diff imagej2_bunwarpj_elastic_transform.py @ 0:bb84f130a4e1 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_bunwarpj_elastic_transform.py	Tue Sep 17 17:04:59 2019 -0400
@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+import argparse
+import shutil
+import subprocess
+import tempfile
+import imagej2_base_utils
+
+# Parse Command Line.
+parser = argparse.ArgumentParser()
+parser.add_argument( '--source_image', dest='source_image', help='Source image' )
+parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
+parser.add_argument( '--target_image', dest='target_image', help='Target image' )
+parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
+parser.add_argument( '--elastic_transformation', dest='elastic_transformation', help='Elastic transformation as saved by bUnwarpJ in elastic format' )
+parser.add_argument( '--source_out', help='Output source image' )
+parser.add_argument( '--source_out_datatype', help='Output registered source image format' )
+parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
+
+args = parser.parse_args()
+
+tmp_dir = imagej2_base_utils.get_temp_dir()
+source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
+tmp_source_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' )
+tmp_source_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.source_out_datatype )
+target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
+elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.elastic_transformation, 'txt' )
+
+# Define command response buffers.
+tmp_out = tempfile.NamedTemporaryFile().name
+tmp_stdout = open( tmp_out, 'wb' )
+tmp_err = tempfile.NamedTemporaryFile().name
+tmp_stderr = open( tmp_err, 'wb' )
+
+# Build the command line to apply the transformation.
+cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
+if cmd is None:
+    imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
+cmd += ' -elastic_transform'
+# Target is sent before source.
+cmd += ' %s' % target_image_path
+cmd += ' %s' % source_image_path
+cmd += ' %s' % elastic_transformation_path
+cmd += ' %s' % tmp_source_out_tiff_path
+
+# Apply the elastic transformation using bUnwarpJ.
+proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
+rc = proc.wait()
+if rc != 0:
+    error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
+    imagej2_base_utils.stop_err( error_message )
+
+# Convert the registered image to the specified output format.
+tmp_out = tempfile.NamedTemporaryFile().name
+tmp_stdout = open( tmp_out, 'wb' )
+tmp_err = tempfile.NamedTemporaryFile().name
+tmp_stderr = open( tmp_err, 'wb' )
+
+cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
+if cmd is None:
+    imagej2_base_utils.stop_err( "ImageJ not found!" )
+cmd += ' %s %s %s' % ( tmp_source_out_tiff_path,
+                       args.source_out_datatype,
+                       tmp_source_out_path )
+
+proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
+rc = proc.wait()
+if rc != 0:
+    error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
+    imagej2_base_utils.stop_err( error_message )
+
+# Save the Registered Source Image to the defined output.
+shutil.move( tmp_source_out_path, args.source_out )
+imagej2_base_utils.cleanup_before_exit( tmp_dir )