spacr 0.4.4__py3-none-any.whl → 0.4.5__py3-none-any.whl

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/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/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.dist-info → spacr-0.4.5.dist-info}/METADATA

@@ -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.dist-info → spacr-0.4.5.dist-info}/RECORD

@@ -9,13 +9,13 @@ spacr/app_sequencing.py,sha256=DjG26jy4cpddnV8WOOAIiExtOe9MleVMY4MFa5uTo5w,157
 spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/cellpose.py,sha256=RBHMs2vwXcfkj0xqAULpALyzJYXddSRycgZSzmwI7v0,14755
 spacr/chat_bot.py,sha256=n3Fhqg3qofVXHmh3H9sUcmfYy9MmgRnr48663MVdY9E,1244
-spacr/core.py,sha256=KYPG28Z-AX1nzZ2Fd6F5RrBU_canp_vyEzZINLYpElw,50496
+spacr/core.py,sha256=9-Vo0ZICGRnqKuIQQdyV4fgczPKBnnLw_5OTti4n2v4,50531
 spacr/deep_spacr.py,sha256=WN64EaQqF87JZg3Uan46t5Y28xsAGD2KMjr2ht6CyDs,54563
 spacr/gui.py,sha256=ARyn9Q_g8HoP-cXh1nzMLVFCKqthY4v2u9yORyaQqQE,8230
 spacr/gui_core.py,sha256=qMHQPY7LZEKQ5c7dIQtRyVBy03xNmwYWO8S85btVeEw,60170
 spacr/gui_elements.py,sha256=Or38I_X9-lJRsyIAtbEfZPXzls0IORagf7vEe6IlI5Y,152647
 spacr/gui_utils.py,sha256=dWVPFwDj793Z3ERG4mMC0hI0MKkOrvXJpUYlcjpCBsU,41357
-spacr/io.py,sha256=bkpBQiLsd69w4GpvrY2NNbZbqHfuRCrbjELlkXBIok8,148414
+spacr/io.py,sha256=itnlAWB3o_GvqyyCpjbFUTK7mCgqmd6wC0Xo0QOv0Ws,148550
 spacr/logger.py,sha256=lJhTqt-_wfAunCPl93xE65Wr9Y1oIHJWaZMjunHUeIw,1538
 spacr/measure.py,sha256=Z3u4BU5RzcY82IZuboQ0OsxuXaPVwOlH65Rw6FrL5z4,55045
 spacr/mediar.py,sha256=FwLvbLQW5LQzPgvJZG8Lw7GniA2vbZx6Jv6vIKu7I5c,14743
@@ -30,7 +30,7 @@ spacr/stats.py,sha256=mbhwsyIqt5upsSD346qGjdCw7CFBa0tIS7zHU9e0jNI,9536
 spacr/submodules.py,sha256=jFlJeVNuIEf63TtCOpTlOZ4iiSLr238kRBiGAAAgKE4,67626
 spacr/timelapse.py,sha256=KGfG4L4-QnFfgbF7L6C5wL_3gd_rqr05Foje6RsoTBg,39603
 spacr/toxo.py,sha256=TmuhejSIPLBvsgeblsUgSvBFCR1gOkApyTKidooJ5Us,26044
-spacr/utils.py,sha256=jjNCA3O7nF-Y_2c2OsAkAm5WdyD1SZ6eqV7PI3WcLdo,228617
+spacr/utils.py,sha256=eaDiP-xsUnPHPvm4Y0abI0vN6f14E7jTx1jGWTvNAXc,228688
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/MEDIAR/.gitignore,sha256=Ff1q9Nme14JUd-4Q3jZ65aeQ5X4uttptssVDgBVHYo8,152
 spacr/resources/MEDIAR/LICENSE,sha256=yEj_TRDLUfDpHDNM0StALXIt6mLqSgaV2hcCwa6_TcY,1065
@@ -153,9 +153,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
-spacr-0.4.4.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.4.4.dist-info/METADATA,sha256=EhQ8CvDWMbq7bJ18Pt_cAcz2uiRz1X7PH5gzwZdw5gw,6095
-spacr-0.4.4.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-spacr-0.4.4.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.4.4.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.4.4.dist-info/RECORD,,
+spacr-0.4.5.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.4.5.dist-info/METADATA,sha256=TflztedXnlEx4zDe5iGkyZ4kGbHPG7ZhRKpBBHwTFWU,6095
+spacr-0.4.5.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+spacr-0.4.5.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.4.5.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.4.5.dist-info/RECORD,,