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-rw-r--r--code/sunlab/globals.py265
1 files changed, 265 insertions, 0 deletions
diff --git a/code/sunlab/globals.py b/code/sunlab/globals.py
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+++ b/code/sunlab/globals.py
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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",
+}
generated by cgit v1.2.1 (git 2.18.0) at 2024-11-21 13:34:39 +0000