help="All preprocessed image patches"
"Contains rgb or grayscale image patches (may vary)",
required=True)
args = parser.parse_args()
input_folder_path = args.input_folder_path
image_patches_with_nuclei_counts_path = args.input_folder_path + '/' + "image_patches_with_nuclei_counts" + "/"
preprocessed_high_res_image_patches_path = args.input_folder_path + '/' + "preprocessed_high_res_image_patches" + "/"
output_folder_path = args.output_folder_path
image_mode = args.image_mode
path_utils.halt_script_if_path_does_not_exist(
image_patches_with_nuclei_counts_path)
path_utils.create_directory_if_directory_does_not_exist_at_path(
output_folder_path)
output_folder_path_for_images_with_highest_nuclei_count = output_folder_path + '/' + "image_patches_with_highest_nuclei_count"
path_utils.create_directory_if_directory_does_not_exist_at_path(
output_folder_path_for_images_with_highest_nuclei_count)
case_directory_paths = path_utils.create_full_paths_to_directories_in_directory_path(
image_patches_with_nuclei_counts_path)
for case_directory_path in case_directory_paths:
path_to_image_patches = case_directory_path + "/" + "images_original"
case_id = case_directory_path.split('/')[-1]
case_id_output_path = output_folder_path_for_images_with_highest_nuclei_count + "/images_original/" + case_id
path_utils.create_directory_if_directory_does_not_exist_at_path(
case_id_output_path)
required=True)
args = parser.parse_args()
input_folder_path = args.input_folder_path
input_folder_path_for_high_res_image_patches = args.input_folder_path + "/image_patches_with_highest_nuclei_count/images_original"
svs_input_folder_path = args.svs_input_folder_path
output_folder_path = args.output_folder_path
visualizations_output_path = output_folder_path + "/visualizations"
copy_tree(input_folder_path + "/visualizations", visualizations_output_path)
highest_nuclei_count_visualization_output_path = visualizations_output_path + "/highest_nuclei_count_annotations_on_most_salient_high_res_image_patch"
svs_loader = svs_l.SVSLoader(svs_input_folder_path)
path_utils.halt_script_if_path_does_not_exist(input_folder_path)
path_utils.create_directory_if_directory_does_not_exist_at_path(
output_folder_path)
most_salient_image_patch_case_directory_paths = path_utils.create_full_paths_to_directories_in_directory_path(
input_folder_path + "/visualizations/most_salient_image_patch_high_res")
CID_indexed_high_saliency_image_patch_metadata_objects_dict = image_patch_metadata_object_utils.case_directory_paths_containing_image_patches_to_dict_indexed_by_CID(
most_salient_image_patch_case_directory_paths)
high_nuclei_count_case_directory_paths = path_utils.create_full_paths_to_directories_in_directory_path(
input_folder_path_for_high_res_image_patches)
for high_nuclei_count_case_directory_path in high_nuclei_count_case_directory_paths:
high_nuclei_count_case_image_patches_paths = path_utils.create_full_paths_to_files_in_directory_path(
high_nuclei_count_case_directory_path)
first_image_patch_path = high_nuclei_count_case_image_patches_paths[0]
help="The path to the input folder.",
required=True)
parser.add_argument("-o",
"--output_folder_path",
type=str,
help="The path to the output folder."
" If output folder doesn't exists at runtime "
"the script will create it.",
required=True)
args = parser.parse_args()
input_folder_path = args.input_folder_path
input_folder_path_for_classifier = input_folder_path + '/' + "preprocessed_image_patches_organized_for_classifier"
output_folder_path = args.output_folder_path
image_patches_with_nuclei_counts_output_folder_path = args.output_folder_path + '/' + "image_patches_with_nuclei_counts"
path_utils.halt_script_if_path_does_not_exist(input_folder_path_for_classifier)
path_utils.create_directory_if_directory_does_not_exist_at_path(
output_folder_path)
case_directory_paths = path_utils.create_full_paths_to_directories_in_directory_path(
input_folder_path_for_classifier)
for case_directory_path in case_directory_paths:
case_id = case_directory_path.split('/')[-1]
case_id_output_path = image_patches_with_nuclei_counts_output_folder_path + "/" + case_id
path_utils.create_directory_if_directory_does_not_exist_at_path(
case_id_output_path)
is_case_already_classified = auto_resume_utils.is_case_already_classified_into_output_directory(
case_directory_path, case_id_output_path + "/" + "images_original")
if is_case_already_classified:
continue
