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comparison constants.py @ 11:c5150cceab47 draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam.git commit 0fe927b618cd4dfc87af7baaa827034cc6813225
author goeckslab
date Sat, 18 Oct 2025 03:17:09 +0000
parents 85e6f4b2ad18
children
comparison
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10:b0d893d04d4c 11:c5150cceab47
5 LABEL_COLUMN_NAME = "label" 5 LABEL_COLUMN_NAME = "label"
6 IMAGE_PATH_COLUMN_NAME = "image_path" 6 IMAGE_PATH_COLUMN_NAME = "image_path"
7 DEFAULT_SPLIT_PROBABILITIES = [0.7, 0.1, 0.2] 7 DEFAULT_SPLIT_PROBABILITIES = [0.7, 0.1, 0.2]
8 TEMP_CSV_FILENAME = "processed_data_for_ludwig.csv" 8 TEMP_CSV_FILENAME = "processed_data_for_ludwig.csv"
9 TEMP_CONFIG_FILENAME = "ludwig_config.yaml" 9 TEMP_CONFIG_FILENAME = "ludwig_config.yaml"
10 TEMP_DIR_PREFIX = "ludwig_api_work_" 10 TEMP_DIR_PREFIX = "gleam_image_work_"
11 PREDICTIONS_PARQUET_FILE_NAME = "predictions.parquet"
12 TEST_STATISTICS_FILE_NAME = "test_statistics.json"
13 TRAIN_SET_METADATA_FILE_NAME = "train_set_metadata.json"
14 DESCRIPTION_FILE_NAME = "description.json"
15 TRAINING_STATISTICS_FILE_NAME = "training_statistics.json"
16 PREDICTIONS_SHAPES_FILE_NAME = "predictions.shapes"
11 MODEL_ENCODER_TEMPLATES: Dict[str, Any] = { 17 MODEL_ENCODER_TEMPLATES: Dict[str, Any] = {
12 "stacked_cnn": "stacked_cnn", 18 "stacked_cnn": "stacked_cnn",
13 "resnet18": {"type": "resnet", "model_variant": 18}, 19 "resnet18": {"type": "resnet", "model_variant": 18},
14 "resnet34": {"type": "resnet", "model_variant": 34}, 20 "resnet34": {"type": "resnet", "model_variant": 34},
15 "resnet50": {"type": "resnet", "model_variant": 50}, 21 "resnet50": {"type": "resnet", "model_variant": 50},
71 "vit_b_16": {"type": "vit", "model_variant": "b_16"}, 77 "vit_b_16": {"type": "vit", "model_variant": "b_16"},
72 "vit_b_32": {"type": "vit", "model_variant": "b_32"}, 78 "vit_b_32": {"type": "vit", "model_variant": "b_32"},
73 "vit_l_16": {"type": "vit", "model_variant": "l_16"}, 79 "vit_l_16": {"type": "vit", "model_variant": "l_16"},
74 "vit_l_32": {"type": "vit", "model_variant": "l_32"}, 80 "vit_l_32": {"type": "vit", "model_variant": "l_32"},
75 "vit_h_14": {"type": "vit", "model_variant": "h_14"}, 81 "vit_h_14": {"type": "vit", "model_variant": "h_14"},
82 "vit_huge_timm": {"type": "vit", "model_variant": "huge_timm", "custom_encoder": True},
83 # MetaFormer family (support all variants via custom_model)
84 "identityformer_s12": {"type": "stacked_cnn", "custom_model": "identityformer_s12", "use_pretrained": True, "trainable": True},
85 "identityformer_s24": {"type": "stacked_cnn", "custom_model": "identityformer_s24", "use_pretrained": True, "trainable": True},
86 "identityformer_s36": {"type": "stacked_cnn", "custom_model": "identityformer_s36", "use_pretrained": True, "trainable": True},
87 "identityformer_m36": {"type": "stacked_cnn", "custom_model": "identityformer_m36", "use_pretrained": True, "trainable": True},
88 "identityformer_m48": {"type": "stacked_cnn", "custom_model": "identityformer_m48", "use_pretrained": True, "trainable": True},
89
90 "randformer_s12": {"type": "stacked_cnn", "custom_model": "randformer_s12", "use_pretrained": True, "trainable": True},
91 "randformer_s24": {"type": "stacked_cnn", "custom_model": "randformer_s24", "use_pretrained": True, "trainable": True},
92 "randformer_s36": {"type": "stacked_cnn", "custom_model": "randformer_s36", "use_pretrained": True, "trainable": True},
