Create make_isotropic.py

Author: volker-baecker

volker/scripts/make_isotropic.py

@@ -0,0 +1,46 @@
+# make_isotropic.py
+# 
+# Author: Volker Baecker
+# Date: 22/03/2024
+# This script is in the public domain
+#
+# Jython script translated from the plugin (java):
+#
+    #     Author: Julian Cooper
+    #    Contact: Julian.Cooper [at] uhb.nhs.uk
+    #    First version: 2009/05/22
+    #    Licence: Public Domain  */
+    
+    #  Acknowledgements: Erik Meijering, author of TransformJ*/
+    
+    #  This plugin scales an anisotropically calibrated stack of images so that the
+    #    calibration is isotropic (the pixel depth becomes the same as the pixel
+    #    width). The plugin will not rescale XY anisotropy.
+     
+    #    Note: If the pixel depth of the source stack is less than then the width
+    #    there will be fewer slices in the output stack resulting in a potential loss
+    #    of information.
+    
+    # Requires imagescience.jar to be installed in plugins folder
+    # Available as part of TransformJ written by Erik Meijering
+    # http://www.imagescience.org/meijering/software/transformj/ 
+
+
+from ij import IJ
+from fr.cnrs.mri.cialib.plasmodium import MakeIsotropic
+
+
+URL = "https://github.com/MontpellierRessourcesImagerie/plasmodium-organelle-analysis"
+PROJECT = "plasmodium-organelle-analysis"
+
+
+def main():
+    image = IJ.getImage()
+    makeIsotropic = MakeIsotropic(PROJECT, URL)
+    makeIsotropic.setImage(image)
+    makeIsotropic.run()
+    resultImage = makeIsotropic.getResultImage()
+    resultImage.show()
+    
+    
+main()