diff imagej2_sharpen.py @ 0:aeb9bb864b8c 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_sharpen.py	Tue Sep 17 16:56:37 2019 -0400
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+import argparse
+import os
+import shutil
+import subprocess
+import tempfile
+import imagej2_base_utils
+
+parser = argparse.ArgumentParser()
+parser.add_argument( '--input', dest='input', help='Path to the input file' )
+parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' )
+parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
+parser.add_argument( '--output', dest='output', help='Path to the output file' )
+parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' )
+args = parser.parse_args()
+
+tmp_dir = imagej2_base_utils.get_temp_dir()
+# ImageJ expects valid image file extensions, so the Galaxy .dat extension does not
+# work for some features.  The following creates a symlink with an appropriate file
+# extension that points to the Galaxy dataset.  This symlink is used by ImageJ.
+tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
+tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
+
+# 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' )
+# Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
+error_log = tempfile.NamedTemporaryFile( delete=False ).name
+
+# Build the command line.
+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' % error_log
+cmd += ' %s' % tmp_input_path
+cmd += ' %s' % tmp_output_path
+cmd += ' %s' % args.output_datatype
+
+# Run the command.
+proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
+rc = proc.wait()
+
+# Handle execution errors.
+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 )
+
+# Handle processing errors.
+if os.path.getsize( error_log ) > 0:
+    error_message = open( error_log, 'r' ).read()
+    imagej2_base_utils.stop_err( error_message )
+
+# Save the output image.
+shutil.move( tmp_output_path, args.output )
+imagej2_base_utils.cleanup_before_exit( tmp_dir )