spacr 0.1.50__py3-none-any.whl → 0.1.61__py3-none-any.whl

spacr/gui_wrappers.py

@@ -0,0 +1,137 @@
+import traceback, matplotlib, spacr
+import matplotlib.pyplot as plt
+matplotlib.use('Agg')
+
+fig_queue = None
+
+def my_show():
+    """
+    Replacement for plt.show() that queues figures instead of displaying them.
+    """
+    fig = plt.gcf()
+    fig_queue.put(fig)
+    plt.close(fig)
+
+def measure_crop_wrapper(settings, q, fig_queue):
+    """
+    Wraps the measure_crop function to integrate with GUI processes.
+    
+    Parameters:
+    - settings: dict, The settings for the measure_crop function.
+    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
+    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
+    """
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        print('start')
+        spacr.measure.measure_crop(settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)
+        traceback.print_exc()
+    finally:
+        plt.show = original_show  
+        
+def preprocess_generate_masks_wrapper(settings, q, fig_queue):
+    """
+    Wraps the measure_crop function to integrate with GUI processes.
+    
+    Parameters:
+    - settings: dict, The settings for the measure_crop function.
+    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
+    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
+    """
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        spacr.core.preprocess_generate_masks(src=settings['src'], settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)
+        traceback.print_exc()
+    finally:
+        plt.show = original_show
+
+def sequencing_wrapper(settings, q, fig_queue):
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        spacr.sequencing.analyze_reads(settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)
+        traceback.print_exc()
+    finally:
+        plt.show = original_show
+
+def umap_wrapper(settings, q, fig_queue):
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        spacr.core.generate_image_umap(settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)
+        traceback.print_exc()
+    finally:
+        plt.show = original_show
+
+def train_test_model_wrapper(settings, q, fig_queue):
+    """
+    Wraps the measure_crop function to integrate with GUI processes.
+    
+    Parameters:
+    - settings: dict, The settings for the measure_crop function.
+    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
+    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
+    """
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        spacr.core.train_test_model(settings['src'], settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)  # Send the error message to the GUI via the queue
+        traceback.print_exc()
+    finally:
+        plt.show = original_show  # Restore the original plt.show function
+        
+        
+def run_multiple_simulations_wrapper(settings, q, fig_queue):
+    """
+    Wraps the run_multiple_simulations function to integrate with GUI processes.
+    
+    Parameters:
+    - settings: dict, The settings for the run_multiple_simulations function.
+    - q: multiprocessing.Queue, Queue for logging messages to the GUI.
+    - fig_queue: multiprocessing.Queue, Queue for sending figures to the GUI.
+    """
+
+    # Temporarily override plt.show
+    original_show = plt.show
+    plt.show = my_show
+
+    try:
+        spacr.sim.run_multiple_simulations(settings=settings)
+    except Exception as e:
+        errorMessage = f"Error during processing: {e}"
+        q.put(errorMessage)  # Send the error message to the GUI via the queue
+        traceback.print_exc()
+    finally:
+        plt.show = original_show  # Restore the original plt.show function

spacr/measure.py

@@ -16,12 +16,6 @@ from skimage.util import img_as_bool
 
 from .logger import log_function_call
 
-#from .io import create_database, _save_settings_to_db
-#from .timelapse import _timelapse_masks_to_gif, _scmovie
-#from .plot import _plot_cropped_arrays, _save_scimg_plot
-#from .utils import _merge_overlapping_objects, _filter_object, _relabel_parent_with_child_labels, _exclude_objects
-#from .utils import _merge_and_save_to_database, _crop_center, _find_bounding_box, _generate_names, _get_percentiles, normalize_to_dtype, _map_wells_png, _list_endpoint_subdirectories, _generate_representative_images
-
 def get_components(cell_mask, nucleus_mask, pathogen_mask):
     """
     Get the components (nucleus and pathogens) for each cell in the given masks.
@@ -626,8 +620,13 @@ def _measure_crop_core(index, time_ls, file, settings):
 
