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Merged
merged 4 commits into from
Feb 21, 2020
Merged

ENH: Re-sync examples with nipype #2

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714868d
RF: Drop NUMPY_MMAP constant
effigies Feb 20, 2020
1a85711
RF: Import workflows from niflow-nipype1-workflows
effigies Feb 20, 2020
37a7b2b
DOC/STY: Cleanups
effigies Feb 20, 2020
b4ebdc3
CI: Force reinstall neurdflib to fix prov
effigies Feb 20, 2020
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23 changes: 17 additions & 6 deletions .circleci/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
# Generated by Neurodocker version 0.4.2-6-g18c7a8b
# Timestamp: 2019-01-04 21:09:17 UTC
# Your version: 0.6.0+5.g74cb187.dirty Latest version: 0.6.0
# Generated by Neurodocker version 0.6.0+5.g74cb187.dirty
# Timestamp: 2020-02-20 20:39:36 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
Expand All @@ -23,11 +24,17 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
&& conda config --system --prepend channels conda-forge \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
&& sync && conda clean -tipsy && sync \
&& sync && conda clean --all && sync \
&& conda install -y -q --name base \
'python=3.6' \
'nipype' \
&& sync && conda clean -tipsy && sync
"python=3.6" \
"nipype" \
&& sync && conda clean --all && sync \
&& bash -c "source activate base \
&& pip install --no-cache-dir \
'--force-reinstall' \
'neurdflib'" \
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@satra Just a heads up that it doesn't look like our strategy of placing neurdflib after prov in either PyPI or conda-forge metadata is sufficient to ensure order.

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thanks - will have to figure out something.

&& rm -rf ~/.cache/pip/* \
&& sync

COPY [".", "/niflow-src"]

Expand All @@ -51,6 +58,10 @@ RUN echo '{ \
\n "conda_install": [ \
\n "python=3.6", \
\n "nipype" \
\n ], \
\n "pip_install": [ \
\n "--force-reinstall", \
\n "neurdflib" \
\n ] \
\n } \
\n ], \
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9 changes: 3 additions & 6 deletions package/niflow/nipype1/examples/dmri_camino_dti.py
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Expand Up @@ -35,30 +35,27 @@

def get_vox_dims(volume):
import nibabel as nb
from nipype.utils import NUMPY_MMAP
if isinstance(volume, list):
volume = volume[0]
nii = nb.load(volume, mmap=NUMPY_MMAP)
nii = nb.load(volume)
hdr = nii.header
voxdims = hdr.get_zooms()
return [float(voxdims[0]), float(voxdims[1]), float(voxdims[2])]


def get_data_dims(volume):
import nibabel as nb
from nipype.utils import NUMPY_MMAP
if isinstance(volume, list):
volume = volume[0]
nii = nb.load(volume, mmap=NUMPY_MMAP)
nii = nb.load(volume)
hdr = nii.header
datadims = hdr.get_data_shape()
return [int(datadims[0]), int(datadims[1]), int(datadims[2])]


def get_affine(volume):
import nibabel as nb
from nipype.utils import NUMPY_MMAP
nii = nb.load(volume, mmap=NUMPY_MMAP)
nii = nb.load(volume)
return nii.affine


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14 changes: 5 additions & 9 deletions package/niflow/nipype1/examples/dmri_connectivity.py
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Expand Up @@ -26,9 +26,8 @@

* http://db.tt/1vx4vLeP

Along with `Camino <http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Main.HomePage>`_,
`Camino-Trackvis <http://www.nitrc.org/projects/camino-trackvis/>`_, `FSL <http://www.fmrib.ox.ac.uk/fsl/>`_,
and `Freesurfer <http://surfer.nmr.mgh.harvard.edu/>`_, you must also have the Connectome File Format
Along with Camino_, Camino2Trackvis_, FSL_, and FreeSurfer_,
you must also have the Connectome File Format
library installed as well as the Connectome Mapper.

