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PlethoraChutney / myheader.py
Created April 4, 2024 20:55
Header to read 16-bit MRC files
#!/usr/bin/env python
import sys
import struct
with open(sys.argv[1], "rb") as f:
[nx, ny, nz] = [x[0] for x in struct.iter_unpack('i', f.read(12))]
# don't care about mode, start
_ = f.read(16)
#!/usr/bin/env python
from cryosparc.tools import CryoSPARC
import json
import argparse
import numpy as np
# you would need to enter your information for CryoSPARC here
with open('/u/rposert/instance-info.json', 'r') as f:
instance_info = json.load(f)
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@PlethoraChutney
PlethoraChutney / revert_symmexp_particles.py
Created October 5, 2023 19:51
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
return {
Span = function (elem)
if quarto.doc.is_format('docx') then
if elem.classes:includes('aside') then
return ""
else
return elem
end
end
end
#!/usr/bin/env python
import numpy as np
import pandas as pd
import umap
import sys
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.preprocessing import StandardScaler
from cryosparc.dataset import Dataset