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FIX: Correctly pin niworkflows branch and use new interface #25

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Merged
merged 3 commits into from
May 11, 2020
Merged

FIX: Correctly pin niworkflows branch and use new interface #25

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1ddc0c1
FIX: Correctly pin niworkflows branch and use new interface
oesteban May 10, 2020
aa2ae98
enh: better pin specific commit
oesteban May 10, 2020
3d09d34
Update brainextraction.py
eilidhmacnicol May 11, 2020
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76 changes: 25 additions & 51 deletions nirodents/workflows/brainextraction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,30 +3,30 @@
"""Nipype translation of ANTs' workflows."""

# general purpose
import os
from multiprocessing import cpu_count
from pkg_resources import resource_filename as pkgr_fn
from packaging.version import parse as parseversion, Version
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@oesteban oesteban May 10, 2020

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cleaning up some stuff that is not ever used anymore

from warnings import warn

# nipype
from nipype.pipeline import engine as pe
from nipype.interfaces import utility as niu
from nipype.interfaces.ants import N4BiasFieldCorrection, Atropos
from nipype.interfaces.ants.utils import AI # , ImageMath, ResampleImageBySpacing,
from nipype.interfaces.ants.utils import AI
from nipype.interfaces.afni import MaskTool
from nipype.interfaces.io import DataSink

# niworkflows
from niworkflows.interfaces.ants import ImageMath
from niworkflows.utils.images import resample_by_spacing
from niworkflows.interfaces.images import RegridToZooms
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@oesteban oesteban May 10, 2020

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this is the new interface

from niworkflows.interfaces.nibabel import ApplyMask
from niworkflows.interfaces.fixes import (
FixHeaderRegistration as Registration,
FixHeaderApplyTransforms as ApplyTransforms)

from templateflow.api import get as get_template

LOWRES_ZOOMS = (0.4, 0.4, 0.4)


def init_rodent_brain_extraction_wf(
atropos_model=None,
atropos_refine=True,
Expand Down Expand Up @@ -71,25 +71,20 @@ def init_rodent_brain_extraction_wf(
tpl_brain_mask = get_template(in_template, resolution=debug + 1, desc='cerebrum', suffix='mask')

# resample template and target
res_tmpl = pe.Node(niu.Function(function=res_by_spc,
input_names=['in_file'], output_names=['out_file']), name='res_tmpl')
if tpl_target_path:
res_tmpl.inputs.in_file = tpl_target_path
res_tmpl = pe.Node(RegridToZooms(
in_file=tpl_target_path, zooms=LOWRES_ZOOMS), name="res_tmpl")

res_target = pe.Node(niu.Function(function=res_by_spc,
input_names=['in_file'], output_names=['out_file']), name='res_target')
res_target2 = pe.Node(niu.Function(function=res_by_spc,
input_names=['in_file'], output_names=['out_file']), name='res_target2')
res_target = pe.Node(RegridToZooms(zooms=LOWRES_ZOOMS), name="res_target")
res_target2 = pe.Node(RegridToZooms(zooms=LOWRES_ZOOMS), name="res_target2")

dil_mask = pe.Node(MaskTool(), name = 'dil_mask')
dil_mask.inputs.outputtype = 'NIFTI_GZ'
dil_mask.inputs.dilate_inputs = '2'
dil_mask.inputs.fill_holes = True
dil_mask = pe.Node(MaskTool(
outputtype='NIFTI_GZ', dilate_inputs='2', fill_holes=True),
name='dil_mask')

# truncate target intensity for N4 correction
trunc_opts = {"T1w": "0.005 0.999 256", "T2w": "0.01 0.999 256"}
trunc = pe.MapNode(ImageMath(operation='TruncateImageIntensity', op2=trunc_opts[bids_suffix]),
name='truncate_images', iterfield=['op1'])
name='truncate_images', iterfield=['op1'])

# Initial N4 correction
inu_n4 = pe.MapNode(
Expand All @@ -104,7 +99,7 @@ def init_rodent_brain_extraction_wf(
if tpl_target_path:
lap_tmpl.inputs.op1 = tpl_target_path
lap_target = pe.Node(ImageMath(operation='Laplacian', op2='0.4'), name='lap_target')

norm_lap_tmpl = pe.Node(ImageMath(operation='Normalize'), name='norm_lap_tmpl')
norm_lap_target = pe.Node(ImageMath(operation='Normalize'), name='norm_lap_target')

Expand All @@ -129,9 +124,6 @@ def init_rodent_brain_extraction_wf(
warp_mask = pe.Node(ApplyTransforms(
interpolation='Linear', invert_transform_flags=True), name='warp_mask')

fixed_mask_trait = 'fixed_image_masks'
moving_mask_trait = 'moving_image_masks'

# Set up initial spatial normalization
init_settings_file = f'data/brainextraction_{init_normalization_quality}_{modality}.json'
init_norm = pe.Node(Registration(from_file=pkgr_fn(
Expand All @@ -145,12 +137,12 @@ def init_rodent_brain_extraction_wf(
inu_n4_final = pe.MapNode(
N4BiasFieldCorrection(
dimension=3, save_bias=True, copy_header=True,
n_iterations=[50] * 5, convergence_threshold=1e-7,
n_iterations=[50] * 5, convergence_threshold=1e-7,
bspline_fitting_distance=bspline_fitting_distance,
rescale_intensities = True, shrink_factor=4),
rescale_intensities=True, shrink_factor=4),
n_procs=omp_nthreads, name='inu_n4_final', iterfield=['input_image'])

split_init_transforms = pe.Node(niu.Split(splits=[1,1]), name='split_init_transforms')
split_init_transforms = pe.Node(niu.Split(splits=[1, 1]), name='split_init_transforms')
mrg_init_transforms = pe.Node(niu.Merge(2), name='mrg_init_transforms')

# Use more precise transforms to warp mask to subject space
Expand All @@ -159,10 +151,8 @@ def init_rodent_brain_extraction_wf(
name='warp_mask_final')

# morphological closing of warped mask
close_mask = pe.Node(MaskTool(), name = 'close_mask')
close_mask.inputs.outputtype = 'NIFTI_GZ'
close_mask.inputs.dilate_inputs = '5 -5'
close_mask.inputs.fill_holes = True
close_mask = pe.Node(MaskTool(outputtype='NIFTI_GZ', dilate_inputs='5 -5', fill_holes=True),
name='close_mask')

# Use subject-space mask to skull-strip subject
skullstrip_tar = pe.Node(ApplyMask(), name='skullstrip_tar')
Expand All @@ -179,7 +169,7 @@ def init_rodent_brain_extraction_wf(
mem_gb=mem_gb)
final_norm.inputs.float = use_float

split_final_transforms = pe.Node(niu.Split(splits=[1,1]), name='split_final_transforms')
split_final_transforms = pe.Node(niu.Split(splits=[1, 1]), name='split_final_transforms')
mrg_final_transforms = pe.Node(niu.Merge(2), name='mrg_final_transforms')

warp_seg_mask = pe.Node(ApplyTransforms(
Expand All @@ -188,8 +178,8 @@ def init_rodent_brain_extraction_wf(
if tpl_brain_mask:
warp_seg_mask.inputs.input_image = tpl_brain_mask

warp_seg_labels =pe.Node(ApplyTransforms(
interpolation='Linear', invert_transform_flags=[False, True]),
warp_seg_labels = pe.Node(ApplyTransforms(
interpolation='Linear', invert_transform_flags=[False, True]),
name='warp_seg_labels')
if tpl_tissue_labels:
warp_seg_labels.inputs.input_image = tpl_tissue_labels
Expand Down Expand Up @@ -287,7 +277,7 @@ def init_rodent_brain_extraction_wf(
(inputnode, res_target, [('in_files', 'in_file')]),
(inputnode, lap_target, [('in_files', 'op1')]),
(lap_target, norm_lap_target, [('output_image', 'op1')]),
(norm_lap_target, mrg_target, [('output_image', 'in2')]),
(norm_lap_target, mrg_target, [('output_image', 'in2')]),
(res_target, mrg_target, [('out_file', 'in1')]),

(res_tmpl, mrg_tmpl, [('out_file', 'in1')]),
Expand All @@ -309,7 +299,7 @@ def init_rodent_brain_extraction_wf(

# normalisation inputs
(mrg_tmpl, init_norm, [('out', 'fixed_image')]),
(mrg_target, init_norm, [('out', 'moving_image')]),
(mrg_target, init_norm, [('out', 'moving_image')]),
(dil_mask, init_norm, [('out_file', 'fixed_image_masks')]),
(warp_mask, init_norm, [('output_image', 'moving_image_masks')]),
(init_aff, init_norm, [('output_transform', 'initial_moving_transform')]),
Expand Down Expand Up @@ -347,26 +337,10 @@ def init_rodent_brain_extraction_wf(
(skullstrip_tar, segment, [('out_file', 'intensity_images')]),
(warp_seg_labels, segment, [('output_image', 'prior_image')]),
(warp_seg_mask, segment, [('output_image', 'mask_image')]),
])
])
return wf

def _pop(in_files):
if isinstance(in_files, (list, tuple)):
return in_files[0]
return in_files

def res_by_spc(in_file, out_file = None):
import os.path as op
from niworkflows.utils.images import resample_by_spacing
import nibabel as nib
resampled = resample_by_spacing(in_file, (0.4, 0.4, 0.4), clip = False)

if out_file is None:
fname, ext = op.splitext(op.basename(in_file))
if ext == '.gz':
fname, ext2 = op.splitext(fname)
ext = ext2 + ext
out_file = op.abspath('{}_resampled{}'.format(fname, ext))

nib.save(resampled, out_file)
return out_file
8 changes: 2 additions & 6 deletions setup.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -23,15 +23,14 @@ install_requires =
attrs
nibabel >= 3.0.1
nipype @ git+https://github.com/nipy/nipype.git@master
niworkflows @ git+https://github.com/nipreps/niworkflows.git@master
templateflow >= 0.5.2
niworkflows @ git+https://github.com/oesteban/niworkflows.git@6d2286268d09215045161e534d0bf84dc34f38fc
templateflow ~= 0.6
test_requires =
coverage < 5
pytest >= 4.4
pytest-cov
pytest-xdist >= 1.28
packages = find:
include_package_data = True

[options.entry_points]
console_scripts =
Expand Down Expand Up @@ -59,8 +58,6 @@ docs =
%(doc)s
duecredit =
duecredit
pointclouds =
pyntcloud
style =
flake8 >= 3.7.0
test =
Expand All @@ -73,7 +70,6 @@ tests =
all =
%(doc)s
%(duecredit)s
%(pointclouds)s
%(style)s
%(test)s

Expand Down