comparison imagej2_base_utils.py @ 0:66d9e595dff2 draft

planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty

0:66d9e595dff2

import os
import shutil
import sys
import tempfile

FIJI_JAR_DIR = os.environ.get( 'FIJI_JAR_DIR', None )
FIJI_OSX_JAVA3D_DIR = os.environ.get( 'FIJI_OSX_JAVA3D_DIR', None )
FIJI_PLUGIN_DIR = os.environ.get( 'FIJI_PLUGIN_DIR', None )
FIJI_ROOT_DIR = os.environ.get( 'FIJI_ROOT_DIR', None )

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 FIJI_JAR_DIR is not None and FIJI_PLUGIN_DIR is not None:
        if jvm_memory in [ None, 'None' ]:
            jvm_memory_str = ''
        else:
            jvm_memory_str = '-Xmx%s' % jvm_memory
        bunwarpj_base_cmd = "java %s -cp %s/ij-1.49k.jar:%s/bUnwarpJ_-2.6.1.jar bunwarpj.bUnwarpJ_" % \
            ( jvm_memory_str, FIJI_JAR_DIR, FIJI_PLUGIN_DIR )
        return bunwarpj_base_cmd
    return None

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, so figure out which name we need.
    """
    platform_dict = get_platform_info_dict()
    if platform_dict.get( 'architecture', None ) in [ 'x86_64' ]:
        if platform_dict.get( 'os', None ) in [ 'darwin' ]:
            return 'ImageJ-macosx'
        if platform_dict.get( 'os', None ) in [ 'linux' ]:
            return 'ImageJ-linux64'
    return None
    
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_max_heap_size_value( max_heap_size_type, max_heap_size ):
    """
    Return a string that can be used by the javabridge to set the size
    of the memory allocation pool used by the JVM.  The value must be
    determined to be a multiple of 1024 or it will be ignored.
    """
    if max_heap_size_type == 'default':
        return None
    if max_heap_size_type == 'megabytes':
        if int( max_heap_size ) % 1024 not in [ 0, 256, 512 ]:
            return None
        return '%sm' % str( max_heap_size )
    if max_heap_size_type == 'gigabytes':
        return '%sg' % str( max_heap_size )

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 ' %.1f' % val
        elif val_type == 'int':
            return ' %d' % val

def stop_err( msg ):
    sys.stderr.write( msg )
    sys.exit( 1 )