spacr 0.2.4__py3-none-any.whl → 0.2.5__py3-none-any.whl

spacr/io.py

@@ -588,20 +588,20 @@ def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=Fals
     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):
         all_filenames = [filename for filename in os.listdir(src) if filename.endswith(img_format)]
-        print(f'All_files:{len(all_filenames)} in {src}')
+        print(f'All_files: {len(all_filenames)} in {src}')
         time_ls = []
-        processed = 0
-        for i in range(0, len(all_filenames), batch_size):
+
+        for idx in range(0, len(all_filenames), batch_size):
             start = time.time()
-            batch_filenames = all_filenames[i:i+batch_size]
-            processed += len(batch_filenames)
+            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)
-
+            
             if pick_slice:
-                for key in images_by_key:
+                for i, key in enumerate(images_by_key):
                     plate, well, field, channel, mode = key
                     max_intensity_slice = max(images_by_key[key], key=lambda x: np.percentile(x, 90))
                     mip_image = Image.fromarray(max_intensity_slice)
@@ -609,21 +609,19 @@ def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=Fals
                     os.makedirs(output_dir, exist_ok=True)
                     output_filename = f'{plate}_{well}_{field}.tif'
                     output_path = os.path.join(output_dir, output_filename)
-
-                    if os.path.exists(output_path):                        
-                        print(f'WARNING: A file with the same name already exists at location {output_filename}')
-                    else:
-                        mip_image.save(output_path)
-                    
+                    files_processed += 1
                     stop = time.time()
                     duration = stop - start
                     time_ls.append(duration)
-                    files_processed = processed
                     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:
+                        mip_image.save(output_path)
             else:
-                for key, images in images_by_key.items():
+                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]
@@ -631,18 +629,17 @@ def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=Fals
                     os.makedirs(output_dir, exist_ok=True)
                     output_filename = f'{plate}_{well}_{field}.tif'
                     output_path = os.path.join(output_dir, output_filename)
-
-                    if os.path.exists(output_path):                        
-                        print(f'WARNING: A file with the same name already exists at location {output_filename}')
-                    else:
-                        mip_image.save(output_path)
+                    files_processed += 1
                     stop = time.time()
                     duration = stop - start
                     time_ls.append(duration)
-                    files_processed = processed
                     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:
+                        mip_image.save(output_path)
             images_by_key.clear()
 
         # Move original images to a new directory
@@ -656,6 +653,7 @@ def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=Fals
                     print(f'WARNING: A file with the same name already exists at location {move}')
                 else:
                     shutil.move(os.path.join(src, filename), move)
+    files_processed = 0
     return
 
 def _merge_file(chan_dirs, stack_dir, file_name):
@@ -975,7 +973,7 @@ def _concatenate_channel(src, channels, randomize=True, timelapse=False, batch_s
                 time_ls.append(duration)
                 files_processed = i+1
                 files_to_process = time_stack_path_lists
-                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=None, batch_size=None, operation_type="Concatinating")
+                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=batch_size, operation_type="Concatinating")
                 stack = np.stack(stack_region)
                 save_loc = os.path.join(channel_stack_loc, f'{name}.npz')
                 np.savez(save_loc, data=stack, filenames=filenames_region)
@@ -1006,7 +1004,7 @@ def _concatenate_channel(src, channels, randomize=True, timelapse=False, batch_s
             time_ls.append(duration)
             files_processed = i+1
             files_to_process = nr_files
-            print_progress(files_processed, files_to_process, n_jobs=1, time_ls=None, batch_size=None, operation_type="Concatinating")
+            print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=batch_size, operation_type="Concatinating")
             if (i+1) % batch_size == 0 or i+1 == nr_files:
                 unique_shapes = {arr.shape[:-1] for arr in stack_ls}
                 if len(unique_shapes) > 1:
@@ -1104,7 +1102,7 @@ def _normalize_img_batch(stack, channels, save_dtype, settings):
         time_ls.append(duration)
         files_processed = i+1
         files_to_process = len(channels)
-        print_progress(files_processed, files_to_process, n_jobs=1, time_ls=None, batch_size=None, operation_type=f"Normalizing: Channel: {channel}")
+        print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type=f"Normalizing")
 
     return normalized_stack.astype(save_dtype)
 
