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annotate imagej2_bunwarpj_align.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 os
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 shutil
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5 import subprocess
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6 import tempfile
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7 import imagej2_base_utils
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8
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9 # Parse Command Line.
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10 parser = argparse.ArgumentParser()
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11 parser.add_argument( '--source_image', dest='source_image', help='Source image' )
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12 parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
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13 parser.add_argument( '--source_mask', dest='source_mask', default=None, help='Source mask' )
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14 parser.add_argument( '--source_mask_format', dest='source_mask_format', default=None, help='Source mask image format' )
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15 parser.add_argument( '--target_image', dest='target_image', help='Target image' )
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16 parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
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17 parser.add_argument( '--target_mask', dest='target_mask', default=None, help='Target mask' )
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18 parser.add_argument( '--target_mask_format', dest='target_mask_format', default=None, help='Target mask image format' )
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19 parser.add_argument( '--min_scale_def', dest='min_scale_def', type=int, help='Initial deformation' )
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20 parser.add_argument( '--max_scale_def', dest='max_scale_def', type=int, help='Final deformation' )
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21 parser.add_argument( '--max_subsamp_fact', dest='max_subsamp_fact', type=int, help='Image sub-sample factor' )
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22 parser.add_argument( '--divergence_weight', dest='divergence_weight', type=float, help='Divergence weight' )
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23 parser.add_argument( '--curl_weight', dest='curl_weight', type=float, help='Curl weight' )
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24 parser.add_argument( '--image_weight', dest='image_weight', type=float, help='Image weight' )
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25 parser.add_argument( '--consistency_weight', dest='consistency_weight', type=float, help='Consistency weight' )
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26 parser.add_argument( '--landmarks_weight', dest='landmarks_weight', type=float, help='Landmarks weight' )
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27 parser.add_argument( '--landmarks_file', dest='landmarks_file', default=None, help='Landmarks file' )
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28 parser.add_argument( '--source_affine_file', dest='source_affine_file', default=None, help='Initial source affine matrix transformation' )
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29 parser.add_argument( '--target_affine_file', dest='target_affine_file', default=None, help='Initial target affine matrix transformation' )
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30 parser.add_argument( '--mono', dest='mono', default=False, help='Unidirectional registration (source to target)' )
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31 parser.add_argument( '--source_trans_out', dest='source_trans_out', default=None, help='Direct source transformation matrix' )
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32 parser.add_argument( '--target_trans_out', dest='target_trans_out', default=None, help='Inverse target transformation matrix' )
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33 parser.add_argument( '--source_out', help='Output source image' )
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34 parser.add_argument( '--source_out_datatype', help='Output registered source image format' )
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35 parser.add_argument( '--target_out', default=None, help='Output target image' )
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36 parser.add_argument( '--target_out_datatype', default=None, help='Output registered target image format' )
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37 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
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38
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39 args = parser.parse_args()
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41 if args.source_trans_out is not None and args.target_trans_out is not None:
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42 save_transformation = True
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43 else:
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44 save_transformation = False
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45
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46 tmp_dir = imagej2_base_utils.get_temp_dir()
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47 source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
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48 tmp_source_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' )
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49 tmp_source_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.source_out_datatype )
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50 target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
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51 if not args.mono:
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52 tmp_target_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' )
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53 tmp_target_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.target_out_datatype )
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54 if args.source_mask is not None and args.target_mask is not None:
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55 tmp_source_mask_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_mask, args.source_mask_format )
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56 tmp_target_mask_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_mask, args.target_mask_format )
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57 if save_transformation:
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58 # bUnwarpJ automatically names the transformation files based on the names
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59 # of the source and target image file names. We've defined symlinks to
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60 # temporary files with valid image extensions since ImageJ does not handle
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61 # the Galaxy "dataset.dat" file extensions.
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62 source_file_name = imagej2_base_utils.get_file_name_without_extension( tmp_source_out_tiff_path )
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63 tmp_source_out_transf_path = os.path.join( tmp_dir, '%s_transf.txt' % source_file_name )
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64 target_file_name = imagej2_base_utils.get_file_name_without_extension( tmp_target_out_tiff_path )
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65 tmp_target_out_transf_path = os.path.join( tmp_dir, '%s_transf.txt' % target_file_name )
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66
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67 # Define command response buffers.
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68 tmp_out = tempfile.NamedTemporaryFile().name
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69 tmp_stdout = open( tmp_out, 'wb' )
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70 tmp_err = tempfile.NamedTemporaryFile().name
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71 tmp_stderr = open( tmp_err, 'wb' )
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72
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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73 # Build the command line to align the two images.
