Mercurial > repos > goeckslab > image_learner

annotate image_learner_cli.py @ 8:85e6f4b2ad18 draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
author goeckslab
date Thu, 14 Aug 2025 14:53:10 +0000
parents 801a8b6973fb
children
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54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1 import argparse
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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2 import json
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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3 import logging
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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4 import os
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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5 import shutil
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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6 import sys
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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7 import tempfile
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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8 import zipfile
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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9 from pathlib import Path
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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10 from typing import Any, Dict, Optional, Protocol, Tuple
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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11
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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12 import numpy as np
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54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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13 import pandas as pd
2
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14 import pandas.api.types as ptypes
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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15 import yaml
2
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16 from constants import (
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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17 IMAGE_PATH_COLUMN_NAME,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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18 LABEL_COLUMN_NAME,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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19 METRIC_DISPLAY_NAMES,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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20 MODEL_ENCODER_TEMPLATES,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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21 SPLIT_COLUMN_NAME,
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22 TEMP_CONFIG_FILENAME,
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23 TEMP_CSV_FILENAME,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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24 TEMP_DIR_PREFIX
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25 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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26 from ludwig.globals import (
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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27 DESCRIPTION_FILE_NAME,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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28 PREDICTIONS_PARQUET_FILE_NAME,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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29 TEST_STATISTICS_FILE_NAME,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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30 TRAIN_SET_METADATA_FILE_NAME,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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31 )
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32 from ludwig.utils.data_utils import get_split_path
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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33 from ludwig.visualize import get_visualizations_registry
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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34 from plotly_plots import build_classification_plots
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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35 from sklearn.model_selection import train_test_split
2
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36 from utils import (
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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37 build_tabbed_html,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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38 encode_image_to_base64,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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39 get_html_closing,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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40 get_html_template,
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41 get_metrics_help_modal
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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42 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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43
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44 # --- Logging Setup ---
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45 logging.basicConfig(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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46 level=logging.INFO,
2
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47 format='%(asctime)s %(levelname)s %(name)s: %(message)s',
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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48 )
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49 logger = logging.getLogger("ImageLearner")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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50
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51
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52 def format_config_table_html(
1
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53 config: dict,
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54 split_info: Optional[str] = None,
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55 training_progress: dict = None,
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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56 output_type: Optional[str] = None,
1
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57 ) -> str:
0
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58 display_keys = [
2
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59 "task_type",
0
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60 "model_name",
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61 "epochs",
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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62 "batch_size",
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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63 "fine_tune",
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64 "use_pretrained",
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65 "learning_rate",
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66 "random_seed",
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67 "early_stop",
8
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68 "threshold",
0
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69 ]
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70 rows = []
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71 for key in display_keys:
8
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72 val = config.get(key, None)
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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73 if key == "threshold":
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74 if output_type != "binary":
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75 continue
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76 val = val if val is not None else 0.5
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77 val_str = f"{val:.2f}"
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78 if val == 0.5:
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79 val_str += " (default)"
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80 else:
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81 if key == "task_type":
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82 val_str = val.title() if isinstance(val, str) else "N/A"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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83 elif key == "batch_size":
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84 if val is not None:
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85 val_str = int(val)
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86 else:
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87 if training_progress:
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88 resolved_val = training_progress.get("batch_size")
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89 val_str = (
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90 "Auto-selected batch size by Ludwig:<br>"
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91 f"<span style='font-size: 0.85em;'>{resolved_val}</span><br>"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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92 )
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93 else:
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94 val_str = "auto"
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95 elif key == "learning_rate":
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96 if val is not None and val != "auto":
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97 val_str = f"{val:.6f}"
0
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98 else:
8
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99 if training_progress:
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100 resolved_val = training_progress.get("learning_rate")
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101 val_str = (
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102 "Auto-selected learning rate by Ludwig:<br>"
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103 f"<span style='font-size: 0.85em;'>"
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104 f"{resolved_val if resolved_val else 'auto'}</span><br>"
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105 "<span style='font-size: 0.85em;'>"
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106 "Based on model architecture and training setup "
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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107 "(e.g., fine-tuning).<br>"
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108 "</span>"
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109 )
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110 else:
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111 val_str = (
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112 "Auto-selected by Ludwig<br>"
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113 "<span style='font-size: 0.85em;'>"
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114 "Automatically tuned based on architecture and dataset.<br>"
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115 "See <a href='https://ludwig.ai/latest/configuration/trainer/"
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116 "#trainer-parameters' target='_blank'>"
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117 "Ludwig Trainer Parameters</a> for details."
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118 "</span>"
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119 )
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120 elif key == "epochs":
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121 if val is None:
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122 val_str = "N/A"
0
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123 else:
8
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124 if (
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125 training_progress
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126 and "epoch" in training_progress
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127 and val > training_progress["epoch"]
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128 ):
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129 val_str = (
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130 f"Because of early stopping: the training "
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131 f"stopped at epoch {training_progress['epoch']}"
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132 )
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133 else:
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134 val_str = val
0
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135 else:
8
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136 val_str = val if val is not None else "N/A"
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137 if val_str == "N/A" and key not in ["task_type"]: # Skip if N/A for non-essential
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138 continue
0
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139 rows.append(
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140 f"<tr>"
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141 f"<td style='padding: 6px 12px; border: 1px solid #ccc; text-align: left;'>"
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142 f"{key.replace('_', ' ').title()}</td>"
1
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143 f"<td style='padding: 6px 12px; border: 1px solid #ccc; text-align: center;'>"
8
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144 f"{val_str}</td>"
0
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145 f"</tr>"
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146 )
2
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147 aug_cfg = config.get("augmentation")
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148 if aug_cfg:
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149 types = [str(a.get("type", "")) for a in aug_cfg]
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150 aug_val = ", ".join(types)
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151 rows.append(
8
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152 f"<tr><td style='padding: 6px 12px; border: 1px solid #ccc; text-align: left;'>Augmentation</td>"
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153 f"<td style='padding: 6px 12px; border: 1px solid #ccc; text-align: center;'>{aug_val}</td></tr>"
2
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154 )
0
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155 if split_info:
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156 rows.append(
8
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157 f"<tr><td style='padding: 6px 12px; border: 1px solid #ccc; text-align: left;'>Data Split</td>"
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158 f"<td style='padding: 6px 12px; border: 1px solid #ccc; text-align: center;'>{split_info}</td></tr>"
0
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159 )
8
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160 html = f"""
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
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161 <h2 style="text-align: center;">Model and Training Summary</h2>
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162 <div style="display: flex; justify-content: center;">
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163 <table style="border-collapse: collapse; width: 100%; table-layout: fixed;">
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164 <thead><tr>
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165 <th style="padding: 10px; border: 1px solid #ccc; text-align: left; white-space: nowrap; overflow: hidden; text-overflow: ellipsis;">Parameter</th>
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166 <th style="padding: 10px; border: 1px solid #ccc; text-align: center; white-space: nowrap; overflow: hidden; text-overflow: ellipsis;">Value</th>
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167 </tr></thead>
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168 <tbody>
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169 {''.join(rows)}
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170 </tbody>
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171 </table>
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172 </div><br>
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173 <p style="text-align: center; font-size: 0.9em;">
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174 Model trained using <a href="https://ludwig.ai/" target="_blank" rel="noopener noreferrer">Ludwig</a>.
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175 <a href="https://ludwig.ai/latest/configuration/" target="_blank" rel="noopener noreferrer">
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176 Ludwig documentation provides detailed information about default model and training parameters
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177 </a>
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178 </p><hr>
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179 """
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180 return html
0
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181
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182
1
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183 def detect_output_type(test_stats):
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184 """Detects if the output type is 'binary' or 'category' based on test statistics."""
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185 label_stats = test_stats.get("label", {})
2
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186 if "mean_squared_error" in label_stats:
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187 return "regression"
1
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188 per_class = label_stats.get("per_class_stats", {})
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189 if len(per_class) == 2:
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190 return "binary"
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191 return "category"
0
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192
1
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193
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194 def extract_metrics_from_json(
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195 train_stats: dict,
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196 test_stats: dict,
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197 output_type: str,
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198 ) -> dict:
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199 """Extracts relevant metrics from training and test statistics based on the output type."""
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200 metrics = {"training": {}, "validation": {}, "test": {}}
0
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201
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202 def get_last_value(stats, key):
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203 val = stats.get(key)
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204 if isinstance(val, list) and val:
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205 return val[-1]
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206 elif isinstance(val, (int, float)):
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207 return val
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208 return None
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209
1
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210 for split in ["training", "validation"]:
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211 split_stats = train_stats.get(split, {})
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212 if not split_stats:
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213 logging.warning(f"No statistics found for {split} split")
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214 continue
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215 label_stats = split_stats.get("label", {})
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216 if not label_stats:
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217 logging.warning(f"No label statistics found for {split} split")
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218 continue
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219 if output_type == "binary":
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220 metrics[split] = {
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221 "accuracy": get_last_value(label_stats, "accuracy"),
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222 "loss": get_last_value(label_stats, "loss"),
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223 "precision": get_last_value(label_stats, "precision"),
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224 "recall": get_last_value(label_stats, "recall"),
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225 "specificity": get_last_value(label_stats, "specificity"),
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226 "roc_auc": get_last_value(label_stats, "roc_auc"),
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227 }
2
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228 elif output_type == "regression":
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229 metrics[split] = {
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230 "loss": get_last_value(label_stats, "loss"),
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231 "mean_absolute_error": get_last_value(
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232 label_stats, "mean_absolute_error"
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233 ),
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234 "mean_absolute_percentage_error": get_last_value(
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235 label_stats, "mean_absolute_percentage_error"
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236 ),
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237 "mean_squared_error": get_last_value(label_stats, "mean_squared_error"),
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238 "root_mean_squared_error": get_last_value(
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239 label_stats, "root_mean_squared_error"
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240 ),
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241 "root_mean_squared_percentage_error": get_last_value(
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242 label_stats, "root_mean_squared_percentage_error"
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243 ),
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244 "r2": get_last_value(label_stats, "r2"),
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245 }
1
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246 else:
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247 metrics[split] = {
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248 "accuracy": get_last_value(label_stats, "accuracy"),
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249 "accuracy_micro": get_last_value(label_stats, "accuracy_micro"),
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250 "loss": get_last_value(label_stats, "loss"),
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251 "roc_auc": get_last_value(label_stats, "roc_auc"),
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252 "hits_at_k": get_last_value(label_stats, "hits_at_k"),
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253 }
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254 # Test metrics: dynamic extraction according to exclusions
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255 test_label_stats = test_stats.get("label", {})
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256 if not test_label_stats:
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257 logging.warning("No label statistics found for test split")
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258 else:
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259 combined_stats = test_stats.get("combined", {})
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260 overall_stats = test_label_stats.get("overall_stats", {})
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261 # Define exclusions
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262 if output_type == "binary":
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263 exclude = {"per_class_stats", "precision_recall_curve", "roc_curve"}
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264 else:
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265 exclude = {"per_class_stats", "confusion_matrix"}
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266 # 1. Get all scalar test_label_stats not excluded
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267 test_metrics = {}
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268 for k, v in test_label_stats.items():
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269 if k in exclude:
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270 continue
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271 if k == "overall_stats":
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272 continue
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273 if isinstance(v, (int, float, str, bool)):
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274 test_metrics[k] = v
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275 # 2. Add overall_stats (flattened)
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276 for k, v in overall_stats.items():
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277 test_metrics[k] = v
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278 # 3. Optionally include combined/loss if present and not already
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279 if "loss" in combined_stats and "loss" not in test_metrics:
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280 test_metrics["loss"] = combined_stats["loss"]
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281 metrics["test"] = test_metrics
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282 return metrics
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283
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284
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285 def generate_table_row(cells, styles):
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286 """Helper function to generate an HTML table row."""
0
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287 return (
1
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288 "<tr>"
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289 + "".join(f"<td style='{styles}'>{cell}</td>" for cell in cells)
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290 + "</tr>"
0
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291 )
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292
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293
8
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294 # -----------------------------------------
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295 # 2) MODEL PERFORMANCE (Train/Val/Test) TABLE
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296 # -----------------------------------------
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297
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298
1
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299 def format_stats_table_html(train_stats: dict, test_stats: dict) -> str:
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300 """Formats a combined HTML table for training, validation, and test metrics."""
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301 output_type = detect_output_type(test_stats)
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302 all_metrics = extract_metrics_from_json(train_stats, test_stats, output_type)
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303 rows = []
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304 for metric_key in sorted(all_metrics["training"].keys()):
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305 if (
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306 metric_key in all_metrics["validation"]
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307 and metric_key in all_metrics["test"]
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308 ):
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309 display_name = METRIC_DISPLAY_NAMES.get(
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310 metric_key,
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311 metric_key.replace("_", " ").title(),
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312 )
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313 t = all_metrics["training"].get(metric_key)
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314 v = all_metrics["validation"].get(metric_key)
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315 te = all_metrics["test"].get(metric_key)
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316 if all(x is not None for x in [t, v, te]):
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317 rows.append([display_name, f"{t:.4f}", f"{v:.4f}", f"{te:.4f}"])
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318 if not rows:
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319 return "<table><tr><td>No metric values found.</td></tr></table>"
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320 html = (
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321 "<h2 style='text-align: center;'>Model Performance Summary</h2>"
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322 "<div style='display: flex; justify-content: center;'>"
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323 "<table class='performance-summary' style='border-collapse: collapse;'>"
1
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324 "<thead><tr>"
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325 "<th class='sortable' style='padding: 10px; border: 1px solid #ccc; text-align: left; white-space: nowrap;'>Metric</th>"
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326 "<th class='sortable' style='padding: 10px; border: 1px solid #ccc; text-align: center; white-space: nowrap;'>Train</th>"
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327 "<th class='sortable' style='padding: 10px; border: 1px solid #ccc; text-align: center; white-space: nowrap;'>Validation</th>"
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328 "<th class='sortable' style='padding: 10px; border: 1px solid #ccc; text-align: center; white-space: nowrap;'>Test</th>"
1
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329 "</tr></thead><tbody>"
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330 )
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331 for row in rows:
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332 html += generate_table_row(
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333 row,
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334 "padding: 10px; border: 1px solid #ccc; text-align: center; white-space: nowrap;"
1
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335 )
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336 html += "</tbody></table></div><br>"
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337 return html
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338
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339
8
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340 # -------------------------------------------
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341 # 3) TRAIN/VALIDATION PERFORMANCE SUMMARY TABLE
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342 # -------------------------------------------
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343
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344
1
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345 def format_train_val_stats_table_html(train_stats: dict, test_stats: dict) -> str:
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346 """Formats an HTML table for training and validation metrics."""
