Particle Import Error

Import and Export
1

Dear all,

I’m having errors when trying to import particle stacks into cryosparc with the following error log:

Traceback (most recent call last):
  File "cryosparc2_master/cryosparc2_compute/run.py", line 78, in cryosparc2_compute.run.main (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_master/cryosparc2_compute/run.c:3954)
  File "cryosparc2_compute/jobs/imports/run.py", line 286, in run_import_particles
    particles.data['alignments3D/psize_A'] = blobdf['psize_A'] # assume shifts are in pixel units on this psize
  File "/home/hongjiang/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pandas/core/frame.py", line 2139, in __getitem__
    return self._getitem_column(key)
  File "/home/hongjiang/cryosparc/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 "/home/hongjiang/cryosparc/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 "/home/hongjiang/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pandas/core/internals.py", line 3838, in get
    loc = self.items.get_loc(item)
  File "/home/hongjiang/cryosparc/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'

It only happens when I ignore the raw data in other words only import the coordinates and link to source micrograph.

Thank you all!

2

I’m also getting this error – did you ever find a solution?

thanks!

3

I was able to get this to work by making a simplified version of my .star file for import, containing just the micrograph name and X/Y coords. eg:

data_images

loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnMicrographName #3

Of course this means that you’re losing any shifts and angles for you particles, however.

Other than changing the .star file, I was following the process described here: