spacr 0.3.0__tar.gz → 0.3.1__tar.gz

{spacr-0.3.0/spacr.egg-info → spacr-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.0
+Version: 0.3.1
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.3.0 → spacr-0.3.1}/setup.py

@@ -60,7 +60,7 @@ dependencies = [
 
 setup(
     name="spacr",
-    version="0.3.0",
+    version="0.3.01",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",

{spacr-0.3.0 → spacr-0.3.1}/spacr/core.py

@@ -1672,9 +1672,9 @@ def preprocess_generate_masks(src, settings={}):
             time_ls=[]
             if check_mask_folder(src, 'cell_mask_stack'):
                 start = time.time()
-                if settings['segmantation_model'] == 'cellpose':
+                if settings['segmentation_mode'] == 'cellpose':
                     generate_cellpose_masks(mask_src, settings, 'cell')
-                elif settings['segmantation_model'] == 'mediar':
+                elif settings['segmentation_mode'] == 'mediar':
                     generate_mediar_masks(mask_src, settings, 'cell')
                 stop = time.time()
                 duration = (stop - start)
@@ -1686,9 +1686,9 @@ def preprocess_generate_masks(src, settings={}):
             time_ls=[]
             if check_mask_folder(src, 'nucleus_mask_stack'):
                 start = time.time()
-                if settings['segmantation_model'] == 'cellpose':
+                if settings['segmentation_mode'] == 'cellpose':
                     generate_cellpose_masks(mask_src, settings, 'nucleus')
-                elif settings['segmantation_model'] == 'mediar':
+                elif settings['segmentation_mode'] == 'mediar':
                     generate_mediar_masks(mask_src, settings, 'nucleus')
                 stop = time.time()
                 duration = (stop - start)
@@ -1700,9 +1700,9 @@ def preprocess_generate_masks(src, settings={}):
             time_ls=[]
             if check_mask_folder(src, 'pathogen_mask_stack'):
                 start = time.time()
-                if settings['segmantation_model'] == 'cellpose':
+                if settings['segmentation_mode'] == 'cellpose':
                     generate_cellpose_masks(mask_src, settings, 'pathogen')
-                elif settings['segmantation_model'] == 'mediar':
+                elif settings['segmentation_mode'] == 'mediar':
                     generate_mediar_masks(mask_src, settings, 'pathogen')
                 stop = time.time()
                 duration = (stop - start)
@@ -1757,7 +1757,7 @@ def preprocess_generate_masks(src, settings={}):
                             files_processed = i+1
                             files_to_process = settings['examples_to_plot']
                             print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Plot mask outlines")
-                            print("Successfully completed run")
+                            
                 except Exception as e:
                     print(f'Failed to plot image mask overly. Error: {e}')
             else:

{spacr-0.3.0 → spacr-0.3.1}/spacr/io.py

@@ -653,7 +653,6 @@ def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=Fals
     from .utils import _extract_filename_metadata, print_progress
     
     regular_expression = re.compile(regex)
-    images_by_key = defaultdict(list)
     stack_path = os.path.join(src, 'stack')
     files_processed = 0
     if not os.path.exists(stack_path) or (os.path.isdir(stack_path) and len(os.listdir(stack_path)) == 0):
@@ -665,7 +664,7 @@ def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=Fals
             start = time.time()
             batch_filenames = all_filenames[idx:idx+batch_size]
             for filename in batch_filenames:
-                images_by_key = _extract_filename_metadata(batch_filenames, src, images_by_key, regular_expression, metadata_type, pick_slice, skip_mode)
+                images_by_key = _extract_filename_metadata(batch_filenames, src, regular_expression, metadata_type, pick_slice, skip_mode)
             
             if pick_slice:
                 for i, key in enumerate(images_by_key):
@@ -683,16 +682,16 @@ def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=Fals
                     files_to_process = len(all_filenames)
                     print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=batch_size, operation_type='Preprocessing filenames')
 
