def update_mask(self):
"""
Regenerate the masks for MaskRCNN and free-hand added (in case they are changed), and show in imageview.
!!!ISSUE: getLocalHandlePositions: moving handles changes the position read out, dragging roi as a whole doesn't.
"""
# Binary mask from ML detection
if len(self.selected_ML_Index) > 0:
# Delete items in dictionary that are not roi items
roi_dict = self.selected_cells_infor_dict.copy()
del_key_list = []
for key in roi_dict:
print(key)
if 'ROIitem' not in key:
del_key_list.append(key)
for key in del_key_list:
del roi_dict[key]
self.MLmask = ProcessImage.ROIitem2Mask(
roi_dict,
mask_resolution=(self.MLtargetedImg.shape[0],
self.MLtargetedImg.shape[1]))
# Binary mask of added rois
self.addedROIitemMask = ProcessImage.ROIitem2Mask(
self.roi_list_freehandl_added,
mask_resolution=(self.MLtargetedImg.shape[0],
self.MLtargetedImg.shape[1]))
self.intergrate_into_final_mask()
def intergrate_into_final_mask(self):
# Binary mask of added rois
self.addedROIitemMask = ProcessImage.ROIitem2Mask(
self.roi_list_freehandl_added,
mask_resolution=(self.MLtargetedImg.shape[0],
self.MLtargetedImg.shape[1]))
#Display the RGB mask, ML mask plus free-hand added.
self.Mask_edit_viewItem.setImage(gray2rgb(self.addedROIitemMask) * self.mask_color_multiplier + \
gray2rgb(self.MLmask) * self.mask_color_multiplier + gray2rgb(self.MLtargetedImg))
self.final_mask = self.MLmask + self.addedROIitemMask
# In case the input image is 2048*2048, and it is resized to fit in MaskRCNN, need to convert back to original size for DMD tranformation.
if self.final_mask.shape[0] != self.Rawimage.shape[
0] or self.final_mask.shape[1] != self.Rawimage.shape[1]:
self.final_mask = resize(
self.final_mask,
[self.Rawimage.shape[0], self.Rawimage.shape[1]],
preserve_range=True).astype(self.final_mask.dtype)
# self.final_mask = np.where(self.final_mask <= 1, self.final_mask, int(1))
plt.figure()
plt.imshow(self.final_mask)
plt.show()