spacr 0.2.56__py3-none-any.whl → 0.2.61__py3-none-any.whl

spacr/settings.py

@@ -3,8 +3,8 @@ import os, ast
 def set_default_plot_merge_settings():
     settings = {}
     settings.setdefault('include_noninfected', True)
-    settings.setdefault('include_multiinfected', True)
-    settings.setdefault('include_multinucleated', True)
+    settings.setdefault('include_multiinfected', 10)
+    settings.setdefault('include_multinucleated', 1)
     settings.setdefault('remove_background', False)
     settings.setdefault('filter_min_max', None)
     settings.setdefault('channel_dims', [0,1,2,3])
@@ -20,7 +20,7 @@ def set_default_plot_merge_settings():
     settings.setdefault('normalize', True)
     settings.setdefault('print_object_number', True)
     settings.setdefault('nr', 1)
-    settings.setdefault('figuresize', 50)
+    settings.setdefault('figuresize', 10)
     settings.setdefault('cmap', 'inferno')
     settings.setdefault('verbose', True)
     return settings
@@ -70,7 +70,7 @@ def set_default_settings_preprocess_generate_masks(src, settings={}):
     
     # Plot settings
     settings.setdefault('plot', False)
-    settings.setdefault('figuresize', 50)
+    settings.setdefault('figuresize', 10)
     settings.setdefault('cmap', 'inferno')
     settings.setdefault('normalize', True)
     settings.setdefault('normalize_plots', True)
@@ -116,7 +116,7 @@ def set_default_settings_preprocess_img_data(settings):
     skip_mode = settings.setdefault('skip_mode', False)
 
     cmap = settings.setdefault('cmap', 'inferno')
-    figuresize = settings.setdefault('figuresize', 50)
+    figuresize = settings.setdefault('figuresize', 10)
     normalize = settings.setdefault('normalize', True)
     save_dtype = settings.setdefault('save_dtype', 'uint16')
     
@@ -189,7 +189,7 @@ def set_default_umap_image_settings(settings={}):
     settings.setdefault('remove_cluster_noise', True)
     settings.setdefault('remove_highly_correlated', True)
     settings.setdefault('log_data', False)
-    settings.setdefault('figuresize', 60)
+    settings.setdefault('figuresize', 10)
     settings.setdefault('black_background', True)
     settings.setdefault('remove_image_canvas', False)
     settings.setdefault('plot_outlines', True)
@@ -314,7 +314,6 @@ def set_default_train_test_model(settings):
     settings.setdefault('batch_size',64)
     settings.setdefault('epochs',100)
     settings.setdefault('val_split',0.1)
-    settings.setdefault('train_mode','erm')
     settings.setdefault('learning_rate',0.001)
     settings.setdefault('weight_decay',0.00001)
     settings.setdefault('dropout_rate',0.1)
@@ -324,7 +323,7 @@ def set_default_train_test_model(settings):
     settings.setdefault('gradient_accumulation',True)
     settings.setdefault('gradient_accumulation_steps',4)
     settings.setdefault('intermedeate_save',True)
-    settings.setdefault('pin_memory',True)
+    settings.setdefault('pin_memory',False)
     settings.setdefault('n_jobs',cores)
     settings.setdefault('train_channels',['r','g','b'])
     settings.setdefault('augment',False)
@@ -334,7 +333,7 @@ def set_default_train_test_model(settings):
 def set_generate_training_dataset_defaults(settings):
 
     settings.setdefault('src','path')
-    settings.setdefault('dataset_mode','annotation')
+    settings.setdefault('dataset_mode','metadata')
     settings.setdefault('annotation_column','test')
     settings.setdefault('annotated_classes',[1,2])
     settings.setdefault('classes',['nc','pc'])
@@ -351,10 +350,10 @@ def set_generate_training_dataset_defaults(settings):
 
 def deep_spacr_defaults(settings):
     
