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Merge pull request #229 from FCP-INDI/dev-1.7.0
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ci-build committed Jul 23, 2020
1 parent 9d9dd7f commit bf98823
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98 changes: 84 additions & 14 deletions C-PAC/.circleci/config.yml
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Original file line number Diff line number Diff line change
@@ -1,36 +1,93 @@
version: 2
jobs:
pytest:
docker:
- image: fcpindi/c-pac:python3
pytest-docker:
machine: true
steps:
- checkout
- attach_workspace:
# Must be absolute path or relative path from working_directory
at: /home/circleci/
- run:
name: "Set Python Version"
command: |
pyenv install 3.6.3
pyenv global 3.6.3
- run:
name: Get Sample BIDS Data
command: git clone https://github.com/bids-standard/bids-examples.git
- run:
name: pytest
command: |
pip install -r dev/circleci_data/requirements.txt
coverage run -m pytest --junitxml=test-results/junit.xml --doctest-ignore-import-errors --continue-on-collection-errors --doctest-modules --ignore=CPAC/cwas/tests/test_mdmr_cython.py dev/circleci_data/
coverage report --include="./*" --omit="/home/circleci/.local/*"
coverage html
docker load < cpac-docker-image.tar.gz
docker run -dit -P -v /home/circleci/project/test-results:/code/test-results -v /home/circleci/project/htmlcov:/code/htmlcov --entrypoint=/bin/bash --name docker_test fcpindi/c-pac:${CIRCLE_BRANCH//\//_}
docker exec docker_test /bin/bash ./code/dev/circleci_data/test_in_image.sh
- store_test_results:
path: test-results
- store_artifacts:
path: test-results
- store_artifacts:
path: htmlcov
no_output_timeout: 5h
pytest-singularity:
machine: true
steps:
- attach_workspace:
# Must be absolute path or relative path from working_directory
at: /home/circleci/
- run:
name: "Set Python Version"
command: |
pyenv install 3.6.3
pyenv global 3.6.3
- run:
name: test_install
command: |
sudo apt-get update && sudo apt-get install flawfinder squashfs-tools uuid-dev libuuid1 libffi-dev libssl-dev libssl1.0.0 libarchive-dev libgpgme11-dev libseccomp-dev -y
cd singularity
./autogen.sh
./configure --prefix=/usr/local --sysconfdir=/etc
make
sudo make install
cd ..
pip install -r dev/circleci_data/requirements.txt
coverage run -m pytest --junitxml=test-results/junit.xml --continue-on-collection-errors dev/circleci_data/test_install.py
build:
machine: true
steps:
- checkout
- run:
name: build
name: "Set Python Version"
command: |
pyenv install 3.6.3
pyenv global 3.6.3
- run:
name: build-docker
command: |
docker build -t cpac:${CIRCLE_BRANCH//\//_} .
docker save cpac:${CIRCLE_BRANCH//\//_} | gzip > cpac-docker-image.tar.gz
docker build -t fcpindi/c-pac:${CIRCLE_BRANCH//\//_} .
docker save fcpindi/c-pac:${CIRCLE_BRANCH//\//_} | gzip > cpac-docker-image.tar.gz
# Persist the specified paths (workspace/echo-output) into the workspace for use in downstream job.
- run:
name: local-registry
command: docker run -d -p 5000:5000 --restart=always --name registry registry:2
- run:
name: build-singularity
command: |
sudo apt-get update && sudo apt-get install flawfinder squashfs-tools uuid-dev libuuid1 libffi-dev libssl-dev libssl1.0.0 libarchive-dev libgpgme11-dev libseccomp-dev -y
git clone -b 2.5.2 https://github.com/sylabs/singularity
cd singularity
./autogen.sh
./configure --prefix=/usr/local --sysconfdir=/etc
make
sudo make install
cd ..
docker load < cpac-docker-image.tar.gz
docker tag fcpindi/c-pac:${CIRCLE_BRANCH//\//_} localhost:5000/fcpindi/c-pac:${CIRCLE_BRANCH//\//_}
docker push localhost:5000/fcpindi/c-pac:${CIRCLE_BRANCH//\//_}
SINGULARITY_NOHTTPS=1 singularity build C-PAC-CI.simg docker://localhost:5000/fcpindi/c-pac:${CIRCLE_BRANCH//\//_}
- store_artifacts:
path: cpac-docker-image.tar.gz
- store_artifacts:
path: C-PAC-CI.simg
destination: cpac-singularity-image.simg
- persist_to_workspace:
# Must be an absolute path, or relative path from working_directory. This is a directory on the container which is
# taken to be the root directory of the workspace.
Expand All @@ -43,6 +100,11 @@ jobs:
- attach_workspace:
# Must be absolute path or relative path from working_directory
at: /home/circleci/
- run:
name: "Set Python Version"
command: |
pyenv install 3.6.3
pyenv global 3.6.3
- run:
name: ≟
command: python dev/circleci_data/scripts/compare.py
Expand All @@ -52,6 +114,11 @@ jobs:
- attach_workspace:
# Must be absolute path or relative path from working_directory
at: /home/circleci/
- run:
name: "Set Python Version"
command: |
pyenv install 3.6.3
pyenv global 3.6.3
- run:
name: Run C-PAC
command: |
Expand Down Expand Up @@ -84,6 +151,9 @@ workflows:
filters:
branches:
only: feature/auto-heatmaps
unit_tests:
jobs:
- pytest
- pytest-docker:
requires:
- build
- pytest-singularity:
requires:
- build
46 changes: 35 additions & 11 deletions C-PAC/CPAC/anat_preproc/anat_preproc.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
# -*- coding: utf-8 -*-
import os
from nipype.interfaces import afni
from nipype.interfaces import ants
from nipype.interfaces import fsl
Expand All @@ -9,6 +10,23 @@
from CPAC.utils.datasource import create_check_for_s3_node
from CPAC.unet.function import predict_volumes

