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 .h5 file from BMicro #21

Closed juko1 closed 2 years ago

juko1 commented 2 years ago

Unhandled exception in Impose version 0.1.1: Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/impose/gui/colocalize.py", line 174, 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 105, 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 145, 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 38, in load channels, meta = suffix_dictpath.suffix File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/impose/formats/fmt_h5.py", line 18, 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-0.h5.zip

raimund-schluessler commented 2 years ago

As discussed recently, this is not yet implemented, so expected to fail. The corresponding issue is #18.