93 "randformer_m36": {"type": "stacked_cnn", "custom_model": "randformer_m36", "use_pretrained": True, "trainable": True},
94 "randformer_m48": {"type": "stacked_cnn", "custom_model": "randformer_m48", "use_pretrained": True, "trainable": True},
95
96 "poolformerv2_s12": {"type": "stacked_cnn", "custom_model": "poolformerv2_s12", "use_pretrained": True, "trainable": True},
97 "poolformerv2_s24": {"type": "stacked_cnn", "custom_model": "poolformerv2_s24", "use_pretrained": True, "trainable": True},
98 "poolformerv2_s36": {"type": "stacked_cnn", "custom_model": "poolformerv2_s36", "use_pretrained": True, "trainable": True},
99 "poolformerv2_m36": {"type": "stacked_cnn", "custom_model": "poolformerv2_m36", "use_pretrained": True, "trainable": True},
100 "poolformerv2_m48": {"type": "stacked_cnn", "custom_model": "poolformerv2_m48", "use_pretrained": True, "trainable": True},
101
102 "convformer_s18": {"type": "stacked_cnn", "custom_model": "convformer_s18", "use_pretrained": True, "trainable": True},
103 "convformer_s18_384": {"type": "stacked_cnn", "custom_model": "convformer_s18_384", "use_pretrained": True, "trainable": True},
104 "convformer_s18_in21ft1k": {"type": "stacked_cnn", "custom_model": "convformer_s18_in21ft1k", "use_pretrained": True, "trainable": True},
105 "convformer_s18_384_in21ft1k": {"type": "stacked_cnn", "custom_model": "convformer_s18_384_in21ft1k", "use_pretrained": True, "trainable": True},
106 "convformer_s18_in21k": {"type": "stacked_cnn", "custom_model": "convformer_s18_in21k", "use_pretrained": True, "trainable": True},
107 "convformer_s36": {"type": "stacked_cnn", "custom_model": "convformer_s36", "use_pretrained": True, "trainable": True},
108 "convformer_s36_384": {"type": "stacked_cnn", "custom_model": "convformer_s36_384", "use_pretrained": True, "trainable": True},
109 "convformer_s36_in21ft1k": {"type": "stacked_cnn", "custom_model": "convformer_s36_in21ft1k", "use_pretrained": True, "trainable": True},
110 "convformer_s36_384_in21ft1k": {"type": "stacked_cnn", "custom_model": "convformer_s36_384_in21ft1k", "use_pretrained": True, "trainable": True},
111 "convformer_s36_in21k": {"type": "stacked_cnn", "custom_model": "convformer_s36_in21k", "use_pretrained": True, "trainable": True},
112 "convformer_m36": {"type": "stacked_cnn", "custom_model": "convformer_m36", "use_pretrained": True, "trainable": True},
113 "convformer_m36_384": {"type": "stacked_cnn", "custom_model": "convformer_m36_384", "use_pretrained": True, "trainable": True},
114 "convformer_m36_in21ft1k": {"type": "stacked_cnn", "custom_model": "convformer_m36_in21ft1k", "use_pretrained": True, "trainable": True},
115 "convformer_m36_384_in21ft1k": {"type": "stacked_cnn", "custom_model": "convformer_m36_384_in21ft1k", "use_pretrained": True, "trainable": True},
116 "convformer_m36_in21k": {"type": "stacked_cnn", "custom_model": "convformer_m36_in21k", "use_pretrained": True, "trainable": True},
117 "convformer_b36": {"type": "stacked_cnn", "custom_model": "convformer_b36", "use_pretrained": True, "trainable": True},
118 "convformer_b36_384": {"type": "stacked_cnn", "custom_model": "convformer_b36_384", "use_pretrained": True, "trainable": True},
119 "convformer_b36_in21ft1k": {"type": "stacked_cnn", "custom_model": "convformer_b36_in21ft1k", "use_pretrained": True, "trainable": True},
120 "convformer_b36_384_in21ft1k": {"type": "stacked_cnn", "custom_model": "convformer_b36_384_in21ft1k", "use_pretrained": True, "trainable": True},
