spacr 0.2.3__py3-none-any.whl → 0.2.5__py3-none-any.whl

spacr/settings.py

@@ -220,6 +220,7 @@ def get_measure_crop_settings(settings):
 
     settings.setdefault('src', 'path')
     settings.setdefault('verbose', False)
+    settings.setdefault('experiment', 'exp')
     
     # Test mode
     settings.setdefault('test_mode', False)
@@ -252,8 +253,6 @@ def get_measure_crop_settings(settings):
 
     # Operational settings
     settings.setdefault('plot',False)
-    settings.setdefault('plot_filtration',False)
-    settings.setdefault('representative_images', False)
     settings.setdefault('n_jobs', os.cpu_count()-2)
 
     # Object settings
@@ -268,24 +267,9 @@ def get_measure_crop_settings(settings):
     settings.setdefault('cytoplasm_min_size',0)
     settings.setdefault('merge_edge_pathogen_cells', True)
 
-    # Miscellaneous settings
-    settings.setdefault('experiment', 'exp')
-    settings.setdefault('cells', ['HeLa'])
-    settings.setdefault('cell_loc', None)
-    settings.setdefault('pathogens', ['ME49Dku80WT', 'ME49Dku80dgra8:GRA8', 'ME49Dku80dgra8', 'ME49Dku80TKO'])
-    settings.setdefault('pathogen_loc', [['c1', 'c2', 'c3', 'c4', 'c5', 'c6'], ['c7', 'c8', 'c9', 'c10', 'c11', 'c12'], ['c13', 'c14', 'c15', 'c16', 'c17', 'c18'], ['c19', 'c20', 'c21', 'c22', 'c23', 'c24']])
-    settings.setdefault('treatments', ['BR1', 'BR2', 'BR3'])
-    settings.setdefault('treatment_loc', [['c1', 'c2', 'c7', 'c8', 'c13', 'c14', 'c19', 'c20'], ['c3', 'c4', 'c9', 'c10', 'c15', 'c16', 'c21', 'c22'], ['c5', 'c6', 'c11', 'c12', 'c17', 'c18', 'c23', 'c24']])
-    settings.setdefault('channel_of_interest', 2)
-    settings.setdefault('compartments', ['pathogen', 'cytoplasm'])
-    settings.setdefault('measurement', 'mean_intensity')
-    settings.setdefault('nr_imgs', 32)
-    settings.setdefault('um_per_pixel', 0.1)
-
     if settings['test_mode']:
         settings['verbose'] = True
         settings['plot'] = True
-        settings['plot_filtration'] = True
         test_imgs = settings['test_nr']
         print(f'Test mode enabled with {test_imgs} images, plotting set to True')
 
@@ -554,8 +538,6 @@ expected_types = {
     "png_dims": list,
     "normalize_by": str,
     "save_measurements": bool,
-    "representative_images": bool,
-    "plot_filtration": bool,
     "include_uninfected": bool,
     "dialate_pngs": bool,
     "dialate_png_ratios": list,
@@ -742,60 +724,6 @@ expected_types = {
     "fraction_threshold": float,
 }
 
