Ali Khan akhanf
akhanf
/ write_to_openstack.py
Last active
November 27, 2025 15:02
ome-zarr-py writing to openstack example
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| import numpy as np | |
| import zarr | |
| import s3fs | |
| from zarr.storage import FsspecStore | |
| from ome_zarr.writer import write_image | |
| import os | |
| # Create data | |
| size_xy = 128 |
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| import zarr | |
| group = zarr.open_group('/home/UWO/akhan488/graham/lightsheet/test_eed/SPIMprep/bids/sub-M1A1Te3/micr/sub-M1A1Te3_sample-brain_acq-imaris_SPIM.ome.zarr.zip',mode='r') | |
| from cvpl_tools.ome_zarr.napari.add import group as add_group | |
| add_group(viewer=viewer,zarr_group=group,merge_channels=False) |
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| #!/usr/bin/env bash | |
| set -euo pipefail | |
| shopt -s expand_aliases | |
| alias osf='uvx --from osfclient osf' | |
| CACHE_DIR=".osfcli.cache" | |
| CACHE_FILE="${CACHE_DIR}/filelist.txt" | |
| CACHE_TTL=3600 |
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| rule screenshot_unfold: | |
| input: | |
| surf_gii=bids( | |
| root=work, | |
| datatype="surf", | |
| suffix="midthickness.surf.gii", | |
| desc="nostruct", | |
| space="unfold", | |
| hemi="{hemi}", |
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| subjects,=glob_wildcards('sub-{subject}/qc.html') | |
| print(subjects) | |
| snaps,=glob_wildcards(f'sub-{subjects[0]}/{{snap}}.png') | |
| print(snaps) | |
| rule all: | |
| input: | |
| expand('{ext}s/{snap}.{ext}',ext=['gif','pdf'],snap=snaps) |
akhanf
/ example_calc_surf_metrics.py
Created
September 28, 2022 21:07
Hippunfold - calculating mean surface metrics over subfields
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| import nibabel as nib | |
| subjects = ['01'] | |
| hemis = ['L','R'] | |
| subfield_labels={1:'Sub',2:'CA1',3:'CA2',4:'CA3',5:'CA4'} | |
| hipp_metrics = ['thickness','gyrification'] | |
| dentate_metrics = ['gyrification'] | |
| with open('table.csv','w') as f: |
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| from snakebids.utils.snakemake_io import glob_wildcards | |
| configfile: 'config.yml' | |
| subject,session,task = glob_wildcards(config['bold']) | |
| print(subject) | |
| print(session) | |
| print(task) |
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| bids_dir: '/path/to/bids_dir' | |
| output_dir: '/path/to/output_dir' | |
| #enable printing debug statements during parsing -- disable if generating dag visualization | |
| debug: False | |
| derivatives: False #will search in bids/derivatives if True; can also be path(s) to derivatives datasets | |
| #list of analysis levels in the bids app | |
| analysis_levels: &analysis_levels |
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| def bids (root=None, prefix=None, suffix=None, subject=None, session=None,include_subject_dir=True,include_session_dir=True,**entities): | |
| """Helper function for generating bids paths for snakemake workflows | |
| File path is of the form: | |
| [root]/[sub-{subject}]/[ses-{session]/[prefix]_[sub-{subject}]_[ses-{session}]_[{key}-{val}_ ... ]_[suffix] | |
| root -- root folder to include in the path (e.g. 'results')) | |
| prefix -- string to prepend to the file name (typically not defined, unless you want tpl-{tpl}, or a subfolder) | |
| suffix -- bids suffix including extension (e.g. 'T1w.nii.gz') |
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