Mercurial > repos > iuc > imagej2_math

comparison imagej2_base_utils.py @ 0:de912ce81cb9 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 23:24:33 -0400
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-1:000000000000 0:de912ce81cb9
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
14 def cleanup_before_exit(tmp_dir):
15 """
16 Remove temporary files and directories prior to tool exit.
17 """
18 if tmp_dir and os.path.exists(tmp_dir):
19 shutil.rmtree(tmp_dir)
20
21
22 def get_base_cmd_bunwarpj(jvm_memory):
23 if FIJI_JAR_DIR is not None and FIJI_PLUGIN_DIR is not None:
24 if jvm_memory in [None, 'None']:
25 jvm_memory_str = ''
26 else:
27 jvm_memory_str = '-Xmx%s' % jvm_memory
28 # bunwarpj_base_cmd = "java %s -cp %s/ij-1.49k.jar:%s/bUnwarpJ_-2.6.1.jar bunwarpj.bUnwarpJ_" % \
29 # (jvm_memory_str, FIJI_JAR_DIR, FIJI_PLUGIN_DIR)
30 bunwarpj_base_cmd = "bunwarpj %s" % jvm_memory_str
31 return bunwarpj_base_cmd
32 return None
33
34
35 def get_base_command_imagej2(memory_size=None, macro=None, jython_script=None):
36 imagej2_executable = get_imagej2_executable()
37 if imagej2_executable is None:
38 return None
39 cmd = '%s --ij2 --headless --debug' % imagej2_executable
40 if memory_size is not None:
41 memory_size_cmd = ' -DXms=%s -DXmx=%s' % (memory_size, memory_size)
42 cmd += memory_size_cmd
43 if macro is not None:
44 cmd += ' --macro %s' % os.path.abspath(macro)
45 if jython_script is not None:
46 cmd += ' --jython %s' % os.path.abspath(jython_script)
47 return cmd
48
49
50 def get_file_extension(image_format):
51 """
52 Return a valid bioformats file extension based on the received
53 value of image_format(e.g., "gif" is returned as ".gif".
54 """
55 return '.%s' % image_format
56
57
58 def get_file_name_without_extension(file_path):
59 """
60 Eliminate the .ext from the received file name, assuming that
61 the file name consists of only a single '.'.
62 """
63 if os.path.exists(file_path):
64 path, name = os.path.split(file_path)
65 name_items = name.split('.')
66 return name_items[0]
67 return None
68
69
70 def get_imagej2_executable():
71 """
72 Fiji names the ImageJ executable different names for different
73 architectures, but our bioconda recipe allows us to do this.
74 """
75 return 'ImageJ'
76
77
78 def get_input_image_path(tmp_dir, input_file, image_format):
79 """
80 Bioformats uses file extensions (e.g., .job, .gif, etc)
81 when reading and writing image files, so the Galaxy dataset
82 naming convention of setting all file extensions as .dat
83 must be handled.
84 """
85 image_path = get_temporary_image_path(tmp_dir, image_format)
86 # Remove the file so we can create a symlink.
87 os.remove(image_path)
88 os.symlink(input_file, image_path)
89 return image_path
90
91
92 def get_platform_info_dict():
93 '''Return a dict with information about the current platform.'''
94 platform_dict = {}
95 sysname, nodename, release, version, machine = os.uname()
96 platform_dict['os'] = sysname.lower()
97 platform_dict['architecture'] = machine.lower()
98 return platform_dict
99
100
101 def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False):
102 tmp_stderr.close()
103 """
104 Return a stderr string of reasonable size.
105 """
106 # Get stderr, allowing for case where it's very large.
107 tmp_stderr = open(tmp_err, 'rb')
108 stderr_str = ''
109 buffsize = BUFF_SIZE
110 try:
111 while True:
112 stderr_str += tmp_stderr.read(buffsize)
113 if not stderr_str or len(stderr_str) % buffsize != 0:
114 break
115 except OverflowError:
116 pass
117 tmp_stderr.close()
118 if include_stdout:
119 tmp_stdout = open(tmp_out, 'rb')
120 stdout_str = ''
121 buffsize = BUFF_SIZE
122 try:
123 while True:
124 stdout_str += tmp_stdout.read(buffsize)
125 if not stdout_str or len(stdout_str) % buffsize != 0:
126 break
127 except OverflowError:
128 pass
129 tmp_stdout.close()
130 if include_stdout:
131 return 'STDOUT\n%s\n\nSTDERR\n%s\n' % (stdout_str, stderr_str)
132 return stderr_str
133
134
135 def get_temp_dir(prefix='tmp-imagej-', dir=None):
136 """
137 Return a temporary directory.
138 """
139 return tempfile.mkdtemp(prefix=prefix, dir=dir)
140
141
142 def get_tempfilename(dir=None, suffix=None):
143 """
144 Return a temporary file name.
145 """
146 fd, name = tempfile.mkstemp(suffix=suffix, dir=dir)
147 os.close(fd)
148 return name
149
150
151 def get_temporary_image_path(tmp_dir, image_format):
152 """
153 Return the path to a temporary file with a valid image format
154 file extension that can be used with bioformats.
155 """
156 file_extension = get_file_extension(image_format)
157 return get_tempfilename(tmp_dir, file_extension)
158
159
160 def handle_none_type(val, val_type='float'):
161 if val is None:
162 return ' None'
163 else:
164 if val_type == 'float':
165 return ' %.3f' % val
166 elif val_type == 'int':
167 return ' %d' % val
168 return ' %s' % val
169
170
171 def stop_err(msg):
172 sys.stderr.write(msg)
173 sys.exit(1)