-    cores = os.cpu_count()-2
+    cores = os.cpu_count()-4
     
     settings.setdefault('src','path')
-    settings.setdefault('dataset_mode','annotation')
+    settings.setdefault('dataset_mode','metadata')
     settings.setdefault('annotation_column','test')
     settings.setdefault('annotated_classes',[1,2])
     settings.setdefault('classes',['nc','pc'])
@@ -379,7 +378,6 @@ def deep_spacr_defaults(settings):
     settings.setdefault('batch_size',64)
     settings.setdefault('epochs',100)
     settings.setdefault('val_split',0.1)
-    settings.setdefault('train_mode','erm')
     settings.setdefault('learning_rate',0.001)
     settings.setdefault('weight_decay',0.00001)
     settings.setdefault('dropout_rate',0.1)
@@ -389,12 +387,13 @@ def deep_spacr_defaults(settings):
     settings.setdefault('gradient_accumulation',True)
     settings.setdefault('gradient_accumulation_steps',4)
     settings.setdefault('intermedeate_save',True)
-    settings.setdefault('pin_memory',True)
+    settings.setdefault('pin_memory',False)
     settings.setdefault('n_jobs',cores)
     settings.setdefault('train_channels',['r','g','b'])
     settings.setdefault('augment',False)
-    settings.setdefault('verbose',False)
-    settings.setdefault('apply_model_to_dataset',False)
+    settings.setdefault('preload_batches', 3)
+    settings.setdefault('verbose',True)
+    settings.setdefault('apply_model_to_dataset',True)
     settings.setdefault('file_metadata',None)
     settings.setdefault('sample',None)
     settings.setdefault('experiment','exp.')
@@ -404,10 +403,10 @@ def deep_spacr_defaults(settings):
     settings.setdefault('file_type','cell_png')
     settings.setdefault('generate_training_dataset', True)
     settings.setdefault('train_DL_model', True)
-
     return settings
 
 def get_analyze_recruitment_default_settings(settings):
+    settings.setdefault('src','path')
     settings.setdefault('target','protein')
     settings.setdefault('cell_types',['HeLa'])
     settings.setdefault('cell_plate_metadata',None)
@@ -427,12 +426,10 @@ def get_analyze_recruitment_default_settings(settings):
     settings.setdefault('plot',True)
     settings.setdefault('plot_nr',10)
     settings.setdefault('plot_control',True)
-    settings.setdefault('figuresize',20)
-    settings.setdefault('remove_background',False)
-    settings.setdefault('backgrounds',100)
+    settings.setdefault('figuresize',10)
     settings.setdefault('include_noninfected',True)
-    settings.setdefault('include_multiinfected',True)
-    settings.setdefault('include_multinucleated',True)
+    settings.setdefault('include_multiinfected',10)
+    settings.setdefault('include_multinucleated',1)
     settings.setdefault('cells_per_well',0)
     settings.setdefault('pathogen_size_range',[0,100000])
     settings.setdefault('nucleus_size_range',[0,100000])
@@ -631,8 +628,8 @@ expected_types = {
     "nr_imgs": int,
     "um_per_pixel": (int, float),
     "include_noninfected": bool,
-    "include_multiinfected": bool,
-    "include_multinucleated": bool,
+    "include_multiinfected": int,
+    "include_multinucleated": int,
     "filter_min_max": (list, type(None)),
     "channel_dims": list,
     "backgrounds": list,
@@ -726,7 +723,6 @@ expected_types = {
     "image_size": int,
     "epochs": int,
     "val_split": float,
-    "train_mode": str,
     "learning_rate": float,
     "weight_decay": float,
     "dropout_rate": float,
@@ -741,7 +737,7 @@ expected_types = {
     "augment": bool,
     "target": str,
     "cell_types": list,
-    "cell_plate_metadata": (list, type(None)),
+    "cell_plate_metadata": (list, list),
     "pathogen_types": list,
     "pathogen_plate_metadata": (list, list),  # This can be a list of lists 
     "treatment_plate_metadata": (list, list),  # This can be a list of lists
@@ -832,6 +828,7 @@ expected_types = {
     "png_type":str,
     "custom_model_path":str,
     "generate_training_dataset":bool,
+    'preload_batches':int,
     "train_DL_model":bool,
 }
 
