--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_base_utils.py	Wed Aug 26 14:37:25 2015 -0400
@@ -0,0 +1,164 @@
+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_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
+    return ' %s' % val
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit( 1 )