-def check_settings_v1(vars_dict, expected_types,q=None):
-    from .gui_utils import parse_list
-    settings = {}
-    # Define the expected types for each key, including None where applicable
-
-    for key, (label, widget, var) in vars_dict.items():
-        if key not in expected_types:
-            if key not in ["General","Nucleus","Cell","Pathogen","Timelapse","Plot","Object Image","Annotate Data","Measurements","Advanced","Miscellaneous","Test"]:
-                q.put(f"Key {key} not found in expected types.")
-                continue
-
-        value = var.get()
-        expected_type = expected_types.get(key, str)
-
-        try:
-            if key in ["png_size", "pathogen_plate_metadata", "treatment_plate_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):
-                        settings[key] = parsed_value
-                    else:
-                        raise ValueError("Invalid format: Mixed list and list of lists")
-                else:
-                    raise ValueError("Invalid format for list or list of lists")
-            elif expected_type == list:
-                settings[key] = parse_list(value) if value else None
-            elif expected_type == bool:
-                settings[key] = value if isinstance(value, bool) else value.lower() in ['true', '1', 't', 'y', 'yes']
-            elif expected_type == (int, type(None)):
-                settings[key] = int(value) if value else None
-            elif expected_type == (float, type(None)):
-                settings[key] = float(value) if value else None
-            elif expected_type == (int, float):
-                settings[key] = float(value) if '.' in value else int(value)
-            elif expected_type == (str, type(None)):
-                settings[key] = str(value) if value else None
-            elif isinstance(expected_type, tuple):
-                for typ in expected_type:
-                    try:
-                        settings[key] = typ(value) if value else None
-                        break
-                    except (ValueError, TypeError):
-                        continue
-                else:
-                    raise ValueError
-            else:
-                settings[key] = expected_type(value) if value else None
-        except (ValueError, SyntaxError):
-            expected_type_name = ' or '.join([t.__name__ for t in expected_type]) if isinstance(expected_type, tuple) else expected_type.__name__
-            q.put(f"Error: Invalid format for {key}. Expected type: {expected_type_name}.")
-            return
-
-    return settings
-
 def check_settings(vars_dict, expected_types, q=None):
     from .gui_utils import parse_list
 
@@ -805,7 +733,7 @@ def check_settings(vars_dict, expected_types, q=None):
 
     settings = {}
 
-    for key, (label, widget, var) in vars_dict.items():
+    for key, (label, widget, var, _) in vars_dict.items():
         if key not in expected_types:
             if key not in ["General", "Nucleus", "Cell", "Pathogen", "Timelapse", "Plot", "Object Image", "Annotate Data", "Measurements", "Advanced", "Miscellaneous", "Test"]:
                 q.put(f"Key {key} not found in expected types.")
@@ -856,7 +784,7 @@ def check_settings(vars_dict, expected_types, q=None):
 
 def generate_fields(variables, scrollable_frame):
     from .gui_utils import create_input_field
-    from .gui_elements import spacrToolTip
+    from .gui_elements import set_dark_style, spacrToolTip
     row = 1
     vars_dict = {}
     tooltips = {
@@ -1014,7 +942,6 @@ def generate_fields(variables, scrollable_frame):
         "plot_by_cluster": "(bool) - Whether to plot images by clusters.",
         "plot_cluster_grids": "(bool) - Whether to plot grids of clustered images.",
         "plot_control": "(dict) - Control settings for plotting.",
-        "plot_filtration": "(bool) - Whether to plot the filtration steps.",
         "plot_images": "(bool) - Whether to plot images.",
         "plot_nr": "(int) - Number of plots to generate.",
         "plot_outlines": "(bool) - Whether to plot outlines of segmented objects.",
@@ -1036,7 +963,6 @@ def generate_fields(variables, scrollable_frame):
         "remove_image_canvas": "(bool) - Whether to remove the image canvas after plotting.",
         "remove_low_variance_features": "(bool) - Whether to remove low variance features from the analysis.",
         "remove_row_column_effect": "(bool) - Whether to remove row and column effects from the data.",
-        "representative_images": "(bool) - Whether to save representative images of the segmented objects (Not working yet).",
         "resize": "(bool) - Resize factor for the images.",
         "resample": "(bool) - Whether to resample the images during processing.",
         "rescale": "(float) - Rescaling factor for the images.",
@@ -1080,17 +1006,19 @@ def generate_fields(variables, scrollable_frame):
         "um_per_pixel": "(float) - The micrometers per pixel for the images."
     }
 
-
     for key, (var_type, options, default_value) in variables.items():
-        label, widget, var = create_input_field(scrollable_frame.scrollable_frame, key, row, var_type, options, default_value)
-        vars_dict[key] = (label, widget, var)  # Store the label, widget, and variable
+        label, widget, var, frame = create_input_field(scrollable_frame.scrollable_frame, key, row, var_type, options, default_value)
+        vars_dict[key] = (label, widget, var, frame)  # Store the label, widget, and variable
         
         # Add tooltip to the label if it exists in the tooltips dictionary
         if key in tooltips:
             spacrToolTip(label, tooltips[key])
+
         row += 1
+        
     return vars_dict
 
