Wgh (what does it stand for)

Troubleshooting
1

What is wgh? I am getting the following error:

Loading Dataset ... 
---- Loading File Set. Type: star Path: /raid/kaelber/cryosparc/run/bulk/./raid/raphael/combined_star.star
     Loaded meta data for 94706 images.
     Found raw data for 94706 images.
Traceback (most recent call last):

File “/raid/kaelber/cryosparc/cryosparc-compute/sparcjob.py”, line 110, in
dataset = dataio.dataset_factory(current_dataset_params, do_cache=False, do_datasign_estimation=False)
File “/raid/kaelber/cryosparc/cryosparc-compute/dataio/init.py”, line 18, in dataset_factory
do_cache=do_cache)
File “/raid/kaelber/cryosparc/cryosparc-compute/dataio/load.py”, line 70, in filesets_into_dataset
“%s is not the same in all images!” % k
AssertionError: wgh is not the same in all images!

2

Could not find this anywhere in the documentation but load.py contains:
assert ‘rlnAmplitudeContrast’ in labels or ‘wgh’ in dataset.mscope_params, “The input star file does not contain rlnAmplitudeContrast and ampitude contrast (wgh) was not set in dataset creation.”

Apparently all particles must have the same amplitude contrast. For particles that have a varying amplitude contrast, you must override the amplitude contrast in the star file by manually specifying an amplitude contrast to be applied to all particles in the “New Dataset” -> “Configure” and this allows particles to be imported. So, problem solved.

3

Hi Jason,

Glad you figured that out - wgh is indeed the amplitude contrast.
I can’t recall if there is a good reason that all particles should have the same amplitude contrast… I think we can probably remove that restriction. I’ve created an issue ticket for that.

Thanks,
Ali

4