spacr 0.0.35__tar.gz → 0.0.36__tar.gz

{spacr-0.0.35/spacr.egg-info → spacr-0.0.36}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.0.35
+Version: 0.0.36
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.0.35 → spacr-0.0.36}/setup.py

@@ -35,7 +35,7 @@ dependencies = [
 
 setup(
     name="spacr",
-    version="0.0.35",
+    version="0.0.36",
     author="Einar Birnir Olafsson",
     author_email="olafsson@med.umich.com",
     description="Spatial phenotype analysis of crisp screens (SpaCr)",

{spacr-0.0.35 → spacr-0.0.36}/spacr/annotate_app.py

@@ -419,7 +419,7 @@ def check_for_duplicates(db):
     conn.commit()
     conn.close()
 
-@log_function_call
+#@log_function_call
 def initiate_annotation_app_root(width, height):
     theme = 'breeze'
     root = ThemedTk(theme=theme)

{spacr-0.0.35 → spacr-0.0.36}/spacr/gui_classify_app.py

@@ -21,7 +21,7 @@ from .gui_utils import classify_variables, check_classify_gui_settings, train_te
 
 thread_control = {"run_thread": None, "stop_requested": False}
 
-@log_function_call
+#@log_function_call
 def initiate_abort():
     global thread_control
     if thread_control.get("stop_requested") is not None:
@@ -33,7 +33,7 @@ def initiate_abort():
             thread_control["run_thread"].terminate()
         thread_control["run_thread"] = None
         
-@log_function_call
+#@log_function_call
 def run_classify_gui(q, fig_queue, stop_requested):
     global vars_dict
     process_stdout_stderr(q)
@@ -49,7 +49,7 @@ def run_classify_gui(q, fig_queue, stop_requested):
     finally:
         stop_requested.value = 1
     
-@log_function_call
+#@log_function_call
 def start_process(q, fig_queue):
     global thread_control
     if thread_control.get("run_thread") is not None:
@@ -69,7 +69,7 @@ def import_settings(scrollable_frame):
     new_settings = update_settings_from_csv(variables, csv_settings)
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
-@log_function_call
+#@log_function_call
 def initiate_classify_root(parent_frame, width, height):
     global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control
     

{spacr-0.0.35 → spacr-0.0.36}/spacr/gui_mask_app.py

@@ -50,7 +50,7 @@ def toggle_advanced_settings():
             label.grid()  # Show the label
             widget.grid()  # Show the widget
 
-@log_function_call
+#@log_function_call
 def initiate_abort():
     global thread_control
     if thread_control.get("stop_requested") is not None:
@@ -62,7 +62,7 @@ def initiate_abort():
             thread_control["run_thread"].terminate()
         thread_control["run_thread"] = None
 
-@log_function_call
+#@log_function_call
 def run_mask_gui(q, fig_queue, stop_requested):
     global vars_dict
     process_stdout_stderr(q)
@@ -75,7 +75,7 @@ def run_mask_gui(q, fig_queue, stop_requested):
     finally:
         stop_requested.value = 1
 
-@log_function_call
+#@log_function_call
 def start_process(q, fig_queue):
     global thread_control
     if thread_control.get("run_thread") is not None:
@@ -95,7 +95,7 @@ def import_settings(scrollable_frame):
     new_settings = update_settings_from_csv(variables, csv_settings)
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
-@log_function_call
+#@log_function_call
 def initiate_mask_root(parent_frame, width, height):
     global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control, advanced_var, scrollable_frame
 

{spacr-0.0.35 → spacr-0.0.36}/spacr/gui_measure_app.py

@@ -50,7 +50,7 @@ def toggle_advanced_settings():
             label.grid()  # Show the label
             widget.grid()  # Show the widget
 
-@log_function_call
+#@log_function_call
 def run_measure_gui(q, fig_queue, stop_requested):
     global vars_dict
     process_stdout_stderr(q)
@@ -64,7 +64,7 @@ def run_measure_gui(q, fig_queue, stop_requested):
     finally:
         stop_requested.value = 1
 
-@log_function_call
+#@log_function_call
 def start_process(q, fig_queue):
     global thread_control
     if thread_control.get("run_thread") is not None:
@@ -75,7 +75,7 @@ def start_process(q, fig_queue):
     thread_control["run_thread"] = Process(target=run_measure_gui, args=(q, fig_queue, stop_requested))
     thread_control["run_thread"].start()
 
-@log_function_call
+#@log_function_call
 def initiate_abort():
     global thread_control
     if thread_control.get("stop_requested") is not None:
@@ -87,7 +87,7 @@ def initiate_abort():
             thread_control["run_thread"].terminate()
         thread_control["run_thread"] = None
 
-@log_function_call
+#@log_function_call
 def import_settings(scrollable_frame):
     global vars_dict
 
@@ -97,7 +97,7 @@ def import_settings(scrollable_frame):
     new_settings = update_settings_from_csv(variables, csv_settings)
     vars_dict = generate_fields(new_settings, scrollable_frame)
 