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347 output_type = detect_output_type(test_stats)
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348 all_metrics = extract_metrics_from_json(train_stats, test_stats, output_type)
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349 rows = []
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350 for metric_key in sorted(all_metrics["training"].keys()):
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351 if metric_key in all_metrics["validation"]:
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352 display_name = METRIC_DISPLAY_NAMES.get(
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353 metric_key,
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354 metric_key.replace("_", " ").title(),
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355 )
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356 t = all_metrics["training"].get(metric_key)
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357 v = all_metrics["validation"].get(metric_key)
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358 if t is not None and v is not None:
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359 rows.append([display_name, f"{t:.4f}", f"{v:.4f}"])
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360 if not rows:
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361 return "<table><tr><td>No metric values found for Train/Validation.</td></tr></table>"
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362 html = (
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363 "<h2 style='text-align: center;'>Train/Validation Performance Summary</h2>"
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364 "<div style='display: flex; justify-content: center;'>"
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365 "<table class='performance-summary' style='border-collapse: collapse;'>"
1
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366 "<thead><tr>"
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367 "<th class='sortable' style='padding: 10px; border: 1px solid #ccc; text-align: left; white-space: nowrap;'>Metric</th>"
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368 "<th class='sortable' style='padding: 10px; border: 1px solid #ccc; text-align: center; white-space: nowrap;'>Train</th>"
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369 "<th class='sortable' style='padding: 10px; border: 1px solid #ccc; text-align: center; white-space: nowrap;'>Validation</th>"
1
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370 "</tr></thead><tbody>"
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371 )
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372 for row in rows:
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373 html += generate_table_row(
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374 row,
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375 "padding: 10px; border: 1px solid #ccc; text-align: center; white-space: nowrap;"
1
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376 )
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377 html += "</tbody></table></div><br>"
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378 return html
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379
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380
8
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381 # -----------------------------------------
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382 # 4) TEST‐ONLY PERFORMANCE SUMMARY TABLE
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383 # -----------------------------------------
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384
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385
2
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diff changeset
386 def format_test_merged_stats_table_html(
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
387 test_metrics: Dict[str, Optional[float]],
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
388 ) -> str:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
389 """Formats an HTML table for test metrics."""
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
390 rows = []
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
391 for key in sorted(test_metrics.keys()):
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
392 display_name = METRIC_DISPLAY_NAMES.get(key, key.replace("_", " ").title())
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
393 value = test_metrics[key]
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
394 if value is not None:
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
395 rows.append([display_name, f"{value:.4f}"])
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
396 if not rows:
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
397 return "<table><tr><td>No test metric values found.</td></tr></table>"
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
398 html = (
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
399 "<h2 style='text-align: center;'>Test Performance Summary</h2>"
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
400 "<div style='display: flex; justify-content: center;'>"
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
401 "<table class='performance-summary' style='border-collapse: collapse;'>"
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
402 "<thead><tr>"
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
403 "<th class='sortable' style='padding: 10px; border: 1px solid #ccc; text-align: left; white-space: nowrap;'>Metric</th>"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
404 "<th class='sortable' style='padding: 10px; border: 1px solid #ccc; text-align: center; white-space: nowrap;'>Test</th>"
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
405 "</tr></thead><tbody>"
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
406 )
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
407 for row in rows:
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
408 html += generate_table_row(
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
409 row,
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
410 "padding: 10px; border: 1px solid #ccc; text-align: center; white-space: nowrap;"
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
411 )
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
412 html += "</tbody></table></div><br>"
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
413 return html
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
414
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
415
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
416 def split_data_0_2(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
417 df: pd.DataFrame,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
418 split_column: str,
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
419 validation_size: float = 0.1,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
420 random_state: int = 42,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
421 label_column: Optional[str] = None,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
422 ) -> pd.DataFrame:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
423 """Given a DataFrame whose split_column only contains {0,2}, re-assign a portion of the 0s to become 1s (validation)."""
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
424 out = df.copy()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
425 out[split_column] = pd.to_numeric(out[split_column], errors="coerce").astype(int)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
426 idx_train = out.index[out[split_column] == 0].tolist()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
427 if not idx_train:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
428 logger.info("No rows with split=0; nothing to do.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
429 return out
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
430 # Always use stratify if possible
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
431 stratify_arr = None
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
432 if label_column and label_column in out.columns:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
433 label_counts = out.loc[idx_train, label_column].value_counts()
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
434 if label_counts.size > 1:
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
435 # Force stratify even with fewer samples - adjust validation_size if needed
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
436 min_samples_per_class = label_counts.min()
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
437 if min_samples_per_class * validation_size < 1:
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
438 # Adjust validation_size to ensure at least 1 sample per class, but do not exceed original validation_size
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
439 adjusted_validation_size = min(validation_size, 1.0 / min_samples_per_class)
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
440 if adjusted_validation_size != validation_size:
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
441 validation_size = adjusted_validation_size
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
442 logger.info(f"Adjusted validation_size to {validation_size:.3f} to ensure at least one sample per class in validation")
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
443 stratify_arr = out.loc[idx_train, label_column]
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
444 logger.info("Using stratified split for validation set")
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
445 else:
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
446 logger.warning("Only one label class found; cannot stratify")
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
447 if validation_size <= 0:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
448 logger.info("validation_size <= 0; keeping all as train.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
449 return out
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
450 if validation_size >= 1:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
451 logger.info("validation_size >= 1; moving all train → validation.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
452 out.loc[idx_train, split_column] = 1
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
453 return out
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
454 # Always try stratified split first
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
455 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
456 train_idx, val_idx = train_test_split(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
457 idx_train,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
458 test_size=validation_size,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
459 random_state=random_state,
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
460 stratify=stratify_arr,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
461 )
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
462 logger.info("Successfully applied stratified split")
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
463 except ValueError as e:
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
464 logger.warning(f"Stratified split failed ({e}); falling back to random split.")
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
465 train_idx, val_idx = train_test_split(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
466 idx_train,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
467 test_size=validation_size,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
468 random_state=random_state,
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
469 stratify=None,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
470 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
471 out.loc[train_idx, split_column] = 0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
472 out.loc[val_idx, split_column] = 1
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
473 out[split_column] = out[split_column].astype(int)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
474 return out
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
475
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
476
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
477 def create_stratified_random_split(
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
478 df: pd.DataFrame,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
479 split_column: str,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
480 split_probabilities: list = [0.7, 0.1, 0.2],
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
481 random_state: int = 42,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
482 label_column: Optional[str] = None,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
483 ) -> pd.DataFrame:
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
484 """Create a stratified random split when no split column exists."""
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
485 out = df.copy()
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
486 # initialize split column
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
487 out[split_column] = 0
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
488 if not label_column or label_column not in out.columns:
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
489 logger.warning("No label column found; using random split without stratification")
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
490 # fall back to simple random assignment
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
491 indices = out.index.tolist()
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
492 np.random.seed(random_state)
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
493 np.random.shuffle(indices)
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
494 n_total = len(indices)
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
495 n_train = int(n_total * split_probabilities[0])
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
496 n_val = int(n_total * split_probabilities[1])
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
497 out.loc[indices[:n_train], split_column] = 0
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
498 out.loc[indices[n_train:n_train + n_val], split_column] = 1
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
499 out.loc[indices[n_train + n_val:], split_column] = 2
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
500 return out.astype({split_column: int})
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
501 # check if stratification is possible
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
502 label_counts = out[label_column].value_counts()
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
503 min_samples_per_class = label_counts.min()
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
504 # ensure we have enough samples for stratification:
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
505 # Each class must have at least as many samples as the number of splits,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
506 # so that each split can receive at least one sample per class.
