Error reading file with links in NXdata

[DanPorter]

Example NXxas file downloaded from:

https://pynxxas.readthedocs.io/en/latest/

Reading the file with:

hdfmap.create_nexus_map('KEK_PFdata.h5')

Gives error:

Traceback (most recent call last):
  File "C:\Users\grp66007\OneDrive - Diamond Light Source Ltd\PythonProjects\hdfmap\examples\nxxas_error_may25.py", line 10, in <module>
    m = hdfmap.create_nexus_map(f)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\grp66007\OneDrive - Diamond Light Source Ltd\PythonProjects\hdfmap\src\hdfmap\file_functions.py", line 55, in create_nexus_map
    hdf_map.populate(hdf, groups=groups, default_entry_only=default_entry_only)
  File "C:\Users\grp66007\OneDrive - Diamond Light Source Ltd\PythonProjects\hdfmap\src\hdfmap\nexus.py", line 388, in populate
    self.generate_image_data_from_nxdetector()
  File "C:\Users\grp66007\OneDrive - Diamond Light Source Ltd\PythonProjects\hdfmap\src\hdfmap\nexus.py", line 309, in generate_image_data_from_nxdetector
    image_ndim = len(self.scannables_shape()) + 2 if self.scannables else 3
                     ^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\grp66007\OneDrive - Diamond Light Source Ltd\PythonProjects\hdfmap\src\hdfmap\hdfmap_class.py", line 379, in scannables_shape
    return self.datasets[path].shape
           ~~~~~~~~~~~~~^^^^^^
KeyError: '/fe010/plot/energy'

[DanPorter]

Analysis

Error arises because in this file, scannables are generated by the default NXdata and the fields within /fe010/plot:NXdata are both h5py.SoftLinks.

Scannables generated by HdfMap.generate_scannables_from_group require datasets within a group to exist in HdfMap.datasets:

hdfmap/src/hdfmap/hdfmap_class.py

Lines 415 to 420 in 5567093

	array_size = min(hdf_group[name].size for name in dataset_names)
	self._populate(hdf_group, root=hdf_path, recursive=False)
	self.scannables = {
	name: build_hdf_path(hdf_path, name)
	for name in dataset_names if hdf_group[name].size == array_size
	}

However HdfMap._populate doesn't add links to datasets:

hdfmap/src/hdfmap/hdfmap_class.py

Lines 317 to 318 in 5567093

	elif isinstance(obj, h5py.Dataset) and not isinstance(link, h5py.SoftLink):
	self._store_dataset(obj, hdf_path, name)

Potential solution - remove requirement for dataset not to be a link.

[DanPorter]

Issue fixed in #19 and additional tests for this file have been added.