T4mmi

# -*- coding: utf-8 -*-
import re
import warnings
from collections import namedtuple
from pathlib import Path

"""GOCAD Object file template:

GOCAD <type> <version>
HEADER {

T4mmi

macro "Batch rotate images and annotations" { 
	/* Read images in a chosen directory and rotate them along
        with the annotations (points) and store them inplace */
	
	source_dir = getDirectory("Choose an input Directory ");  // window to select the input directory
	dest_dir = getDirectory("Choose an output Directory ");  // window to select the output directory
	list = getFileList(source_dir);  // list files in it
  	angle = getNumber("choose the clockwise rotation angle", 90);
	
	setBatchMode(true); // activate batch process

T4mmi

import numpy as np
from numba import jit
from typing import Sequence

# @jit(nopython=True)
def flood_fill_labels(data: np.ndarray, seeds: Sequence[Sequence[int]]=[]) -> np.ndarray:
    """Labels an array using a flood fill algorithm

    The function implements a flooding algorithm 
    considering a connectivity equals to the 2*data.ndim

T4mmi

# Contact: Thomas Janvier <thomas.p.janvier@gmail.com>
itk_fetch_module(Thickness3D
  "Tools for 3D thickness measurement"
  GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKBinaryThinning3D.git
  GIT_TAG <TODO: add the latest valid commit tag found on https://github.com/InsightSoftwareConsortium/ITKThickness3D/commits/master>
)

T4mmi

macro "Batch export XY coordinates" { 
	/* Read images in a chosen directory and export measurements
        XY coordinates (in pixels) in a .txt file with the same name */
	
	dir = getDirectory("Choose a Directory ");  // window to select the input directory
	list = getFileList(dir); // list files in it
	setBatchMode(true); // activate batch process
	for (i=0; i<list.length; i++) { // loop over files
		showProgress(i, list.length); // update progressbar
		file_name = list[i];