-                    if os.path.exists(output_path):                        
-                        print(f'WARNING: A file with the same name already exists at location {output_filename}')
-                    else:
+                    #if os.path.exists(output_path):                        
+                    #    print(f'WARNING: A file with the same name already exists at location {output_filename}')
+                    if not os.path.exists(output_path):
                         mip_image.save(output_path)
             else:
                 for i, (key, images) in enumerate(images_by_key.items()):
-                    mip = np.max(np.stack(images), axis=0)
-                    mip_image = Image.fromarray(mip)
                     plate, well, field, channel = key[:4]
                     output_dir = os.path.join(src, channel)
+                    mip = np.max(np.stack(images), axis=0)
+                    mip_image = Image.fromarray(mip)
                     os.makedirs(output_dir, exist_ok=True)
                     output_filename = f'{plate}_{well}_{field}.tif'
                     output_path = os.path.join(output_dir, output_filename)
@@ -703,9 +702,9 @@ def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=Fals
                     files_to_process = len(all_filenames)
                     print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=batch_size, operation_type='Preprocessing filenames')
 
-                    if os.path.exists(output_path):                        
-                        print(f'WARNING: A file with the same name already exists at location {output_filename}')
-                    else:
+                    #if os.path.exists(output_path):                        
+                    #    print(f'WARNING: A file with the same name already exists at location {output_filename}')
+                    if not os.path.exists(output_path):
                         mip_image.save(output_path)
             images_by_key.clear()
 
@@ -972,8 +971,8 @@ def _mip_all(src, include_first_chan=True):
         if filename.endswith('.npy'):
             # Load the array from the file.
             array = np.load(os.path.join(src, filename))
-            # Normalize the array using custom parameters (q1=2, q2=98).
-            array = normalize_to_dtype(array, q1=2, q2=98, percentiles=None)
+            # Normalize the array 
+            #array = normalize_to_dtype(array, q1=0, q2=99, percentiles=None)
 
             if array.ndim != 3: # Check if the array is not 3-dimensional.
                 # Log a message indicating a zero array will be generated due to unexpected dimensions.
@@ -1671,6 +1670,7 @@ def preprocess_img_data(settings):
                 if plot:
                     print(f'plotting {nr} images from {src}/stack')
                     plot_arrays(src+'/stack', figuresize, cmap, nr=nr, normalize=normalize)
+
                 if all_to_mip:
                     _mip_all(src+'/stack')
                     if plot:

{spacr-0.3.0 → spacr-0.3.1}/spacr/mediar.py

@@ -22,8 +22,6 @@ try:
     # Now import the dependencies from MEDIAR
     from core.MEDIAR import Predictor, EnsemblePredictor
     from train_tools.models import MEDIARFormer
-
-    print("Imports successful.")
 finally:
     # Remove the temporary __init__.py file after the import
     if os.path.exists(init_file):

{spacr-0.3.0 → spacr-0.3.1}/spacr/plot.py

@@ -123,7 +123,7 @@ def plot_image_mask_overlay(file, channels, cell_channel, nucleus_channel, patho
 
     fig = _plot_merged_plot(image=image, outlines=outlines, outline_colors=outline_colors, figuresize=figuresize, thickness=thickness)
 
-    return
+    return fig
 
 def plot_masks(batch, masks, flows, cmap='inferno', figuresize=10, nr=1, file_type='.npz', print_object_number=True):
     """

{spacr-0.3.0 → spacr-0.3.1}/spacr/utils.py

@@ -303,7 +303,10 @@ def _get_cellpose_batch_size():
     except Exception as e:
         return 8
 
-def _extract_filename_metadata(filenames, src, images_by_key, regular_expression, metadata_type='cellvoyager', pick_slice=False, skip_mode='01'):
+def _extract_filename_metadata(filenames, src, regular_expression, metadata_type='cellvoyager', pick_slice=False, skip_mode='01'):
+    
+    images_by_key = defaultdict(list)
+    
     for filename in filenames:
         match = regular_expression.match(filename)
         if match:
@@ -328,7 +331,6 @@ def _extract_filename_metadata(filenames, src, images_by_key, regular_expression
                 if metadata_type =='cq1':
                     orig_wellID = wellID
                     wellID = _convert_cq1_well_id(wellID)
-                    #clear_output(wait=True)
                     print(f'Converted Well ID: {orig_wellID} to {wellID}', end='\r', flush=True)
 
                 if pick_slice:
@@ -338,7 +340,7 @@ def _extract_filename_metadata(filenames, src, images_by_key, regular_expression
                         sliceid = '00'
 
                     if mode == skip_mode:
-                        continue      
+                        continue
                         
                 key = (plate, well, field, channel, mode)
                 with Image.open(os.path.join(src, filename)) as img:

{spacr-0.3.0 → spacr-0.3.1/spacr.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.0
+Version: 0.3.1
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson