[JUNGFRAU] [Correct] Fix index location for ROI instrument output
Description
Yohei told me that accessing JUNGFRAU ROI data was broken - doing this resulted in an error:
run = open_run(3495, 7, data='proc')
run['FXE_XAD_JF1M/ROIPROC/JNGFR02:output']['data.roi1.data'].ndarray()Traceback
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
/software/anaconda3/2021.05/lib/python3.8/site-packages/extra_data/file_access.py in get_index(self, source, group)
314 try:
--> 315 return self._index_cache[(source, group)]
316 except KeyError:
KeyError: ('FXE_XAD_JF1M/ROIPROC/JNGFR02:output', 'data')
During handling of the above exception, another exception occurred:
KeyError Traceback (most recent call last)
/tmp/ipykernel_199459/308304994.py in <module>
----> 1 run['FXE_XAD_JF1M/ROIPROC/JNGFR02:output']['data.roi1.data'].ndarray()
/software/anaconda3/2021.05/lib/python3.8/site-packages/extra_data/keydata.py in ndarray(self, roi, out)
227 roi = (roi,)
228
--> 229 req_shape = self.shape[:1] + roi_shape(self.entry_shape, roi)
230
231 if out is None:
/software/anaconda3/2021.05/lib/python3.8/site-packages/extra_data/keydata.py in shape(self)
88 Finding the shape may require getting index data from several files
89 """
---> 90 return (sum(c.total_count for c in self._data_chunks),) + self.entry_shape
91
92 def select_trains(self, trains):
/software/anaconda3/2021.05/lib/python3.8/site-packages/extra_data/keydata.py in _data_chunks(self)
56 """An ordered list of chunks containing data"""
57 if self._cached_chunks is None:
---> 58 self._cached_chunks = sorted(
59 self._find_chunks(), key=lambda c: c.train_ids[0]
60 )
/software/anaconda3/2021.05/lib/python3.8/site-packages/extra_data/keydata.py in _find_chunks(self)
34 continue
35
---> 36 firsts, counts = file.get_index(self.source, self._key_group)
37
38 # Of trains in this file, which are in selection
/software/anaconda3/2021.05/lib/python3.8/site-packages/extra_data/file_access.py in get_index(self, source, group)
315 return self._index_cache[(source, group)]
316 except KeyError:
--> 317 ix = self._read_index(source, group)
318 self._index_cache[(source, group)] = ix
319 return ix
/software/anaconda3/2021.05/lib/python3.8/site-packages/extra_data/file_access.py in _read_index(self, source, group)
325 """
326 ntrains = len(self.train_ids)
--> 327 ix_group = self.file['/INDEX/{}/{}'.format(source, group)]
328 firsts = ix_group['first'][:ntrains]
329 if 'count' in ix_group:
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
/software/anaconda3/2021.05/lib/python3.8/site-packages/h5py/_hl/group.py in __getitem__(self, name)
303 raise ValueError("Invalid HDF5 object reference")
304 elif isinstance(name, (bytes, str)):
--> 305 oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
306 else:
307 raise TypeError("Accessing a group is done with bytes or str, "
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/h5o.pyx in h5py.h5o.open()
KeyError: "Unable to open object (object 'data' doesn't exist)"I'm hoping we can do this as a hotfix.
How Has This Been Tested?
I ran a new calibration of the same data with the command line, and tried the same thing:
run2 = RunDirectory('/gpfs/exfel/data/scratch/kluyvert/jf-calib-p3495-r7/')
run2['FXE_XAD_JF1M/ROIPROC/JNGFR02:output']['data.roi1.data'].ndarray()This gave me an array, not an error.
Types of changes
- Bug fix (non-breaking change which fixes an issue)
Checklist:
- My code follows the code style of this project.