Bug report: Import particles does not read provided pixel size

Import and Export
1

Hi, in version 2.15, when I try to import a particle star file with “ignore raw data”, it fails with this error. Looks like pixel size is not set, even though I explicitly povide it in the import job window.

 File "cryosparc2_master/cryosparc2_compute/run.py", line 85, in cryosparc2_compute.run.main
  File "cryosparc2_compute/jobs/imports/run.py", line 310, in run_import_particles
    particles.data['alignments3D/psize_A'] = blobdf['psize_A'] # assume shifts are in pixel units on this psize
  File "/apps/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 2139, in __getitem__
    return self._getitem_column(key)
  File "/apps/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 2146, in _getitem_column
    return self._get_item_cache(key)
  File "/apps/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pandas/core/generic.py", line 1842, in _get_item_cache
    values = self._data.get(item)
  File "/apps/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pandas/core/internals.py", line 3838, in get
    loc = self.items.get_loc(item)
  File "/apps/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pandas/core/indexes/base.py", line 2524, in get_loc
    return self._engine.get_loc(self._maybe_cast_indexer(key))
  File "pandas/_libs/index.pyx", line 117, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/index.pyx", line 139, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 1265, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 1273, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'psize_A'

If “ignore raw data” is not selected, the import job goes to completion.

2

Hi @rbehrouzi,

Can you take a look at this post which includes a workaround for now? This looks like a bug in the Import Particles job, we’ll investigate this and try to release a fix in the next version of cryoSPARC.

3

Thanks Stephan. I needed the pose data so couldn’t go that route. Luckily, it works fine when the raw data are present, so I could work around it.