@@ -850,12 +847,12 @@ categories = {"General": ["src", "metadata_type", "custom_regex", "experiment",
              "Annotation": ["nc_loc", "pc_loc", "nc", "pc", "cell_plate_metadata","pathogen_types", "pathogen_plate_metadata", "treatment_plate_metadata", "metadata_types", "cell_types", "target","positive_control","negative_control", "location_column", "treatment_loc", "cells", "cell_loc", "pathogens", "pathogen_loc", "channel_of_interest", "measurement", "treatments", "um_per_pixel", "nr_imgs", "exclude", "exclude_conditions", "mix", "pos", "neg"],
              "Machine Learning":[],
              "Deep Learning": ["png_type","score_threshold","file_type", "train_channels", "epochs", "loss_type", "optimizer_type","image_size","val_split","learning_rate","weight_decay","dropout_rate", "init_weights", "train", "classes", "augment"],
-             "Generate Dataset":["file_metadata","class_metadata", "annotation_column","annotated_classes", "dataset_mode", "metadata_type_by","custom_measurement", "sample", "size"],
+             "Generate Dataset":["preload_batches", "file_metadata","class_metadata", "annotation_column","annotated_classes", "dataset_mode", "metadata_type_by","custom_measurement", "sample", "size"],
              "Cellpose":["from_scratch", "n_epochs", "width_height", "model_name", "custom_model", "resample", "rescale", "CP_prob", "flow_threshold", "percentiles", "circular", "invert", "diameter", "grayscale", "background", "Signal_to_noise", "resize", "target_height", "target_width"],
              "Regression":["class_1_threshold", "plate", "other", "fraction_threshold", "alpha", "remove_row_column_effect", "regression_type", "min_cell_count", "agg_type", "transform", "dependent_variable", "gene_weights_csv"],
              "Miscellaneous": ["all_to_mip", "pick_slice", "skip_mode", "upscale", "upscale_factor"],
              "Test": ["test_mode", "test_images", "random_test", "test_nr", "test", "test_split"],
-             "Advanced": ["target_intensity_min", "cells_per_well", "include_multinucleated", "include_multiinfected", "include_noninfected", "backgrounds", "plot", "timelapse", "schedule", "test_size","exclude","n_repeats","top_features", "model_type_ml", "model_type","minimum_cell_count","n_estimators","preprocess", "remove_background", "normalize", "lower_percentile", "merge_pathogens", "batch_size", "filter", "save", "masks", "verbose", "randomize", "n_jobs", "train_mode","amsgrad","use_checkpoint","gradient_accumulation","gradient_accumulation_steps","intermedeate_save","pin_memory"]
+             "Advanced": ["target_intensity_min", "cells_per_well", "include_multinucleated", "include_multiinfected", "include_noninfected", "backgrounds", "plot", "timelapse", "schedule", "test_size","exclude","n_repeats","top_features", "model_type_ml", "model_type","minimum_cell_count","n_estimators","preprocess", "remove_background", "normalize", "lower_percentile", "merge_pathogens", "batch_size", "filter", "save", "masks", "verbose", "randomize", "n_jobs", "amsgrad","use_checkpoint","gradient_accumulation","gradient_accumulation_steps","intermedeate_save","pin_memory"]
              }
 
 category_keys = list(categories.keys())
@@ -879,7 +876,7 @@ def check_settings(vars_dict, expected_types, q=None):
         expected_type = expected_types.get(key, str)
 
