Mercurial > repos > imgteam > imagej2_analyze_particles_binary

annotate imagej2_bunwarpj_adapt_transform.py @ 0:aeb9bb864b8c 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 16:56:37 -0400
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aeb9bb864b8c "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
aeb9bb864b8c "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
aeb9bb864b8c "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
aeb9bb864b8c "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
aeb9bb864b8c "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
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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aeb9bb864b8c "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.
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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8 parser = argparse.ArgumentParser()
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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9 parser.add_argument( '--source_image', dest='source_image', help='Source image' )
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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10 parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
aeb9bb864b8c "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( '--target_image', dest='target_image', help='Target image' )
aeb9bb864b8c "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' )
aeb9bb864b8c "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( '--input_elastic_transformation', dest='input_elastic_transformation', help='Input elastic transformation matrix' )
aeb9bb864b8c "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( '--image_size_factor', dest='image_size_factor', type=float, help='Image size factor' )
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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()
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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20 source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
aeb9bb864b8c "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 )
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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22 input_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input_elastic_transformation, 'txt' )
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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24 # Define command response buffers.
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25 tmp_out = tempfile.NamedTemporaryFile().name
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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26 tmp_stdout = open( tmp_out, 'wb' )
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27 tmp_err = tempfile.NamedTemporaryFile().name
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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28 tmp_stderr = open( tmp_err, 'wb' )
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30 def is_power2( val ):
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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31 if val < 0:
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32 return False
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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33 if val < 1:
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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34 val = 1.0 / val
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35 val = int( val )
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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36 return ( ( val & ( val - 1 ) ) == 0 )
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38 # Build the command line to adapt the transformation.
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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39 cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
aeb9bb864b8c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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40 if cmd is None:
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41 imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
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42 cmd += ' -adapt_transform'
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44 # Make sure the value of image_size_factor is a power of 2 (positive or negative).
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45 if is_power2( args.image_size_factor ):
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46 image_size_factor = args.image_size_factor
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47 else:
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48 msg = "Image size factor must be a positive or negative power of 2 (0.25, 0.5, 2, 4, 8, etc)."
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49 imagej2_base_utils.stop_err( msg )
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51 # Target is sent before source.
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52 cmd += ' %s' % target_image_path
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53 cmd += ' %s' % source_image_path
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54 cmd += ' %s' % input_elastic_transformation_path
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55 cmd += ' %s' % args.output
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56 cmd += ' %2.f' % image_size_factor
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58 # Adapt the transformation based on the image size factor using bUnwarpJ.
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59 proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True )
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60 rc = proc.wait()
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61 if rc != 0:
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62 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
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63 imagej2_base_utils.stop_err( error_message )
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64
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65 imagej2_base_utils.cleanup_before_exit( tmp_dir )