spacr 0.2.2__py3-none-any.whl → 0.2.21__py3-none-any.whl

spacr/old_code.py

@@ -1,358 +0,0 @@
-def process_fig_queue_v1():
-    while not fig_queue.empty():
-        update_task = fig_queue.get()
-        try:
-            update_task()
-        except Exception as e:
-            print(f"Error processing fig_queue: {e}")
-    root.after(100, process_fig_queue)
-
-def update_figure_in_gui_v1(fig):
-    
-
-    def task():
-        global canvas, canvas_widget, fig_queue
-        disconnect_all_event_handlers(fig)
-        canvas.figure = fig
-        fig.set_size_inches(10, 10, forward=True)
-        for axis in fig.axes:
-            axis.set_visible(False)        
-        canvas.draw()
-        canvas_widget.draw()  
-           
-    fig_queue.put(task)
-    
-def my_show_v1():
-    fig = plt.gcf()
-    update_figure_in_gui(fig)
-    
-    def disconnect_all_event_handlers(fig):
-    canvas = fig.canvas
-    if canvas.callbacks.callbacks:
-        for event, callback_list in list(canvas.callbacks.callbacks.items()):
-            for cid in list(callback_list.keys()):
-                canvas.mpl_disconnect(cid)
-    return canvas
-
-def resize_figure_to_canvas(fig, canvas):
-    canvas_width = canvas.winfo_width()
-    canvas_height = canvas.winfo_height()
-
-    # Convert pixels to inches for matplotlib
-    fig_width = canvas_width / fig.dpi
-    fig_height = canvas_height / fig.dpi
-
-    # Resizing the figure
-    fig.set_size_inches(fig_width, fig_height, forward=True)
-
-    # Optionally, hide axes
-    for ax in fig.axes:
-        ax.set_visible(False)
-        
-    return fig
-    
-def process_fig_queue_v1():
-    global canvas
-    while not fig_queue.empty():
-        try:
-            fig = fig_queue.get_nowait()
-            canvas.figure = fig  
-            canvas.draw()
-        except queue.Empty:
-            pass
-        except Exception as e:
-            print(f"Error processing fig_queue: {e}")
-            traceback.print_exc()
-    root.after(100, process_fig_queue)
-    
-def process_fig_queue():
-    while not fig_queue.empty():
-        try:
-            fig = fig_queue.get_nowait()
-            # Signal the main thread to update the GUI with the new figure
-            root.after_idle(update_canvas_with_figure, fig)
-        except queue.Empty:
-            pass
-        except Exception as e:
-            print(f"Error processing fig_queue: {e}")
-            traceback.print_exc()
-    # Reschedule itself to run again
-    root.after(100, process_fig_queue)
-    
-def update_canvas_with_figure(fig):
-    global canvas
-    # Resize the figure to fit the canvas
-    canvas_width = canvas.get_tk_widget().winfo_width()
-    canvas_height = canvas.get_tk_widget().winfo_height()
-    fig_width = canvas_width / fig.dpi
-    fig_height = canvas_height / fig.dpi
-    fig.set_size_inches(fig_width, fig_height, forward=True)
-    # Hide the axes if needed
-    for ax in fig.axes:
-        ax.set_visible(False)
-    # Update the canvas with the new figure
-    canvas.figure = fig
-    canvas.draw_idle()  # Use draw_idle for efficiency and thread safety
-
-def run_mask_gui(q):
-    global vars_dict
-    try:
-        settings = check_mask_gui_settings(vars_dict)
-        settings = add_mask_gui_defaults(settings)
-        preprocess_generate_masks_wrapper(settings['src'], settings=settings, advanced_settings={})
-    except Exception as e:
-        q.put(f"Error during processing: {e}\n")
-
-#@log_function_call   
-def main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label):
-    try:
-        while not q.empty():
-            message = q.get_nowait()
-            if message.startswith("Progress"):
-                progress_label.config(text=message)
-            elif message.startswith("Processing"):
-                progress_label.config(text=message)
-            elif message == "" or message == "\r":
-                pass
-            elif message.startswith("/"):
-                pass
-            elif message.startswith("\\"):
-                pass
-            elif message.startswith(""):
-                pass
-            else:
-                print(message)
-    except Exception as e:
-        print(f"Error updating GUI canvas: {e}")
-    #try:    
-    #    while not fig_queue.empty():
-    #        fig = fig_queue.get_nowait()
-    #        #if hasattr(canvas_widget, 'figure'):
-    #        #clear_canvas(canvas_widget)
-    #        canvas_widget.figure = fig
-    #except Exception as e:
-    #    print(f"Error updating GUI figure: {e}")
-    finally:
-        root.after(100, lambda: main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label))
-        
-    class MPNN(MessagePassing):
-    def __init__(self, node_in_features, edge_in_features, out_features):
-        super(MPNN, self).__init__(aggr='mean')  # 'mean' aggregation.
-        self.message_mlp = Sequential(
-            Linear(node_in_features + edge_in_features, 128),
-            ReLU(),
-            Linear(128, out_features)
