spacr 0.4.4__tar.gz → 0.4.5__tar.gz

{spacr-0.4.4 → spacr-0.4.5}/MANIFEST.in

@@ -35,3 +35,13 @@ prune notebooks
 prune spacr/notebooks
 prune spacr/datasets
 
+# Exclude model files from distribution
+#exclude spacr/resources/models/cp/*
+#prune spacr/resources/models/cp
+
+# Exclude all notebooks (including old ones)
+prune notebooks
+prune spacr/notebooks
+prune spacr/notebooks/submodules
+prune spacr/notebooks/old
+

{spacr-0.4.4/spacr.egg-info → spacr-0.4.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.4.4
+Version: 0.4.5
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.4.4 → spacr-0.4.5}/setup.py

@@ -71,7 +71,7 @@ dependencies = [
 
 setup(
     name="spacr",
-    version="0.4.4",
+    version="0.4.5",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",

{spacr-0.4.4 → spacr-0.4.5}/spacr/core.py

@@ -13,7 +13,7 @@ def preprocess_generate_masks(settings):
     from .plot import plot_image_mask_overlay, plot_arrays
     from .utils import _pivot_counts_table, check_mask_folder, adjust_cell_masks, print_progress, save_settings, delete_intermedeate_files, format_path_for_system, normalize_src_path
     from .settings import set_default_settings_preprocess_generate_masks
-    
+        
     if 'src' in settings:
         if not isinstance(settings['src'], (str, list)):
             ValueError(f'src must be a string or a list of strings')
@@ -33,7 +33,7 @@ def preprocess_generate_masks(settings):
             
             print(f'Processing folder: {source_folder}')
             
-            source_folder = format_path_for_system(source_folder)            
+            source_folder = format_path_for_system(source_folder)   
             settings['src'] = source_folder
             src = source_folder
             settings = set_default_settings_preprocess_generate_masks(settings)
@@ -61,9 +61,9 @@ def preprocess_generate_masks(settings):
             if settings['cell_channel'] is None and settings['nucleus_channel'] is None and settings['pathogen_channel'] is None:
                 print(f'Error: At least one of cell_channel, nucleus_channel or pathogen_channel must be defined')
                 return
-
+            
             save_settings(settings, name='gen_mask_settings')
-
+            
             if not settings['pathogen_channel'] is None:
                 custom_model_ls = ['toxo_pv_lumen','toxo_cyto']
                 if settings['pathogen_model'] not in custom_model_ls:
@@ -83,7 +83,7 @@ def preprocess_generate_masks(settings):
                 settings_df = pd.DataFrame(list(settings.items()), columns=['setting_key', 'setting_value'])
                 settings_df['setting_value'] = settings_df['setting_value'].apply(str)
                 display(settings_df)
-
+                
             if settings['test_mode']:
                 print(f'Starting Test mode ...')
 

{spacr-0.4.4 → spacr-0.4.5}/spacr/io.py

@@ -1574,7 +1574,7 @@ def preprocess_img_data(settings):
     Returns:
         None
     """
-
+    
     src = settings['src']
     valid_ext = ['tif', 'tiff', 'png', 'jpeg']
     files = os.listdir(src)
@@ -1602,11 +1602,11 @@ def preprocess_img_data(settings):
         
     mask_channels = [settings['nucleus_channel'], settings['cell_channel'], settings['pathogen_channel']]
     backgrounds = [settings['nucleus_background'], settings['cell_background'], settings['pathogen_background']]
-
+    
     settings, metadata_type, custom_regex, nr, plot, batch_size, timelapse, lower_percentile, randomize, all_to_mip, pick_slice, skip_mode, cmap, figuresize, normalize, save_dtype, test_mode, test_images, random_test = set_default_settings_preprocess_img_data(settings)
-
+    
     regex = _get_regex(metadata_type, img_format, custom_regex)
-
+    
     if test_mode:
 
         print(f'Running spacr in test mode')
@@ -1615,6 +1615,8 @@ def preprocess_img_data(settings):
             os.rmdir(os.path.join(src, 'test'))
             print(f"Deleted test directory: {os.path.join(src, 'test')}")
         except OSError as e:
+            print(f"Error deleting test directory: {e}")
+            print(f"Delete manually before running test mode")
             pass
 
         src = _run_test_mode(settings['src'], regex, timelapse, test_images, random_test)

{spacr-0.4.4 → spacr-0.4.5}/spacr/utils.py

@@ -321,21 +321,24 @@ def load_settings(csv_file_path, show=False, setting_key='setting_key', setting_
 
 def save_settings(settings, name='settings', show=False):
     
-    settings_df = pd.DataFrame(list(settings.items()), columns=['Key', 'Value'])
-    if show:
-        display(settings_df)
+    settings_2 = settings.copy()
     
-    if isinstance(settings['src'], list):
-        src = settings['src'][0]
+    if isinstance(settings_2['src'], list):
+        src = settings_2['src'][0]
         name = f"{name}_list"
     else:
-        src = settings['src']
+        src = settings_2['src']
         
-    if 'test_mode' in settings.keys():
-        settings['test_mode'] = False
+    if 'test_mode' in settings_2.keys():
+        settings_2['test_mode'] = False
         
-        if 'plot' in settings.keys():
-            settings['plot'] = False
+        if 'plot' in settings_2.keys():
+            settings_2['plot'] = False
+            
+    settings_df = pd.DataFrame(list(settings_2.items()), columns=['Key', 'Value'])
+    
+    if show:
+        display(settings_df)
 
     settings_csv = os.path.join(src,'settings',f'{name}.csv')
     os.makedirs(os.path.join(src,'settings'), exist_ok=True)
@@ -3144,7 +3147,7 @@ def _run_test_mode(src, regex, timelapse=False, test_images=10, random_test=True
 
     if os.path.exists(os.path.join(src, 'orig')):
         src = os.path.join(src, 'orig')
-    
+        
     all_filenames = [filename for filename in os.listdir(src) if regular_expression.match(filename)]
     print(f'Found {len(all_filenames)} files')
     images_by_set = defaultdict(list)

{spacr-0.4.4 → spacr-0.4.5/spacr.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.4.4
+Version: 0.4.5
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson