spacr 0.9.0__py3-none-any.whl → 0.9.1__py3-none-any.whl

spacr/gui_core.py

@@ -1083,81 +1083,6 @@ def process_console_queue():
     # **Continue processing if no error was detected**
     after_id = console_output.after(uppdate_frequency, process_console_queue)
     parent_frame.after_tasks.append(after_id)
-    
-def process_console_queue_v2():
-    global q, console_output, parent_frame, progress_bar, process_console_queue
-
-    # Initialize function attribute if it doesn't exist
-    if not hasattr(process_console_queue, "completed_tasks"):
-        process_console_queue.completed_tasks = []
-    if not hasattr(process_console_queue, "current_maximum"):
-        process_console_queue.current_maximum = None
-
-    ansi_escape_pattern = re.compile(r'\x1B\[[0-?]*[ -/]*[@-~]')
-
-    while not q.empty():
-        message = q.get_nowait()
-        clean_message = ansi_escape_pattern.sub('', message)
-
-        # **Abort Execution if an Error Message is Detected**
-        if clean_message.startswith("Error:"):
-            console_output.insert(tk.END, clean_message + "\n", "error")
-            console_output.see(tk.END)
-            print("Run aborted due to error:", clean_message)  # Debug message
-            return  # **Exit immediately to stop further execution**
-
-        # Check if the message contains progress information
-        if clean_message.startswith("Progress:"):
-            try:
-                # Extract the progress information
-                match = re.search(r'Progress: (\d+)/(\d+), operation_type: ([\w\s]*),(.*)', clean_message)
-
-                if match:
-                    current_progress = int(match.group(1))
-                    total_progress = int(match.group(2))
-                    operation_type = match.group(3).strip()
-                    additional_info = match.group(4).strip()  # Capture everything after operation_type
-                    
-                    # Check if the maximum value has changed
-                    if process_console_queue.current_maximum != total_progress:
-                        process_console_queue.current_maximum = total_progress
-                        process_console_queue.completed_tasks = []
-
-                    # Add the task to the completed set
-                    process_console_queue.completed_tasks.append(current_progress)
-                    
-                    # Calculate the unique progress count
-                    unique_progress_count = len(np.unique(process_console_queue.completed_tasks))
-
-                    # Update the progress bar
-                    if progress_bar:
-                        progress_bar['maximum'] = total_progress
-                        progress_bar['value'] = unique_progress_count
-
-                    # Store operation type and additional info
-                    if operation_type:
-                        progress_bar.operation_type = operation_type
-                        progress_bar.additional_info = additional_info
-
-                    # Update the progress label
-                    if progress_bar.progress_label:
-                        progress_bar.update_label()
-
-                    # Clear completed tasks when progress is complete
-                    if unique_progress_count >= total_progress:
-                        process_console_queue.completed_tasks.clear()
-
-            except Exception as e:
-                print(f"Error parsing progress message: {e}")
-
-        else:
-            # Insert non-progress messages into the console
-            console_output.insert(tk.END, clean_message + "\n")
-            console_output.see(tk.END)
-
-    # **Continue processing if no error was detected**
-    after_id = console_output.after(uppdate_frequency, process_console_queue)
-    parent_frame.after_tasks.append(after_id)
 
 def main_thread_update_function(root, q, fig_queue, canvas_widget):
     global uppdate_frequency

spacr/plot.py

@@ -1241,103 +1241,6 @@ def _display_gif(path):
     """
     with open(path, 'rb') as file:
         display(ipyimage(file.read()))
-
-def _plot_recruitment_v2(df, df_type, channel_of_interest, columns=[], figuresize=10):
-    """
-    Plot recruitment data for different conditions and pathogens.
-
-    Args:
-        df (DataFrame): The input DataFrame containing the recruitment data.
-        df_type (str): The type of DataFrame (e.g., 'train', 'test').
-        channel_of_interest (str): The channel of interest for plotting.
-        target (str): The target variable for plotting.
-        columns (list, optional): Additional columns to plot. Defaults to an empty list.
-        figuresize (int, optional): The size of the figure. Defaults to 50.
-
-    Returns:
-        None
-    """
-
-    color_list = [(55/255, 155/255, 155/255), 
-                  (155/255, 55/255, 155/255), 
-                  (55/255, 155/255, 255/255), 
-                  (255/255, 55/255, 155/255)]
-
-    sns.set_palette(sns.color_palette(color_list))
-    font = figuresize/2
-    width=figuresize
-    height=figuresize/4
-
-    # Create the subplots
-    fig, axes = plt.subplots(nrows=1, ncols=4, figsize=(width, height))
-
-    # Plot for 'cell_channel' on axes[0]
-    plotter_cell = spacrGraph(df,grouping_column='condition', data_column=f'cell_channel_{channel_of_interest}_mean_intensity')
-    plotter_cell.create_plot(ax=axes[0])
-    axes[0].set_xlabel(f'pathogen {df_type}', fontsize=font)
-    axes[0].set_ylabel(f'cell_channel_{channel_of_interest}_mean_intensity', fontsize=font)
-
-    # Plot for 'nucleus_channel' on axes[1]
-    plotter_nucleus = spacrGraph(df,grouping_column='condition', data_column=f'nucleus_channel_{channel_of_interest}_mean_intensity')
-    plotter_nucleus.create_plot(ax=axes[1])
-    axes[1].set_xlabel(f'pathogen {df_type}', fontsize=font)
-    axes[1].set_ylabel(f'nucleus_channel_{channel_of_interest}_mean_intensity', fontsize=font)
-
-    # Plot for 'cytoplasm_channel' on axes[2]
-    plotter_cytoplasm = spacrGraph(df, grouping_column='condition', data_column=f'cytoplasm_channel_{channel_of_interest}_mean_intensity')
-    plotter_cytoplasm.create_plot(ax=axes[2])
-    axes[2].set_xlabel(f'pathogen {df_type}', fontsize=font)
-    axes[2].set_ylabel(f'cytoplasm_channel_{channel_of_interest}_mean_intensity', fontsize=font)
-
-    # Plot for 'pathogen_channel' on axes[3]
-    plotter_pathogen = spacrGraph(df, grouping_column='condition', data_column=f'pathogen_channel_{channel_of_interest}_mean_intensity')
-    plotter_pathogen.create_plot(ax=axes[3])
-    axes[3].set_xlabel(f'pathogen {df_type}', fontsize=font)
-    axes[3].set_ylabel(f'pathogen_channel_{channel_of_interest}_mean_intensity', fontsize=font)
-
-    #axes[0].legend_.remove()
-    #axes[1].legend_.remove()
-    #axes[2].legend_.remove()
-    #axes[3].legend_.remove()
-
-    handles, labels = axes[3].get_legend_handles_labels()
-    axes[3].legend(handles, labels, bbox_to_anchor=(1.05, 0.5), loc='center left')
-    for i in [0,1,2,3]:
-        axes[i].tick_params(axis='both', which='major', labelsize=font)
-        axes[i].set_xticklabels(axes[i].get_xticklabels(), rotation=45)
-
-    plt.tight_layout()
-    plt.show()
-
-    columns = columns + ['pathogen_cytoplasm_mean_mean', 'pathogen_cytoplasm_q75_mean', 'pathogen_periphery_cytoplasm_mean_mean', 'pathogen_outside_cytoplasm_mean_mean', 'pathogen_outside_cytoplasm_q75_mean']
-    #columns = columns + [f'pathogen_slope_channel_{channel_of_interest}', f'pathogen_cell_distance_channel_{channel_of_interest}', f'nucleus_cell_distance_channel_{channel_of_interest}']
-
-    width = figuresize*2
-    columns_per_row = math.ceil(len(columns) / 2)
-    height = (figuresize*2)/columns_per_row
-
-    fig, axes = plt.subplots(nrows=2, ncols=columns_per_row, figsize=(width, height * 2))
-    axes = axes.flatten()
-
-    print(f'{columns}')
-    for i, col in enumerate(columns):
-        ax = axes[i]
-        plotter_col = spacrGraph(df, grouping_column='condition', data_column=col)
-        plotter_col.create_plot(ax=ax)
-        ax.set_xlabel(f'pathogen {df_type}', fontsize=font)
-        ax.set_ylabel(f'{col}', fontsize=int(font * 2))
-        #ax.legend_.remove()
-        ax.tick_params(axis='both', which='major', labelsize=font)
-        ax.set_xticklabels(ax.get_xticklabels(), rotation=45)
-        if i <= 5:
-            ax.set_ylim(1, None)
-
-    # Turn off any unused axes
-    for i in range(len(columns), len(axes)):
-        axes[i].axis('off')
-
-    plt.tight_layout()
-    plt.show()
         
 def _plot_recruitment(df, df_type, channel_of_interest, columns=[], figuresize=10):
     """
@@ -1843,31 +1746,6 @@ def print_mask_and_flows(stack, mask, flows, overlay=True, max_size=1000, thickn
     fig.tight_layout()
     plt.show()
     