-        )
-        self.update_mlp = Sequential(
-            Linear(out_features, out_features),
-            ReLU(),
-            Linear(out_features, out_features)
-        )
-
-    def forward(self, x, edge_index, edge_attr):
-        # x: Node features [N, node_in_features]
-        # edge_index: Graph connectivity [2, E]
-        # edge_attr: Edge attributes/features [E, edge_in_features]
-        return self.propagate(edge_index, x=x, edge_attr=edge_attr)
-
-    def message(self, x_j, edge_attr):
-        # x_j: Input features of neighbors [E, node_in_features]
-        # edge_attr: Edge attributes [E, edge_in_features]
-        tmp = torch.cat([x_j, edge_attr], dim=-1)  # Concatenate node features with edge attributes
-        return self.message_mlp(tmp)
-
-    def update(self, aggr_out):
-        # aggr_out: Aggregated messages [N, out_features]
-        return self.update_mlp(aggr_out)
-    
-def weighted_mse_loss(output, target, score_threshold=0.8, high_score_weight=10):
-    # Assumes output and target are the predicted and true scores, respectively
-    weights = torch.ones_like(target)
-    high_score_mask = target >= score_threshold
-    weights[high_score_mask] = high_score_weight
-    return ((output - target) ** 2 * weights).mean()
-
-def generate_single_graph(sequencing, scores):
-    # Load and preprocess sequencing data
-    gene_df = pd.read_csv(sequencing)
-    gene_df = gene_df.rename(columns={"prc": "well_id", "grna": "gene_id", "count": "read_count"})
-    total_reads_per_well = gene_df.groupby('well_id')['read_count'].sum().reset_index(name='total_reads')
-    gene_df = gene_df.merge(total_reads_per_well, on='well_id')
-    gene_df['well_read_fraction'] = gene_df['read_count']/gene_df['total_reads']
-
-    # Load and preprocess cell score data
-    cell_df = pd.read_csv(scores)
-    cell_df = cell_df[['prcfo', 'prc', 'pred']].rename(columns={'prcfo': 'cell_id', 'prc': 'well_id', 'pred': 'score'})
-
-    # Initialize mappings
-    gene_id_to_index = {gene: i for i, gene in enumerate(gene_df['gene_id'].unique())}
-    cell_id_to_index = {cell: i + len(gene_id_to_index) for i, cell in enumerate(cell_df['cell_id'].unique())}
-
-    # Initialize edge indices and attributes
-    edge_index = []
-    edge_attr = []
-
-    # Associate each cell with all genes in the same well
-    for well_id, group in gene_df.groupby('well_id'):
-        if well_id in cell_df['well_id'].values:
-            cell_indices = cell_df[cell_df['well_id'] == well_id]['cell_id'].map(cell_id_to_index).values
-            gene_indices = group['gene_id'].map(gene_id_to_index).values
-            fractions = group['well_read_fraction'].values
-            
-            for cell_idx in cell_indices:
-                for gene_idx, fraction in zip(gene_indices, fractions):
-                    edge_index.append([cell_idx, gene_idx])
-                    edge_attr.append([fraction])
-
-    # Convert lists to PyTorch tensors
-    edge_index = torch.tensor(edge_index, dtype=torch.long).t().contiguous()
-    edge_attr = torch.tensor(edge_attr, dtype=torch.float)
-    cell_scores = torch.tensor(cell_df['score'].values, dtype=torch.float)
-
-    # One-hot encoding for genes, and zero features for cells (could be replaced with real features if available)
-    gene_features = torch.eye(len(gene_id_to_index))
-    cell_features = torch.zeros(len(cell_id_to_index), gene_features.size(1))
-
-    # Combine features
-    x = torch.cat([cell_features, gene_features], dim=0)
-
-    # Create the graph data object
-    data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, y=cell_scores)
-
-    return data, gene_id_to_index, len(gene_id_to_index)
-
-# in _normalize_and_outline
-    outlines = []
-    
-        overlayed_image = rgb_image.copy()
-        for i, mask_dim in enumerate(mask_dims):
-            mask = np.take(image, mask_dim, axis=2)
-            outline = np.zeros_like(mask)
-            # Find the contours of the objects in the mask
-            for j in np.unique(mask)[1:]:
-                contours = find_contours(mask == j, 0.5)
-                for contour in contours:
-                    contour = contour.astype(int)
-                    outline[contour[:, 0], contour[:, 1]] = j
-            # Make the outline thicker
-            outline = dilation(outline, square(outline_thickness))
-            outlines.append(outline)
-            # Overlay the outlines onto the RGB image
-            for j in np.unique(outline)[1:]:
-                overlayed_image[outline == j] = outline_colors[i % len(outline_colors)]
-
-def _extract_filename_metadata(filenames, src, images_by_key, regular_expression, metadata_type='cellvoyager', pick_slice=False, skip_mode='01'):
-    for filename in filenames:
-        match = regular_expression.match(filename)
-        if match:
-            try:
-                try:
-                    plate = match.group('plateID')
-                except:
-                    plate = os.path.basename(src)
