napari_ndev._apoc_feature_stack

ApocFeatureStack

Bases: Container

Create and apply image features in the napari viewer.

Parameters:

• viewer (Viewer, default: None ) –

  The napari viewer instance to which this feature stack is attached. Default is None.

Attributes:

• _viewer (Viewer or None) –

  The napari viewer instance.

• _original (CheckBox) –

  Checkbox to keep the original image.

• _gaussian_blur (LineEdit) –

  LineEdit for specifying Gaussian Blur parameters.

• _DoG (LineEdit) –

  LineEdit for specifying Difference of Gaussian parameters.

• _LoG (LineEdit) –

  LineEdit for specifying Laplacian of Gaussian parameters.

• _SoG (LineEdit) –

  LineEdit for specifying Sobel of Gaussian parameters.

• _sHoG (LineEdit) –

  LineEdit for specifying Small Hessian of Gaussian parameters.

• _lHoG (LineEdit) –

  LineEdit for specifying Large Hessian of Gaussian parameters.

• _median (LineEdit) –

  LineEdit for specifying Median filter parameters.

• _tophat (LineEdit) –

  LineEdit for specifying Top Hat filter parameters.

• _generate_string_button (PushButton) –

  Button to generate the feature string.

• _feature_string (TextEdit) –

  TextEdit to display the custom feature string.

• _image_layer (ComboBox) –

  ComboBox to select the image layer.

• _apply_button (PushButton) –

  Button to apply the feature stack to the selected image.

• _progress_bar (ProgressBar) –

  Progress bar to display the progress of feature application.

Methods:

• _filter_layers –

  Filters the layers in the viewer by the specified layer type.

• _update_layer_choices –

  Updates the choices in the image layer ComboBox.

• generate_feature_string –

  Generates a feature string based on the user inputs.

• layer_to_feature_stack –

  Applies the generated feature stack to the selected image layer.

Source code in src/napari_ndev/_apoc_feature_stack.py

class ApocFeatureStack(Container):
    """
    Create and apply image features in the napari viewer.

    Parameters
    ----------
    viewer : napari.viewer.Viewer, optional
        The napari viewer instance to which this feature stack is attached. Default is None.

    Attributes
    ----------
    _viewer : napari.viewer.Viewer or None
        The napari viewer instance.
    _original : CheckBox
        Checkbox to keep the original image.
    _gaussian_blur : LineEdit
        LineEdit for specifying Gaussian Blur parameters.
    _DoG : LineEdit
        LineEdit for specifying Difference of Gaussian parameters.
    _LoG : LineEdit
        LineEdit for specifying Laplacian of Gaussian parameters.
    _SoG : LineEdit
        LineEdit for specifying Sobel of Gaussian parameters.
    _sHoG : LineEdit
        LineEdit for specifying Small Hessian of Gaussian parameters.
    _lHoG : LineEdit
        LineEdit for specifying Large Hessian of Gaussian parameters.
    _median : LineEdit
        LineEdit for specifying Median filter parameters.
    _tophat : LineEdit
        LineEdit for specifying Top Hat filter parameters.
    _generate_string_button : PushButton
        Button to generate the feature string.
    _feature_string : TextEdit
        TextEdit to display the custom feature string.
    _image_layer : ComboBox
        ComboBox to select the image layer.
    _apply_button : PushButton
        Button to apply the feature stack to the selected image.
    _progress_bar : ProgressBar
        Progress bar to display the progress of feature application.

    Methods
    -------
    _filter_layers(layer_type)
        Filters the layers in the viewer by the specified layer type.
    _update_layer_choices()
        Updates the choices in the image layer ComboBox.
    generate_feature_string()
        Generates a feature string based on the user inputs.
    layer_to_feature_stack()
        Applies the generated feature stack to the selected image layer.

    """

    def __init__(
        self,
        viewer: 'napari.viewer.Viewer' = None,
    ):
        super().__init__()
        self._viewer = viewer if viewer is not None else None

        self._original = CheckBox(label='Keep Original Image')
        self._gaussian_blur = LineEdit(label='Gaussian Blur')
        self._DoG = LineEdit(label='Difference of Gauss.')
        self._LoG = LineEdit(label='Laplacian of Gauss.')
        self._SoG = LineEdit(label='Sobel of Gauss.')
        self._sHoG = LineEdit(label='Small Hessian of Gauss.')
        self._lHoG = LineEdit(label='Large Hessian of Gauss.')
        self._median = LineEdit(label='Median')
        self._tophat = LineEdit(label='Top Hat')

        self._generate_string_button = PushButton(
            label='Generate Feature String'
        )
        self._feature_string = TextEdit(label='Custom Feature String')

        self._image_layer = ComboBox(
            choices=self._filter_layers(layers.Image), label='Image Layer'
        )
        self._apply_button = PushButton(label='Apply to selected image')
        self._progress_bar = ProgressBar(label='Progress: ')

        self.extend(
            [
                self._original,
                self._gaussian_blur,
                self._DoG,
                self._LoG,
                self._SoG,
                self._sHoG,
                self._lHoG,
                self._median,
                self._tophat,
                self._generate_string_button,
                self._feature_string,
                self._image_layer,
                self._apply_button,
                self._progress_bar,
            ]
        )

        self._generate_string_button.clicked.connect(
            self.generate_feature_string
        )
        self._apply_button.clicked.connect(self.layer_to_feature_stack)

        if self._viewer is not None:
            self._viewer.layers.events.removed.connect(
                self._update_layer_choices
            )
            self._viewer.layers.events.inserted.connect(
                self._update_layer_choices
            )

    def _filter_layers(self, layer_type):
        if self._viewer is None:
            return []
        return [x for x in self._viewer.layers if isinstance(x, layer_type)]

    def _update_layer_choices(self):
        self._image_layer.choices = self._filter_layers(layers.Image)

    def generate_feature_string(self):
        def process_feature(prefix, input_str):
            return [
                prefix + num.strip()
                for num in input_str.split(',')
                if num.strip()
            ]

        feature_list = []
        if self._original.value:
            feature_list.append('original')
        feature_list.extend(
            process_feature('gaussian_blur=', self._gaussian_blur.value)
        )
        feature_list.extend(
            process_feature('difference_of_gaussian=', self._DoG.value)
        )
        feature_list.extend(
            process_feature('laplace_box_of_gaussian_blur=', self._LoG.value)
        )
        feature_list.extend(
            process_feature('sobel_of_gaussian_blur=', self._SoG.value)
        )
        feature_list.extend(
            process_feature(
                'small_hessian_eigenvalue_of_gaussian_blur=', self._sHoG.value
            )
        )
        feature_list.extend(
            process_feature(
                'large_hessian_eigenvalue_of_gaussian_blur=',
                self._lHoG.value,
            )
        )
        feature_list.extend(
            process_feature('median_sphere=', self._median.value)
        )
        feature_list.extend(
            process_feature('top_hat_sphere=', self._tophat.value)
        )

        self._feature_string.value = ' '.join(feature_list)

    def layer_to_feature_stack(self):
        from apoc import generate_feature_stack

        image = self._image_layer.value.data
        feature_stack = generate_feature_stack(
            image, self._feature_string.value
        )

        feature_strings = self._feature_string.value.split()

        self._progress_bar.max = len(feature_stack)
        self._progress_bar.value = 0

        for idx, (feature, string) in enumerate(
            zip(reversed(feature_stack), reversed(feature_strings))
        ):
            self._viewer.add_image(data=feature, name=string)
            self._progress_bar.value = idx + 1