Mercurial > repos > imgteam > imagej2_find_edges
comparison imagej2_base_utils.py @ 0:8e608a6e44ac draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
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date | Tue, 17 Sep 2019 16:59:03 -0400 |
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-1:000000000000 | 0:8e608a6e44ac |
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1 import os | |
2 import shutil | |
3 import sys | |
4 import tempfile | |
5 | |
6 BUFF_SIZE = 1048576 | |
7 | |
8 | |
9 def cleanup_before_exit(tmp_dir): | |
10 """ | |
11 Remove temporary files and directories prior to tool exit. | |
12 """ | |
13 if tmp_dir and os.path.exists(tmp_dir): | |
14 shutil.rmtree(tmp_dir) | |
15 | |
16 | |
17 def get_base_cmd_bunwarpj(jvm_memory): | |
18 if jvm_memory in [None, 'None']: | |
19 jvm_memory_str = '' | |
20 else: | |
21 jvm_memory_str = '-Xmx%s' % jvm_memory | |
22 # The following bunwarpj_base_cmd string will look something like this: | |
23 # "java %s -cp $JAR_DIR/ij-1.49k.jar:$PLUGINS_DIR/bUnwarpJ_-2.6.1.jar \ | |
24 # bunwarpj.bUnwarpJ_" % (jvm_memory_str) | |
25 # See the bunwarpj.sh script for the fiji 20151222 | |
26 # bioconda recipe in github. | |
27 bunwarpj_base_cmd = "bunwarpj %s" % jvm_memory_str | |
28 return bunwarpj_base_cmd | |
29 | |
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 | |
46 def get_file_extension(image_format): | |
47 """ | |
48 Return a valid bioformats file extension based on the received | |
49 value of image_format(e.g., "gif" is returned as ".gif". | |
50 """ | |
51 return '.%s' % image_format | |
52 | |
53 | |
54 def get_file_name_without_extension(file_path): | |
55 """ | |
56 Eliminate the .ext from the received file name, assuming that | |
57 the file name consists of only a single '.'. | |
58 """ | |
59 if os.path.exists(file_path): | |
60 path, name = os.path.split(file_path) | |
61 name_items = name.split('.') | |
62 return name_items[0] | |
63 return None | |
64 | |
65 | |
66 def get_imagej2_executable(): | |
67 """ | |
68 Fiji names the ImageJ executable different names for different | |
69 architectures, but our bioconda recipe allows us to do this. | |
70 """ | |
71 return 'ImageJ' | |
72 | |
73 | |
74 def get_input_image_path(tmp_dir, input_file, image_format): | |
75 """ | |
76 Bioformats uses file extensions (e.g., .job, .gif, etc) | |
77 when reading and writing image files, so the Galaxy dataset | |
78 naming convention of setting all file extensions as .dat | |
79 must be handled. | |
80 """ | |
81 image_path = get_temporary_image_path(tmp_dir, image_format) | |
82 # Remove the file so we can create a symlink. | |
83 os.remove(image_path) | |
84 os.symlink(input_file, image_path) | |
85 return image_path | |
86 | |
87 | |
88 def get_platform_info_dict(): | |
89 '''Return a dict with information about the current platform.''' | |
90 platform_dict = {} | |
91 sysname, nodename, release, version, machine = os.uname() | |
92 platform_dict['os'] = sysname.lower() | |
93 platform_dict['architecture'] = machine.lower() | |
94 return platform_dict | |
95 | |
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 | |
131 def get_temp_dir(prefix='tmp-imagej-', dir=None): | |
132 """ | |
133 Return a temporary directory. | |
134 """ | |
135 return tempfile.mkdtemp(prefix=prefix, dir=dir) | |
136 | |
137 | |
138 def get_tempfilename(dir=None, suffix=None): | |
139 """ | |
140 Return a temporary file name. | |
141 """ | |
142 fd, name = tempfile.mkstemp(suffix=suffix, dir=dir) | |
143 os.close(fd) | |
144 return name | |
145 | |
146 | |
147 def get_temporary_image_path(tmp_dir, image_format): | |
148 """ | |
149 Return the path to a temporary file with a valid image format | |
150 file extension that can be used with bioformats. | |
151 """ | |
152 file_extension = get_file_extension(image_format) | |
153 return get_tempfilename(tmp_dir, file_extension) | |
154 | |
155 | |
156 def handle_none_type(val, val_type='float'): | |
157 if val is None: | |
158 return ' None' | |
159 else: | |
160 if val_type == 'float': | |
161 return ' %.3f' % val | |
162 elif val_type == 'int': | |
163 return ' %d' % val | |
164 return ' %s' % val | |
165 | |
166 | |
167 def stop_err(msg): | |
168 sys.stderr.write(msg) | |
169 sys.exit(1) |