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 __init__(self, ds_type, st_type, st_path):
"""Prepare the dataset object.
Parameters
----------
ds_type : str
One of ('mosaic', 'stack', 'single')
st_type : str
'single' : a single file container with the full dataset
'tree' : a directory hierarchy
'sequence' : a sequence of files
st_path : str
The full path to either a file or directory, depending on the
storage type of this dataset.
supplement : dict
An auxiliary dict to keep supplementary information.
Instance Variables
------------------
ds_type : str
storage : pathtools.parse_path
"""
log.debug("Creating a 'Dataset' object.")
ds_type_allowed = ('mosaic', 'stack', 'single')
st_type_allowed = ('single', 'tree', 'sequence')
if not ds_type in ds_type_allowed:
raise TypeError("Illegal dataset type: %s." % ds_type)
if not st_type in st_type_allowed:
raise TypeError("Illegal storage type: %s." % st_type)
self.ds_type = ds_type
self.storage = parse_path(st_path)
self.storage['type'] = st_type
if st_type == 'single' and self.storage['fname'] == '':
raise TypeError("File name missing for storage type 'single'.")
self.supplement = {}
def __init__(self, infile):
"""Set up the common experiment properties.
Parameters
----------
infile : str
The experiment file or folder.
Instance Variables
------------------
infile : pathtools.parse_path
datasets : list(Dataset)
"""
super(Experiment, self).__init__()
log.info("Creating an 'Experiment' object.")
self.infile = parse_path(infile)
log.debug(self.infile)
