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annotate imagej2_bunwarpj_elastic_transform.py @ 0:dd20ee3092e3 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 17:04:21 -0400
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dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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1 #!/usr/bin/env python
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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2 import argparse
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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3 import shutil
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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4 import subprocess
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 import tempfile
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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6 import imagej2_base_utils
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dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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8 # Parse Command Line.
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9 parser = argparse.ArgumentParser()
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10 parser.add_argument( '--source_image', dest='source_image', help='Source image' )
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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11 parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
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12 parser.add_argument( '--target_image', dest='target_image', help='Target image' )
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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13 parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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14 parser.add_argument( '--elastic_transformation', dest='elastic_transformation', help='Elastic transformation as saved by bUnwarpJ in elastic format' )
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15 parser.add_argument( '--source_out', help='Output source image' )
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16 parser.add_argument( '--source_out_datatype', help='Output registered source image format' )
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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17 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
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19 args = parser.parse_args()
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21 tmp_dir = imagej2_base_utils.get_temp_dir()
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22 source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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23 tmp_source_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' )
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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24 tmp_source_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.source_out_datatype )
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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25 target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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26 elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.elastic_transformation, 'txt' )
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28 # Define command response buffers.
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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29 tmp_out = tempfile.NamedTemporaryFile().name
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30 tmp_stdout = open( tmp_out, 'wb' )
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31 tmp_err = tempfile.NamedTemporaryFile().name
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32 tmp_stderr = open( tmp_err, 'wb' )
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34 # Build the command line to apply the transformation.
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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35 cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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36 if cmd is None:
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37 imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
dd20ee3092e3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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38 cmd += ' -elastic_transform'
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39 # Target is sent before source.
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40 cmd += ' %s' % target_image_path
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41 cmd += ' %s' % source_image_path
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42 cmd += ' %s' % elastic_transformation_path
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43 cmd += ' %s' % tmp_source_out_tiff_path
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45 # Apply the elastic transformation using bUnwarpJ.
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46 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
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47 rc = proc.wait()
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48 if rc != 0:
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49 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
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50 imagej2_base_utils.stop_err( error_message )
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52 # Convert the registered image to the specified output format.
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53 tmp_out = tempfile.NamedTemporaryFile().name
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54 tmp_stdout = open( tmp_out, 'wb' )
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55 tmp_err = tempfile.NamedTemporaryFile().name
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56 tmp_stderr = open( tmp_err, 'wb' )
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58 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
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59 if cmd is None:
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60 imagej2_base_utils.stop_err( "ImageJ not found!" )
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61 cmd += ' %s %s %s' % ( tmp_source_out_tiff_path,
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62 args.source_out_datatype,
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63 tmp_source_out_path )
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65 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
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66 rc = proc.wait()
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67 if rc != 0:
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68 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
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69 imagej2_base_utils.stop_err( error_message )
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71 # Save the Registered Source Image to the defined output.
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72 shutil.move( tmp_source_out_path, args.source_out )
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73 imagej2_base_utils.cleanup_before_exit( tmp_dir )