+
 categories = {
     "General": ["src", "metadata_type", "custom_regex", "experiment", "channels", "magnification", "channel_dims"],
     "Paths":["grna", "barcodes"],
@@ -1100,9 +1028,9 @@ categories = {
     "Cell": ["cell_intensity_range", "cell_size_range", "cell_chann_dim", "cell_channel", "cell_background", "cell_Signal_to_noise", "cell_CP_prob", "cell_FT", "remove_background_cell", "cell_min_size", "cell_mask_dim", "cytoplasm", "cytoplasm_min_size", "include_uninfected", "merge_edge_pathogen_cells", "adjust_cells"],
     "Pathogen": ["pathogen_intensity_range", "pathogen_size_range", "pathogen_chann_dim", "pathogen_channel", "pathogen_background", "pathogen_Signal_to_noise", "pathogen_CP_prob", "pathogen_FT", "pathogen_model", "remove_background_pathogen", "pathogen_min_size", "pathogen_mask_dim"],
     "Timelapse": ["fps", "timelapse_displacement", "timelapse_memory", "timelapse_frame_limits", "timelapse_remove_transient", "timelapse_mode", "timelapse_objects", "compartments"],
-    "Plot": ["plot_control", "plot_nr", "plot_filtration", "examples_to_plot", "normalize_plots", "normalize", "cmap", "figuresize", "plot_cluster_grids", "img_zoom", "row_limit", "color_by", "plot_images", "smooth_lines", "plot_points", "plot_outlines", "black_background", "plot_by_cluster", "heatmap_feature","grouping","min_max","cmap","save_figure"],
+    "Plot": ["plot_control", "plot_nr", "examples_to_plot", "normalize_plots", "normalize", "cmap", "figuresize", "plot_cluster_grids", "img_zoom", "row_limit", "color_by", "plot_images", "smooth_lines", "plot_points", "plot_outlines", "black_background", "plot_by_cluster", "heatmap_feature","grouping","min_max","cmap","save_figure"],
     "Object Image": ["save_png", "dialate_pngs", "dialate_png_ratios", "png_size", "png_dims", "save_arrays", "normalize_by", "dialate_png_ratios", "crop_mode", "dialate_pngs", "normalize", "use_bounding_box"],
-    "Annotate Data": ["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", "representative_images", "um_per_pixel", "nr_imgs", "exclude", "exclude_conditions", "mix", "pos", "neg"],
+    "Annotate Data": ["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"],
     "Measurements": ["remove_image_canvas", "remove_highly_correlated", "homogeneity", "homogeneity_distances", "radial_dist", "calculate_correlation", "manders_thresholds", "save_measurements", "tables", "image_nr", "dot_size", "filter_by", "remove_highly_correlated_features", "remove_low_variance_features", "channel_of_interest"],
     "Advanced": ["plate_dict", "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","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","n_jobs","channels","augment"],
     "Clustering": ["eps","min_samples","analyze_clusters","clustering","remove_cluster_noise"],
@@ -1114,7 +1042,7 @@ categories = {
 }
 
 descriptions = {
-    'mask': "Generate Cellpose masks for Cells, Nuclei, and Pathogens. Function: preprocess_generate_masks from spacr.core.\n\nKey Features:\n- Automated Mask Generation: Automatically generate accurate masks for various cellular components using Cellpose, a robust deep learning model for cell segmentation.\n- Versatility: Capable of handling different types of biological samples, including cells, nuclei, and pathogens.\n- Integration: Directly integrates with other modules, providing the foundational masks required for subsequent analysis.",
+    'mask': "\n\nHelp:\n- Generate Cells, Nuclei, Pathogens, and Cytoplasm masks from intensity images in src.\n- To ensure that spacr is installed correctly:\n- 1. Downloade the training set (click Download).\n- 2. Import settings (click settings navigate to downloaded dataset settings folder and import preprocess_generate_masks_settings.csv).\n- 3. Run the module.\n- 4. Proceed to the Measure module (click Measure in the menue bar).\n- For further help, click the Help button in the menue bar.",
     