         try:
-            if key in ["timelapse_frame_limits", "png_size", "pathogen_loc", "treatment_loc", "pathogen_plate_metadata", "treatment_plate_metadata", "barcode_coordinates", "class_metadata"]:
+            if key in ["cell_plate_metadata", "timelapse_frame_limits", "png_size", "pathogen_loc", "treatment_loc", "pathogen_plate_metadata", "treatment_plate_metadata", "barcode_coordinates", "class_metadata"]:
                 parsed_value = ast.literal_eval(value) if value else None
                 if isinstance(parsed_value, list):
                     if all(isinstance(i, list) for i in parsed_value) or all(not isinstance(i, list) for i in parsed_value):
@@ -1014,8 +1011,8 @@ def generate_fields(variables, scrollable_frame):
         "image_nr": "(int) - Number of images to process.",
         "image_size": "(int) - Size of the images for training.",
         "img_zoom": "(float) - Zoom factor for the images in plots.",
-        "include_multinucleated": "(bool) - Whether to include multinucleated cells in the analysis.",
-        "include_multiinfected": "(bool) - Whether to include multi-infected cells in the analysis.",
+        "include_multinucleated": "(int) - Whether to include multinucleated cells in the analysis.",
+        "include_multiinfected": "(int) - Whether to include multi-infected cells in the analysis.",
         "include_noninfected": "(bool) - Whether to include non-infected cells in the analysis.",
         "include_uninfected": "(bool) - Whether to include uninfected cells in the analysis.",
         "init_weights": "(bool) - Whether to initialize weights for the model.",
@@ -1139,7 +1136,6 @@ def generate_fields(variables, scrollable_frame):
         "treatments": "(list) - The treatments to include in the analysis.",
         "top_features": "(int) - Top features to include in the analysis.",
         "train": "(bool) - Whether to train the model.",
-        "train_mode": "(str) - Mode to use for training the model.",
         "transform": "(dict) - Transformation to apply to the data.",
         "upscale": "(bool) - Whether to upscale the images.",
         "upscale_factor": "(float) - Factor by which to upscale the images.",

spacr/utils.py

@@ -87,8 +87,14 @@ from scipy.stats import f_oneway, kruskal
 from sklearn.cluster import KMeans
 from scipy import stats
 
+def save_settings(settings, name='settings'):
+    
+    settings_df = pd.DataFrame(list(settings.items()), columns=['Key', 'Value'])
+    settings_csv = os.path.join(settings['src'],'settings',f'{name}.csv')
+    os.makedirs(os.path.join(settings['src'],'settings'), exist_ok=True)
+    settings_df.to_csv(settings_csv, index=False)
 
-def print_progress(files_processed, files_to_process, n_jobs, time_ls=None, batch_size=None, operation_type="", metricks=None):
+def print_progress(files_processed, files_to_process, n_jobs, time_ls=None, batch_size=None, operation_type=""):
     if isinstance(files_processed, list):
         files_processed = len(set(files_processed))
     if isinstance(files_to_process, list):
@@ -116,11 +122,8 @@ def print_progress(files_processed, files_to_process, n_jobs, time_ls=None, batc
         else:
             average_time_img = average_time / batch_size
             time_info = f'Time/batch: {average_time:.3f}sec, Time/image: {average_time_img:.3f}sec, Time_left: {time_left:.3f} min.'
-
-    if metricks is None:
-        print(f'Progress: {files_processed}/{files_to_process}, operation_type: {operation_type} {time_info}')
     else:
-        print(f'Progress: {files_processed}/{files_to_process}, {metricks}, operation_type: {operation_type} {time_info}')
+        print(f'Progress: {files_processed}/{files_to_process}, operation_type: {operation_type} {time_info}')
 
 def reset_mp():
     current_method = get_start_method()
@@ -1650,7 +1653,7 @@ def split_my_dataset(dataset, split_ratio=0.1):
     val_dataset = Subset(dataset, val_indices)
     return train_dataset, val_dataset
 
-def classification_metrics(all_labels, prediction_pos_probs, loader_name, loss, epoch):
+def classification_metrics(all_labels, prediction_pos_probs, loss, epoch):
     """
     Calculate classification metrics for binary classification.
 