         file_name = os.path.splitext(file)[0]
         data = np.load(os.path.join(settings['input_folder'], file))
-
         data_type = data.dtype
+        if data_type not in ['uint8','uint16']:
+            data_type_before = data_type
+            data = data.astype(np.uint16)
+            data_type = data.dtype
+            print(f'Converted data from {data_type_before} to {data_type}')
+
         if settings['save_measurements']:
             os.makedirs(source_folder+'/measurements', exist_ok=True)
             _create_database(source_folder+'/measurements/measurements.db')    
@@ -832,7 +831,6 @@ def _measure_crop_core(index, time_ls, file, settings):
                                     png_channels = normalize_to_dtype(png_channels, settings['normalize'][0], settings['normalize'][1], percentile_list=percentile_list)
                             else:
                                 png_channels = normalize_to_dtype(png_channels, 0, 100)
-
                             os.makedirs(png_folder, exist_ok=True)
 
                             if png_channels.shape[2] == 2:

spacr/plot.py

@@ -1565,4 +1565,56 @@ def plot_feature_importance(feature_importance_df):
     ax.set_xlabel('Feature Importance', fontsize=font_size)
     ax.tick_params(axis='both', which='major', labelsize=font_size)
     plt.tight_layout()
-    return fig
+    return fig
+
+def read_and_plot__vision_results(base_dir, y_axis='accuracy', name_split='_time', y_lim=[0.8, 0.9]):
+    # List to store data from all CSV files
+    data_frames = []
+
+    dst = os.path.join(base_dir, 'result')
+    os.mkdir(dst,exists=True)
+
+    # Walk through the directory
+    for root, dirs, files in os.walk(base_dir):
+        for file in files:
+            if file.endswith("_test_result.csv"):
+                file_path = os.path.join(root, file)
+                # Extract model information from the file name
+                file_name = os.path.basename(file_path)
+                model = file_name.split(f'{name_split}')[0]
+                
+                # Extract epoch information from the file name
+                epoch_info = file_name.split('_time')[1]
+                base_folder = os.path.dirname(file_path)
+                epoch = os.path.basename(base_folder)
+                
+                # Read the CSV file
+                df = pd.read_csv(file_path)
+                df['model'] = model
+                df['epoch'] = epoch
+                
+                # Append the data frame to the list
+                data_frames.append(df)
+    
+    # Concatenate all data frames
+    if data_frames:
+        result_df = pd.concat(data_frames, ignore_index=True)
+        
+        # Calculate average y_axis per model
+        avg_metric = result_df.groupby('model')[y_axis].mean().reset_index()
+        avg_metric = avg_metric.sort_values(by=y_axis)
+        print(avg_metric)
+        
+        # Plotting the results
+        plt.figure(figsize=(10, 6))
+        plt.bar(avg_metric['model'], avg_metric[y_axis])
+        plt.xlabel('Model')
+        plt.ylabel(f'{y_axis}')
+        plt.title(f'Average {y_axis.capitalize()} per Model')
+        plt.xticks(rotation=45)
+        plt.tight_layout()
+        if y_lim is not None:
+            plt.ylim(y_lim)
+        plt.show()
+    else:
+        print("No CSV files found in the specified directory.")

spacr/sequencing.py

@@ -37,22 +37,6 @@ def analyze_reads(settings):
         None
     """
     
-    def save_chunk_to_hdf5_v1(output_file_path, data_chunk, chunk_counter):
-        """
-        Save a data chunk to an HDF5 file.
-
-        Parameters:
-        - output_file_path (str): The path to the output HDF5 file.
-        - data_chunk (list): The data chunk to be saved.
-        - chunk_counter (int): The counter for the current chunk.
-
-        Returns:
-        None
-        """
-        df = pd.DataFrame(data_chunk, columns=['combined_read', 'grna', 'plate_row', 'column', 'sample'])
-        with pd.HDFStore(output_file_path, mode='a', complevel=5, complib='blosc') as store:
-            store.put(f'reads/chunk_{chunk_counter}', df, format='table', append=True)
-
     def save_chunk_to_hdf5(output_file_path, data_chunk, chunk_counter):
         """
         Save a data chunk to an HDF5 file.
@@ -306,7 +290,7 @@ def analyze_reads(settings):
                 qc_df = pd.DataFrame([qc])
                 qc_df.to_csv(qc_file_path, index=False)
                 
-    from .utils import get_analyze_reads_default_settings
+    from .settings import get_analyze_reads_default_settings
 
     settings = get_analyze_reads_default_settings(settings)