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
507 min_samples_required = len(split_probabilities)
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
508 if min_samples_per_class < min_samples_required:
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
509 logger.warning(
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
510 f"Insufficient samples per class for stratification (min: {min_samples_per_class}, required: {min_samples_required}); using random split"
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
511 )
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
512 # fall back to simple random assignment
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
513 indices = out.index.tolist()
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
514 np.random.seed(random_state)
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
515 np.random.shuffle(indices)
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
516 n_total = len(indices)
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
517 n_train = int(n_total * split_probabilities[0])
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
518 n_val = int(n_total * split_probabilities[1])
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
519 out.loc[indices[:n_train], split_column] = 0
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
520 out.loc[indices[n_train:n_train + n_val], split_column] = 1
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
521 out.loc[indices[n_train + n_val:], split_column] = 2
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
522 return out.astype({split_column: int})
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
523 logger.info("Using stratified random split for train/validation/test sets")
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
524 # first split: separate test set
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
525 train_val_idx, test_idx = train_test_split(
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
526 out.index.tolist(),
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
527 test_size=split_probabilities[2],
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
528 random_state=random_state,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
529 stratify=out[label_column],
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
530 )
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
531 # second split: separate training and validation from remaining data
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
532 val_size_adjusted = split_probabilities[1] / (split_probabilities[0] + split_probabilities[1])
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
533 train_idx, val_idx = train_test_split(
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
534 train_val_idx,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
535 test_size=val_size_adjusted,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
536 random_state=random_state,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
537 stratify=out.loc[train_val_idx, label_column],
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
538 )
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
539 # assign split values
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
540 out.loc[train_idx, split_column] = 0
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
541 out.loc[val_idx, split_column] = 1
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
542 out.loc[test_idx, split_column] = 2
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
543 logger.info("Successfully applied stratified random split")
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
544 logger.info(f"Split counts: Train={len(train_idx)}, Val={len(val_idx)}, Test={len(test_idx)}")
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
545 return out.astype({split_column: int})
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
546
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
547
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
548 class Backend(Protocol):
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
549 """Interface for a machine learning backend."""
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
550 def prepare_config(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
551 self,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
552 config_params: Dict[str, Any],
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
553 split_config: Dict[str, Any],
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
554 ) -> str:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
555 ...
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
556
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
557 def run_experiment(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
558 self,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
559 dataset_path: Path,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
560 config_path: Path,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
561 output_dir: Path,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
562 random_seed: int,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
563 ) -> None:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
564 ...
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
565
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
566 def generate_plots(self, output_dir: Path) -> None:
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
567 ...
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
568
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
569 def generate_html_report(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
570 self,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
571 title: str,
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
572 output_dir: str,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
573 config: Dict[str, Any],
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
574 split_info: str,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
575 ) -> Path:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
576 ...
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
577
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
578
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
579 class LudwigDirectBackend:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
580 """Backend for running Ludwig experiments directly via the internal experiment_cli function."""
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
581 def prepare_config(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
582 self,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
583 config_params: Dict[str, Any],
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
584 split_config: Dict[str, Any],
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
585 ) -> str:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
586 logger.info("LudwigDirectBackend: Preparing YAML configuration.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
587 model_name = config_params.get("model_name", "resnet18")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
588 use_pretrained = config_params.get("use_pretrained", False)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
589 fine_tune = config_params.get("fine_tune", False)
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
590 if use_pretrained:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
591 trainable = bool(fine_tune)
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
592 else:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
593 trainable = True
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
594 epochs = config_params.get("epochs", 10)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
595 batch_size = config_params.get("batch_size")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
596 num_processes = config_params.get("preprocessing_num_processes", 1)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
597 early_stop = config_params.get("early_stop", None)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
598 learning_rate = config_params.get("learning_rate")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
599 learning_rate = "auto" if learning_rate is None else float(learning_rate)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
600 raw_encoder = MODEL_ENCODER_TEMPLATES.get(model_name, model_name)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
601 if isinstance(raw_encoder, dict):
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
602 encoder_config = {
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
603 **raw_encoder,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
604 "use_pretrained": use_pretrained,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
605 "trainable": trainable,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
606 }
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
607 else:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
608 encoder_config = {"type": raw_encoder}
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
609 batch_size_cfg = batch_size or "auto"
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
610 label_column_path = config_params.get("label_column_data_path")
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
611 label_series = None
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
612 if label_column_path is not None and Path(label_column_path).exists():
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
613 try:
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
614 label_series = pd.read_csv(label_column_path)[LABEL_COLUMN_NAME]
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
615 except Exception as e:
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
616 logger.warning(f"Could not read label column for task detection: {e}")
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
617 if (
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
618 label_series is not None
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
619 and ptypes.is_numeric_dtype(label_series.dtype)
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
620 and label_series.nunique() > 10
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
621 ):
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
622 task_type = "regression"
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
623 else:
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
624 task_type = "classification"
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
625 config_params["task_type"] = task_type
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
626 image_feat: Dict[str, Any] = {
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
627 "name": IMAGE_PATH_COLUMN_NAME,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
628 "type": "image",
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
629 "encoder": encoder_config,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
630 }
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
631 if config_params.get("augmentation") is not None:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
632 image_feat["augmentation"] = config_params["augmentation"]
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
633 if task_type == "regression":
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
634 output_feat = {
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
635 "name": LABEL_COLUMN_NAME,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
636 "type": "number",
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
637 "decoder": {"type": "regressor"},
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
638 "loss": {"type": "mean_squared_error"},
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
639 "evaluation": {
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
640 "metrics": [
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
641 "mean_squared_error",
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
642 "mean_absolute_error",
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
643 "r2",
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
644 ]
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
645 },
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
646 }
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
647 val_metric = config_params.get("validation_metric", "mean_squared_error")
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
648 else:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
649 num_unique_labels = (
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
650 label_series.nunique() if label_series is not None else 2
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
651 )
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
652 output_type = "binary" if num_unique_labels == 2 else "category"
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
653 output_feat = {"name": LABEL_COLUMN_NAME, "type": output_type}
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
654 if output_type == "binary" and config_params.get("threshold") is not None:
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
655 output_feat["threshold"] = float(config_params["threshold"])
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
656 val_metric = None
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
657 conf: Dict[str, Any] = {
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
658 "model_type": "ecd",
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
659 "input_features": [image_feat],
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
660 "output_features": [output_feat],
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
661 "combiner": {"type": "concat"},
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
662 "trainer": {
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
663 "epochs": epochs,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
664 "early_stop": early_stop,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
665 "batch_size": batch_size_cfg,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
666 "learning_rate": learning_rate,
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
667 # only set validation_metric for regression
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
668 **({"validation_metric": val_metric} if val_metric else {}),
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
669 },
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
670 "preprocessing": {
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
671 "split": split_config,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
672 "num_processes": num_processes,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
673 "in_memory": False,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
674 },
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
675 }
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
676 logger.debug("LudwigDirectBackend: Config dict built.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
677 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
678 yaml_str = yaml.dump(conf, sort_keys=False, indent=2)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
679 logger.info("LudwigDirectBackend: YAML config generated.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
680 return yaml_str
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
681 except Exception:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
682 logger.error(
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
683 "LudwigDirectBackend: Failed to serialize YAML.",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
684 exc_info=True,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
685 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
686 raise
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
687
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
688 def run_experiment(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
689 self,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
690 dataset_path: Path,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
691 config_path: Path,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
692 output_dir: Path,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
693 random_seed: int = 42,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
694 ) -> None:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
695 """Invoke Ludwig's internal experiment_cli function to run the experiment."""
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
696 logger.info("LudwigDirectBackend: Starting experiment execution.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
697 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
698 from ludwig.experiment import experiment_cli
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
699 except ImportError as e:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
700 logger.error(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
701 "LudwigDirectBackend: Could not import experiment_cli.",
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
702 exc_info=True,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
703 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
704 raise RuntimeError("Ludwig import failed.") from e
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
705 output_dir.mkdir(parents=True, exist_ok=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
706 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
707 experiment_cli(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
708 dataset=str(dataset_path),
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
709 config=str(config_path),
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
710 output_directory=str(output_dir),
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
711 random_seed=random_seed,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
712 )
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
713 logger.info(
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
714 f"LudwigDirectBackend: Experiment completed. Results in {output_dir}"
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
715 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
716 except TypeError as e:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
717 logger.error(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
718 "LudwigDirectBackend: Argument mismatch in experiment_cli call.",
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
719 exc_info=True,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
720 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
721 raise RuntimeError("Ludwig argument error.") from e
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
722 except Exception:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
723 logger.error(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
724 "LudwigDirectBackend: Experiment execution error.",
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
725 exc_info=True,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
726 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
727 raise
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
728
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
729 def get_training_process(self, output_dir) -> Optional[Dict[str, Any]]:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
730 """Retrieve the learning rate used in the most recent Ludwig run."""
