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|
DIR_ROOT = "../"
FILES = {
"TRAINING_DATASET": DIR_ROOT + "data/spheroid26_011523_filtered.csv",
"TRAINING_DATASET_WIDE_BERTH": DIR_ROOT + "data/spheroid26_011523_exc.csv",
"PRETRAINED_MODEL_DIR": DIR_ROOT + "models/current_model/",
"PEN_TRACKED": {
"AUTO": DIR_ROOT + "data/PEN_automatically_tracked.csv",
"MANUAL": DIR_ROOT + "data/PEN_manually_tracked.csv",
},
"RHO": {
"3": DIR_ROOT + "data/Rho_act_Cell3.csv",
"4": DIR_ROOT + "data/Rho_act_Cell4.csv",
"6": DIR_ROOT + "data/Rho_act_Cell6.csv",
"7": DIR_ROOT + "data/Rho_act_Cell7.csv",
"8": DIR_ROOT + "data/Rho_act_Cell8.csv",
"9": DIR_ROOT + "data/Rho_act_Cell9.csv",
"10": DIR_ROOT + "data/Rho_act_Cell10.csv",
"11": DIR_ROOT + "data/Rho_act_Cell11.csv",
},
"CN03": {
"3": DIR_ROOT + "data/Rho_act_Cell3.csv",
"4": DIR_ROOT + "data/Rho_act_Cell4.csv",
"6": DIR_ROOT + "data/Rho_act_Cell6.csv",
"7": DIR_ROOT + "data/Rho_act_Cell7.csv",
"8": DIR_ROOT + "data/Rho_act_Cell8.csv",
"9": DIR_ROOT + "data/Rho_act_Cell9.csv",
"10": DIR_ROOT + "data/Rho_act_Cell10.csv",
"11": DIR_ROOT + "data/Rho_act_Cell11.csv",
},
"Y27632": {
"1": DIR_ROOT + "data/Y27632_Cell1.csv",
"2": DIR_ROOT + "data/Y27632_Cell2.csv",
"3": DIR_ROOT + "data/Y27632_Cell3.csv",
"4": DIR_ROOT + "data/Y27632_Cell4.csv",
"5": DIR_ROOT + "data/Y27632_Cell5.csv",
},
"HISTOLOGIES": {
"J1": DIR_ROOT + "../HistologyProject/J1/svm/svm.csv",
"image001": DIR_ROOT + "../HistologyProject/image001/svm/svm.csv",
"H4": DIR_ROOT + "../HistologyProject/H4/svm/svm.csv",
"H9": DIR_ROOT + "../HistologyProject/H9/svm/svm.csv",
},
"SPHEROID": {
"1p5mgml": DIR_ROOT + "data/spheroid26_011523_filtered.csv",
"3mgml": DIR_ROOT + "data/spheroid20_011923_filtered.csv",
"4mgml": DIR_ROOT + "data/spheroid22_012323_filtered.csv",
"6mgml": DIR_ROOT + "data/spheroid26_012423_filtered.csv",
},
"SPHEROID_RAW": {
"REG": {
"1p5mgml": [
DIR_ROOT + "data/" + "spheroid15_030322_RegularCollagen_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid16_030322_RegularCollagen_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid17_041022_RegularCollagen_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid18_041022_RegularCollagen_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid26_011523_RegularCollagen_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid27_090323_RegularCollagen_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid28_090523_RegularCollagen_1p5mgml.csv",
],
"3mgml": [
DIR_ROOT + "data/" + "spheroid15_031022_RegularCollagen_3mgml.csv",
DIR_ROOT + "data/" + "spheroid16_031522_RegularCollagen_3mgml.csv",
DIR_ROOT + "data/" + "spheroid17_041022_RegularCollagen_3mgml.csv",
DIR_ROOT + "data/" + "spheroid18_083022_RegularCollagen_3mgml.csv",
DIR_ROOT + "data/" + "spheroid19_083022_RegularCollagen_3mgml.csv",
DIR_ROOT + "data/" + "spheroid20_011923_RegularCollagen_3mgml.csv",
],
"4mgml": [
DIR_ROOT + "data/" + "spheroid17_031022_RegularCollagen_4mgml.csv",
DIR_ROOT + "data/" + "spheroid18_031022_RegularCollagen_4mgml.csv",
DIR_ROOT + "data/" + "spheroid19_031022_RegularCollagen_4mgml.csv",
DIR_ROOT + "data/" + "spheroid20_083022_RegularCollagen_4mgml.csv",
DIR_ROOT + "data/" + "spheroid21_083022_RegularCollagen_4mgml.csv",
DIR_ROOT + "data/" + "spheroid22_012323_RegularCollagen_4mgml.csv",
],
"6mgml": [
DIR_ROOT + "data/" + "spheroid22_031022_RegularCollagen_6mgml.csv",
