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GuckLab / impose

Align microscopy images using custom-defined structural patterns and superimpose those on data from other imaging modalities.
GNU General Public License v3.0
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Cannot open file #41

Closed juko1 closed 2 years ago

juko1 commented 2 years ago

Unhandled exception in Impose version 0.2.3: Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/impose/gui/colocalize.py", line 177, in on_add_data self.add_paths(paths) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/impose/gui/colocalize.py", line 108, in add_paths self.session_scheme.append(pp) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/impose/session.py", line 155, in append data_source = DataSource(path) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/impose/data.py", line 43, in init self._initialize_from_path(path) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/impose/data.py", line 89, in _initialize_from_path data_channels, meta_orig = load(path) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/impose/formats/init.py", line 45, in load channels, meta = suffix_dictpath.suffix File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/impose/formats/fmt_bm_bmlab.py", line 64, in loadh5 axes = np.string(h5[k0].attrs["axisOrder"]).decode("utf-8") File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/h5py/_hl/attrs.py", line 56, in getitem attr = h5a.open(self._id, self._e(name)) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5a.pyx", line 80, in h5py.h5a.open KeyError: "Can't open attribute (can't locate attribute: 'axisOrder')"

Brillouin-7.h5.zip

raimund-schluessler commented 2 years ago

@juko1 Thanks, but you have already posted this error multiple times in #35 and #38. Also, the session file from bmlab is not enough to reproduce this, because Impose always also needs the rawdata file to open the Brillouin data. I will enhance the error messages to state this properly. In the meantime, please check that you have the raw data files alongside your session files either in a RawData / EvalData structure, or in the same folder with the session file having the same file name plus a .session part.

juko1 commented 2 years ago

I'm in the process of uploading the rawdata and will send you the link. The last time the solution was to update bmalb, which I already did. I have a RawData / EvalData structure.

raimund-schluessler commented 2 years ago

The problem is solved.