Error reading files saved by py4DSTEM

[matao1984]

Hi,

I was trying to read some files saved by py4DSTEM and got the following error:

s = ncem_reader.read(file)
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
File /opt/anaconda3/envs/temcompanion/lib/python3.12/site-packages/emdfile/classes/utils.py:39, in _get_class(grp)
     38 classname = grp.attrs['python_class']
---> [39](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/temcompanion/lib/python3.12/site-packages/emdfile/classes/utils.py:39) __class__ = lookup[classname]
     40 return __class__

KeyError: 'Calibration'

During handling of the above exception, another exception occurred:

Exception                                 Traceback (most recent call last)
Cell In[5], [line 1](vscode-notebook-cell:?execution_count=5&line=1)
----> [1](vscode-notebook-cell:?execution_count=5&line=1) s = ncem_reader.read(file)

File /opt/anaconda3/envs/temcompanion/lib/python3.12/site-packages/emdfile/read.py:110, in read(filepath, emdpath, tree, **legacy_options)
    108         nodegroup = nodegroup[name]
    109 # Read the root
--> [110](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/temcompanion/lib/python3.12/site-packages/emdfile/read.py:110) root = Root.from_h5(rootgroup)
    111 # if this is all that was requested, return
    112 if nodegroup is rootgroup and tree is False:

File /opt/anaconda3/envs/temcompanion/lib/python3.12/site-packages/emdfile/classes/node.py:635, in Node.from_h5(cls, group)
    632 if md.attrs['python_class'] != 'Metadata':
    633     # and attempt promotion
    634     try:
--> [635](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/temcompanion/lib/python3.12/site-packages/emdfile/classes/node.py:635)         cls = _get_class(md)
    636         inst = cls( name=basename(md.name) )
    637         inst._params.update(node.metadata[basename(md.name)]._params)

File /opt/anaconda3/envs/temcompanion/lib/python3.12/site-packages/emdfile/classes/utils.py:42, in _get_class(grp)
     40     return __class__
     41 except KeyError:
---> [42](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/temcompanion/lib/python3.12/site-packages/emdfile/classes/utils.py:42)     raise Exception(f"Unknown classname {classname}")

Exception: Unknown classname Calibration

The file was saved by the recent release of py4DSTEM which is described as "NCEM EMD v1.0" format. However, it seems it cannot handle "Calibration" that was saved by py4DSTEM.

[sezelt]

Do you have py4DSTEM installed in the environment?

[matao1984]

I realized that it actually needs py4DSTEM and also needs import py4DSTEM to be able to work. However, I am looking for an easier way to load data from this format to implement in TemCompanion. Is it possible?

[sezelt]

Because of the way that custom data types are implemented, I think it is necessary to have whatever package defined the data layout installed in the environment.