     'measure': "Capture Measurements from Cells, Nuclei, Pathogens, and Cytoplasm objects. Generate single object PNG images for one or several objects. (Requires masks from the Mask module). Function: measure_crop from spacr.measure.\n\nKey Features:\n- Comprehensive Measurement Capture: Obtain detailed measurements for various cellular components, including area, perimeter, intensity, and more.\n- Image Generation: Create high-resolution PNG images of individual objects, facilitating further analysis and visualization.\n- Mask Dependency: Requires accurate masks generated by the Mask module to ensure precise measurements.",
     
@@ -1143,10 +1071,7 @@ def set_annotate_default_settings(settings):
     settings.setdefault('src', 'path')
     settings.setdefault('image_type', 'cell_png')
     settings.setdefault('channels', 'r,g,b')
-    settings.setdefault('geom', "3200x2000")
-    settings.setdefault('img_size', [200, 200])
-    settings.setdefault('rows', 10)
-    settings.setdefault('columns', 18)
+    settings.setdefault('img_size', 200)
     settings.setdefault('annotation_column', 'test')
     settings.setdefault('normalize', 'False')
     settings.setdefault('percentiles', [2, 98])

spacr/utils.py

@@ -1,4 +1,4 @@
-import sys, os, re, sqlite3, torch, torchvision, random, string, shutil, cv2, tarfile, glob, psutil, platform, signal
+import sys, os, re, sqlite3, torch, torchvision, random, string, shutil, cv2, tarfile, glob, psutil, platform
 
 import numpy as np
 from cellpose import models as cp_models
@@ -87,6 +87,40 @@ from scipy.stats import f_oneway, kruskal
 from sklearn.cluster import KMeans
 from scipy import stats
 
+
+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):
+        files_to_process = len(set(files_to_process))
+    if isinstance(batch_size, list):
+        batch_size = len(batch_size)
+
+    if not isinstance(files_processed, int):
+        try:
+            files_processed = int(files_processed)
+        except:
+            files_processed = 0
+    if not isinstance(files_to_process, int):
+        try:
+            files_to_process = int(files_to_process)
+        except:
+            files_to_process = 0
+
+    time_info = ""
+    if time_ls is not None:
+        average_time = np.mean(time_ls) if len(time_ls) > 0 else 0
+        time_left = (((files_to_process - files_processed) * average_time) / n_jobs) / 60
+        if batch_size is None:
+            time_info = f'Time/image: {average_time:.3f}sec, Time_left: {time_left:.3f} min.'
+        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.'
+
+    print(f'Progress: {files_processed}/{files_to_process}, operation_type: {operation_type} {time_info}')
+
+
+
 def reset_mp():
     current_method = get_start_method()
     system = platform.system()
@@ -2934,11 +2968,13 @@ def _choose_model(model_name, device, object_type='cell', restore_type=None, obj
     if restore_type == None:
         if model_name in ['cyto', 'cyto2', 'cyto3', 'nuclei']:
             model = cp_models.Cellpose(gpu=torch.cuda.is_available(), model_type=model_name, device=device)
-
+            return model
     else:
         if object_type == 'nucleus':
             restore = f'{type}_nuclei'
             model = denoise.CellposeDenoiseModel(gpu=torch.cuda.is_available(), model_type="nuclei",restore_type=restore, chan2_restore=False, device=device)
+            return model
+
         else:
             restore = f'{type}_cyto3'
             if model_name =='cyto2':
@@ -2946,8 +2982,7 @@ def _choose_model(model_name, device, object_type='cell', restore_type=None, obj
             if model_name =='cyto':
                 chan2_restore = False
             model = denoise.CellposeDenoiseModel(gpu=torch.cuda.is_available(), model_type="cyto3",restore_type=restore, chan2_restore=chan2_restore, device=device)
-    
-    return model
+            return model
 
 class SelectChannels:
     def __init__(self, channels):
@@ -3593,22 +3628,22 @@ def delete_folder(folder_path):
 def measure_test_mode(settings):    
 
     if settings['test_mode']:
-        if not os.path.basename(settings['input_folder']) == 'test':
-            all_files = os.listdir(settings['input_folder'])
+        if not os.path.basename(settings['src']) == 'test':
+            all_files = os.listdir(settings['src'])
             random_files = random.sample(all_files, settings['test_nr'])
 
