def validate_filepath(self):
"""Fix the broken filenames in FluoView experiment files.
The FluoView software usually stores corrupted filenames in its
experiment description files, that have a missing suffix, e.g.
Slide1sec001\\Slide1sec001.oib
whereas the correct filename would be
Slide1sec001\\Slide1sec001_01.oib
This function attempts to fix this by checking if the supplied path is
actually existing and trying the default suffix if not. Raises an
IOError exception if no corresponding file can be found.
Returns
-------
storage : pathtools.parse_path
"""
fpath = self.storage
ext = fpath['ext']
log.debug("Validating file path: %s" % fpath)
if not exists(fpath['full']):
fpath = parse_path(fpath['orig'].replace(ext, '_01' + ext))
log.debug("Trying next path: %s" % fpath['full'])
if not exists(fpath['full']):
raise IOError("Can't find file: %s" % fpath)
return fpath
def gen_stitching_macro_code(experiment, pfx, path='', tplpath='', opts={}):
"""Generate code in ImageJ's macro language to stitch the mosaics.
Take two template files ("head" and "body") and generate an ImageJ
macro to stitch the mosaics. Using the splitted templates allows for
setting default values in the head that can be overridden in this
generator method (the ImageJ macro language doesn't have a command to
check if a variable is set or not, it just exits with an error).
Parameters
----------
experiment : volpy.experiment.MosaicExperiment
The object containing all information about the mosaic.
pfx : str
The prefix for the two template files, will be completed with the
corresponding suffixes "_head.ijm" and "_body.ijm".
path : str
The path to use as input directory *INSIDE* the macro.
tplpath : str
The path to a directory or zip file containing the templates.
opts : dict (optional)
A dict with key-value pairs to be put into the macro between the head
and body to override the macro's default settings.
NOTE: the values are placed literally in the macro code, this means
that strings have to be quoted, e.g. opts['foo'] = '"bar baz"'
Returns
-------
ijm : list(str) or str
The generated macro code as a list of str (one str per line) or as
a single long string if requested via the "flat" parameter.
"""
# pylint: disable-msg=E1103
# the type of 'ijm' is not correctly inferred by pylint and it complains
# by default templates are expected in a subdir of the current package:
if (tplpath == ''):
tplpath = join(dirname(__file__), 'ijm_templates')
log.debug('Looking for template directory: %s' % tplpath)
if not exists(tplpath):
tplpath += '.zip'
log.debug('Looking for template directory: %s' % tplpath)
if not exists(tplpath):
raise IOError("Template directory can't be found!")
log.info('Template directory: %s' % tplpath)
ijm = []
try:
import imcf
ijm.append('// Generated by %s (%s).\n\n' % (__name__, imcf.VERSION))
except ImportError:
pass
ijm += readtxt(pfx + '_head.ijm', tplpath)
ijm.append('\n')
ijm.append('name = "%s";\n' % experiment.infile['dname'])
# windows path separator (in)sanity:
path = path.replace('\\', '\\\\')
ijm.append('input_dir="%s";\n' % path)
ijm.append('use_batch_mode = true;\n')
for option, value in opts.items():
ijm.append('%s = %s;\n' % (option, value))
# If the overlap is below a certain level (5 percent), we disable
# computing the actual positions and subpixel accuracy:
if (experiment[0].get_overlap('pct') < 5.0):
ijm.append('compute = false;\n')
ijm.append('\n')
ijm += readtxt(pfx + '_body.ijm', tplpath)
log.debug('--- ijm ---\n%s\n--- ijm ---' % ijm)
return(ijm)