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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
@@ -0,0 +1,265 @@
+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",
+}