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@PlethoraChutney
Created October 5, 2023 19:51
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Un-downsample a symmetry-expanded particle stack
from cryosparc.tools import CryoSPARC
import numpy as np
cs = CryoSPARC(
# you'll need env variables here, or just set stuff directly
)
cs.test_connection()
# we will filter fullsize_particles so that only the intersection with
# downsampled particles are retained. ctf, alignments, etc. will all
# still come from fullsize_particles
#
# if you want alignments from the downsampled job, you have to change
# pixel size and scale the shifts, which we don't do here. It's not as
# simple as just changing the passthrough!
select_project = "P294"
select_workspace = "W2"
job_fullsize_particles = "J31"
job_downsampled_particles = "J34"
ds_particles = cs.find_job(select_project, job_downsampled_particles).load_output(
"particles"
)
full_particles = cs.find_job(select_project, job_fullsize_particles).load_output(
"particles"
)
# pseudoparticles are uniquely identified by the combination
# of their source UID and symmetry expansion index
full_particles.add_fields(["intersect_field"], ["str"])
full_particles["intersect_field"] = [
f"{r['sym_expand/src_uid']}.{r['sym_expand/idx']}" for r in full_particles.rows()
]
ds_particles.add_fields(["intersect_field"], ["str"])
ds_particles["intersect_field"] = [
f"{r['sym_expand/src_uid']}.{r['sym_expand/idx']}" for r in ds_particles.rows()
]
# this is a little slow --- lots of string comparisons
intersection = full_particles.query(
{"intersect_field": ds_particles["intersect_field"]}
)
cs.save_external_result(
select_project,
select_workspace,
intersection,
type="particle",
name="sym_expand_intersection",
slots=["blob"],
passthrough=(job_fullsize_particles, "particles"),
title="Filtered Subset",
)
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