DIR_ROOT + "data/" + "spheroid23_031022_RegularCollagen_6mgml.csv",
DIR_ROOT + "data/" + "spheroid24_031022_RegularCollagen_6mgml.csv",
DIR_ROOT + "data/" + "spheroid25_031022_RegularCollagen_6mgml.csv",
DIR_ROOT + "data/" + "spheroid26_012423_RegularCollagen_6mgml.csv",
],
},
"PC": {
"1p5mgml": [
DIR_ROOT + "data/" + "spheroid1_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid2_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid3_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid4_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid5_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid7_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid8_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid9_012723_PhotoCol_1p5mgml.csv",
],
"3mgml": [
DIR_ROOT + "data/" + "spheroid5_022022_PhotoCol_3mgml.csv",
DIR_ROOT + "data/" + "spheroid6_022022_PhotoCol_3mgml.csv",
DIR_ROOT + "data/" + "spheroid7_030322_PhotoCol_3mgml.csv",
DIR_ROOT + "data/" + "spheroid8_030322_PhotoCol_3mgml.csv",
DIR_ROOT + "data/" + "spheroid12_060923_PhotoCol_3mgml.csv",
],
"4mgml": [
DIR_ROOT + "data/" + "spheroid2_022022_PhotoCol_4mgml.csv",
DIR_ROOT + "data/" + "spheroid3_053122_PhotoCol_4mgml.csv",
DIR_ROOT + "data/" + "spheroid4_053122_PhotoCol_4mgml.csv",
DIR_ROOT + "data/" + "spheroid5_053122_PhotoCol_4mgml.csv",
DIR_ROOT + "data/" + "spheroid6_053122_PhotoCol_4mgml.csv",
DIR_ROOT + "data/" + "spheroid7_091222_PhotoCol_4mgml.csv",
DIR_ROOT + "data/" + "spheroid8_091822_PhotoCol_4mgml.csv",
],
"6mgml": [
DIR_ROOT + "data/" + "spheroid1_021922_PhotoCol_6mgml.csv",
DIR_ROOT + "data/" + "spheroid2_021922_PhotoCol_6mgml.csv",
DIR_ROOT + "data/" + "spheroid3_021922_PhotoCol_6mgml.csv",
DIR_ROOT + "data/" + "spheroid4_021922_PhotoCol_6mgml.csv",
DIR_ROOT + "data/" + "spheroid6_091222_PhotoCol_6mgml.csv",
DIR_ROOT + "data/" + "spheroid8_022323_PhotoCol_6mgml.csv",
],
},
},
"SPHEROID_RAW_RIC": {
"NAME": "(R)esolution (I)mage type (C)oncentration",
"QUARTER_HOUR": {
"REG": {
"1p5mgml": [
DIR_ROOT
+ "data/"
+ "spheroid28_090523_RegularCollagen_1p5mgml.csv",
],
"3mgml": [
DIR_ROOT + "data/" + "spheroid20_011923_RegularCollagen_3mgml.csv",
],
"4mgml": [
DIR_ROOT + "data/" + "spheroid22_012323_RegularCollagen_4mgml.csv",
],
"6mgml": [
DIR_ROOT + "data/" + "spheroid26_012423_RegularCollagen_6mgml.csv",
],
},
"PC": {
"1p5mgml": [
DIR_ROOT + "data/" + "spheroid9_012723_PhotoCol_1p5mgml.csv",
],
"3mgml": [
DIR_ROOT + "data/" + "spheroid12_060923_PhotoCol_3mgml.csv",
],
"4mgml": [],
"6mgml": [
DIR_ROOT + "data/" + "spheroid8_022323_PhotoCol_6mgml.csv",
],
},
},
"DAILY": {
"REG": {
"1p5mgml": [
DIR_ROOT
+ "data/"
+ "spheroid15_030322_RegularCollagen_1p5mgml.csv",
DIR_ROOT
+ "data/"
+ "spheroid16_030322_RegularCollagen_1p5mgml.csv",
DIR_ROOT
+ "data/"
+ "spheroid17_041022_RegularCollagen_1p5mgml.csv",
DIR_ROOT
+ "data/"
+ "spheroid18_041022_RegularCollagen_1p5mgml.csv",
DIR_ROOT
+ "data/"
+ "spheroid26_011523_RegularCollagen_1p5mgml.csv",
DIR_ROOT
+ "data/"
+ "spheroid27_090323_RegularCollagen_1p5mgml.csv",
],
"3mgml": [
DIR_ROOT + "data/" + "spheroid15_031022_RegularCollagen_3mgml.csv",
DIR_ROOT + "data/" + "spheroid16_031522_RegularCollagen_3mgml.csv",
DIR_ROOT + "data/" + "spheroid17_041022_RegularCollagen_3mgml.csv",
DIR_ROOT + "data/" + "spheroid18_083022_RegularCollagen_3mgml.csv",
DIR_ROOT + "data/" + "spheroid19_083022_RegularCollagen_3mgml.csv",
],
"4mgml": [
