68 create a widget for vesicle pool assignments #73
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,219 @@ | ||
| import napari | ||
| import napari.layers | ||
| import napari.viewer | ||
| import numpy as np | ||
| import pandas as pd | ||
|
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||
| from napari.utils.notifications import show_info | ||
| from qtpy.QtWidgets import QWidget, QVBoxLayout, QPushButton | ||
|
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| from .base_widget import BaseWidget | ||
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| try: | ||
| from napari_skimage_regionprops import add_table | ||
| except ImportError: | ||
| add_table = None | ||
|
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| class VesiclePoolWidget(BaseWidget): | ||
| def __init__(self): | ||
| super().__init__() | ||
|
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| self.viewer = napari.current_viewer() | ||
| layout = QVBoxLayout() | ||
|
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| self.image_selector_name = "Distances to Structure" | ||
| self.image_selector_name1 = "Vesicles Segmentation" | ||
| # # Create the image selection dropdown. | ||
| self.image_selector_widget = self._create_layer_selector(self.image_selector_name, layer_type="Shapes") | ||
| self.segmentation1_selector_widget = self._create_layer_selector(self.image_selector_name1, layer_type="Labels") | ||
|
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||
| # Create new layer name | ||
| self.new_layer_name_param, new_layer_name_layout = self._add_string_param( | ||
| name="New Layer Name", | ||
| value="", | ||
| ) | ||
|
|
||
| # pooled group name | ||
| self.pooled_group_name_param, pooled_group_name_layout = self._add_string_param( | ||
| name="Pooled Group Name", | ||
| value="", | ||
| ) | ||
|
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||
| # Create query string | ||
| self.query_param, query_layout = self._add_string_param( | ||
| name="Query String", | ||
| value="", | ||
| tooltip="Enter a comma separated query string (e.g., 'radius > 15, distance > 250') " | ||
| "Possible filters: radius, distance, area, intensity_max, intensity_mean, intensity_min, intensity_std" | ||
| ) | ||
|
|
||
| # Create advanced settings. | ||
| self.settings = self._create_settings_widget() | ||
|
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| # Create and connect buttons. | ||
| self.measure_button1 = QPushButton("Create Vesicle Pool") | ||
| self.measure_button1.clicked.connect(self.on_pool_vesicles) | ||
|
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||
| # Add the widgets to the layout. | ||
| layout.addWidget(self.image_selector_widget) | ||
| layout.addWidget(self.segmentation1_selector_widget) | ||
| layout.addLayout(query_layout) | ||
| layout.addLayout(new_layer_name_layout) | ||
| layout.addLayout(pooled_group_name_layout) | ||
| layout.addWidget(self.measure_button1) | ||
|
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| self.setLayout(layout) | ||
|
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| def on_pool_vesicles(self): | ||
| distances_layer = self._get_layer_selector_layer(self.image_selector_name) | ||
| distances = distances_layer.properties | ||
| segmentation = self._get_layer_selector_data(self.image_selector_name1) | ||
| morphology_layer = self._get_layer_selector_layer(self.image_selector_name1) | ||
| morphology = morphology_layer.properties | ||
|
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||
| if segmentation is None: | ||
| show_info("INFO: Please choose a segmentation.") | ||
| return | ||
| if self.query_param.text() == "": | ||
| show_info("INFO: Please enter a query string.") | ||
| return | ||
| # resolve string | ||
| query = self.query_param.text() | ||
|
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||
| if self.new_layer_name_param.text() == "": | ||
| show_info("INFO: Please enter a new layer name.") | ||
| return | ||
| new_layer_name = self.new_layer_name_param.text() | ||
| if self.pooled_group_name_param.text() == "": | ||
| show_info("INFO: Please enter a pooled group name.") | ||
| return | ||
| pooled_group_name = self.pooled_group_name_param.text() | ||
|
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||
| if distances is None: | ||
| show_info("INFO: Distances layer could not be found or has no values.") | ||
| return | ||
| self._compute_vesicle_pool(segmentation, distances, morphology, new_layer_name, pooled_group_name, query) | ||
|
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| def _compute_vesicle_pool(self, segmentation, distances, morphology, new_layer_name, pooled_group_name, query): | ||
| """ | ||
| Compute a vesicle pool based on the provided query parameters. | ||
| Args: | ||
| segmentation (array): Segmentation data (e.g., labeled regions). | ||
| distances (dict): Properties from the distances layer. | ||
| morphology (dict): Properties from the morphology layer. | ||
| new_layer_name (str): Name for the new layer to be created. | ||
| pooled_group_name (str): Name for the pooled group to be assigned. | ||
| query (dict): Query parameters. | ||
| """ | ||
|
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| distances_ids = distances.get("id", []) | ||
| morphology_ids = morphology.get("label_id", []) | ||
|
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| # Check if IDs are identical | ||
| if set(distances_ids) != set(morphology_ids): | ||
| show_info("ERROR: The IDs in distances and morphology are not identical.") | ||
| return | ||
|
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||
| distances = pd.DataFrame(distances) | ||
| morphology = pd.DataFrame(morphology) | ||
|
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| # Merge dataframes on the 'id' column | ||
| merged_df = morphology.merge(distances, left_on="label_id", right_on="id", suffixes=("_morph", "_dist")) | ||
|
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| # Apply the query string to filter the data | ||
| filtered_df = self._parse_query(query, merged_df) | ||
|
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| # Extract valid vesicle IDs | ||
| valid_vesicle_ids = filtered_df["label_id"].tolist() | ||
|
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| new_layer_data = np.zeros(segmentation.shape, dtype=np.uint8) | ||
| pool_id = 1 | ||
| layer = None | ||
|
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| # check if group already exists | ||
| if new_layer_name in self.viewer.layers: | ||
| layer = self.viewer.layers[new_layer_name] | ||
| if pooled_group_name not in layer.properties["pool"]: | ||
| new_layer_data = layer.data | ||
| pool_id = len(np.unique(layer.properties["pool"])) + 1 | ||
| # compute vesicles with new pool_id and properties | ||
| for vesicle_id in valid_vesicle_ids: | ||
| new_layer_data[segmentation == vesicle_id] = pool_id | ||
|
||
| new_properties = { | ||
| "id": valid_vesicle_ids, | ||
| "radius": filtered_df["radius"].tolist(), | ||
| "distance": filtered_df["distance"].tolist(), | ||
| "pool": [pooled_group_name] * len(valid_vesicle_ids) | ||
| } | ||
| if new_layer_name in self.viewer.layers: | ||
| layer = self.viewer.layers[new_layer_name] | ||
| # override current vesicles with new pooled vesicles | ||
| if pooled_group_name in layer.properties["pool"]: | ||
| layer.data = new_layer_data | ||
| layer.properties = new_properties | ||
| show_info(f"Vesicle pool '{pooled_group_name}' overriden with {len(valid_vesicle_ids)} vesicles.") | ||
| else: | ||
| # add new vesicles and pool to existing layer | ||
| current_properties = pd.DataFrame(layer.properties) | ||
| new_properties = pd.DataFrame(new_properties) | ||
| merged = pd.concat([current_properties, new_properties], ignore_index=True) | ||
| layer.data = new_layer_data | ||
| layer.properties = merged | ||
| show_info(f"Vesicle pool '{pooled_group_name}' updated with {len(valid_vesicle_ids)} vesicles.") | ||
| else: | ||
| # Create a new layer in the viewer | ||
| self.viewer.add_labels( | ||
| new_layer_data, | ||
| name=new_layer_name, | ||
| properties=new_properties | ||
| ) | ||
| show_info( | ||
| f"Added new layer '{new_layer_name}' with {len(valid_vesicle_ids)} " | ||
| f"vesicles in group '{pooled_group_name}'." | ||
| ) | ||
| if add_table is not None: | ||
| add_table(self.viewer.layers[new_layer_name], self.viewer) | ||
| return { | ||
| "id": valid_vesicle_ids, | ||
| "radius": filtered_df["radius"].tolist(), | ||
| "distance": filtered_df["distance"].tolist(), | ||
| } | ||
|
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||
| def _parse_query(self, query, data): | ||
| """ | ||
| Parse and apply a query string to filter data. | ||
| Args: | ||
| query (str): Comma-separated query string (e.g., "radius > 15, distance > 250"). | ||
| data (pd.DataFrame): DataFrame containing the data to filter. | ||
| Returns: | ||
| pd.DataFrame: Filtered DataFrame. | ||
| """ | ||
| filters = query.split(",") # Split the query into individual conditions | ||
| filters = [f.strip() for f in filters] # Remove extra spaces | ||
| for condition in filters: | ||
| try: | ||
| # Apply each condition to filter the DataFrame | ||
| data = data.query(condition) | ||
| except Exception as e: | ||
| print(f"Failed to apply condition '{condition}': {e}") | ||
| continue | ||
| return data | ||
|
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| def _create_settings_widget(self): | ||
| setting_values = QWidget() | ||
| setting_values.setLayout(QVBoxLayout()) | ||
|
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| self.save_path, layout = self._add_path_param(name="Save Table", select_type="file", value="") | ||
| setting_values.layout().addLayout(layout) | ||
|
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| self.voxel_size_param, layout = self._add_float_param( | ||
| "voxel_size", 0.0, min_val=0.0, max_val=100.0, | ||
| ) | ||
| setting_values.layout().addLayout(layout) | ||
|
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| settings = self._make_collapsible(widget=setting_values, title="Advanced Settings") | ||
| return settings | ||
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The proper spelling is
"Vesicle Morphology".