@@ -1151,7 +1149,6 @@ def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={})
                         parts = file.split('_')
                         name = parts[0] + '_' + parts[1] + '_' + parts[2]
                     array = np.load(path)
-                    #array = np.take(array, channels, axis=2)
                     stack_region.append(array)
                     filenames_region.append(os.path.basename(path))
                 stop = time.time()
@@ -1159,7 +1156,7 @@ def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={})
                 time_ls.append(duration)
                 files_processed = i+1
                 files_to_process = len(time_stack_path_lists)
-                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=None, batch_size=None, operation_type="Concatinating")
+                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Concatinating")
                 stack = np.stack(stack_region)
 
                 normalized_stack = _normalize_img_batch(stack=stack,
@@ -1188,18 +1185,18 @@ def concatenate_and_normalize(src, channels, save_dtype=np.float32, settings={})
         stack_ls = []
         filenames_batch = []
         time_ls = []
+        files_processed = 0
         for i, path in enumerate(paths):
             start = time.time()
             array = np.load(path)
-            #array = np.take(array, channels, axis=2)
             stack_ls.append(array)
             filenames_batch.append(os.path.basename(path))
             stop = time.time()
             duration = stop - start
             time_ls.append(duration)
-            files_processed = i+1
+            files_processed += 1
             files_to_process = nr_files
-            print_progress(files_processed, files_to_process, n_jobs=1, time_ls=None, batch_size=None, operation_type="Concatinating")
+            print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Concatinating")
 
             if (i + 1) % settings['batch_size'] == 0 or i + 1 == nr_files:
                 unique_shapes = {arr.shape[:-1] for arr in stack_ls}
@@ -1350,12 +1347,12 @@ def _normalize_stack(src, backgrounds=[100, 100, 100], remove_backgrounds=[False
                 average_time = np.mean(time_ls) if len(time_ls) > 0 else 0
                 print(f'channels:{chan_index}/{stack.shape[-1] - 1}, arrays:{array_index + 1}/{single_channel.shape[0]}, Signal:{upper:.1f}, noise:{lower:.1f}, Signal-to-noise:{average_stnr:.1f}, Time/channel:{average_time:.2f}sec')
 
-                stop = time.time()
-                duration = stop - start
-                time_ls.append(duration)
-                files_processed = file_index + 1
-                files_to_process = len(paths)
-                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Normalizing")
+                #stop = time.time()
+                #duration = stop - start
+                #time_ls.append(duration)
+                #files_processed = file_index + 1
+                #files_to_process = len(paths)
+                #print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Normalizing")
                 
             normalized_stack[:, :, :, channel] = arr_2d_normalized
         
@@ -1405,12 +1402,12 @@ def _normalize_timelapse(src, lower_percentile=2, save_dtype=np.float32):
 
                 print(f'channels:{chan_index+1}/{stack.shape[-1]}, arrays:{array_index+1}/{single_channel.shape[0]}', end='\r')
 
-                stop = time.time()
-                duration = stop - start
-                time_ls.append(duration)
-                files_processed = file_index+1
-                files_to_process = len(paths)
-                print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Normalizing")
+                #stop = time.time()
+                #duration = stop - start
+                #time_ls.append(duration)
+                #files_processed = file_index+1
+                #files_to_process = len(paths)
+                #print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Normalizing")
 
         save_loc = os.path.join(output_fldr, f'{name}_norm_timelapse.npz')
         np.savez(save_loc, data=normalized_stack, filenames=filenames)
@@ -1620,8 +1617,8 @@ def preprocess_img_data(settings):
                               save_dtype=np.float32,
                               settings=settings)
 
-    if plot:
-        _plot_4D_arrays(src+'/norm_channel_stack', nr_npz=1, nr=nr)
+    #if plot:
+    #    _plot_4D_arrays(src+'/norm_channel_stack', nr_npz=1, nr=nr)
 
     return settings, src
     
@@ -1951,7 +1948,7 @@ def _load_and_concatenate_arrays(src, channels, cell_chann_dim, nucleus_chann_di
     all_imgs = len(os.listdir(reference_folder))
     time_ls = []
     # Iterate through each file in the reference folder
-    for filename in os.listdir(reference_folder):
+    for idx, filename in enumerate(os.listdir(reference_folder)):
         start = time.time()
         stack_ls = []
         if filename.endswith('.npy'):
@@ -2012,7 +2009,7 @@ def _load_and_concatenate_arrays(src, channels, cell_chann_dim, nucleus_chann_di
         stop = time.time()
         duration = stop - start
         time_ls.append(duration)
-        files_processed = count
+        files_processed = idx+1
         files_to_process = all_imgs
         print_progress(files_processed, files_to_process, n_jobs=1, time_ls=time_ls, batch_size=None, operation_type="Merging Arrays")
 
@@ -2550,7 +2547,6 @@ def _read_mask(mask_path):
         mask = img_as_uint(mask)
     return mask
 
-
 def convert_numpy_to_tiff(folder_path, limit=None):
     """
     Converts all numpy files in a folder to TIFF format and saves them in a subdirectory 'tiff'.