akhanf

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)

akhanf

#!/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

akhanf

rule screenshot_unfold:
    input:
        surf_gii=bids(
            root=work,
            datatype="surf",
            suffix="midthickness.surf.gii",
            desc="nostruct",
            space="unfold",
            hemi="{hemi}",

akhanf

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

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:

akhanf

from snakebids.utils.snakemake_io import glob_wildcards

configfile: 'config.yml'

subject,session,task = glob_wildcards(config['bold'])

print(subject)
print(session)
print(task)

akhanf

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

akhanf

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')

akhanf

from os.path import join

configfile: 'config.yml'

container: config['container']


rule create_protocol:
    input:
        bvec = join(config['in_dir'],config['bvec']),

akhanf

input_images = ['A','B','C']
shell('touch {input_images}')

max_iters = 4

#need this to make sure iterations don't go below 0!
wildcard_constraints:
    iteration="[0-9]+"