@@ -1699,11 +1702,9 @@ def classification_metrics(all_labels, prediction_pos_probs, loader_name, loss,
     else:
         acc_nc = np.nan
     data_dict = {'accuracy': acc_all, 'neg_accuracy': acc_nc, 'pos_accuracy': acc_pc, 'loss':loss.item(),'prauc':pr_auc, 'optimal_threshold':optimal_threshold}
-    data_df = pd.DataFrame(data_dict, index=[str(epoch)+'_'+loader_name]) 
+    data_df = pd.DataFrame(data_dict, index=[str(epoch)]) 
     return data_df
     
-
-
 def compute_irm_penalty(losses, dummy_w, device):
     """
     Computes the Invariant Risk Minimization (IRM) penalty.
@@ -1741,7 +1742,7 @@ def compute_irm_penalty(losses, dummy_w, device):
 #    summary(base_model, (channels, height, width))
 #    return
 
-def choose_model(model_type, device, init_weights=True, dropout_rate=0, use_checkpoint=False, channels=3, height=224, width=224, chan_dict=None, num_classes=2):
+def choose_model(model_type, device, init_weights=True, dropout_rate=0, use_checkpoint=False, channels=3, height=224, width=224, chan_dict=None, num_classes=2, verbose=False):
     """
     Choose a model for classification.
 
@@ -1773,7 +1774,7 @@ def choose_model(model_type, device, init_weights=True, dropout_rate=0, use_chec
         print(f'Invalid model_type: {model_type}. Compatible model_types: {model_types}')
         return
 
-    print(f'\rModel parameters: Architecture: {model_type} init_weights: {init_weights} dropout_rate: {dropout_rate} use_checkpoint: {use_checkpoint}', end='\r', flush=True)
+    print(f'Model parameters: Architecture: {model_type} init_weights: {init_weights} dropout_rate: {dropout_rate} use_checkpoint: {use_checkpoint}', end='\r', flush=True)
     
     if model_type == 'custom':
         
@@ -1784,8 +1785,8 @@ def choose_model(model_type, device, init_weights=True, dropout_rate=0, use_chec
     else:
         print(f'Compatible model_types: {model_types}')
         raise ValueError(f"Invalid model_type: {model_type}")
-
-    print(base_model)
+    if verbose:
+        print(base_model)
     
     return base_model
 

{spacr-0.2.56.dist-info → spacr-0.2.61.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.56
+Version: 0.2.61
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.2.56.dist-info → spacr-0.2.61.dist-info}/RECORD