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74 cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
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75 if cmd is None:
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76 imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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77 cmd += ' -align'
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78 # Target is sent before source.
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79 cmd += ' %s' % target_image_path
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80 if args.target_mask is None:
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81 target_mask_str = ' NULL'
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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82 else:
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83 target_mask_str = ' %s' % tmp_target_mask_path
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84 cmd += target_mask_str
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85 cmd += ' %s' % source_image_path
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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86 if args.source_mask is None:
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87 source_mask_str = ' NULL'
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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88 else:
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89 source_mask_str = ' %s' % tmp_source_mask_path
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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90 cmd += source_mask_str
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91 cmd += ' %d' % args.min_scale_def
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92 cmd += ' %d' % args.max_scale_def
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93 cmd += ' %d' % args.max_subsamp_fact
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94 cmd += ' %.1f' % args.divergence_weight
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95 cmd += ' %.1f' % args.curl_weight
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96 cmd += ' %.1f' % args.image_weight
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97 cmd += ' %.1f' % args.consistency_weight
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98 # Source is produced before target.
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99 cmd += ' %s' % tmp_source_out_tiff_path
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100 if not args.mono:
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101 cmd += ' %s' % tmp_target_out_tiff_path
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102 if args.landmarks_file is not None:
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103 # We have to create a temporary file with a .txt extension here so that
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104 # bUnwarpJ will not ignore the Galaxy "dataset.dat" file.
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105 tmp_landmarks_file_path = imagej2_base_utils.get_input_image_path( tmp_dir,
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106 args.landmarks_file,
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107 'txt' )
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108 cmd += ' -landmarks'
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109 cmd += ' %.1f' % args.landmarks_weight
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110 cmd += ' %s' % tmp_landmarks_file_path
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111 if args.source_affine_file is not None and args.target_affine_file is not None:
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112 # Target is sent before source.
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113 cmd += ' -affine'
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114 cmd += ' %s' % args.target_affine_file
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115 cmd += ' %s' % args.source_affine_file
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116 if args.mono:
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117 cmd += ' -mono'
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118 if save_transformation:
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119 cmd += ' -save_transformation'
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120
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121 # Align the two images using bUnwarpJ.
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122 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
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123 rc = proc.wait()
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124 if rc != 0:
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125 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
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126 imagej2_base_utils.stop_err( error_message )
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127
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128 # bUnwarpJ produces tiff image stacks consisting of 3 slices which can be viewed in ImageJ.
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129 # The 3 slices are:: 1) the registered image, 2) the target image and 3) the black/white
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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130 # warp image. Galaxy supports only single-layered images, so we'll convert the images so they
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131 # can be viewed in Galaxy.
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132
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133 # Define command response buffers.
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134 tmp_out = tempfile.NamedTemporaryFile().name
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135 tmp_stdout = open( tmp_out, 'wb' )
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136 tmp_err = tempfile.NamedTemporaryFile().name
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137 tmp_stderr = open( tmp_err, 'wb' )
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138
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139 # Build the command line to handle the multi-slice tiff images.
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140 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
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141 if cmd is None:
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142 imagej2_base_utils.stop_err( "ImageJ not found!" )
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143 if args.mono:
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144 # bUnwarpJ will produce only a registered source image.
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145 cmd += ' %s %s %s %s' % ( tmp_source_out_tiff_path,
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146 args.source_out_datatype,
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147 tmp_source_out_path,
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148 args.mono )
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149 else:
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150 # bUnwarpJ will produce registered source and target images.
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151 cmd += ' %s %s %s %s %s %s %s' % ( tmp_source_out_tiff_path,
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152 args.source_out_datatype,
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153 tmp_source_out_path,
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154 tmp_target_out_tiff_path,
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155 args.target_out_datatype,
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156 tmp_target_out_path,
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157 args.mono )
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158
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159 # Merge the multi-slice tiff layers into an image that can be viewed in Galaxy.
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160 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
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161 rc = proc.wait()
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162 if rc != 0:
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163 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
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164 imagej2_base_utils.stop_err( error_message )
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165
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166 # Save the Registered Source Image to the output dataset.
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167 shutil.move( tmp_source_out_path, args.source_out )
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168 if not args.mono:
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169 # Move the Registered Target Image to the output dataset.
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170 shutil.move( tmp_target_out_path, args.target_out )
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171
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172 # If requested, save matrix transformations as additional datasets.
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173 if save_transformation:
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174 shutil.move( tmp_source_out_transf_path, args.source_trans_out )
855fa4bb8a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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175 if not args.mono:
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176 shutil.move( tmp_target_out_transf_path, args.target_trans_out )
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177
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178 imagej2_base_utils.cleanup_before_exit( tmp_dir )