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
731 output_dir = Path(output_dir)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
732 exp_dirs = sorted(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
733 output_dir.glob("experiment_run*"),
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
734 key=lambda p: p.stat().st_mtime,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
735 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
736 if not exp_dirs:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
737 logger.warning(f"No experiment run directories found in {output_dir}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
738 return None
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
739 progress_file = exp_dirs[-1] / "model" / "training_progress.json"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
740 if not progress_file.exists():
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
741 logger.warning(f"No training_progress.json found in {progress_file}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
742 return None
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
743 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
744 with progress_file.open("r", encoding="utf-8") as f:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
745 data = json.load(f)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
746 return {
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
747 "learning_rate": data.get("learning_rate"),
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
748 "batch_size": data.get("batch_size"),
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
749 "epoch": data.get("epoch"),
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
750 }
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
751 except Exception as e:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
752 logger.warning(f"Failed to read training progress info: {e}")
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
753 return {}
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
754
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
755 def convert_parquet_to_csv(self, output_dir: Path):
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
756 """Convert the predictions Parquet file to CSV."""
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
757 output_dir = Path(output_dir)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
758 exp_dirs = sorted(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
759 output_dir.glob("experiment_run*"),
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
760 key=lambda p: p.stat().st_mtime,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
761 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
762 if not exp_dirs:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
763 logger.warning(f"No experiment run dirs found in {output_dir}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
764 return
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
765 exp_dir = exp_dirs[-1]
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
766 parquet_path = exp_dir / PREDICTIONS_PARQUET_FILE_NAME
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
767 csv_path = exp_dir / "predictions.csv"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
768 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
769 df = pd.read_parquet(parquet_path)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
770 df.to_csv(csv_path, index=False)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
771 logger.info(f"Converted Parquet to CSV: {csv_path}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
772 except Exception as e:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
773 logger.error(f"Error converting Parquet to CSV: {e}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
774
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
775 def generate_plots(self, output_dir: Path) -> None:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
776 """Generate all registered Ludwig visualizations for the latest experiment run."""
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
777 logger.info("Generating all Ludwig visualizations…")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
778 test_plots = {
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
779 "compare_performance",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
780 "compare_classifiers_performance_from_prob",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
781 "compare_classifiers_performance_from_pred",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
782 "compare_classifiers_performance_changing_k",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
783 "compare_classifiers_multiclass_multimetric",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
784 "compare_classifiers_predictions",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
785 "confidence_thresholding_2thresholds_2d",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
786 "confidence_thresholding_2thresholds_3d",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
787 "confidence_thresholding",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
788 "confidence_thresholding_data_vs_acc",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
789 "binary_threshold_vs_metric",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
790 "roc_curves",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
791 "roc_curves_from_test_statistics",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
792 "calibration_1_vs_all",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
793 "calibration_multiclass",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
794 "confusion_matrix",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
795 "frequency_vs_f1",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
796 }
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
797 train_plots = {
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
798 "learning_curves",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
799 "compare_classifiers_performance_subset",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
800 }
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
801 output_dir = Path(output_dir)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
802 exp_dirs = sorted(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
803 output_dir.glob("experiment_run*"),
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
804 key=lambda p: p.stat().st_mtime,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
805 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
806 if not exp_dirs:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
807 logger.warning(f"No experiment run dirs found in {output_dir}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
808 return
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
809 exp_dir = exp_dirs[-1]
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
810 viz_dir = exp_dir / "visualizations"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
811 viz_dir.mkdir(exist_ok=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
812 train_viz = viz_dir / "train"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
813 test_viz = viz_dir / "test"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
814 train_viz.mkdir(parents=True, exist_ok=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
815 test_viz.mkdir(parents=True, exist_ok=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
816
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
817 def _check(p: Path) -> Optional[str]:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
818 return str(p) if p.exists() else None
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
819
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
820 training_stats = _check(exp_dir / "training_statistics.json")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
821 test_stats = _check(exp_dir / TEST_STATISTICS_FILE_NAME)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
822 probs_path = _check(exp_dir / PREDICTIONS_PARQUET_FILE_NAME)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
823 gt_metadata = _check(exp_dir / "model" / TRAIN_SET_METADATA_FILE_NAME)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
824 dataset_path = None
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
825 split_file = None
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
826 desc = exp_dir / DESCRIPTION_FILE_NAME
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
827 if desc.exists():
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
828 with open(desc, "r") as f:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
829 cfg = json.load(f)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
830 dataset_path = _check(Path(cfg.get("dataset", "")))
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
831 split_file = _check(Path(get_split_path(cfg.get("dataset", ""))))
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
832 output_feature = ""
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
833 if desc.exists():
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
834 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
835 output_feature = cfg["config"]["output_features"][0]["name"]
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
836 except Exception:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
837 pass
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
838 if not output_feature and test_stats:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
839 with open(test_stats, "r") as f:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
840 stats = json.load(f)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
841 output_feature = next(iter(stats.keys()), "")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
842 viz_registry = get_visualizations_registry()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
843 for viz_name, viz_func in viz_registry.items():
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
844 if viz_name in train_plots:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
845 viz_dir_plot = train_viz
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
846 elif viz_name in test_plots:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
847 viz_dir_plot = test_viz
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
848 else:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
849 continue
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
850 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
851 viz_func(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
852 training_statistics=[training_stats] if training_stats else [],
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
853 test_statistics=[test_stats] if test_stats else [],
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
854 probabilities=[probs_path] if probs_path else [],
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
855 output_feature_name=output_feature,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
856 ground_truth_split=2,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
857 top_n_classes=[0],
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
858 top_k=3,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
859 ground_truth_metadata=gt_metadata,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
860 ground_truth=dataset_path,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
861 split_file=split_file,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
862 output_directory=str(viz_dir_plot),
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
863 normalize=False,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
864 file_format="png",
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
865 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
866 logger.info(f"✔ Generated {viz_name}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
867 except Exception as e:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
868 logger.warning(f"✘ Skipped {viz_name}: {e}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
869 logger.info(f"All visualizations written to {viz_dir}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
870
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
871 def generate_html_report(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
872 self,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
873 title: str,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
874 output_dir: str,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
875 config: dict,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
876 split_info: str,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
877 ) -> Path:
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
878 """Assemble an HTML report from visualizations under train_val/ and test/ folders."""
