Mercurial > repos > iuc > imagej2_analyze_particles_binary

comparison 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
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children dd9041dc3c27
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-1:000000000000 0:d065ec177dcd
1 import os
2 import shutil
3 import sys
4 import tempfile
5
6 FIJI_JAR_DIR = os.environ.get( 'FIJI_JAR_DIR', None )
7 FIJI_OSX_JAVA3D_DIR = os.environ.get( 'FIJI_OSX_JAVA3D_DIR', None )
8 FIJI_PLUGIN_DIR = os.environ.get( 'FIJI_PLUGIN_DIR', None )
9 FIJI_ROOT_DIR = os.environ.get( 'FIJI_ROOT_DIR', None )
10
11 BUFF_SIZE = 1048576
12
13 def cleanup_before_exit( tmp_dir ):
14 """
15 Remove temporary files and directories prior to tool exit.
16 """
17 if tmp_dir and os.path.exists( tmp_dir ):
18 shutil.rmtree( tmp_dir )
19
20 def get_base_cmd_bunwarpj( jvm_memory ):
21 if FIJI_JAR_DIR is not None and FIJI_PLUGIN_DIR is not None:
22 if jvm_memory in [ None, 'None' ]:
23 jvm_memory_str = ''
24 else:
25 jvm_memory_str = '-Xmx%s' % jvm_memory
26 bunwarpj_base_cmd = "java %s -cp %s/ij-1.49k.jar:%s/bUnwarpJ_-2.6.1.jar bunwarpj.bUnwarpJ_" % \
27 ( jvm_memory_str, FIJI_JAR_DIR, FIJI_PLUGIN_DIR )
28 return bunwarpj_base_cmd
29 return None
30
31 def get_base_command_imagej2( memory_size=None, macro=None, jython_script=None ):
32 imagej2_executable = get_imagej2_executable()
33 if imagej2_executable is None:
34 return None
35 cmd = '%s --ij2 --headless --debug' % imagej2_executable
36 if memory_size is not None:
37 memory_size_cmd = ' -DXms=%s -DXmx=%s' % ( memory_size, memory_size )
38 cmd += memory_size_cmd
39 if macro is not None:
40 cmd += ' --macro %s' % os.path.abspath( macro )
41 if jython_script is not None:
42 cmd += ' --jython %s' % os.path.abspath( jython_script )
43 return cmd
44
45 def get_file_extension( image_format ):
46 """
47 Return a valid bioformats file extension based on the received
48 value of image_format( e.g., "gif" is returned as ".gif".
49 """
50 return '.%s' % image_format
51
52 def get_file_name_without_extension( file_path ):
53 """
54 Eliminate the .ext from the received file name, assuming that
55 the file name consists of only a single '.'.
56 """
57 if os.path.exists( file_path ):
58 path, name = os.path.split( file_path )
59 name_items = name.split( '.' )
60 return name_items[ 0 ]
61 return None
62
63 def get_imagej2_executable():
64 """
65 Fiji names the ImageJ executable different names for different
66 architectures, so figure out which name we need.
67 """
68 platform_dict = get_platform_info_dict()
69 if platform_dict.get( 'architecture', None ) in [ 'x86_64' ]:
70 if platform_dict.get( 'os', None ) in [ 'darwin' ]:
71 return 'ImageJ-macosx'
72 if platform_dict.get( 'os', None ) in [ 'linux' ]:
73 return 'ImageJ-linux64'
74 return None
75
76 def get_input_image_path( tmp_dir, input_file, image_format ):
77 """
78 Bioformats uses file extensions (e.g., .job, .gif, etc)
79 when reading and writing image files, so the Galaxy dataset
80 naming convention of setting all file extensions as .dat
81 must be handled.
82 """
83 image_path = get_temporary_image_path( tmp_dir, image_format )
84 # Remove the file so we can create a symlink.
85 os.remove( image_path )
86 os.symlink( input_file, image_path )
87 return image_path
88
89 def get_platform_info_dict():
90 '''Return a dict with information about the current platform.'''
91 platform_dict = {}
92 sysname, nodename, release, version, machine = os.uname()
93 platform_dict[ 'os' ] = sysname.lower()
94 platform_dict[ 'architecture' ] = machine.lower()
95 return platform_dict
96
97 def get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False ):
98 tmp_stderr.close()
99 """
100 Return a stderr string of reasonable size.
101 """
102 # Get stderr, allowing for case where it's very large.
103 tmp_stderr = open( tmp_err, 'rb' )
104 stderr_str = ''
105 buffsize = BUFF_SIZE
106 try:
107 while True:
108 stderr_str += tmp_stderr.read( buffsize )
109 if not stderr_str or len( stderr_str ) % buffsize != 0:
110 break
111 except OverflowError:
112 pass
113 tmp_stderr.close()
114 if include_stdout:
115 tmp_stdout = open( tmp_out, 'rb' )
116 stdout_str = ''
117 buffsize = BUFF_SIZE
118 try:
119 while True:
120 stdout_str += tmp_stdout.read( buffsize )
121 if not stdout_str or len( stdout_str ) % buffsize != 0:
122 break
123 except OverflowError:
124 pass
125 tmp_stdout.close()
126 if include_stdout:
127 return 'STDOUT\n%s\n\nSTDERR\n%s\n' % ( stdout_str, stderr_str )
128 return stderr_str
129
130 def get_temp_dir( prefix='tmp-imagej-', dir=None ):
131 """
132 Return a temporary directory.
133 """
134 return tempfile.mkdtemp( prefix=prefix, dir=dir )
135
136 def get_tempfilename( dir=None, suffix=None ):
137 """
138 Return a temporary file name.
139 """
140 fd, name = tempfile.mkstemp( suffix=suffix, dir=dir )
141 os.close( fd )
142 return name
143
144 def get_temporary_image_path( tmp_dir, image_format ):
145 """
146 Return the path to a temporary file with a valid image format
147 file extension that can be used with bioformats.
148 """
149 file_extension = get_file_extension( image_format )
150 return get_tempfilename( tmp_dir, file_extension )
151
152 def handle_none_type( val, val_type='float' ):
153 if val is None:
154 return ' None'
155 else:
156 if val_type == 'float':
157 return ' %.1f' % val
158 elif val_type == 'int':
159 return ' %d' % val
160 return ' %s' % val
161
162 def stop_err( msg ):
163 sys.stderr.write( msg )
164 sys.exit( 1 )