DIR_ROOT + "data/" + "spheroid17_031022_RegularCollagen_4mgml.csv",
DIR_ROOT + "data/" + "spheroid18_031022_RegularCollagen_4mgml.csv",
DIR_ROOT + "data/" + "spheroid19_031022_RegularCollagen_4mgml.csv",
DIR_ROOT + "data/" + "spheroid20_083022_RegularCollagen_4mgml.csv",
DIR_ROOT + "data/" + "spheroid21_083022_RegularCollagen_4mgml.csv",
],
"6mgml": [
DIR_ROOT + "data/" + "spheroid22_031022_RegularCollagen_6mgml.csv",
DIR_ROOT + "data/" + "spheroid23_031022_RegularCollagen_6mgml.csv",
DIR_ROOT + "data/" + "spheroid24_031022_RegularCollagen_6mgml.csv",
DIR_ROOT + "data/" + "spheroid25_031022_RegularCollagen_6mgml.csv",
],
},
"PC": {
"1p5mgml": [
DIR_ROOT + "data/" + "spheroid1_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid2_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid3_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid4_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid5_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid7_021922_PhotoCol_1p5mgml.csv",
DIR_ROOT + "data/" + "spheroid8_021922_PhotoCol_1p5mgml.csv",
],
"3mgml": [
DIR_ROOT + "data/" + "spheroid5_022022_PhotoCol_3mgml.csv",
DIR_ROOT + "data/" + "spheroid6_022022_PhotoCol_3mgml.csv",
DIR_ROOT + "data/" + "spheroid7_030322_PhotoCol_3mgml.csv",
DIR_ROOT + "data/" + "spheroid8_030322_PhotoCol_3mgml.csv",
DIR_ROOT + "data/" + "spheroid12_060923_PhotoCol_3mgml.csv",
],
"4mgml": [
DIR_ROOT + "data/" + "spheroid2_022022_PhotoCol_4mgml.csv",
DIR_ROOT + "data/" + "spheroid3_053122_PhotoCol_4mgml.csv",
DIR_ROOT + "data/" + "spheroid4_053122_PhotoCol_4mgml.csv",
DIR_ROOT + "data/" + "spheroid5_053122_PhotoCol_4mgml.csv",
DIR_ROOT + "data/" + "spheroid6_053122_PhotoCol_4mgml.csv",
DIR_ROOT + "data/" + "spheroid7_091222_PhotoCol_4mgml.csv",
],
"6mgml": [
DIR_ROOT + "data/" + "spheroid1_021922_PhotoCol_6mgml.csv",
DIR_ROOT + "data/" + "spheroid2_021922_PhotoCol_6mgml.csv",
DIR_ROOT + "data/" + "spheroid3_021922_PhotoCol_6mgml.csv",
DIR_ROOT + "data/" + "spheroid4_021922_PhotoCol_6mgml.csv",
DIR_ROOT + "data/" + "spheroid6_091222_PhotoCol_6mgml.csv",
],
},
},
},
"SPHEROID_PC": {
"1p5mgml": DIR_ROOT + "data/spheroid9_012723_pc_1p5.csv",
"3mgml": DIR_ROOT + "data/spheroid12_060923_pc_3.csv",
},
"SPHEROID_MASKS": {
"1p5mgml": DIR_ROOT + "data/spheroid_1p5mgml_spheroid26_011523/images/",
"3mgml": DIR_ROOT + "data/spheroid_3mgml_spheroid20_011923/images/",
"4mgml": DIR_ROOT + "data/spheroid_4mgml_spheroid22_012323/images/",
"6mgml": DIR_ROOT + "data/spheroid_6mgml_spheroid26_012423/images/",
"3mgml_pc": DIR_ROOT + "data/spheroid_photocol_3mgml_spheroid12_060923/images/",
},
"FIGURES": {
"2": {
"PHENOTYPES_SMOOTHED": DIR_ROOT
+ "extra_data/PhenotypeGaussianSmoothed.npy",
},
"3": {
"SAMPLED_DATASET": DIR_ROOT + "extra_data/Figure3.SampledDataset.npy",
"PAIRWISE_DISTANCES": DIR_ROOT + "extra_data/Figure3.PairwiseDistances.npy",
"PAIRWISE_DOT_PRODUCTS": DIR_ROOT
+ "extra_data/Figure3.PairwiseDotProducts.npy",
"TRAJECTORIES": DIR_ROOT + "extra_data/Figure3.Trajectories.npy",
},
},
"PHENOTYPE_GRID": {
"IN": DIR_ROOT + "extra_data/PhenotypeGrid.npy",
"OUT": DIR_ROOT + "extra_data/PhenotypeGrid_out.npy",
},
"PHENOTYPE_RGB": DIR_ROOT + "extra_data/PhenotypeColors.npy",
"SVM": {
"MODEL": DIR_ROOT + "other/svm/SVC_rbf_010820_16942_new.pkl",
"SCALER": DIR_ROOT + "other/svm/SVC_rbf_scaler_010820_16942_new.pkl",
},
"NONPHYSICAL_MASK": DIR_ROOT + "extra_data/NonPhysicalMask.npy",
}
|