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
879 cwd = Path.cwd()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
880 report_name = title.lower().replace(" ", "_") + "_report.html"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
881 report_path = cwd / report_name
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
882 output_dir = Path(output_dir)
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
883 output_type = None
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
884 exp_dirs = sorted(
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
885 output_dir.glob("experiment_run*"),
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
886 key=lambda p: p.stat().st_mtime,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
887 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
888 if not exp_dirs:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
889 raise RuntimeError(f"No 'experiment*' dirs found in {output_dir}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
890 exp_dir = exp_dirs[-1]
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
891 base_viz_dir = exp_dir / "visualizations"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
892 train_viz_dir = base_viz_dir / "train"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
893 test_viz_dir = base_viz_dir / "test"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
894 html = get_html_template()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
895 html += f"<h1>{title}</h1>"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
896 metrics_html = ""
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
897 train_val_metrics_html = ""
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
898 test_metrics_html = ""
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
899 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
900 train_stats_path = exp_dir / "training_statistics.json"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
901 test_stats_path = exp_dir / TEST_STATISTICS_FILE_NAME
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
902 if train_stats_path.exists() and test_stats_path.exists():
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
903 with open(train_stats_path) as f:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
904 train_stats = json.load(f)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
905 with open(test_stats_path) as f:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
906 test_stats = json.load(f)
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
907 output_type = detect_output_type(test_stats)
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
908 metrics_html = format_stats_table_html(train_stats, test_stats)
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
909 train_val_metrics_html = format_train_val_stats_table_html(
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
910 train_stats, test_stats
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
911 )
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
912 test_metrics_html = format_test_merged_stats_table_html(
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
913 extract_metrics_from_json(train_stats, test_stats, output_type)[
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
914 "test"
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
915 ]
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
916 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
917 except Exception as e:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
918 logger.warning(
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
919 f"Could not load stats for HTML report: {type(e).__name__}: {e}"
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
920 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
921 config_html = ""
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
922 training_progress = self.get_training_process(output_dir)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
923 try:
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
924 config_html = format_config_table_html(
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
925 config, split_info, training_progress
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
926 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
927 except Exception as e:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
928 logger.warning(f"Could not load config for HTML report: {e}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
929
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
930 def render_img_section(
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
931 title: str, dir_path: Path, output_type: str = None
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
932 ) -> str:
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
933 if not dir_path.exists():
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
934 return f"<h2>{title}</h2><p><em>Directory not found.</em></p>"
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
935 # collect every PNG
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
936 imgs = list(dir_path.glob("*.png"))
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
937 # --- EXCLUDE Ludwig's base confusion matrix and any top-N confusion_matrix files ---
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
938 imgs = [
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
939 img for img in imgs
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
940 if not (
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
941 img.name == "confusion_matrix.png"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
942 or img.name.startswith("confusion_matrix__label_top")
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
943 or img.name == "roc_curves.png"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
944 )
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
945 ]
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
946 if not imgs:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
947 return f"<h2>{title}</h2><p><em>No plots found.</em></p>"
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
948 if output_type == "binary":
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
949 order = [
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
950 "roc_curves_from_prediction_statistics.png",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
951 "compare_performance_label.png",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
952 "confusion_matrix_entropy__label_top2.png",
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
953 # ...you can tweak ordering as needed
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
954 ]
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
955 img_names = {img.name: img for img in imgs}
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
956 ordered = [img_names[n] for n in order if n in img_names]
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
957 others = sorted(img for img in imgs if img.name not in order)
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
958 imgs = ordered + others
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
959 elif output_type == "category":
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
960 unwanted = {
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
961 "compare_classifiers_multiclass_multimetric__label_best10.png",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
962 "compare_classifiers_multiclass_multimetric__label_top10.png",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
963 "compare_classifiers_multiclass_multimetric__label_worst10.png",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
964 }
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
965 display_order = [
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
966 "roc_curves.png",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
967 "compare_performance_label.png",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
968 "compare_classifiers_performance_from_prob.png",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
969 "confusion_matrix_entropy__label_top10.png",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
970 ]
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
971 # filter and order
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
972 valid_imgs = [img for img in imgs if img.name not in unwanted]
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
973 img_map = {img.name: img for img in valid_imgs}
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
974 ordered = [img_map[n] for n in display_order if n in img_map]
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
975 others = sorted(img for img in valid_imgs if img.name not in display_order)
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
976 imgs = ordered + others
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
977 else:
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
978 # regression: just sort whatever's left
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
979 imgs = sorted(imgs)
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
980 # render each remaining PNG
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
981 html = ""
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
982 for img in imgs:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
983 b64 = encode_image_to_base64(str(img))
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
984 img_title = img.stem.replace("_", " ").title()
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
985 html += (
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
986 f"<h2 style='text-align: center;'>{img_title}</h2>"
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
987 f'<div class="plot" style="margin-bottom:20px;text-align:center;">'
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
988 f'<img src="data:image/png;base64,{b64}" '
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
989 f'style="max-width:90%;max-height:600px;border:1px solid #ddd;" />'
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
990 f"</div>"
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
991 )
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
992 return html
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
993
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
994 tab1_content = config_html + metrics_html
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
995 tab2_content = train_val_metrics_html + render_img_section(
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
996 "Training and Validation Visualizations", train_viz_dir
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
997 )
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
998 # --- Predictions vs Ground Truth table ---
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
999 preds_section = ""
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1000 parquet_path = exp_dir / PREDICTIONS_PARQUET_FILE_NAME
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1001 if output_type == "regression" and parquet_path.exists():
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1002 try:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1003 # 1) load predictions from Parquet
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1004 df_preds = pd.read_parquet(parquet_path).reset_index(drop=True)
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1005 # assume the column containing your model's prediction is named "prediction"
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1006 pred_col = next(
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1007 (c for c in df_preds.columns if "prediction" in c.lower()),
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1008 None,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1009 )
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1010 if pred_col is None:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1011 raise ValueError("No prediction column found in Parquet output")
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1012 df_pred = df_preds[[pred_col]].rename(columns={pred_col: "prediction"})
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1013 # 2) load ground truth for the test split from prepared CSV
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1014 df_all = pd.read_csv(config["label_column_data_path"])
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1015 df_gt = df_all[df_all[SPLIT_COLUMN_NAME] == 2][LABEL_COLUMN_NAME].reset_index(drop=True)
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1016 # 3) concatenate side-by-side
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1017 df_table = pd.concat([df_gt, df_pred], axis=1)
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1018 df_table.columns = [LABEL_COLUMN_NAME, "prediction"]
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1019 # 4) render as HTML
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1020 preds_html = df_table.to_html(index=False, classes="predictions-table")
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1021 preds_section = (
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1022 "<h2 style='text-align: center;'>Ground Truth vs. Predictions</h2>"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1023 "<div style='overflow-y:auto; max-height:400px; overflow-x:auto; margin-bottom:20px;'>"
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1024 + preds_html
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1025 + "</div>"
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1026 )
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1027 except Exception as e:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1028 logger.warning(f"Could not build Predictions vs GT table: {e}")
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1029 tab3_content = test_metrics_html + preds_section
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1030 if output_type in ("binary", "category"):
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1031 training_stats_path = exp_dir / "training_statistics.json"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1032 interactive_plots = build_classification_plots(
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1033 str(test_stats_path),
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1034 str(training_stats_path),
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1035 )
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1036 for plot in interactive_plots:
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1037 # 2) inject the static "roc_curves_from_prediction_statistics.png"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1038 if plot["title"] == "ROC-AUC":
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1039 static_img = test_viz_dir / "roc_curves_from_prediction_statistics.png"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1040 if static_img.exists():
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1041 b64 = encode_image_to_base64(str(static_img))
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1042 tab3_content += (
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1043 "<h2 style='text-align: center;'>"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1044 "Roc Curves From Prediction Statistics"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1045 "</h2>"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1046 f'<div class="plot" style="margin-bottom:20px;text-align:center;">'
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1047 f'<img src="data:image/png;base64,{b64}" '
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1048 f'style="max-width:90%;max-height:600px;border:1px solid #ddd;" />'
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1049 "</div>"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1050 )
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1051 # always render the plotly panels exactly as before
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1052 tab3_content += (
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1053 f"<h2 style='text-align: center;'>{plot['title']}</h2>"
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1054 + plot["html"]
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1055 )
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1056 tab3_content += render_img_section(
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1057 "Test Visualizations",
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1058 test_viz_dir,
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1059 output_type
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1060 )
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1061 # assemble the tabs and help modal
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1062 tabbed_html = build_tabbed_html(tab1_content, tab2_content, tab3_content)
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1063 modal_html = get_metrics_help_modal()
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1064 html += tabbed_html + modal_html + get_html_closing()
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1065 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1066 with open(report_path, "w") as f:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1067 f.write(html)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1068 logger.info(f"HTML report generated at: {report_path}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1069 except Exception as e:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1070 logger.error(f"Failed to write HTML report: {e}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1071 raise
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1072 return report_path
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1073
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1074
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1075 class WorkflowOrchestrator:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1076 """Manages the image-classification workflow."""