121 "convformer_b36_in21k": {"type": "stacked_cnn", "custom_model": "convformer_b36_in21k", "use_pretrained": True, "trainable": True},
122
123 "caformer_s18": {
124 "type": "stacked_cnn",
125 "custom_model": "caformer_s18",
126 "use_pretrained": True,
127 "trainable": True,
128 },
129 "caformer_s36": {
130 "type": "stacked_cnn",
131 "custom_model": "caformer_s36",
132 "use_pretrained": True,
133 "trainable": True,
134 },
135 "caformer_m36": {
136 "type": "stacked_cnn",
137 "custom_model": "caformer_m36",
138 "use_pretrained": True,
139 "trainable": True,
140 },
141 "caformer_b36": {
142 "type": "stacked_cnn",
143 "custom_model": "caformer_b36",
144 "use_pretrained": True,
145 "trainable": True,
146 },
147 "caformer_s18_384": {"type": "stacked_cnn", "custom_model": "caformer_s18_384", "use_pretrained": True, "trainable": True},
148 "caformer_s18_in21ft1k": {"type": "stacked_cnn", "custom_model": "caformer_s18_in21ft1k", "use_pretrained": True, "trainable": True},
149 "caformer_s18_384_in21ft1k": {"type": "stacked_cnn", "custom_model": "caformer_s18_384_in21ft1k", "use_pretrained": True, "trainable": True},
150 "caformer_s18_in21k": {"type": "stacked_cnn", "custom_model": "caformer_s18_in21k", "use_pretrained": True, "trainable": True},
151 "caformer_s36_384": {"type": "stacked_cnn", "custom_model": "caformer_s36_384", "use_pretrained": True, "trainable": True},
152 "caformer_s36_in21ft1k": {"type": "stacked_cnn", "custom_model": "caformer_s36_in21ft1k", "use_pretrained": True, "trainable": True},
153 "caformer_s36_384_in21ft1k": {"type": "stacked_cnn", "custom_model": "caformer_s36_384_in21ft1k", "use_pretrained": True, "trainable": True},
154 "caformer_s36_in21k": {"type": "stacked_cnn", "custom_model": "caformer_s36_in21k", "use_pretrained": True, "trainable": True},
155 "caformer_m36_384": {"type": "stacked_cnn", "custom_model": "caformer_m36_384", "use_pretrained": True, "trainable": True},
156 "caformer_m36_in21ft1k": {"type": "stacked_cnn", "custom_model": "caformer_m36_in21ft1k", "use_pretrained": True, "trainable": True},
157 "caformer_m36_384_in21ft1k": {"type": "stacked_cnn", "custom_model": "caformer_m36_384_in21ft1k", "use_pretrained": True, "trainable": True},
158 "caformer_m36_in21k": {"type": "stacked_cnn", "custom_model": "caformer_m36_in21k", "use_pretrained": True, "trainable": True},
159 "caformer_b36_384": {"type": "stacked_cnn", "custom_model": "caformer_b36_384", "use_pretrained": True, "trainable": True},
160 "caformer_b36_in21ft1k": {"type": "stacked_cnn", "custom_model": "caformer_b36_in21ft1k", "use_pretrained": True, "trainable": True},
161 "caformer_b36_384_in21ft1k": {"type": "stacked_cnn", "custom_model": "caformer_b36_384_in21ft1k", "use_pretrained": True, "trainable": True},
162 "caformer_b36_in21k": {"type": "stacked_cnn", "custom_model": "caformer_b36_in21k", "use_pretrained": True, "trainable": True},
76 "convnext_tiny": {"type": "convnext", "model_variant": "tiny"}, 163 "convnext_tiny": {"type": "convnext", "model_variant": "tiny"},
77 "convnext_small": {"type": "convnext", "model_variant": "small"}, 164 "convnext_small": {"type": "convnext", "model_variant": "small"},
78 "convnext_base": {"type": "convnext", "model_variant": "base"}, 165 "convnext_base": {"type": "convnext", "model_variant": "base"},
79 "convnext_large": {"type": "convnext", "model_variant": "large"}, 166 "convnext_large": {"type": "convnext", "model_variant": "large"},
80 "maxvit_t": {"type": "maxvit", "model_variant": "t"}, 167 "maxvit_t": {"type": "maxvit", "model_variant": "t"},