-@log_function_call
+#@log_function_call
 def initiate_measure_root(parent_frame, width, height):
     global vars_dict, q, canvas, fig_queue, canvas_widget, thread_control, variables, advanced_var, scrollable_frame
     

{spacr-0.0.35 → spacr-0.0.36}/spacr/gui_utils.py

@@ -744,7 +744,7 @@ def set_dark_style(style):
     style.configure('TEntry', background='black', foreground='white')
     style.configure('TCheckbutton', background='black', foreground='white')
 
-#@log_function_call   
+##@log_function_call   
 def main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label):
     try:
         ansi_escape_pattern = re.compile(r'\x1B\[[0-?]*[ -/]*[@-~]')
@@ -833,7 +833,7 @@ def measure_crop_wrapper(settings, q, fig_queue):
     finally:
         plt.show = original_show  # Restore the original plt.show function
         
-@log_function_call
+#@log_function_call
 def preprocess_generate_masks_wrapper(settings, q, fig_queue):
     """
     Wraps the measure_crop function to integrate with GUI processes.

{spacr-0.0.35 → spacr-0.0.36}/spacr/io.py

@@ -529,7 +529,7 @@ class TarImageDataset(Dataset):
         
         return img, m.name
 
-@log_function_call
+#@log_function_call
 def _rename_and_organize_image_files(src, regex, batch_size=100, pick_slice=False, skip_mode='01', metadata_type='', img_format='.tif'):
     """
     Convert z-stack images to maximum intensity projection (MIP) images.
@@ -930,7 +930,7 @@ def _mip_all(src, include_first_chan=True):
             np.save(os.path.join(src, filename), concatenated)
     return
 
-@log_function_call
+#@log_function_call
 def _concatenate_channel(src, channels, randomize=True, timelapse=False, batch_size=100):
     """
     Concatenates channel data from multiple files and saves the concatenated data as numpy arrays.
@@ -1257,7 +1257,7 @@ def delete_empty_subdirectories(folder_path):
                 # An error occurred, likely because the directory is not empty
                 #print(f"Skipping non-empty directory: {full_dir_path}")
 
-@log_function_call
+#@log_function_call
 def preprocess_img_data(settings):
     
     from .plot import plot_arrays, _plot_4D_arrays

{spacr-0.0.35 → spacr-0.0.36}/spacr/mask_app.py

@@ -753,7 +753,7 @@ class modify_masks:
                 self.mask[labeled_mask == i] = 0  # Remove small objects
         self.update_display()
 
-@log_function_call
+##@log_function_call
 def initiate_mask_app_root(width, height):
     theme = 'breeze'
     root = ThemedTk(theme=theme)

{spacr-0.0.35 → spacr-0.0.36}/spacr/measure.py

@@ -157,7 +157,7 @@ def _analyze_cytoskeleton(array, mask, channel):
 
     return pd.DataFrame(properties_list)
 
-@log_function_call
+#@log_function_call
 def _morphological_measurements(cell_mask, nucleus_mask, pathogen_mask, cytoplasm_mask, settings, zernike=True, degree=8):
     """
     Calculate morphological measurements for cells, nucleus, pathogens, and cytoplasms based on the given masks.
@@ -501,7 +501,7 @@ def _estimate_blur(image):
     # Compute and return the variance of the Laplacian
     return lap.var()
 
-@log_function_call
+#@log_function_call
 def _intensity_measurements(cell_mask, nucleus_mask, pathogen_mask, cytoplasm_mask, channel_arrays, settings, sizes=[3, 6, 12, 24], periphery=True, outside=True):
     """
     Calculate various intensity measurements for different regions in the image.
@@ -589,7 +589,7 @@ def _intensity_measurements(cell_mask, nucleus_mask, pathogen_mask, cytoplasm_ma
     
     return pd.concat(cell_dfs, axis=1), pd.concat(nucleus_dfs, axis=1), pd.concat(pathogen_dfs, axis=1), pd.concat(cytoplasm_dfs, axis=1)
 
-@log_function_call
+#@log_function_call
 def _measure_crop_core(index, time_ls, file, settings):
 
     """
@@ -887,7 +887,7 @@ def _measure_crop_core(index, time_ls, file, settings):
     average_time = np.mean(time_ls) if len(time_ls) > 0 else 0
     return average_time, cells
 
-@log_function_call
+#@log_function_call
 def measure_crop(settings):
     
     """

{spacr-0.0.35 → spacr-0.0.36}/spacr/old_code.py

@@ -103,7 +103,7 @@ def run_mask_gui(q):
     except Exception as e:
         q.put(f"Error during processing: {e}\n")
 
-@log_function_call   
+#@log_function_call   
 def main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label):
     try:
         while not q.empty():

{spacr-0.0.35 → spacr-0.0.36/spacr.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.0.35
+Version: 0.0.36
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson