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lable image halves
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@niksirbi
niksirbi committed May 22, 2024
1 parent 857d38b commit d5adf27
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Showing 2 changed files with 21 additions and 68 deletions.
36 changes: 7 additions & 29 deletions brainglobe_template_builder/napari/align_widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,14 +95,6 @@ def _create_align_group(self):
self.align_image_button.clicked.connect(self._on_align_button_click)
self.align_groupbox.layout().addRow(self.align_image_button)

# Add button to split image down the midplane
self.split_image_button = QPushButton(
"Split and refect image", parent=self.align_groupbox
)
self.split_image_button.setEnabled(False)
self.split_image_button.clicked.connect(self._on_split_button_click)
self.align_groupbox.layout().addRow(self.split_image_button)

def _get_layers_by_type(self, layer_type: Layer) -> list:
"""Return a list of napari layers of a given type."""
return [
Expand Down Expand Up @@ -150,7 +142,7 @@ def _on_estimate_button_click(self):
# Move viewer to show z-plane of first point
self.viewer.dims.set_point(0, points[0][0])
# Enable "Select points" mode
self.viewer.layers["midplane points"].mode = "select"
self.viewer.layers["midplane_points"].mode = "select"
show_info("Please move all 9 estimated points exactly to the midplane")

def _on_align_button_click(self):
Expand All @@ -172,33 +164,19 @@ def _on_align_button_click(self):
self.viewer.add_image(aligned_image, name="aligned_image")
aligned_mask = aligner.transform_image(mask_data)
self.viewer.add_labels(aligned_mask, name="aligned_mask", opacity=0.5)
split_mask = aligner.split_mask(aligned_mask)
self.viewer.add_labels(split_mask, name="split_mask", opacity=0.5)
aligned_halves = aligner.label_halves(aligned_image)
self.viewer.add_labels(
aligned_halves, name="aligned_halves", opacity=0.5
)
# Hide original image, mask, and points layers
self.viewer.layers[image_name].visible = False
self.viewer.layers[mask_name].visible = False
self.viewer.layers[points_name].visible = False
# Enable the split button
self.split_image_button.setEnabled(True)
# Hide aligned mask layer
self.viewer.layers["aligned_mask"].visible = False
# Make aligner object accessible to other methods
self.aligner = aligner

def _on_split_button_click(self):
"""Split the aligned image and its mask down the midplane and reflect
each half."""
aligned_image = self.viewer.layers["aligned_image"].data
split_mask = self.viewer.layers["split_mask"].data
hemi1_image, hemi2_image = self.aligner.split_and_reflect_image(
aligned_image
)
hemi1_mask, hemi2_mask = self.aligner.split_and_reflect_image(
split_mask
)
self.viewer.add_image(hemi1_image, name="hemi1_sym_image")
self.viewer.add_labels(hemi1_mask, name="hemi1_sym_mask", opacity=0.5)
self.viewer.add_image(hemi2_image, name="hemi2_sym_image")
self.viewer.add_labels(hemi2_mask, name="hemi2_sym_mask", opacity=0.5)

def _on_dropdown_selection_change(self):
# Enable estimate button if mask dropdown has a value
if self.select_mask_dropdown.currentText() == "":
Expand Down
53 changes: 14 additions & 39 deletions brainglobe_template_builder/preproc/alignment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -196,59 +196,34 @@ def transform_image(self, image: np.ndarray = None):
self.transformed_image = apply_transform(image, self.transform)
return self.transformed_image

def split_mask(self, mask: np.ndarray) -> np.ndarray:
"""Label each half of the mask along the symmetry axis with different
def label_halves(self, image: np.ndarray) -> np.ndarray:
"""Label each half of the image along the symmetry axis with different
integer values, to help diagnose issues with the splitting process.
Parameters
----------
mask : np.ndarray
The mask to split. Must contain only 1 label
image : np.ndarray
The image to label. This should be aligned along the symmetry axis.
Returns
-------
np.ndarray
An array of the same shape as the input mask, with each half
labelled with a different integer value.
An array of the same shape as the input image, with each half
labelled with a different integer value (2 and 3).
"""
# Ensure mask is binary
mask = mask.astype(bool)
axi = self.symmetry_axis_idx
axis_len = mask.shape[axi]
axis_len = image.shape[axi]
half_len = axis_len // 2
split_mask = np.zeros_like(mask, dtype=int)
labelled_halves = np.zeros_like(image, dtype=int)

# Create slicing objects for each half
slicer_half1 = [slice(None)] * mask.ndim
slicer_half1 = [slice(None)] * image.ndim
slicer_half1[axi] = slice(0, half_len)
slicer_half2 = [slice(None)] * mask.ndim
slicer_half2 = [slice(None)] * image.ndim
slicer_half2[axi] = slice(half_len, axis_len)

# Apply new labels only to the regions labeled in the input mask
split_mask[tuple(slicer_half1)] = mask[tuple(slicer_half1)] * 2
split_mask[tuple(slicer_half2)] = mask[tuple(slicer_half2)] * 3
# Apply different integer values to each half
labelled_halves[tuple(slicer_half1)] = 2
labelled_halves[tuple(slicer_half2)] = 3

return split_mask

def split_and_reflect_image(
self, image: np.ndarray
) -> tuple[np.ndarray, np.ndarray]:
"""Split the transformed image into two halves along the symmetry
axis and reflect each half to produce two full images.
Parameters
----------
image : np.ndarray
The image to split and reflect.
"""
axi = self.symmetry_axis_idx # axis index
axis_len = image.shape[axi]
half_len = axis_len // 2
# take first half_len slices along the symmetry axis (first hald)
hemi1 = image.take(range(half_len), axis=axi)
# take last half_len slices along the symmetry axis (second half)
hemi2 = image.take(range(half_len, axis_len), axis=axi)
# reflect each half to produce two full images
full1 = np.concatenate([hemi1, np.flip(hemi1, axis=axi)], axis=axi)
full2 = np.concatenate([np.flip(hemi2, axis=axi), hemi2], axis=axi)
return full1, full2
return labelled_halves

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