-def plot_resize_v1(images, resized_images, labels, resized_labels):
-    # Display an example image and label before and after resizing
-    fig, ax = plt.subplots(2, 2, figsize=(20, 20))
-    
-    # Check if the image is grayscale; if so, add a colormap and keep dimensions correct
-    if images[0].ndim == 2:  # Grayscale image
-        ax[0, 0].imshow(images[0], cmap='gray')
-    else:  # RGB or RGBA image
-        ax[0, 0].imshow(images[0])
-    ax[0, 0].set_title('Original Image')
-
-    if resized_images[0].ndim == 2:  # Grayscale image
-        ax[0, 1].imshow(resized_images[0], cmap='gray')
-    else:  # RGB or RGBA image
-        ax[0, 1].imshow(resized_images[0])
-    ax[0, 1].set_title('Resized Image')
-
-    # Assuming labels are always grayscale (most common scenario)
-    ax[1, 0].imshow(labels[0], cmap='gray')
-    ax[1, 0].set_title('Original Label')
-    ax[1, 1].imshow(resized_labels[0], cmap='gray')
-    ax[1, 1].set_title('Resized Label')
-    plt.show()
-    
-
 def plot_resize(images, resized_images, labels, resized_labels):
     def prepare_image(img):
         if img.ndim == 2:

spacr/settings.py

@@ -124,33 +124,6 @@ def set_default_plot_data_from_db(settings):
     settings.setdefault('uninfected', False)
     return settings
 
-
-
-def set_default_settings_preprocess_img_data_v1(settings):
-
-    metadata_type = settings.setdefault('metadata_type', 'cellvoyager')
-    custom_regex = settings.setdefault('custom_regex', None)
-    nr = settings.setdefault('nr', 1)
-    plot = settings.setdefault('plot', True)
-    batch_size = settings.setdefault('batch_size', 50)
-    timelapse = settings.setdefault('timelapse', False)
-    lower_percentile = settings.setdefault('lower_percentile', 2)
-    randomize = settings.setdefault('randomize', True)
-    all_to_mip = settings.setdefault('all_to_mip', False)
-    pick_slice = settings.setdefault('pick_slice', False)
-    skip_mode = settings.setdefault('skip_mode', False)
-
-    cmap = settings.setdefault('cmap', 'inferno')
-    figuresize = settings.setdefault('figuresize', 10)
-    normalize = settings.setdefault('normalize', True)
-    save_dtype = settings.setdefault('save_dtype', 'uint16')
-    
-    test_mode = settings.setdefault('test_mode', False)
-    test_images = settings.setdefault('test_images', 10)
-    random_test = settings.setdefault('random_test', True)
-
-    return 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
-
 def set_default_settings_preprocess_img_data(settings):
 
     settings.setdefault('metadata_type', 'cellvoyager')

spacr/timelapse.py

@@ -255,56 +255,6 @@ def _relabel_masks_based_on_tracks(masks, tracks, mode='btrack'):
 
     return relabeled_masks
 
-def _prepare_for_tracking_v1(mask_array):
-    """
-    Prepare the mask array for object tracking.
-
-    Args:
-        mask_array (ndarray): Array of binary masks representing objects.
-
-    Returns:
-        DataFrame: DataFrame containing information about each object in the mask array.
-            The DataFrame has the following columns:
-            - frame: The frame number.
-            - y: The y-coordinate of the object's centroid.
-            - x: The x-coordinate of the object's centroid.
-            - mass: The area of the object.
-            - original_label: The original label of the object.
-
-    """
-    frames = []
-    for t, frame in enumerate(mask_array):
-        props = regionprops(frame)
-        for obj in props:
-            # Include 'label' in the dictionary to capture the original label of the object
-            frames.append({
-                'frame': t, 
-                'y': obj.centroid[0], 
-                'x': obj.centroid[1], 
-                'mass': obj.area,
-                'original_label': obj.label  # Capture the original label
-            })
-    return pd.DataFrame(frames)
-
-def _prepare_for_tracking_v1(mask_array):
-    frames = []
-    for t, frame in enumerate(mask_array):
-        props = regionprops_table(
-            frame,
-            properties=('label', 'centroid-0', 'centroid-1', 'area',
-                        'bbox-0', 'bbox-1', 'bbox-2', 'bbox-3',
-                        'eccentricity')
-        )
-        df = pd.DataFrame(props)
-        df = df.rename(columns={
-            'centroid-0': 'y', 'centroid-1': 'x', 'area': 'mass',
-            'label': 'original_label'
-        })
-        df['frame'] = t
-        frames.append(df[['frame','y','x','mass','original_label',
-                          'bbox-0','bbox-1','bbox-2','bbox-3','eccentricity']])
-    return pd.concat(frames, ignore_index=True)
-
 def _prepare_for_tracking(mask_array):
     frames = []
     for t, frame in enumerate(mask_array):
@@ -522,46 +472,6 @@ def _facilitate_trackin_with_adaptive_removal(masks, search_range=None, max_atte
         f"Failed to track after {max_attempts} attempts; last search_range={search_range}"
     )
 
