added experiments files
Browse files
experiments/results/dataset_audit/report.txt
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@@ -1,86 +1,86 @@
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legacy root : C:/Users/Kaveh/Documents/cellforce/dataset
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dataset root: C:\Users\Kaveh\Documents\Shape2Force\dataset
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legacy all_tune/train n= 280
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legacy all_tune/test n= 81
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legacy fibro_split/train n= 236
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legacy fibro_split/test n= 46
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legacy 1kpa_new/train n= 16
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legacy 1kpa_new/test n= 15
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legacy 10kpa_new/train n= 28
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legacy 10kpa_new/test n= 20
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legacy 1kPa_SET_III n= 17
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legacy DMSO_SET_II n= 11
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legacy Y27632_SET_II n= 20
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legacy Control_SET_I n= 27
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legacy Fibronectin_SET_I n= 40
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legacy TGFB_SET_I n= 15
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legacy Y27632_SET_I n= 16
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legacy U2OS/test n= 39
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legacy Drugs/all n= 98
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legacy spheroid/train n= 129
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legacy spheroid/test n= 28
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repository singlecell/train n= 236
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repository singlecell/test n= 46
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repository spheroid/train n= 129
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repository spheroid/test n= 28
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Folders with samples in the legacy tree that are NOT listed in experiments/layout.py:
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single_cell\01kPa\train (30 samples)
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single_cell\10kPa\train (30 samples)
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single_cell\10kpa_new\all (48 samples)
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single_cell\1kpa_new\all (31 samples)
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single_cell\ds\10kpa (20 samples)
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single_cell\ds\1kpa (15 samples)
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single_cell\ds\u2os (39 samples)
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single_cell\fibros\test (59 samples)
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single_cell\fibros\train (223 samples)
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single_cell\u2os\train (12 samples)
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single_cell\U2OS_best_images\test (8 samples)
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single_cell\U2OS_best_images\train (23 samples)
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Repository dataset vs legacy:
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singlecell/train vs fibro_split/train : shared 236, only repo 0, only legacy 0
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singlecell/test vs fibro_split/test : shared 46, only repo 0, only legacy 0
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| 45 |
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spheroid/train vs spheroid/train : shared 128, only repo 0, only legacy 0
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| 46 |
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spheroid/test vs spheroid/test : shared 28, only repo 0, only legacy 0
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all_tune composition (split x source set):
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train 10kpa_new/train 28
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train 1kpa_new/train 16
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train fibro_split/train 236
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val 10kpa_new/test 20
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val 1kpa_new/test 15
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val fibro_split/test 46
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all_tune images NOT in the repository dataset (Zenodo v1): 79
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train 10kpa_new/train 28
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train 1kpa_new/train 16
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val 10kpa_new/test 20
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val 1kpa_new/test 15
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Substrate code the original code fed for all_tune folders (folder_name[:4]):
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train 'Posi' -> fibroblasts_PDMS 236
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train 'kpan0' -> PDMS_1kPa_3um 16
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train 'kpan1' -> PDMS_10kPa_3um 28
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val 'Posi' -> fibroblasts_PDMS 46
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val 'kpan0' -> PDMS_1kPa_3um 15
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val 'kpan1' -> PDMS_10kPa_3um 20
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Leakage check - independent test sets vs all_tune train+val (must be 0):
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1kPa_SET_III 0 (of 17)
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DMSO_SET_II 0 (of 11)
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Y27632_SET_II 0 (of 20)
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Control_SET_I 0 (of 27)
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Fibronectin_SET_I 0 (of 40)
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TGFB_SET_I 0 (of 15)
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Y27632_SET_I 0 (of 16)
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U2OS/test 0 (of 39)
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Validation-set content - legacy 'test' folders inside all_tune/test (val):
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fibro_split/test 46 of 46 in val; 0 in train
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1kpa_new/test 15 of 15 in val; 0 in train
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10kpa_new/test 20 of 20 in val; 0 in train
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Copying and writing manifests ...