@@ -8,23 +8,23 @@ spacr/app_measure.py,sha256=_K7APYIeOKpV6e_LcqabBjvEi7mfq9Fch8175x1x0k8,162
 spacr/app_sequencing.py,sha256=DjG26jy4cpddnV8WOOAIiExtOe9MleVMY4MFa5uTo5w,157
 spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
-spacr/core.py,sha256=3r32IJlvT6ReN7cgAU2frFkdACQyN48mgUETNzrTrwE,160329
-spacr/deep_spacr.py,sha256=Yge4Tu6k7jjIQhuCAOVZkDS8dQR1cDvYtySfahAp6Lg,40153
+spacr/core.py,sha256=IDme9j7eeC_49KGaNk_xPOKtpxdcXKMhYtoo3xhjQMM,146502
+spacr/deep_spacr.py,sha256=a2YewgkQvLV-95NYJAutnojvJmX4S8z_wv6Tb-XIgUI,34484
 spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
 spacr/gui.py,sha256=dSEQhzZgIOT7SOonbIp07-zXcLaEt6M7sRiIREpDv64,7226
-spacr/gui_core.py,sha256=p2Rx97U92KDM4DW1hfFuYRh_4mQ1aSN_0ieOH0vB2g8,30933
-spacr/gui_elements.py,sha256=grC-_jlyJir3W-GLbnN5zTfq9D7ef-KCt_WnlvKXmpY,111819
-spacr/gui_utils.py,sha256=gWDO-BESGsNR26g9t1xy3BLwSdIDXHSmJ7w34V-A56E,28094
-spacr/io.py,sha256=YVykRy_kgC0LF7oBdJoqtnFoTEGx5mfldboHpZXxe9E,115603
+spacr/gui_core.py,sha256=8aoxVLwt8evl_mZG6xHxhRgf5nq35bfay12OOSJos5Q,40148
+spacr/gui_elements.py,sha256=z00Xk16TxqMUXKat0rGmw2DHDFzuXoY0C1Tlg6LZpEI,110662
+spacr/gui_utils.py,sha256=h84IcxKqcUZfatLybIMszc_xVVsBrdGKWzPdfV1oM3w,28474
+spacr/io.py,sha256=ZtVNbEom8X8p_KfsuWw0glGwLg6S0CfwwevDPGdfiSc,117342
 spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
 spacr/measure.py,sha256=4rmzH_a5Y0s1qALVi6YRut3xpnkJXs5vzeTPCEf3QS8,54871
-spacr/plot.py,sha256=4o9X76ur2kBe6TtOrbIPfo04iC60OZ1rNJoegBxtLmk,72361
+spacr/plot.py,sha256=CICY2h6sNiY6bGKkw6ZYmro_FixXkKxZpIIOoSuMw94,73963
 spacr/sequencing.py,sha256=dt4urG5tL85qh2sGEi2F9rtOqBQR-eCfcqOvcAtQIzg,75849
-spacr/settings.py,sha256=Vbm1F5I926t3CJ0E7Y3m9pMIFZz1DzzSKNil6kDChIM,67904
+spacr/settings.py,sha256=tDvTBWANeuI6YC_fH5vK2HOOuRgQXIkzyNKDmt1vL4c,67745
 spacr/sim.py,sha256=FveaVgBi3eypO2oVB5Dx-v0CC1Ny7UPfXkJiiRRodAk,71212
 spacr/sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 spacr/timelapse.py,sha256=KMYCgHzf9LTZe-lWl5mvH2EjbKRE6OhpwdY13wEumGc,39504
-spacr/utils.py,sha256=Q1MgPMSf6coNta4mcb6UaWGtnGW1JeruJa7SxtOzvMk,188567
+spacr/utils.py,sha256=M0lbpquOIxJi4iMH2_GAu0iB7jysifPNW3wzNuH1V4I,188733
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/font/open_sans/OFL.txt,sha256=bGMoWBRrE2RcdzDiuYiB8A9OVFlJ0sA2imWwce2DAdo,4484
 "spacr/resources/font/open_sans/OpenSans-Italic-VariableFont_wdth,wght.ttf",sha256=QSoWv9h46CRX_fdlqFM3O2d3-PF3R1srnb4zUezcLm0,580280
@@ -92,9 +92,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model,sha256=z8BbHWZPRnE9D_BHO0fBREE85c1vkltDs-incs2ytXQ,26566572
 spacr/resources/models/cp/toxo_plaque_cyto_e25000_X1120_Y1120.CP_model_settings.csv,sha256=fBAGuL_B8ERVdVizO3BHozTDSbZUh1yFzsYK3wkQN68,420
 spacr/resources/models/cp/toxo_pv_lumen.CP_model,sha256=2y_CindYhmTvVwBH39SNILF3rI3x9SsRn6qrMxHy3l0,26562451
-spacr-0.2.56.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.2.56.dist-info/METADATA,sha256=yXp1WrJwtCMC3ha79ztaaqzfvPa95B2mmVCAm9Uirgk,5259
-spacr-0.2.56.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-spacr-0.2.56.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.2.56.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
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