-def _facilitate_trackin_with_adaptive_removal_v1(masks, search_range=500, max_attempts=100, memory=3):
-    """
-    Facilitates object tracking with adaptive removal.
-
-    Args:
-        masks (numpy.ndarray): Array of binary masks representing objects in each frame.
-        search_range (int, optional): Maximum distance objects can move between frames. Defaults to 500.
-        max_attempts (int, optional): Maximum number of attempts to track objects. Defaults to 100.
-        memory (int, optional): Number of frames to remember when linking tracks. Defaults to 3.
-
-    Returns:
-        tuple: A tuple containing the updated masks, features, and tracks_df.
-            masks (numpy.ndarray): Updated array of binary masks.
-            features (pandas.DataFrame): DataFrame containing features for object tracking.
-            tracks_df (pandas.DataFrame): DataFrame containing the tracked object trajectories.
-
-    Raises:
-        Exception: If tracking fails after the maximum number of attempts.
-
-    """
-    attempts = 0
-    first_frame = masks[0]
-    starting_objects = np.unique(first_frame[first_frame != 0])
-    while attempts < max_attempts:
-        try:
-            masks = _remove_objects_from_first_frame(masks, 10)
-            first_frame = masks[0]
-            objects = np.unique(first_frame[first_frame != 0])
-            print(len(objects))
-            features = _prepare_for_tracking(masks)
-            tracks_df = tp.link(features, search_range=search_range, memory=memory)
-            print(f"Success with {len(objects)} objects, started with {len(starting_objects)} objects")
-            return masks, features, tracks_df
-        except Exception as e:  # Consider catching a more specific exception if possible
-            print(f"Retrying with fewer objects. Exception: {e}", flush=True)
-        finally:
-            attempts += 1
-    print(f"Failed to track objects after {max_attempts} attempts. Consider adjusting parameters.")
-    return None, None, None
-
 def _trackpy_track_cells(src, name, batch_filenames, object_type, masks, timelapse_displacement, timelapse_memory, timelapse_remove_transient, plot, save, mode, track_by_iou):
         """
         Track cells using the Trackpy library.

spacr/utils.py

@@ -5210,54 +5210,6 @@ def rename_columns_in_db(db_path):
 
     con.commit()
     con.close()    
-
-def rename_columns_in_db_v1(db_path):
-    with sqlite3.connect(db_path) as conn:
-        cursor = conn.cursor()
-        
-        # Retrieve all table names in the database
-        cursor.execute("SELECT name FROM sqlite_master WHERE type='table';")
-        tables = [table[0] for table in cursor.fetchall()]
-
-        for table in tables:
-            # Retrieve column names for each table
-            cursor.execute(f"PRAGMA table_info({table});")
-            columns_info = cursor.fetchall()
-            column_names = [col[1] for col in columns_info]
-
-            # Check if columns 'rowID' or 'columnID' exist
-            columns_to_rename = {}
-            if 'row' in column_names:
-                columns_to_rename['row'] = 'rowID'
-            if 'col' in column_names:
-                columns_to_rename['col'] = 'columnID'
-            
-            # Rename columns if necessary
-            if columns_to_rename:
-                # Rename existing table to a temporary name
-                temp_table = f"{table}_old"
-                cursor.execute(f"ALTER TABLE `{table}` RENAME TO `{temp_table}`")
-
-                # Define new columns with updated names
-                column_definitions = ", ".join(
-                    [f"`{columns_to_rename.get(col[1], col[1])}` {col[2]}" for col in columns_info]
-                )
-                cursor.execute(f"CREATE TABLE `{table}` ({column_definitions})")
-                
-                # Copy data to the new table
-                old_columns = ", ".join([f"`{col}`" for col in column_names])
-                new_columns = ", ".join(
-                    [f"`{columns_to_rename.get(col, col)}`" for col in column_names]
-                )
-                cursor.execute(f"INSERT INTO `{table}` ({new_columns}) SELECT {old_columns} FROM `{temp_table}`")
-                try:
-                    cursor.execute(f"DROP TABLE `{temp_table}`")
-                except sqlite3.Error as e:
-                    print(f"Error while dropping temporary table '{temp_table}': {e}")
-
-    # After closing the 'with' block, run VACUUM outside of any transaction
-    with sqlite3.connect(db_path) as conn:
-        conn.execute("VACUUM;")
         
 def group_feature_class(df, feature_groups=['cell', 'cytoplasm', 'nucleus', 'pathogen'], name='compartment'):
 

