Mercurial > repos > goeckslab > image_learner
view split_data.py @ 13:1a9c42974a5a draft default tip
planemo upload for repository https://github.com/goeckslab/gleam.git commit 9f96da4ea7ab3b572af86698ff51b870125cd674
| author | goeckslab |
|---|---|
| date | Fri, 21 Nov 2025 17:35:00 +0000 |
| parents | bcfa2e234a80 |
| children |
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import argparse import logging from typing import Optional import numpy as np import pandas as pd from sklearn.model_selection import train_test_split logger = logging.getLogger("ImageLearner") def split_data_0_2( df: pd.DataFrame, split_column: str, validation_size: float = 0.1, random_state: int = 42, label_column: Optional[str] = None, ) -> pd.DataFrame: """Given a DataFrame whose split_column only contains {0,2}, re-assign a portion of the 0s to become 1s (validation).""" out = df.copy() out[split_column] = pd.to_numeric(out[split_column], errors="coerce").astype(int) idx_train = out.index[out[split_column] == 0].tolist() if not idx_train: logger.info("No rows with split=0; nothing to do.") return out stratify_arr = None if label_column and label_column in out.columns: label_counts = out.loc[idx_train, label_column].value_counts() if label_counts.size > 1: # Force stratify even with fewer samples - adjust validation_size if needed min_samples_per_class = label_counts.min() if min_samples_per_class * validation_size < 1: # Adjust validation_size to ensure at least 1 sample per class, but do not exceed original validation_size adjusted_validation_size = min( validation_size, 1.0 / min_samples_per_class ) if adjusted_validation_size != validation_size: validation_size = adjusted_validation_size logger.info( f"Adjusted validation_size to {validation_size:.3f} to ensure at least one sample per class in validation" ) stratify_arr = out.loc[idx_train, label_column] logger.info("Using stratified split for validation set") else: logger.warning("Only one label class found; cannot stratify") if validation_size <= 0: logger.info("validation_size <= 0; keeping all as train.") return out if validation_size >= 1: logger.info("validation_size >= 1; moving all train → validation.") out.loc[idx_train, split_column] = 1 return out # Always try stratified split first try: train_idx, val_idx = train_test_split( idx_train, test_size=validation_size, random_state=random_state, stratify=stratify_arr, ) logger.info("Successfully applied stratified split") except ValueError as e: logger.warning(f"Stratified split failed ({e}); falling back to random split.") train_idx, val_idx = train_test_split( idx_train, test_size=validation_size, random_state=random_state, stratify=None, ) out.loc[train_idx, split_column] = 0 out.loc[val_idx, split_column] = 1 out[split_column] = out[split_column].astype(int) return out def create_stratified_random_split( df: pd.DataFrame, split_column: str, split_probabilities: list = [0.7, 0.1, 0.2], random_state: int = 42, label_column: Optional[str] = None, ) -> pd.DataFrame: """Create a stratified random split when no split column exists.""" out = df.copy() # initialize split column out[split_column] = 0 if not label_column or label_column not in out.columns: logger.warning( "No label column found; using random split without stratification" ) # fall back to simple random assignment indices = out.index.tolist() np.random.seed(random_state) np.random.shuffle(indices) n_total = len(indices) n_train = int(n_total * split_probabilities[0]) n_val = int(n_total * split_probabilities[1]) out.loc[indices[:n_train], split_column] = 0 out.loc[indices[n_train:n_train + n_val], split_column] = 1 out.loc[indices[n_train + n_val:], split_column] = 2 return out.astype({split_column: int}) # check if stratification is possible label_counts = out[label_column].value_counts() min_samples_per_class = label_counts.min() # ensure we have enough samples for stratification: # Each class must have at least as many samples as the number of splits, # so that each split can receive at least one sample per class. min_samples_required = len(split_probabilities) if min_samples_per_class < min_samples_required: logger.warning( f"Insufficient samples per class for stratification (min: {min_samples_per_class}, required: {min_samples_required}); using random split" ) # fall back to simple random assignment indices = out.index.tolist() np.random.seed(random_state) np.random.shuffle(indices) n_total = len(indices) n_train = int(n_total * split_probabilities[0]) n_val = int(n_total * split_probabilities[1]) out.loc[indices[:n_train], split_column] = 0 out.loc[indices[n_train:n_train + n_val], split_column] = 1 out.loc[indices[n_train + n_val:], split_column] = 2 return out.astype({split_column: int}) logger.info("Using stratified random split for train/validation/test sets") # first split: separate test set train_val_idx, test_idx = train_test_split( out.index.tolist(), test_size=split_probabilities[2], random_state=random_state, stratify=out[label_column], ) # second split: separate training and validation from remaining data val_size_adjusted = split_probabilities[1] / ( split_probabilities[0] + split_probabilities[1] ) train_idx, val_idx = train_test_split( train_val_idx, test_size=val_size_adjusted, random_state=random_state, stratify=out.loc[train_val_idx, label_column] if label_column and label_column in out.columns else None, ) # assign split values out.loc[train_idx, split_column] = 0 out.loc[val_idx, split_column] = 1 out.loc[test_idx, split_column] = 2 logger.info("Successfully applied stratified random split") logger.info( f"Split counts: Train={len(train_idx)}, Val={len(val_idx)}, Test={len(test_idx)}" ) return out.astype({split_column: int}) class SplitProbAction(argparse.Action): def __call__(self, parser, namespace, values, option_string=None): train, val, test = values total = train + val + test if abs(total - 1.0) > 1e-6: parser.error( f"--split-probabilities must sum to 1.0; " f"got {train:.3f} + {val:.3f} + {test:.3f} = {total:.3f}" ) setattr(namespace, self.dest, values)
