def poly_mask(self):
"""
Gets the mask array for a ROI polygon on the image.
The mask array's shape will match the image's shape.
Any pixel inside both the ROI polygon and the image will be set to 1 in the mask array;
all other values in the mask will be set to 0.
Returns
-------
ndarray:
Mask array of the ROI polygon within image space (mask shape matches image shape).
"""
result, mapped = self._roiItem.getArrayRegion(np.ones_like(
self.imageItem.image),
self.imageItem,
returnMappedCoords=True)
# TODO -- move this code to own function and test
# Reverse the result array to make indexing calculations easier, then revert back
result = result[::-1, ::-1]
mapped = mapped[::-1, ::-1]
# Pad result mask rect into bounding rect of mask and image
floorRow = np.floor(mapped[0]).astype(int)
floorCol = np.floor(mapped[1]).astype(int)
# Return empty mask if ROI bounding box does not intersect image bounding box
resultRect = QRectF(QPointF(np.min(floorRow), np.min(floorCol)),
QPointF(np.max(floorRow), np.max(floorCol)))
if not self._intersectsImage(resultRect):
# TODO -- is zeros(shape) the right return value for a non-intersecting polygon?
return np.zeros(self.imageItem.image.shape)
# Find the bounds of the ROI polygon
minX = np.min(floorRow)
maxX = np.max(floorRow)
minY = np.min(floorCol)
maxY = np.max(floorCol)
width = self.imageItem.width()
height = self.imageItem.height()
# Pad the ROI polygon into the image shape
# Don't need padding if a polygon boundary is outside of the image shape
padXBefore = minX
if minX < 0:
padXBefore = 0
padXAfter = height - maxX
if padXAfter < 0:
padXAfter = 0
padYBefore = minY
if minY < 0:
padYBefore = 0
padYAfter = width - maxY
if padYAfter < 0:
padYAfter = 0
boundingBox = np.pad(result, ((padYBefore, padYAfter),
(padXBefore, padXAfter)), "constant")
# For trimming, any negative minimums need to be shifted into the image shape
offsetX = 0
offsetY = 0
if minX < 0:
offsetX = abs(minX)
if minY < 0:
offsetY = abs(minY)
trimmed = boundingBox[abs(offsetY):abs(offsetY) + height,
abs(offsetX):abs(offsetX) + width]
# Reorient the trimmed mask array
trimmed = trimmed[::-1, ::-1]
# # TODO remove plotting code below
# from matplotlib import pyplot as plt
# plt.figure('bounding_box, origin="lower"')
# plt.imshow(boundingBox, origin='lower')
# plt.show()
#
#
# plt.figure(f'trimmed, origin="lower", [{abs(offsetY)}:{abs(offsetY)+height}, {abs(offsetX)}:{abs(offsetX)+width}]')
# plt.imshow(trimmed, origin='lower')
# plt.show()
# # TODO remove the plotting code above
return trimmed
def setMarkerBounds(self):
for marker_index in self.marker_dict:
marker = self.marker_dict[marker_index]['marker']
marker.maxBounds = QRectF(
0, 0, self.image_data.shape[0] + marker.size()[0] - 1,
self.image_data.shape[1] + marker.size()[1] - 1)