def patch_cmass_output(lst, index=0):
"""
Parameters
----------
lst : list of tuples
output of afni.CenterMass()
index : int
index in the list of tuples
Returns
-------
tuple
one set of center of mass coordinates
"""
if len(lst) <= index:
raise IndexError("lst index out of range")
return lst[index]

def create_anat_preproc(method='afni', already_skullstripped=False, config=None, wf_name='anat_preproc'):
"""The main purpose of this workflow is to process T1 scans. Raw mprage file is deobliqued, reoriented
Expand Down Expand Up @@ -82,15 +100,20 @@ def create_anat_preproc(method='afni', already_skullstripped=False, config=None,

preproc = pe.Workflow(name=wf_name)

inputnode = pe.Node(util.IdentityInterface(
fields=['anat', 'brain_mask']), name='inputspec')
inputnode = pe.Node(util.IdentityInterface(fields=['anat',
'brain_mask',
'template_brain_only_for_anat',
'template_skull_for_anat',
'template_cmass']),
name='inputspec')

outputnode = pe.Node(util.IdentityInterface(fields=['refit',
'reorient',
'skullstrip',
'brain',
'brain_mask']),
name='outputspec')
'brain_mask',
'center_of_mass']),
name='outputspec')

anat_deoblique = pe.Node(interface=afni.Refit(),
name='anat_deoblique')
Expand Down Expand Up @@ -241,6 +264,7 @@ def create_anat_preproc(method='afni', already_skullstripped=False, config=None,

preproc.connect(anat_reorient, 'out_file',
anat_skullstrip, 'in_file')

preproc.connect(skullstrip_args, 'expr',
anat_skullstrip, 'args')

Expand Down Expand Up @@ -295,7 +319,7 @@ def create_anat_preproc(method='afni', already_skullstripped=False, config=None,
anat_skullstrip = pe.Node(
interface=fsl.BET(), name='anat_skullstrip')
anat_skullstrip.inputs.output_type = 'NIFTI_GZ'

preproc.connect(anat_reorient, 'out_file',
anat_skullstrip, 'in_file')