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1077 def __init__(self, args: argparse.Namespace, backend: Backend):
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1078 self.args = args
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1079 self.backend = backend
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1080 self.temp_dir: Optional[Path] = None
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1081 self.image_extract_dir: Optional[Path] = None
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1082 logger.info(f"Orchestrator initialized with backend: {type(backend).__name__}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1083
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1084 def _create_temp_dirs(self) -> None:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1085 """Create temporary output and image extraction directories."""
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1086 try:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1087 self.temp_dir = Path(
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1088 tempfile.mkdtemp(dir=self.args.output_dir, prefix=TEMP_DIR_PREFIX)
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1089 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1090 self.image_extract_dir = self.temp_dir / "images"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1091 self.image_extract_dir.mkdir()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1092 logger.info(f"Created temp directory: {self.temp_dir}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1093 except Exception:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1094 logger.error("Failed to create temporary directories", exc_info=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1095 raise
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1096
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1097 def _extract_images(self) -> None:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1098 """Extract images from ZIP into the temp image directory."""
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1099 if self.image_extract_dir is None:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1100 raise RuntimeError("Temp image directory not initialized.")
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1101 logger.info(
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1102 f"Extracting images from {self.args.image_zip} → {self.image_extract_dir}"
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1103 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1104 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1105 with zipfile.ZipFile(self.args.image_zip, "r") as z:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1106 z.extractall(self.image_extract_dir)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1107 logger.info("Image extraction complete.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1108 except Exception:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1109 logger.error("Error extracting zip file", exc_info=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1110 raise
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1111
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1112 def _prepare_data(self) -> Tuple[Path, Dict[str, Any], str]:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1113 """Load CSV, update image paths, handle splits, and write prepared CSV."""
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1114 if not self.temp_dir or not self.image_extract_dir:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1115 raise RuntimeError("Temp dirs not initialized before data prep.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1116 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1117 df = pd.read_csv(self.args.csv_file)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1118 logger.info(f"Loaded CSV: {self.args.csv_file}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1119 except Exception:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1120 logger.error("Error loading CSV file", exc_info=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1121 raise
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1122 required = {IMAGE_PATH_COLUMN_NAME, LABEL_COLUMN_NAME}
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1123 missing = required - set(df.columns)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1124 if missing:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1125 raise ValueError(f"Missing CSV columns: {', '.join(missing)}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1126 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1127 df[IMAGE_PATH_COLUMN_NAME] = df[IMAGE_PATH_COLUMN_NAME].apply(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1128 lambda p: str((self.image_extract_dir / p).resolve())
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1129 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1130 except Exception:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1131 logger.error("Error updating image paths", exc_info=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1132 raise
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1133 if SPLIT_COLUMN_NAME in df.columns:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1134 df, split_config, split_info = self._process_fixed_split(df)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1135 else:
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1136 logger.info("No split column; creating stratified random split")
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1137 df = create_stratified_random_split(
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1138 df=df,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1139 split_column=SPLIT_COLUMN_NAME,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1140 split_probabilities=self.args.split_probabilities,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1141 random_state=self.args.random_seed,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1142 label_column=LABEL_COLUMN_NAME,
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1143 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1144 split_config = {
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1145 "type": "fixed",
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1146 "column": SPLIT_COLUMN_NAME,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1147 }
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1148 split_info = (
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1149 f"No split column in CSV. Created stratified random split: "
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1150 f"{[int(p * 100) for p in self.args.split_probabilities]}% "
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1151 f"for train/val/test with balanced label distribution."
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1152 )
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1153 final_csv = self.temp_dir / TEMP_CSV_FILENAME
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1154 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1155 df.to_csv(final_csv, index=False)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1156 logger.info(f"Saved prepared data to {final_csv}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1157 except Exception:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1158 logger.error("Error saving prepared CSV", exc_info=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1159 raise
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1160 return final_csv, split_config, split_info
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1161
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1162 def _process_fixed_split(
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1163 self, df: pd.DataFrame
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1164 ) -> Tuple[pd.DataFrame, Dict[str, Any], str]:
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1165 """Process a fixed split column (0=train,1=val,2=test)."""
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1166 logger.info(f"Fixed split column '{SPLIT_COLUMN_NAME}' detected.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1167 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1168 col = df[SPLIT_COLUMN_NAME]
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1169 df[SPLIT_COLUMN_NAME] = pd.to_numeric(col, errors="coerce").astype(
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1170 pd.Int64Dtype()
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1171 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1172 if df[SPLIT_COLUMN_NAME].isna().any():
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1173 logger.warning("Split column contains non-numeric/missing values.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1174 unique = set(df[SPLIT_COLUMN_NAME].dropna().unique())
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1175 logger.info(f"Unique split values: {unique}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1176 if unique == {0, 2}:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1177 df = split_data_0_2(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1178 df,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1179 SPLIT_COLUMN_NAME,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1180 validation_size=self.args.validation_size,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1181 label_column=LABEL_COLUMN_NAME,
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1182 random_state=self.args.random_seed,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1183 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1184 split_info = (
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1185 "Detected a split column (with values 0 and 2) in the input CSV. "
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1186 f"Used this column as a base and reassigned "
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1187 f"{self.args.validation_size * 100:.1f}% "
7
801a8b6973fb planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents: 6
diff changeset
1188 "of the training set (originally labeled 0) to validation (labeled 1) using stratified sampling."
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1189 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1190 logger.info("Applied custom 0/2 split.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1191 elif unique.issubset({0, 1, 2}):
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1192 split_info = "Used user-defined split column from CSV."
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1193 logger.info("Using fixed split as-is.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1194 else:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1195 raise ValueError(f"Unexpected split values: {unique}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1196 return df, {"type": "fixed", "column": SPLIT_COLUMN_NAME}, split_info
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1197 except Exception:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1198 logger.error("Error processing fixed split", exc_info=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1199 raise
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1200
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1201 def _cleanup_temp_dirs(self) -> None:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1202 if self.temp_dir and self.temp_dir.exists():
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1203 logger.info(f"Cleaning up temp directory: {self.temp_dir}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1204 shutil.rmtree(self.temp_dir, ignore_errors=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1205 self.temp_dir = None
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1206 self.image_extract_dir = None
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1207
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1208 def run(self) -> None:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1209 """Execute the full workflow end-to-end."""
