#!/usr/bin/env python
from __future__ import print_function
from util import logfmt, TemporaryDirectory
from plumbum import local, cli, FG
from plumbum.cmd import ConvertBetweenFileFormats
from util.scripts import activateTensors_py
import logging
logger = logging.getLogger()
logging.basicConfig(level=logging.DEBUG, format=logfmt(__file__))
def nrrd(f):
return '.nhdr' in f.suffixes or '.nrrd' in f.suffixes
class App(cli.Application):
"""Runs tract_querier. Output is <out>/*.vtk"""
ukf = cli.SwitchAttr(
['-i', '--in'],
cli.ExistingFile,
help='tractography file (.vtk or .vtk.gz), must be in RAS space',
mandatory=True)
fsindwi = cli.SwitchAttr(
['-f', '--fsindwi'],
cli.ExistingFile,
help='Freesurfer labelmap in DWI space (nrrd or nifti)',
mandatory=True)
query = cli.SwitchAttr(['-q', '--query'],
help='tract_querier query file (e.g. wmql-2.0.qry)',
from __future__ import print_function
from util import logfmt
from plumbum import local, cli, FG
from plumbum.cmd import unu, ConvertBetweenFileFormats, ComposeMultiTransform, antsApplyTransforms
from util.antspath import antsRegistrationSyN_sh
from util import TemporaryDirectory
from itertools import zip_longest
import pandas as pd
import sys
import psutil
N_CPU = str(psutil.cpu_count())
import logging
logger = logging.getLogger()
logging.basicConfig(level=logging.INFO, format=logfmt(__file__))
ANTSJOINTFUSION_PARAMS = [
'--search-radius', 5, '--patch-radius', 3, '--patch-metric', 'PC',
'--constrain-nonnegative', 1, '--alpha', 0.4, '--beta', 3.0
]
def grouper(iterable, n, fillvalue=None):
"Collect data into fixed-length chunks or blocks"
# grouper('ABCDEFG', 3, 'x') --> ABC DEF Gxx
if n == 1:
return [iterable]
args = [iter(iterable)] * n
return zip_longest(fillvalue=fillvalue, *args)