Expand Down Expand Up @@ -422,29 +446,28 @@ def create_anat_preproc(method='afni', already_skullstripped=False, config=None,
# flirt -v -dof 6 -in brain.nii.gz -ref NMT_SS_0.5mm.nii.gz -o brain_rot2atl -omat brain_rot2atl.mat -interp sinc
# TODO: antsRegistration -z 0 -d 3 -r [NMT_SS_0.5mm.nii.gz,brain.nii.gz,0] -o [transform,brain_rot2atl.nii.gz,brain_inv_rot2atl.nii.gz] -t Rigid[0.1] -m MI[NMT_SS_0.5mm.nii.gz,brain.nii.gz,1,32,Regular,0.25] -c [1000x500x250x100,1e-08,10] -s 3.0x2.0x1.0x0.0 -f 8x4x2x1 -u 1 -t Affine[0.1] -m MI[NMT_SS_0.5mm.nii.gz,brain.nii.gz,1,32,Regular,0.25] -c [1000x500x250x100,1e-08,10] -s 3.0x2.0x1.0x0.0 -f 8x4x2x1 -u 1
native_brain_to_template_brain = pe.Node(interface=fsl.FLIRT(), name='native_brain_to_template_brain')
native_brain_to_template_brain.inputs.reference = config.template_brain_only_for_anat
native_brain_to_template_brain.inputs.dof = 6
native_brain_to_template_brain.inputs.interp = 'sinc'
preproc.connect(unet_masked_brain, 'out_file', native_brain_to_template_brain, 'in_file')
preproc.connect(inputnode, 'template_brain_only_for_anat', native_brain_to_template_brain, 'reference')

# flirt -in head.nii.gz -ref NMT_0.5mm.nii.gz -o head_rot2atl -applyxfm -init brain_rot2atl.mat
# TODO: antsApplyTransforms -d 3 -i head.nii.gz -r NMT_0.5mm.nii.gz -n Linear -o head_rot2atl.nii.gz -v -t transform1Rigid.mat -t transform2Affine.mat -t transform0DerivedInitialMovingTranslation.mat
native_head_to_template_head = pe.Node(interface=fsl.FLIRT(), name='native_head_to_template_head')
native_head_to_template_head.inputs.reference = config.template_skull_for_anat
native_head_to_template_head.inputs.apply_xfm = True
preproc.connect(anat_reorient, 'out_file', native_head_to_template_head, 'in_file')
preproc.connect(native_brain_to_template_brain, 'out_matrix_file', native_head_to_template_head, 'in_matrix_file')

preproc.connect(inputnode, 'template_skull_for_anat', native_head_to_template_head, 'reference')

# fslmaths NMT_SS_0.5mm.nii.gz -bin templateMask.nii.gz
template_brain_mask = pe.Node(interface=fsl.maths.MathsCommand(), name='template_brain_mask')
template_brain_mask.inputs.in_file = config.template_brain_only_for_anat
template_brain_mask.inputs.args = '-bin'
preproc.connect(inputnode, 'template_brain_only_for_anat', template_brain_mask, 'in_file')

# ANTS 3 -m CC[head_rot2atl.nii.gz,NMT_0.5mm.nii.gz,1,5] -t SyN[0.25] -r Gauss[3,0] -o atl2T1rot -i 60x50x20 --use-Histogram-Matching --number-of-affine-iterations 10000x10000x10000x10000x10000 --MI-option 32x16000
ants_template_head_to_template = pe.Node(interface=ants.Registration(), name='template_head_to_template')
ants_template_head_to_template.inputs.metric = ['CC']
ants_template_head_to_template.inputs.metric_weight = [1,5]
ants_template_head_to_template.inputs.moving_image = config.template_skull_for_anat
ants_template_head_to_template.inputs.transforms = ['SyN']
ants_template_head_to_template.inputs.transform_parameters = [(0.25,)]
ants_template_head_to_template.inputs.interpolation = 'NearestNeighbor'
Expand All @@ -453,7 +476,7 @@ def create_anat_preproc(method='afni', already_skullstripped=False, config=None,
ants_template_head_to_template.inputs.shrink_factors = [[4,2,1]]
ants_template_head_to_template.inputs.convergence_threshold = [1.e-8]
preproc.connect(native_head_to_template_head, 'out_file', ants_template_head_to_template, 'fixed_image')

preproc.connect(inputnode, 'template_skull_for_anat', ants_template_head_to_template, 'moving_image')
# antsApplyTransforms -d 3 -i templateMask.nii.gz -t atl2T1rotWarp.nii.gz atl2T1rotAffine.txt -r brain_rot2atl.nii.gz -o brain_rot2atl_mask.nii.gz
template_head_transform_to_template = pe.Node(interface=ants.ApplyTransforms(), name='template_head_transform_to_template')
template_head_transform_to_template.inputs.dimension = 3
Expand Down Expand Up @@ -491,3 +514,4 @@ def create_anat_preproc(method='afni', already_skullstripped=False, config=None,
preproc.connect(refined_brain, 'out_file', outputnode, 'brain')

return preproc

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