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annotate imagej2_bunwarpj_compare_elastic_raw.py @ 0:855fa4bb8a44 draft default tip

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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 17:03:40 -0400
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855fa4bb8a44 "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
855fa4bb8a44 "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
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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3 import subprocess
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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4 import tempfile
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 import imagej2_base_utils
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855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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7 # Parse Command Line.
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8 parser = argparse.ArgumentParser()
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9 parser.add_argument( '--source_image', dest='source_image', help='Source image' )
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10 parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
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11 parser.add_argument( '--target_image', dest='target_image', help='Target image' )
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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12 parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
855fa4bb8a44 "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_elastic_transformation', dest='target_elastic_transformation', help='Target elastic transformation matrix' )
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14 parser.add_argument( '--source_raw_transformation', dest='source_raw_transformation', help='Source raw transformation matrix' )
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15 parser.add_argument( '--output', dest='output', help='Warping index' )
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17 args = parser.parse_args()
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19 tmp_dir = imagej2_base_utils.get_temp_dir()
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20 source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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21 target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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22 target_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_elastic_transformation, 'txt' )
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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23 source_raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_raw_transformation, 'txt' )
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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24 # bUnwarpJ produces several lines of output that we need to discard, so
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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25 # we'll use a temporary output file from which we'll read only the last line.
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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26 tmp_output_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.output, 'txt' )
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28 # Define command response buffers.
855fa4bb8a44 "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 calculate the warping index.
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35 cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
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36 if cmd is None:
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37 imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
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38 cmd += ' -compare_elastic_raw'
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39 cmd += ' %s' % target_image_path
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40 cmd += ' %s' % source_image_path
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41 cmd += ' %s' % target_elastic_transformation_path
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42 cmd += ' %s' % source_raw_transformation_path
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43 cmd += ' > %s' % tmp_output_path
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44
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45 # Calculate the warping index of elastic and raw transformations using bUnwarpJ.
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46 proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, 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 # Example contents of tmp_output_path:
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53 # ['Target image : ~/tmpHdt9Cs.jpg\n',
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54 # 'Source image : ~/tmpu6kyfc.gif\n',
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55 # 'Elastic Transformation file : ~/tmp4vZurG.txt\n',
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56 # 'Raw Transformation file : ~/tmp2PNQcT.txt\n',
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57 # ' Warping index = 25.007467512204983\n']
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58 results = open( tmp_output_path, 'r' ).readlines()
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59 warp_index = results[ -1 ].split( ' ' )[ -1 ]
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60 outf = open( args.output, 'wb' )
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61 outf.write( '%s' % warp_index )
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62 outf.close()
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63
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64 imagej2_base_utils.cleanup_before_exit( tmp_dir )