-
-                well = match.group('wellID')
-                field = match.group('fieldID')
-                channel = match.group('chanID')
-                mode = None
-
-                if well[0].isdigit():
-                    well = str(_safe_int_convert(well))
-                if field[0].isdigit():
-                    field = str(_safe_int_convert(field))
-                if channel[0].isdigit():
-                    channel = str(_safe_int_convert(channel))
-
-                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:
-                    try:
-                        mode = match.group('AID')
-                    except IndexError:
-                        sliceid = '00'
-
-                    if mode == skip_mode:
-                        continue      
-                        
-                key = (plate, well, field, channel, mode)
-                with Image.open(os.path.join(src, filename)) as img:
-                    images_by_key[key].append(np.array(img))
-            except IndexError:
-                print(f"Could not extract information from filename {filename} using provided regex")
-        else:
-            print(f"Filename {filename} did not match provided regex")
-            continue
-        
-    return images_by_key
-
-def compare_cellpose_masks_v1(src, verbose=False, save=False):
-    
-    from .io import _read_mask
-    from .plot import visualize_masks, plot_comparison_results, visualize_cellpose_masks
-    from .utils import extract_boundaries, boundary_f1_score, compute_segmentation_ap, jaccard_index
-
-    import os
-    import numpy as np
-    from skimage.measure import label
-
-    # Collect all subdirectories in src
-    dirs = [os.path.join(src, d) for d in os.listdir(src) if os.path.isdir(os.path.join(src, d))]
-
-    dirs.sort()  # Optional: sort directories if needed
-
-    # Get common files in all directories
-    common_files = set(os.listdir(dirs[0]))
-    for d in dirs[1:]:
-        common_files.intersection_update(os.listdir(d))
-    common_files = list(common_files)
-
-    results = []
-    conditions = [os.path.basename(d) for d in dirs]
-
-    for index, filename in enumerate(common_files):
-        print(f'Processing image {index+1}/{len(common_files)}', end='\r', flush=True)
-        paths = [os.path.join(d, filename) for d in dirs]
-
-        # Check if file exists in all directories
-        if not all(os.path.exists(path) for path in paths):
-            print(f'Skipping {filename} as it is not present in all directories.')
-            continue
-
-        masks = [_read_mask(path) for path in paths]
-        boundaries = [extract_boundaries(mask) for mask in masks]
-
-        if verbose:
-            visualize_cellpose_masks(masks, titles=conditions, comparison_title=f"Masks Comparison for {filename}", save=save, src=src)
-
-        # Initialize data structure for results
-        file_results = {'filename': filename}
-
-        # Compare each mask with each other
-        for i in range(len(masks)):
-            for j in range(i + 1, len(masks)):
-                condition_i = conditions[i]
-                condition_j = conditions[j]
-                mask_i = masks[i]
-                mask_j = masks[j]
-
-                # Compute metrics
-                boundary_f1 = boundary_f1_score(mask_i, mask_j)
-                jaccard = jaccard_index(mask_i, mask_j)
-                average_precision = compute_segmentation_ap(mask_i, mask_j)
-
-                # Store results
-                file_results[f'jaccard_{condition_i}_{condition_j}'] = jaccard
-                file_results[f'boundary_f1_{condition_i}_{condition_j}'] = boundary_f1
-                file_results[f'average_precision_{condition_i}_{condition_j}'] = average_precision
-
-        results.append(file_results)
-
-    fig = plot_comparison_results(results)
-
-    save_results_and_figure(src, fig, results)
-
-    return results, fig

spacr/resources/icons/abort.svg

@@ -1 +0,0 @@
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spacr/resources/icons/annotate.svg

@@ -1 +0,0 @@
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spacr/resources/icons/classify.svg

@@ -1 +0,0 @@
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spacr/resources/icons/download.svg

@@ -1 +0,0 @@
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spacr/resources/icons/make_masks.svg

@@ -1 +0,0 @@
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spacr/resources/icons/map_barcodes.svg

@@ -1 +0,0 @@
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spacr/resources/icons/mask.svg

@@ -1 +0,0 @@
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spacr/resources/icons/measure.svg

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spacr/resources/icons/run.svg

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spacr/resources/icons/run_2.svg

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spacr/resources/icons/train_cellpose.svg

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