Mercurial > repos > imgteam > imagej2_noise
diff imagej2_base_utils.py @ 0:3f6599ec7d30 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 16:58:28 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_base_utils.py Tue Sep 17 16:58:28 2019 -0400 @@ -0,0 +1,169 @@ +import os +import shutil +import sys +import tempfile + +BUFF_SIZE = 1048576 + + +def cleanup_before_exit(tmp_dir): + """ + Remove temporary files and directories prior to tool exit. + """ + if tmp_dir and os.path.exists(tmp_dir): + shutil.rmtree(tmp_dir) + + +def get_base_cmd_bunwarpj(jvm_memory): + if jvm_memory in [None, 'None']: + jvm_memory_str = '' + else: + jvm_memory_str = '-Xmx%s' % jvm_memory + # The following bunwarpj_base_cmd string will look something like this: + # "java %s -cp $JAR_DIR/ij-1.49k.jar:$PLUGINS_DIR/bUnwarpJ_-2.6.1.jar \ + # bunwarpj.bUnwarpJ_" % (jvm_memory_str) + # See the bunwarpj.sh script for the fiji 20151222 + # bioconda recipe in github. + bunwarpj_base_cmd = "bunwarpj %s" % jvm_memory_str + return bunwarpj_base_cmd + + +def get_base_command_imagej2(memory_size=None, macro=None, jython_script=None): + imagej2_executable = get_imagej2_executable() + if imagej2_executable is None: + return None + cmd = '%s --ij2 --headless --debug' % imagej2_executable + if memory_size is not None: + memory_size_cmd = ' -DXms=%s -DXmx=%s' % (memory_size, memory_size) + cmd += memory_size_cmd + if macro is not None: + cmd += ' --macro %s' % os.path.abspath(macro) + if jython_script is not None: + cmd += ' --jython %s' % os.path.abspath(jython_script) + return cmd + + +def get_file_extension(image_format): + """ + Return a valid bioformats file extension based on the received + value of image_format(e.g., "gif" is returned as ".gif". + """ + return '.%s' % image_format + + +def get_file_name_without_extension(file_path): + """ + Eliminate the .ext from the received file name, assuming that + the file name consists of only a single '.'. + """ + if os.path.exists(file_path): + path, name = os.path.split(file_path) + name_items = name.split('.') + return name_items[0] + return None + + +def get_imagej2_executable(): + """ + Fiji names the ImageJ executable different names for different + architectures, but our bioconda recipe allows us to do this. + """ + return 'ImageJ' + + +def get_input_image_path(tmp_dir, input_file, image_format): + """ + Bioformats uses file extensions (e.g., .job, .gif, etc) + when reading and writing image files, so the Galaxy dataset + naming convention of setting all file extensions as .dat + must be handled. + """ + image_path = get_temporary_image_path(tmp_dir, image_format) + # Remove the file so we can create a symlink. + os.remove(image_path) + os.symlink(input_file, image_path) + return image_path + + +def get_platform_info_dict(): + '''Return a dict with information about the current platform.''' + platform_dict = {} + sysname, nodename, release, version, machine = os.uname() + platform_dict['os'] = sysname.lower() + platform_dict['architecture'] = machine.lower() + return platform_dict + + +def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False): + tmp_stderr.close() + """ + Return a stderr string of reasonable size. + """ + # Get stderr, allowing for case where it's very large. + tmp_stderr = open(tmp_err, 'rb') + stderr_str = '' + buffsize = BUFF_SIZE + try: + while True: + stderr_str += tmp_stderr.read(buffsize) + if not stderr_str or len(stderr_str) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if include_stdout: + tmp_stdout = open(tmp_out, 'rb') + stdout_str = '' + buffsize = BUFF_SIZE + try: + while True: + stdout_str += tmp_stdout.read(buffsize) + if not stdout_str or len(stdout_str) % buffsize != 0: + break + except OverflowError: + pass + tmp_stdout.close() + if include_stdout: + return 'STDOUT\n%s\n\nSTDERR\n%s\n' % (stdout_str, stderr_str) + return stderr_str + + +def get_temp_dir(prefix='tmp-imagej-', dir=None): + """ + Return a temporary directory. + """ + return tempfile.mkdtemp(prefix=prefix, dir=dir) + + +def get_tempfilename(dir=None, suffix=None): + """ + Return a temporary file name. + """ + fd, name = tempfile.mkstemp(suffix=suffix, dir=dir) + os.close(fd) + return name + + +def get_temporary_image_path(tmp_dir, image_format): + """ + Return the path to a temporary file with a valid image format + file extension that can be used with bioformats. + """ + file_extension = get_file_extension(image_format) + return get_tempfilename(tmp_dir, file_extension) + + +def handle_none_type(val, val_type='float'): + if val is None: + return ' None' + else: + if val_type == 'float': + return ' %.3f' % val + elif val_type == 'int': + return ' %d' % val + return ' %s' % val + + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit(1)