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1210 logger.info("Starting workflow...")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1211 self.args.output_dir.mkdir(parents=True, exist_ok=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1212 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1213 self._create_temp_dirs()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1214 self._extract_images()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1215 csv_path, split_cfg, split_info = self._prepare_data()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1216 use_pretrained = self.args.use_pretrained or self.args.fine_tune
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1217 backend_args = {
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1218 "model_name": self.args.model_name,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1219 "fine_tune": self.args.fine_tune,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1220 "use_pretrained": use_pretrained,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1221 "epochs": self.args.epochs,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1222 "batch_size": self.args.batch_size,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1223 "preprocessing_num_processes": self.args.preprocessing_num_processes,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1224 "split_probabilities": self.args.split_probabilities,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1225 "learning_rate": self.args.learning_rate,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1226 "random_seed": self.args.random_seed,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1227 "early_stop": self.args.early_stop,
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1228 "label_column_data_path": csv_path,
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1229 "augmentation": self.args.augmentation,
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1230 "threshold": self.args.threshold,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1231 }
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1232 yaml_str = self.backend.prepare_config(backend_args, split_cfg)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1233 config_file = self.temp_dir / TEMP_CONFIG_FILENAME
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1234 config_file.write_text(yaml_str)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1235 logger.info(f"Wrote backend config: {config_file}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1236 self.backend.run_experiment(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1237 csv_path,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1238 config_file,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1239 self.args.output_dir,
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1240 self.args.random_seed,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1241 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1242 logger.info("Workflow completed successfully.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1243 self.backend.generate_plots(self.args.output_dir)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1244 report_file = self.backend.generate_html_report(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1245 "Image Classification Results",
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1246 self.args.output_dir,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1247 backend_args,
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1248 split_info,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1249 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1250 logger.info(f"HTML report generated at: {report_file}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1251 self.backend.convert_parquet_to_csv(self.args.output_dir)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1252 logger.info("Converted Parquet to CSV.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1253 except Exception:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1254 logger.error("Workflow execution failed", exc_info=True)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1255 raise
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1256 finally:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1257 self._cleanup_temp_dirs()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1258
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1259
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1260 def parse_learning_rate(s):
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1261 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1262 return float(s)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1263 except (TypeError, ValueError):
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1264 return None
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1265
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1266
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1267 def aug_parse(aug_string: str):
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1268 """
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1269 Parse comma-separated augmentation keys into Ludwig augmentation dicts.
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1270 Raises ValueError on unknown key.
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1271 """
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1272 mapping = {
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1273 "random_horizontal_flip": {"type": "random_horizontal_flip"},
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1274 "random_vertical_flip": {"type": "random_vertical_flip"},
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1275 "random_rotate": {"type": "random_rotate", "degree": 10},
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1276 "random_blur": {"type": "random_blur", "kernel_size": 3},
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1277 "random_brightness": {"type": "random_brightness", "min": 0.5, "max": 2.0},
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1278 "random_contrast": {"type": "random_contrast", "min": 0.5, "max": 2.0},
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1279 }
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1280 aug_list = []
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1281 for tok in aug_string.split(","):
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1282 key = tok.strip()
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1283 if key not in mapping:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1284 valid = ", ".join(mapping.keys())
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1285 raise ValueError(f"Unknown augmentation '{key}'. Valid choices: {valid}")
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1286 aug_list.append(mapping[key])
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1287 return aug_list
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1288
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1289
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1290 class SplitProbAction(argparse.Action):
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1291 def __call__(self, parser, namespace, values, option_string=None):
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1292 train, val, test = values
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1293 total = train + val + test
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1294 if abs(total - 1.0) > 1e-6:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1295 parser.error(
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1296 f"--split-probabilities must sum to 1.0; "
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1297 f"got {train:.3f} + {val:.3f} + {test:.3f} = {total:.3f}"
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1298 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1299 setattr(namespace, self.dest, values)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1300
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1301
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1302 def main():
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1303 parser = argparse.ArgumentParser(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1304 description="Image Classification Learner with Pluggable Backends",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1305 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1306 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1307 "--csv-file",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1308 required=True,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1309 type=Path,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1310 help="Path to the input CSV",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1311 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1312 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1313 "--image-zip",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1314 required=True,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1315 type=Path,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1316 help="Path to the images ZIP",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1317 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1318 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1319 "--model-name",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1320 required=True,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1321 choices=MODEL_ENCODER_TEMPLATES.keys(),
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1322 help="Which model template to use",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1323 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1324 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1325 "--use-pretrained",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1326 action="store_true",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1327 help="Use pretrained weights for the model",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1328 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1329 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1330 "--fine-tune",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1331 action="store_true",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1332 help="Enable fine-tuning",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1333 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1334 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1335 "--epochs",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1336 type=int,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1337 default=10,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1338 help="Number of training epochs",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1339 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1340 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1341 "--early-stop",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1342 type=int,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1343 default=5,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1344 help="Early stopping patience",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1345 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1346 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1347 "--batch-size",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1348 type=int,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1349 help="Batch size (None = auto)",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1350 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1351 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1352 "--output-dir",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1353 type=Path,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1354 default=Path("learner_output"),
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1355 help="Where to write outputs",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1356 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1357 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1358 "--validation-size",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1359 type=float,
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1360 default=0.15,
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1361 help="Fraction for validation (0.0–1.0)",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1362 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1363 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1364 "--preprocessing-num-processes",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1365 type=int,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1366 default=max(1, os.cpu_count() // 2),
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1367 help="CPU processes for data prep",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1368 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1369 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1370 "--split-probabilities",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1371 type=float,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1372 nargs=3,
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1373 metavar=("train", "val", "test"),
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1374 action=SplitProbAction,
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1375 default=[0.7, 0.1, 0.2],
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1376 help=(
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1377 "Random split proportions (e.g., 0.7 0.1 0.2)."
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1378 "Only used if no split column."
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1379 ),
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1380 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1381 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1382 "--random-seed",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1383 type=int,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1384 default=42,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1385 help="Random seed used for dataset splitting (default: 42)",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1386 )
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1387 parser.add_argument(
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1388 "--learning-rate",
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1389 type=parse_learning_rate,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1390 default=None,
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1391 help="Learning rate. If not provided, Ludwig will auto-select it.",
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1392 )
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1393 parser.add_argument(
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1394 "--augmentation",
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1395 type=str,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1396 default=None,
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1397 help=(
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1398 "Comma-separated list (in order) of any of: "
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1399 "random_horizontal_flip, random_vertical_flip, random_rotate, "
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1400 "random_blur, random_brightness, random_contrast. "
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1401 "E.g. --augmentation random_horizontal_flip,random_rotate"
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1402 ),
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1403 )
8
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1404 parser.add_argument(
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1405 "--threshold",
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1406 type=float,
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1407 default=None,
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1408 help=(
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1409 "Decision threshold for binary classification (0.0–1.0)."
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1410 "Overrides default 0.5."
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1411 )
85e6f4b2ad18 planemo upload for repository https://github.com/goeckslab/gleam.git commit 8a42eb9b33df7e1df5ad5153b380e20b910a05b6
goeckslab
parents: 7
diff changeset
1412 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1413 args = parser.parse_args()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1414 if not 0.0 <= args.validation_size <= 1.0:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1415 parser.error("validation-size must be between 0.0 and 1.0")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1416 if not args.csv_file.is_file():
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1417 parser.error(f"CSV not found: {args.csv_file}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1418 if not args.image_zip.is_file():
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1419 parser.error(f"ZIP not found: {args.image_zip}")
2
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1420 if args.augmentation is not None:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1421 try:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1422 augmentation_setup = aug_parse(args.augmentation)
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1423 setattr(args, "augmentation", augmentation_setup)
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1424 except ValueError as e:
186424a7eca7 planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents: 1
diff changeset
1425 parser.error(str(e))
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1426 backend_instance = LudwigDirectBackend()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1427 orchestrator = WorkflowOrchestrator(args, backend_instance)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1428 exit_code = 0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1429 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1430 orchestrator.run()
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1431 logger.info("Main script finished successfully.")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1432 except Exception as e:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1433 logger.error(f"Main script failed.{e}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1434 exit_code = 1
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1435 finally:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1436 sys.exit(exit_code)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1437
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1438
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1439 if __name__ == "__main__":
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1440 try:
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1441 import ludwig
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1442 logger.debug(f"Found Ludwig version: {ludwig.globals.LUDWIG_VERSION}")
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1443 except ImportError:
1
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1444 logger.error(
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1445 "Ludwig library not found. Please ensure Ludwig is installed "
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1446 "('pip install ludwig[image]')"
39202fe5cf97 planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 0
diff changeset
1447 )
0
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1448 sys.exit(1)
54b871dfc51e planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff changeset
1449 main()