imread error when passing a string

[haesleinhuepf]

Hi @cgohlke ,

I'm retrieving an error when passing a string to the imread function and presume it's a bug. This example works well:

import czifile
from pathlib import Path
image = czifile.imread(Path("../../data/PupalWing.czi"))

But this throws an error:

import czifile
image = czifile.imread("../../data/PupalWing.czi")

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[12], line 2
      1 import czifile
----> 2 image = czifile.imread("../../data/PupalWing.czi")

File ~\mambaforge\envs\bio39\lib\site-packages\czifile\czifile.py:220, in imread(filename, *args, **kwargs)
    214 def imread(filename, *args, **kwargs):
    215     """Return image data from CZI file as numpy array.
    216 
    217     'args' and 'kwargs' are arguments to the CziFile.asarray function.
    218 
    219     """
--> 220     with CziFile(filename) as czi:
    221         result = czi.asarray(*args, **kwargs)
    222     return result

File ~\mambaforge\envs\bio39\lib\site-packages\czifile\czifile.py:275, in CziFile.__init__(self, arg, multifile, filesize, detectmosaic)
    272 if multifile and self.header.file_part and isinstance(arg, basestring):
    273     # open master file instead
    274     self._fh.close()
--> 275     name, _ = match_filename(arg)
    276     self._fh = FileHandle(name)
    277     self.header = Segment(self._fh, 0).data()

File ~\mambaforge\envs\bio39\lib\site-packages\czifile\czifile.py:1148, in match_filename(filename)
   1145 match = re.search(r'(.*?)(?:\((\d+)\))?\.czi$',
   1146                   filename, re.IGNORECASE).groups()
   1147 name = match[0] + '.czi'
-> 1148 part = int(match[1]) if len(match) > 1 else 0
   1149 return name, part

TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'

If you want to reproduce this, you can download the example image here.

Thanks!

Best, Robert

[cgohlke]

Thanks for reporting.

The file is part of a multi-file series but does not follow the CZI multi-file naming schema (section 3.5.1 of the CZI specification). The current version of czifile is not os.Path aware, so it does not attempt to parse the file name. Since multi-file handling was never fully implemented, it's probably best to remove all of it.