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sample folders: {'copied': 264}
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manifests written to experiments/splits/ - commit them to git
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| 1 |
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legacy root : C:/Users/Kaveh/Documents/cellforce/dataset
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dataset root: C:\Users\Kaveh\Documents\Shape2Force\dataset
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+
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legacy all_tune/train n= 280
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legacy all_tune/test n= 81
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legacy fibro_split/train n= 236
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legacy fibro_split/test n= 46
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legacy 1kpa_new/train n= 16
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legacy 1kpa_new/test n= 15
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legacy 10kpa_new/train n= 28
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legacy 10kpa_new/test n= 20
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legacy 1kPa_SET_III n= 17
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legacy DMSO_SET_II n= 11
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| 14 |
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legacy Y27632_SET_II n= 20
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| 15 |
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legacy Control_SET_I n= 27
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legacy Fibronectin_SET_I n= 40
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legacy TGFB_SET_I n= 15
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legacy Y27632_SET_I n= 16
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legacy U2OS/test n= 39
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legacy Drugs/all n= 98
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legacy spheroid/train n= 129
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legacy spheroid/test n= 28
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repository singlecell/train n= 236
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repository singlecell/test n= 46
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repository spheroid/train n= 129
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repository spheroid/test n= 28
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Folders with samples in the legacy tree that are NOT listed in experiments/layout.py:
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| 29 |
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single_cell\01kPa\train (30 samples)
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single_cell\10kPa\train (30 samples)
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single_cell\10kpa_new\all (48 samples)
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single_cell\1kpa_new\all (31 samples)
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single_cell\ds\10kpa (20 samples)
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single_cell\ds\1kpa (15 samples)
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single_cell\ds\u2os (39 samples)
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single_cell\fibros\test (59 samples)
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single_cell\fibros\train (223 samples)
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single_cell\u2os\train (12 samples)
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single_cell\U2OS_best_images\test (8 samples)
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single_cell\U2OS_best_images\train (23 samples)
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Repository dataset vs legacy:
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singlecell/train vs fibro_split/train : shared 236, only repo 0, only legacy 0
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| 44 |
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singlecell/test vs fibro_split/test : shared 46, only repo 0, only legacy 0
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| 45 |
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spheroid/train vs spheroid/train : shared 128, only repo 0, only legacy 0
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| 46 |
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spheroid/test vs spheroid/test : shared 28, only repo 0, only legacy 0
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all_tune composition (split x source set):
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| 49 |
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train 10kpa_new/train 28
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train 1kpa_new/train 16
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train fibro_split/train 236
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val 10kpa_new/test 20
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val 1kpa_new/test 15
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val fibro_split/test 46
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all_tune images NOT in the repository dataset (Zenodo v1): 79
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train 10kpa_new/train 28
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train 1kpa_new/train 16
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val 10kpa_new/test 20
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val 1kpa_new/test 15
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Substrate code the original code fed for all_tune folders (folder_name[:4]):
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train 'Posi' -> fibroblasts_PDMS 236
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train 'kpan0' -> PDMS_1kPa_3um 16
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train 'kpan1' -> PDMS_10kPa_3um 28
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val 'Posi' -> fibroblasts_PDMS 46
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val 'kpan0' -> PDMS_1kPa_3um 15
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val 'kpan1' -> PDMS_10kPa_3um 20
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Leakage check - independent test sets vs all_tune train+val (must be 0):
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1kPa_SET_III 0 (of 17)
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DMSO_SET_II 0 (of 11)
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Y27632_SET_II 0 (of 20)
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Control_SET_I 0 (of 27)
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Fibronectin_SET_I 0 (of 40)
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TGFB_SET_I 0 (of 15)
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Y27632_SET_I 0 (of 16)
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U2OS/test 0 (of 39)
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Validation-set content - legacy 'test' folders inside all_tune/test (val):
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fibro_split/test 46 of 46 in val; 0 in train
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1kpa_new/test 15 of 15 in val; 0 in train
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10kpa_new/test 20 of 20 in val; 0 in train
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Copying and writing manifests ...
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sample folders: {'copied': 264}
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manifests written to experiments/splits/ - commit them to git
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experiments/results/eval/model_params.csv
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@@ -3,3 +3,21 @@ released_singlecell,77.002341,,
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released_spheroid_GN,77.000613,,
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supervised_spheroid_FN,11.783428,,
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stage1_image_only,77.000613,,
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released_spheroid_GN,77.000613,,
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supervised_spheroid_FN,11.783428,,
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stage1_image_only,77.000613,,
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s2f_full_seed0,77.002341,22.0,0.6845365777248289
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s2f_full_seed1,77.002341,32.0,0.7641608729595091
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s2f_no_force_seed0,77.002341,36.0,0.6944503726028814
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s2f_no_force_seed1,77.002341,31.0,0.7536247052797457
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s2f_no_gan_seed0,77.002341,21.0,0.721968437113413
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s2f_no_gan_seed1,77.002341,34.0,0.7040372549033747
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s2f_no_substrate_no_gan_seed0,77.000613,25.0,0.598808929687593
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s2f_no_substrate_no_gan_seed1,77.000613,38.0,0.6280873359703436
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s2f_no_substrate_seed0,77.000613,23.0,0.6303678663765512
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s2f_no_substrate_seed1,77.000613,17.0,0.6032634014036597
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unet_gan_no_substrate_seed0,31.036481,21.0,0.6770522376386131
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unet_gan_no_substrate_seed1,31.036481,1.0,0.6818016338639143
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unet_gan_seed0,31.037633,18.0,0.7331220245942837
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unet_gan_seed1,31.037633,24.0,0.8099774224002186
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unet_no_substrate_seed0,31.036481,12.0,0.646111976809618
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unet_no_substrate_seed1,31.036481,29.0,0.6637544072255855
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unet_seed0,31.037633,21.0,0.7371067419284727
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unet_seed1,31.037633,31.0,0.7615440138956395
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experiments/results/eval/per_image.csv
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experiments/results/eval/summary.csv
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