Mercurial > repos > iuc > imagej2_analyze_particles_binary

annotate imagej2_base_utils.py @ 0:d065ec177dcd draft

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planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:36:17 -0400
parents
children dd9041dc3c27
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0
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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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5
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6 FIJI_JAR_DIR = os.environ.get( 'FIJI_JAR_DIR', None )
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7 FIJI_OSX_JAVA3D_DIR = os.environ.get( 'FIJI_OSX_JAVA3D_DIR', None )
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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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10
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11 BUFF_SIZE = 1048576
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12
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13 def cleanup_before_exit( tmp_dir ):
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14 """
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15 Remove temporary files and directories prior to tool exit.
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16 """
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17 if tmp_dir and os.path.exists( tmp_dir ):
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18 shutil.rmtree( tmp_dir )
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19
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20 def get_base_cmd_bunwarpj( jvm_memory ):
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21 if FIJI_JAR_DIR is not None and FIJI_PLUGIN_DIR is not None:
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22 if jvm_memory in [ None, 'None' ]:
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23 jvm_memory_str = ''
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24 else:
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25 jvm_memory_str = '-Xmx%s' % jvm_memory
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26 bunwarpj_base_cmd = "java %s -cp %s/ij-1.49k.jar:%s/bUnwarpJ_-2.6.1.jar bunwarpj.bUnwarpJ_" % \
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27 ( jvm_memory_str, FIJI_JAR_DIR, FIJI_PLUGIN_DIR )
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28 return bunwarpj_base_cmd
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29 return None
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30
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31 def get_base_command_imagej2( memory_size=None, macro=None, jython_script=None ):
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32 imagej2_executable = get_imagej2_executable()
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33 if imagej2_executable is None:
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34 return None
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35 cmd = '%s --ij2 --headless --debug' % imagej2_executable
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36 if memory_size is not None:
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37 memory_size_cmd = ' -DXms=%s -DXmx=%s' % ( memory_size, memory_size )
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38 cmd += memory_size_cmd
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39 if macro is not None:
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40 cmd += ' --macro %s' % os.path.abspath( macro )
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41 if jython_script is not None:
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42 cmd += ' --jython %s' % os.path.abspath( jython_script )
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43 return cmd
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44
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45 def get_file_extension( image_format ):
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46 """
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47 Return a valid bioformats file extension based on the received
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48 value of image_format( e.g., "gif" is returned as ".gif".
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49 """
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50 return '.%s' % image_format
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51
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52 def get_file_name_without_extension( file_path ):
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53 """
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54 Eliminate the .ext from the received file name, assuming that
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55 the file name consists of only a single '.'.
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56 """
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57 if os.path.exists( file_path ):
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58 path, name = os.path.split( file_path )
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59 name_items = name.split( '.' )
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60 return name_items[ 0 ]
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61 return None
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62
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63 def get_imagej2_executable():
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64 """
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65 Fiji names the ImageJ executable different names for different
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66 architectures, so figure out which name we need.
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67 """
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68 platform_dict = get_platform_info_dict()
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69 if platform_dict.get( 'architecture', None ) in [ 'x86_64' ]:
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70 if platform_dict.get( 'os', None ) in [ 'darwin' ]:
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71 return 'ImageJ-macosx'
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72 if platform_dict.get( 'os', None ) in [ 'linux' ]:
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73 return 'ImageJ-linux64'
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74 return None
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75
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76 def get_input_image_path( tmp_dir, input_file, image_format ):
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77 """
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78 Bioformats uses file extensions (e.g., .job, .gif, etc)
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79 when reading and writing image files, so the Galaxy dataset
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80 naming convention of setting all file extensions as .dat
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81 must be handled.
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82 """
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83 image_path = get_temporary_image_path( tmp_dir, image_format )
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84 # Remove the file so we can create a symlink.
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85 os.remove( image_path )
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86 os.symlink( input_file, image_path )
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87 return image_path
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88
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89 def get_platform_info_dict():
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90 '''Return a dict with information about the current platform.'''
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91 platform_dict = {}
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92 sysname, nodename, release, version, machine = os.uname()
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93 platform_dict[ 'os' ] = sysname.lower()
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94 platform_dict[ 'architecture' ] = machine.lower()
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95 return platform_dict
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96
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97 def get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False ):
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98 tmp_stderr.close()
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99 """
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100 Return a stderr string of reasonable size.
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101 """
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102 # Get stderr, allowing for case where it's very large.
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103 tmp_stderr = open( tmp_err, 'rb' )
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104 stderr_str = ''
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105 buffsize = BUFF_SIZE
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106 try:
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107 while True:
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108 stderr_str += tmp_stderr.read( buffsize )
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109 if not stderr_str or len( stderr_str ) % buffsize != 0:
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110 break
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111 except OverflowError:
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112 pass
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113 tmp_stderr.close()
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114 if include_stdout:
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115 tmp_stdout = open( tmp_out, 'rb' )
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116 stdout_str = ''
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117 buffsize = BUFF_SIZE
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118 try:
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119 while True:
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120 stdout_str += tmp_stdout.read( buffsize )
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121 if not stdout_str or len( stdout_str ) % buffsize != 0:
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122 break
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123 except OverflowError:
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124 pass
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125 tmp_stdout.close()
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126 if include_stdout:
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127 return 'STDOUT\n%s\n\nSTDERR\n%s\n' % ( stdout_str, stderr_str )
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128 return stderr_str
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129
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130 def get_temp_dir( prefix='tmp-imagej-', dir=None ):
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131 """
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132 Return a temporary directory.
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133 """
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134 return tempfile.mkdtemp( prefix=prefix, dir=dir )
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135
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136 def get_tempfilename( dir=None, suffix=None ):
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137 """
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138 Return a temporary file name.
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139 """
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140 fd, name = tempfile.mkstemp( suffix=suffix, dir=dir )
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141 os.close( fd )
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142 return name
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143
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144 def get_temporary_image_path( tmp_dir, image_format ):
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145 """
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146 Return the path to a temporary file with a valid image format
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147 file extension that can be used with bioformats.
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148 """
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149 file_extension = get_file_extension( image_format )
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150 return get_tempfilename( tmp_dir, file_extension )
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151
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152 def handle_none_type( val, val_type='float' ):
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153 if val is None:
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154 return ' None'
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155 else:
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156 if val_type == 'float':
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157 return ' %.1f' % val
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158 elif val_type == 'int':
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159 return ' %d' % val
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160 return ' %s' % val
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161
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162 def stop_err( msg ):
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163 sys.stderr.write( msg )
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164 sys.exit( 1 )