-            src = os.path.join(os.path.dirname(settings['input_folder']),'test', 'merged')
+            src = os.path.join(os.path.dirname(settings['src']),'test', 'merged')
             if os.path.exists(src):
                 delete_folder(src)
             os.makedirs(src, exist_ok=True)
 
             for file in random_files:
-                shutil.copy(os.path.join(settings['input_folder'], file), os.path.join(src,file))
+                shutil.copy(os.path.join(settings['src'], file), os.path.join(src,file))
 
-            settings['input_folder'] = src
+            settings['src'] = src
             print(f'Changed source folder to {src} for test mode')
         else:
-            print(f'Test mode enabled, using source folder {settings["input_folder"]}')
+            print(f'Test mode enabled, using source folder {settings["src"]}')
 
     return settings
 

{spacr-0.2.3.dist-info → spacr-0.2.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.3
+Version: 0.2.5
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -39,6 +39,10 @@ Requires-Dist: ttf-opensans >=2020.10.30
 Requires-Dist: customtkinter <6.0,>=5.2.2
 Requires-Dist: biopython <2.0,>=1.80
 Requires-Dist: lxml <6.0,>=5.1.0
+Requires-Dist: psutil <6.0,>=5.9.8
+Requires-Dist: gputil <2.0,>=1.4.0
+Requires-Dist: gpustat <2.0,>=1.1.1
+Requires-Dist: pyautogui <1.0,>=0.9.54
 Requires-Dist: huggingface-hub <0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest <3.11,>=3.9 ; extra == 'dev'

spacr-0.2.5.dist-info/RECORD

@@ -0,0 +1,100 @@
+spacr/__init__.py,sha256=pJ7Mm7Kb1DhHIdLmNgMILFVWJ9QAG47pT0M6wtiXl8E,1465
+spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
+spacr/app_annotate.py,sha256=nEIL7Fle9CDKGo3sucG_03DgjUQt5W1M1IHBIpVBr08,2171
+spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
+spacr/app_make_masks.py,sha256=pqDhRpluiHZz-kPX2Zh_KbYe4TsU43qYBa_7f-rsjpw,1694
+spacr/app_mask.py,sha256=l-dBY8ftzCMdDe6-pXc2Nh_u-idNL9G7UOARiLJBtds,153
+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=WBVZfuVJPqI7hXaZVLPWCbe-CCLDNjsCB3nHCF2Axmg,148064
+spacr/deep_spacr.py,sha256=ASBsN4JpHp_3S-91JUsB34IWTjTGPYI7jKV2qZnUR5M,37005
+spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
+spacr/gui.py,sha256=NoqaHYjqvyiexfXMsFWrRYjcyqAOhEIYnR-82LkKzdk,7277
+spacr/gui_core.py,sha256=UqX0JE7mCi_4TlVCtEMMTHSUEC2BvZSVUmWzue2HYok,30756
+spacr/gui_elements.py,sha256=ISGt_gEozMx_BWWgXvcgEEKeqvCxfmoCDVHWlrJ1roQ,106811
+spacr/gui_utils.py,sha256=nRH1bEXjrTsfgp01H7ayIkimN0v7G163XjiruGwySP0,28050
+spacr/io.py,sha256=UYISLJgwpwyoTxKy1v1wzFQ6cLX77h2rHh4t5fF1_4w,115461
+spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
+spacr/measure.py,sha256=A_n7y6cF4FL2VDggLaeeKdoWLx8UeHmUZL54NFM_jvI,54742
+spacr/plot.py,sha256=4o9X76ur2kBe6TtOrbIPfo04iC60OZ1rNJoegBxtLmk,72361
+spacr/sequencing.py,sha256=fHZRnoMSxmhMdadkei3lUeBdckqFyptWdQyWsDW3aaU,83304
+spacr/settings.py,sha256=QS8D7zrhxyArRsavfz2w2bh6VnYJk3rUBwoGdE5Qqfc,61254
+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=TT2gb2nmhNSwkHheaOfpDPXhpE90_6Er3nA77gAbO3U,188225
+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
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