def save_heatmaps(heatmap_malignant, heatmap_benign, short_file_path, view,
horizontal_flip, parameters):
"""
Saves the heatmaps after flipping back to the original direction
"""
image_extension = '.hdf5' if parameters['use_hdf5'] else '.png'
heatmap_malignant = loading.flip_image(heatmap_malignant, view,
horizontal_flip)
heatmap_benign = loading.flip_image(heatmap_benign, view, horizontal_flip)
heatmap_save_path_malignant = os.path.join(
parameters['save_heatmap_path'][0], short_file_path + image_extension)
if heatmap_save_path_malignant.endswith("png"):
saving_images.save_image_as_png(heatmap_malignant,
heatmap_save_path_malignant)
elif heatmap_save_path_malignant.endswith("hdf5"):
saving_images.save_image_as_hdf5(heatmap_malignant,
heatmap_save_path_malignant)
else:
raise RuntimeError()
heatmap_save_path_benign = os.path.join(parameters['save_heatmap_path'][1],
short_file_path + image_extension)
if heatmap_save_path_benign.endswith("png"):
saving_images.save_image_as_png(heatmap_benign,
heatmap_save_path_benign)
elif heatmap_save_path_benign.endswith("hdf5"):
saving_images.save_image_as_hdf5(heatmap_benign,
heatmap_save_path_benign)
else:
raise RuntimeError()
def crop_mammogram_one_image(scan, input_file_path,
output_file_path, num_iterations,
buffer_size):
"""
Crops a mammogram, saves as png file, includes the following additional information:
- window_location: location of cropping window w.r.t. original dicom image so that segmentation
map can be cropped in the same way for training.
- rightmost_points: rightmost nonzero pixels after correctly being flipped
- bottommost_points: bottommost nonzero pixels after correctly being flipped
- distance_from_starting_side: number of zero columns between the start of the image and start of
the largest connected component w.r.t. original dicom image.
"""
image = reading_images.read_image_png(input_file_path)
try:
# error detection using erosion. Also get cropping information for this image.
cropping_info = crop_img_from_largest_connected(
image,
image_orientation(scan['horizontal_flip'],
scan['side']), True, num_iterations,
buffer_size, 1 / 3)
except Exception as error:
print(
input_file_path,
"\n\tFailed to crop image because image is invalid.",
str(error))
else:
top, bottom, left, right = cropping_info[0]
target_parent_dir = os.path.split(output_file_path)[0]
if not os.path.exists(target_parent_dir):
os.makedirs(target_parent_dir)
try:
saving_images.save_image_as_png(
image[top:bottom, left:right], output_file_path)
except Exception as error:
print(input_file_path, "\n\tError while saving image.",
str(error))
return cropping_info