From b85ee9d64a536937912544c7bbd5b98b635b7e8d Mon Sep 17 00:00:00 2001 From: Christian C Date: Mon, 11 Nov 2024 12:29:32 -0800 Subject: Initial commit --- code/sunlab/globals.py | 265 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 265 insertions(+) create mode 100644 code/sunlab/globals.py (limited to 'code/sunlab/globals.py') diff --git a/code/sunlab/globals.py b/code/sunlab/globals.py new file mode 100644 index 0000000..eb5800b --- /dev/null +++ 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 + 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+ "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 + 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