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use morphometrics-engine for region props (morphometrics#55)
* fix init * fix widget import * update setup conda version
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,199 +1,2 @@ | ||
| import warnings | ||
| from typing import Any, Dict, List, Union | ||
|
|
||
| import napari | ||
| import numpy as np | ||
| from magicgui import magicgui | ||
| from napari_skimage_regionprops._table import add_table | ||
| from qtpy.QtWidgets import ( | ||
| QCheckBox, | ||
| QHBoxLayout, | ||
| QLabel, | ||
| QPushButton, | ||
| QVBoxLayout, | ||
| QWidget, | ||
| ) | ||
| from superqt.collapsible import QCollapsible | ||
|
|
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| from morphometrics.measure import _measurements, measure_selected | ||
|
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|
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| class QtSingleMeasurement(QWidget): | ||
| def __init__(self, name: str): | ||
| super().__init__() | ||
| self._measurement_name = name | ||
| self._label_widget = QLabel(name) | ||
| self._check_box = QCheckBox() | ||
|
|
||
| self.setLayout(QHBoxLayout()) | ||
| self.layout().addWidget(self._check_box) | ||
| self.layout().addWidget(self._label_widget) | ||
|
|
||
| self.layout().setSpacing(0) | ||
| self.layout().setContentsMargins(0,0,0,0) | ||
|
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| @property | ||
| def measurement_name(self) -> str: | ||
| return self._measurement_name | ||
|
|
||
| @property | ||
| def include_measurement(self) -> bool: | ||
| return self._check_box.isChecked() | ||
|
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|
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| class QtMeasurementSet(QWidget): | ||
| def __init__(self, name: str, choices: List[str]): | ||
| super().__init__() | ||
| self._measurement_name = name | ||
|
|
||
| self._measurement_section = QCollapsible( | ||
| title=self._measurement_name, parent=self | ||
| ) | ||
| self._choice_widgets = [QtSingleMeasurement(name=choice) for choice in choices] | ||
| for choice_widget in self._choice_widgets: | ||
| self._measurement_section.addWidget(choice_widget) | ||
|
|
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| self.setLayout(QVBoxLayout()) | ||
| self.layout().addWidget(self._measurement_section) | ||
|
|
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| self.layout().setSpacing(0) | ||
| self.layout().setContentsMargins(0,0,0,0) | ||
|
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| self._measurement_section.layout().layout().setSpacing(0) | ||
| self._measurement_section.layout().setContentsMargins(0,0,0,0) | ||
|
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| @property | ||
| def measurement_name(self) -> str: | ||
| return self._measurement_name | ||
|
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| @property | ||
| def include_measurement(self) -> bool: | ||
| return np.any([widget.include_measurement for widget in self._choice_widgets]) | ||
|
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| @property | ||
| def measurement_choices(self) -> Dict[str, bool]: | ||
| return { | ||
| widget.measurement_name: widget.include_measurement | ||
| for widget in self._choice_widgets | ||
| } | ||
|
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|
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| def create_measurement_widgets( | ||
| measurements: List[Dict[str, Any]] | ||
| ) -> List[Union[QtSingleMeasurement, QtMeasurementSet]]: | ||
| widgets = [] | ||
| for measurement_name, measurement_config in measurements.items(): | ||
| if measurement_config["type"] == "single": | ||
| widgets.append(QtSingleMeasurement(name=measurement_name)) | ||
| elif measurement_config["type"] == "set": | ||
| widgets.append( | ||
| QtMeasurementSet( | ||
| name=measurement_name, choices=measurement_config["choices"] | ||
| ) | ||
| ) | ||
| return widgets | ||
|
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|
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| class QtMeasurementWidget(QWidget): | ||
| def __init__(self, viewer: napari.Viewer): | ||
| super().__init__() | ||
| self._viewer = viewer | ||
|
|
||
| # create the layer selection widgets | ||
| self._layer_selection_widget = magicgui( | ||
| self._select_layers, | ||
| intensity_image={"choices": self._get_image_layers}, | ||
| label_image={"choices": self._get_labels_layers}, | ||
| auto_call=True, | ||
| call_button=False, | ||
| ) | ||
| self._layer_selection_widget() | ||
|
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| # create the measurement widgets | ||
| self.measurement_widgets = create_measurement_widgets(_measurements) | ||
|
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| self._run_button = QPushButton("Run", self) | ||
| self._run_button.clicked.connect(self._run) | ||
|
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| # add widgets to the layout | ||
| self.setLayout(QVBoxLayout()) | ||
| self.layout().addWidget(self._layer_selection_widget.native) | ||
| for widget in self.measurement_widgets: | ||
| self.layout().addWidget(widget) | ||
| self.layout().addWidget(self._run_button) | ||
|
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| @property | ||
| def measurement_selection(self) -> List[Union[str, Dict[str, Any]]]: | ||
| measurement_selection = [] | ||
| for widget in self.measurement_widgets: | ||
| if not widget.include_measurement: | ||
| continue | ||
| if isinstance(widget, QtSingleMeasurement): | ||
| measurement_selection.append(widget.measurement_name) | ||
| elif isinstance(widget, QtMeasurementSet): | ||
| measurement_selection.append( | ||
| { | ||
| "name": widget.measurement_name, | ||
| "choices": widget.measurement_choices, | ||
| } | ||
| ) | ||
| else: | ||
| raise TypeError( | ||
| "Widgets should be QtSingleMeasurement or QtMeasurementSet" | ||
| ) | ||
|
|
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| return measurement_selection | ||
|
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| def _select_layers( | ||
| self, intensity_image: napari.layers.Image, label_image: napari.layers.Labels | ||
| ): | ||
| self._intensity_image_layer = intensity_image | ||
| self._label_image_layer = label_image | ||
|
|
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| def _get_image_layers(self, combo_widget): | ||
| return [ | ||
| layer | ||
| for layer in self._viewer.layers | ||
| if isinstance(layer, napari.layers.Image) | ||
| ] | ||
|
|
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| def _get_labels_layers(self, combo_widget): | ||
| return [ | ||
| layer | ||
| for layer in self._viewer.layers | ||
| if isinstance(layer, napari.layers.Labels) | ||
| ] | ||
|
|
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| def _run(self): | ||
| for widget in self.measurement_widgets: | ||
| print(f"{widget.measurement_name}: {widget.include_measurement}") | ||
|
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| widget_is_set = isinstance(widget, QtMeasurementSet) | ||
| print(f"{widget.measurement_name} is set: {widget_is_set}") | ||
|
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| labels = self._label_image_layer.data | ||
| image = self._intensity_image_layer.data | ||
|
|
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| # deal with dimensionality of data | ||
| if len(image.shape) > len(labels.shape): | ||
| dim = 0 | ||
| subset = "" | ||
| while len(image.shape) > len(labels.shape): | ||
| current_dim_value = self._viewer.dims.current_step[dim] | ||
| dim = dim + 1 | ||
| image = image[current_dim_value] | ||
| subset = subset + ", " + str(current_dim_value) | ||
| warnings.warn( | ||
| "Not the full image was analysed, just the subset [" | ||
| + subset[2:] | ||
| + "] according to selected timepoint / slice." | ||
| ) | ||
|
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| measurement_table = measure_selected( | ||
| label_image=labels, | ||
| intensity_image=image, | ||
| measurement_selection=self.measurement_selection, | ||
| ) | ||
|
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| self._label_image_layer.properties = measurement_table.reset_index() | ||
| add_table(self._label_image_layer, self._viewer) | ||
| # backwards compatibility import | ||
| from morphometrics_engine._widget import QtMeasurementWidget # noqa |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,18 @@ | ||
| from typing import Callable, List, Optional | ||
|
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| from toolz import curry | ||
|
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| _measurements = dict() | ||
|
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|
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| @curry | ||
| def register_measurement( | ||
| func: Callable, name: Optional[str] = None, uses_intensity_image: bool = True | ||
| ) -> Callable: | ||
| _measurements[name] = { | ||
| "type": "single", | ||
| "callable": func, | ||
| "choices": None, | ||
| "intensity_image": uses_intensity_image, | ||
| } | ||
| return func | ||
|
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|
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| @curry | ||
| def register_measurement_set( | ||
| func: Callable, | ||
| choices: List[str], | ||
| name: Optional[str] = None, | ||
| uses_intensity_image: bool = True, | ||
| ) -> Callable: | ||
| _measurements[name] = { | ||
| "type": "set", | ||
| "callable": func, | ||
| "choices": choices, | ||
| "intensity_image": uses_intensity_image, | ||
| } | ||
| return func | ||
|
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|
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| def available_measurments() -> List[str]: | ||
| return [k for k in _measurements] | ||
|
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| from morphometrics_engine import ( | ||
| available_measurements, | ||
| measure_all_with_defaults, | ||
| measure_selected, | ||
| ) | ||
|
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| from .intensity import measure_boundary_intensity, measure_internal_intensity | ||
| from .label import measure_surface_properties_from_labels, regionprops | ||
| from .measure import measure_all_with_defaults, measure_selected | ||
|
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| __all__ = [ | ||
| "available_measurements", | ||
| "measure_selected", | ||
| "measure_all_with_defaults", | ||
| "measure_boundary_intensity", | ||
| "measure_internal_intensity", | ||
| "measure_surface_properties_from_labels", | ||
| "regionprops", | ||
| ] |
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