Mercurial > repos > iuc > imagej2_skeletonize3d

annotate imagej2_base_utils.py @ 3:39e144c3952b draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
author iuc
date Fri, 22 Jul 2016 23:10:42 -0400
parents 99f75b64cdf3
children
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1 import os
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2 import shutil
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3 import sys
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4 import tempfile
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39e144c3952b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
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6 FIJI_JAR_DIR = os.environ.get('FIJI_JAR_DIR', None)
39e144c3952b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
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7 FIJI_OSX_JAVA3D_DIR = os.environ.get('FIJI_OSX_JAVA3D_DIR', None)
39e144c3952b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
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8 FIJI_PLUGIN_DIR = os.environ.get('FIJI_PLUGIN_DIR', None)
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9 FIJI_ROOT_DIR = os.environ.get('FIJI_ROOT_DIR', None)
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11 BUFF_SIZE = 1048576
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14 def cleanup_before_exit(tmp_dir):
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15 """
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16 Remove temporary files and directories prior to tool exit.
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17 """
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18 if tmp_dir and os.path.exists(tmp_dir):
39e144c3952b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
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19 shutil.rmtree(tmp_dir)
39e144c3952b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
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22 def get_base_cmd_bunwarpj(jvm_memory):
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23 if FIJI_JAR_DIR is not None and FIJI_PLUGIN_DIR is not None:
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24 if jvm_memory in [None, 'None']:
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25 jvm_memory_str = ''
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26 else:
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27 jvm_memory_str = '-Xmx%s' % jvm_memory
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28 # bunwarpj_base_cmd = "java %s -cp %s/ij-1.49k.jar:%s/bUnwarpJ_-2.6.1.jar bunwarpj.bUnwarpJ_" % \
39e144c3952b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
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29 # (jvm_memory_str, FIJI_JAR_DIR, FIJI_PLUGIN_DIR)
39e144c3952b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
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30 bunwarpj_base_cmd = "bunwarpj %s" % jvm_memory_str
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31 return bunwarpj_base_cmd
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32 return None
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35 def get_base_command_imagej2(memory_size=None, macro=None, jython_script=None):
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36 imagej2_executable = get_imagej2_executable()
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37 if imagej2_executable is None:
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38 return None
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39 cmd = '%s --ij2 --headless --debug' % imagej2_executable
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40 if memory_size is not None:
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41 memory_size_cmd = ' -DXms=%s -DXmx=%s' % (memory_size, memory_size)
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42 cmd += memory_size_cmd
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43 if macro is not None:
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44 cmd += ' --macro %s' % os.path.abspath(macro)
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45 if jython_script is not None:
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46 cmd += ' --jython %s' % os.path.abspath(jython_script)
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47 return cmd
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48
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50 def get_file_extension(image_format):
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51 """
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52 Return a valid bioformats file extension based on the received
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53 value of image_format(e.g., "gif" is returned as ".gif".
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54 """
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55 return '.%s' % image_format
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56
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58 def get_file_name_without_extension(file_path):
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59 """
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60 Eliminate the .ext from the received file name, assuming that
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61 the file name consists of only a single '.'.
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62 """
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63 if os.path.exists(file_path):
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64 path, name = os.path.split(file_path)
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65 name_items = name.split('.')
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66 return name_items[0]
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67 return None
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70 def get_imagej2_executable():
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71 """
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72 Fiji names the ImageJ executable different names for different
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73 architectures, but our bioconda recipe allows us to do this.
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74 """
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75 return 'ImageJ'
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78 def get_input_image_path(tmp_dir, input_file, image_format):
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79 """
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80 Bioformats uses file extensions (e.g., .job, .gif, etc)
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81 when reading and writing image files, so the Galaxy dataset
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82 naming convention of setting all file extensions as .dat
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83 must be handled.
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84 """
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85 image_path = get_temporary_image_path(tmp_dir, image_format)
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86 # Remove the file so we can create a symlink.
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87 os.remove(image_path)
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88 os.symlink(input_file, image_path)
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89 return image_path
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90
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91
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92 def get_platform_info_dict():
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93 '''Return a dict with information about the current platform.'''
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94 platform_dict = {}
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95 sysname, nodename, release, version, machine = os.uname()
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96 platform_dict['os'] = sysname.lower()
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97 platform_dict['architecture'] = machine.lower()
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98 return platform_dict
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99
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101 def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False):
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102 tmp_stderr.close()
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103 """
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104 Return a stderr string of reasonable size.
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105 """
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106 # Get stderr, allowing for case where it's very large.
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107 tmp_stderr = open(tmp_err, 'rb')
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108 stderr_str = ''
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109 buffsize = BUFF_SIZE
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110 try:
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111 while True:
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112 stderr_str += tmp_stderr.read(buffsize)
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113 if not stderr_str or len(stderr_str) % buffsize != 0:
0
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114 break
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115 except OverflowError:
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116 pass
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117 tmp_stderr.close()
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118 if include_stdout:
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119 tmp_stdout = open(tmp_out, 'rb')
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120 stdout_str = ''
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121 buffsize = BUFF_SIZE
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122 try:
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123 while True:
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124 stdout_str += tmp_stdout.read(buffsize)
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125 if not stdout_str or len(stdout_str) % buffsize != 0:
0
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126 break
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127 except OverflowError:
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128 pass
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129 tmp_stdout.close()
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130 if include_stdout:
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131 return 'STDOUT\n%s\n\nSTDERR\n%s\n' % (stdout_str, stderr_str)
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132 return stderr_str
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133
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134
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135 def get_temp_dir(prefix='tmp-imagej-', dir=None):
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136 """
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137 Return a temporary directory.
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138 """
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139 return tempfile.mkdtemp(prefix=prefix, dir=dir)
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140
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141
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142 def get_tempfilename(dir=None, suffix=None):
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143 """
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144 Return a temporary file name.
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145 """
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146 fd, name = tempfile.mkstemp(suffix=suffix, dir=dir)
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147 os.close(fd)
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148 return name
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149
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150
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151 def get_temporary_image_path(tmp_dir, image_format):
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152 """
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153 Return the path to a temporary file with a valid image format
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154 file extension that can be used with bioformats.
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155 """
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156 file_extension = get_file_extension(image_format)
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157 return get_tempfilename(tmp_dir, file_extension)
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158
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159
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160 def handle_none_type(val, val_type='float'):
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161 if val is None:
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162 return ' None'
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163 else:
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164 if val_type == 'float':
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165 return ' %.3f' % val
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166 elif val_type == 'int':
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167 return ' %d' % val
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168 return ' %s' % val
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169
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170
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171 def stop_err(msg):
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172 sys.stderr.write(msg)
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173 sys.exit(1)