oesteban

nose.config: INFO: Ignoring files matching ['^\\.', '^_', '^setup\\.py$']
nose.plugins.cover: INFO: Coverage report will include only packages: ['nipype']
nose.selector: INFO: /root/src/nipype/nipype/interfaces/tests/use_resources is executable; skipped
/root/src/nipype/nipype/workflows/dmri/mrtrix/group_connectivity.py:15: UserWarning: cmp not installed
  warnings.warn('cmp not installed')
Doctest: nipype.algorithms.mesh ... ok
Doctest: nipype.algorithms.metrics ... ok
Doctest: nipype.algorithms.metrics.ErrorMap ... ok
Doctest: nipype.algorithms.metrics.FuzzyOverlap ... ok
Doctest: nipype.algorithms.metrics.Overlap ... ok

oesteban

#!/opt/conda/bin/python
"""
Convert files to json objects uploadable to GitHub gists using:

curl -v -H "Authorization: token <insert token here>" -X POST https://api.github.com/gists --data @<filename.json>

"""

import sys
import json

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#!/usr/bin/env python
import re
import sys
from builtins import open

squote_exp = re.compile(r"(?P<ms>u?'(?:[^'\n\r\\]|(?:'')|(?:\\x[0-9a-fA-F]+)|(?:\\.))*')",
                        re.UNICODE)

def add_upref(m):
    ms = m.group('ms')

oesteban

ANTS : http://picsl.upenn.edu/ANTS/ c3d : http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D

export PATH=/software/ANTS-dev:$PATH

c3d_affine_tool -ref [A] -src [B] bbreg.mat -fsl2ras -oitk fsl2antsAffine.txt

WarpImageMultiTransform 3 [B] [C] -R [D] [A_Warp].nii.gz [A_Affine].txt fsl2antsAffine.txt

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CMDLINE python mriqc data/ out/ participant --participant_label 50052 --mem_gb 64 --verbose-reports --n_procs 10 --ants-nthreads 68 -f --profile -m T1w
MEM 0.816406 1490359481.9571
MEM 27.171875 1490359485.5077
MEM 28.769531 1490359488.9861
MEM 40.691406 1490359492.4732
MEM 55.683594 1490359495.9580
MEM 67.445312 1490359499.4542
MEM 71.191406 1490359502.9444
MEM 80.781250 1490359506.4395
MEM 86.386719 1490359509.9397

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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  IEEE.bst  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Bibliography Syle file for articles according to IEEE instructions
% [email protected]     <22-JUN-93>
% modified from unsrt.bib. Contributions by Richard H. Roy

ENTRY
  { address
    author
    booktitle
    chapter

oesteban

#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
from glob import glob
import numpy as np
import json
import datalad

files = glob('sub-*/func/*_bold.json')

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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
import re
import datetime
import subprocess as sp
from textwrap import indent

def get_parser():

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Top 1 lines
#1: traits/has_traits.py:3008: 1.3 KiB
    if not meta_eval( getattr( trait, meta_name ) ):37 other: 14.1 KiB
Total allocated size: 15.3 KiB

Top 1 lines
#1: testnipype.py:50: 8388608.0 KiB
    large_str = ' ' * (8 * 1024**3)94 other: 362.5 KiB
Total allocated size: 8388970.6 KiB

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>>> from pympler import asizeof
... from nipype.interfaces.fsl import BET
... from niworkflows.interfaces.masks import BETRPT
... from nipype.pipeline import engine as pe
... from niworkflows.nipype.pipeline import engine as pe2

>>> bet_old = BET(in_file="/home/oesteban/Data/openfmri/ds000001/sub-01/anat/sub-01_T1w.nii.gz")
>>> bet_rpt = BETRPT(in_file="/home/oesteban/Data/openfmri/ds000001/sub-01/anat/sub-01_T1w.nii.gz", generate_report=True)
>>> asizeof.asizeof(bet_old)
3808