{spacr-0.9.0.dist-info → spacr-0.9.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.9.0
+Version: 0.9.1
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson

{spacr-0.9.0.dist-info → spacr-0.9.1.dist-info}/RECORD

@@ -11,7 +11,7 @@ spacr/chat_bot.py,sha256=n3Fhqg3qofVXHmh3H9sUcmfYy9MmgRnr48663MVdY9E,1244
 spacr/core.py,sha256=w4E3Pg-ZnA8BOK0iUMTjiNO0GeR5YCEs8fUTbESzqjY,47392
 spacr/deep_spacr.py,sha256=055tIo3WP3elGFiIuSZaLURgu2XyUDxAdbw5ezASEqM,54526
 spacr/gui.py,sha256=NhMh96KoArrSAaJBV6PhDQpIC1cQpxgb6SclhRbYG8s,8122
-spacr/gui_core.py,sha256=jQPDQVP43YL_AW7Sm8cIQgdZVaB9Yig8U6ov9clCYOc,56180
+spacr/gui_core.py,sha256=m-AYUmaSXqsGFj9EzPf4fp1irZGN-X-21S4FBO8PoXc,52727
 spacr/gui_elements.py,sha256=5a3BOpctBPklsT1NungqS72h1Bg1FArUndE0OfvWD8Y,152646
 spacr/gui_utils.py,sha256=vv_uBOA0n-04KCCicYHhNt3sRbm0IPLM5r8QX5EkJ1Q,40867
 spacr/io.py,sha256=SYLhupKnOJJscNSGE4N67E32-ywhwrjRccIfZrL38Uk,157966
@@ -20,16 +20,16 @@ spacr/measure.py,sha256=Z3u4BU5RzcY82IZuboQ0OsxuXaPVwOlH65Rw6FrL5z4,55045
 spacr/mediar.py,sha256=p0F515eFbm6_rePSnChsgqrgH-H5Sr_3zWrghtOnAUg,14863
 spacr/ml.py,sha256=XCRZeX7UkbMctQICIoskeWVx8CCmmCoHNauUOAkfFq0,91692
 spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
-spacr/plot.py,sha256=DGQulM2425DFVRMT9ZVvZW8EMxnc3hzjXhcL7fTMrGA,172668
+spacr/plot.py,sha256=M2w9ytR8iMFtsVPhmQ5tzIWTQDmbtCzs1-7hALUIQtg,167339
 spacr/sequencing.py,sha256=EY12RdW5QRKpHDRQCw1QoAlxCq8FK2v6WoVa5uuDBXQ,26745
-spacr/settings.py,sha256=LzJbebCRkDVYJxbojZKQE88MJ8Fg8iR6HZNHjN_np28,88687
+spacr/settings.py,sha256=Fd5RbNxjBmWG6bCCDprVvy8dTjBzSK7L71k_-mJXBsk,87380
 spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
 spacr/sp_stats.py,sha256=mbhwsyIqt5upsSD346qGjdCw7CFBa0tIS7zHU9e0jNI,9536
 spacr/spacr_cellpose.py,sha256=RBHMs2vwXcfkj0xqAULpALyzJYXddSRycgZSzmwI7v0,14755
 spacr/submodules.py,sha256=Z2i4kv_rWdxqoXsOKCF7BaSXtvaCZB69Ow8_FQBnZsY,83093
-spacr/timelapse.py,sha256=YJciEQS15eVC9R9adcen62xx7uttGAr_Gaz1vGX2Ke8,46824
+spacr/timelapse.py,sha256=-5ZupTsCCpbenIQ2zsUmnwXh45B82fO-gPrSXOxu2s8,42980
 spacr/toxo.py,sha256=GoNfgyH-NJx3WOzNQPgzODir7Jp65fs7UM46XpzcrUo,26056
-spacr/utils.py,sha256=ddeLh_KWA1bQsB9R3OtljFmsoWrriWjIJDq7x61J_XI,236185
+spacr/utils.py,sha256=RA4V1EDXsU_Gs6QgplvOA4lVIRFQJVJ1JAzQsaunHiU,234010
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/data/lopit.csv,sha256=ERI5f9W8RdJGiSx_khoaylD374f8kmvLia1xjhD_mII,4421709
 spacr/resources/data/toxoplasma_metadata.csv,sha256=9TXx0VlClDHAxQmaLhoklE8NuETduXaGHZjhR_6lZfs,2969409
@@ -101,9 +101,9 @@ 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
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