These are written by Stephan Gerhard and can be obtained from:
Expand Down Expand Up @@ -73,30 +72,27 @@

def get_vox_dims(volume):
import nibabel as nb
from nipype.utils import NUMPY_MMAP
if isinstance(volume, list):
volume = volume[0]
nii = nb.load(volume, mmap=NUMPY_MMAP)
nii = nb.load(volume)
hdr = nii.header
voxdims = hdr.get_zooms()
return [float(voxdims[0]), float(voxdims[1]), float(voxdims[2])]


def get_data_dims(volume):
import nibabel as nb
from nipype.utils import NUMPY_MMAP
if isinstance(volume, list):
volume = volume[0]
nii = nb.load(volume, mmap=NUMPY_MMAP)
nii = nb.load(volume)
hdr = nii.header
datadims = hdr.get_data_shape()
return [int(datadims[0]), int(datadims[1]), int(datadims[2])]


def get_affine(volume):
import nibabel as nb
from nipype.utils import NUMPY_MMAP
nii = nb.load(volume, mmap=NUMPY_MMAP)
nii = nb.load(volume)
return nii.affine


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8 changes: 4 additions & 4 deletions package/niflow/nipype1/examples/dmri_connectivity_advanced.py
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Expand Up @@ -58,12 +58,12 @@
import inspect
import os
import os.path as op # system functions
from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
from nipype.workflows.dmri.camino.connectivity_mapping import select_aparc_annot
from niflow.nipype1.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
from niflow.nipype1.workflows.dmri.camino.connectivity_mapping import select_aparc_annot
from nipype.utils.misc import package_check
import warnings
from nipype.workflows.dmri.connectivity.nx import create_networkx_pipeline, create_cmats_to_csv_pipeline
from nipype.workflows.smri.freesurfer import create_tessellation_flow
from niflow.nipype1.workflows.dmri.connectivity.nx import create_networkx_pipeline, create_cmats_to_csv_pipeline
from niflow.nipype1.workflows.smri.freesurfer import create_tessellation_flow

try:
package_check('cmp')
Expand Down
2 changes: 1 addition & 1 deletion package/niflow/nipype1/examples/dmri_dtk_dti.py
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Expand Up @@ -26,7 +26,7 @@
import nipype.interfaces.utility as util # utility
import nipype.pipeline.engine as pe # pypeline engine
import os # system functions
from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
from niflow.nipype1.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
"""
Confirm package dependencies are installed. (This is only for the
tutorial, rarely would you put this in your own code.)
Expand Down
2 changes: 1 addition & 1 deletion package/niflow/nipype1/examples/dmri_dtk_odf.py
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Expand Up @@ -26,7 +26,7 @@
import nipype.interfaces.utility as util # utility
import nipype.pipeline.engine as pe # pypeline engine
import os # system functions
from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
from niflow.nipype1.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
"""
Confirm package dependencies are installed. (This is only for the
tutorial, rarely would you put this in your own code.)
Expand Down
2 changes: 1 addition & 1 deletion package/niflow/nipype1/examples/dmri_fsl_dti.py
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Expand Up @@ -25,7 +25,7 @@
import nipype.interfaces.utility as util # utility
import nipype.pipeline.engine as pe # pypeline engine
import os # system functions
from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline,\
from niflow.nipype1.workflows.dmri.fsl.dti import create_eddy_correct_pipeline,\
create_bedpostx_pipeline
"""
Confirm package dependencies are installed. (This is only for the
Expand Down
4 changes: 2 additions & 2 deletions package/niflow/nipype1/examples/dmri_group_connectivity_camino.py
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Expand Up @@ -57,8 +57,8 @@
import nipype.interfaces.freesurfer as fs # freesurfer
import os.path as op # system functions
import cmp
from nipype.workflows.dmri.camino.group_connectivity import create_group_connectivity_pipeline
from nipype.workflows.dmri.connectivity.group_connectivity import (
from niflow.nipype1.workflows.dmri.camino.group_connectivity import create_group_connectivity_pipeline
from niflow.nipype1.workflows.dmri.connectivity.group_connectivity import (
create_merge_networks_by_group_workflow,
create_merge_group_networks_workflow,
create_average_networks_by_group_workflow)
Expand Down
4 changes: 2 additions & 2 deletions package/niflow/nipype1/examples/dmri_group_connectivity_mrtrix.py
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Expand Up @@ -57,8 +57,8 @@
import nipype.interfaces.freesurfer as fs # freesurfer
import os.path as op # system functions
import cmp
from nipype.workflows.dmri.mrtrix.group_connectivity import create_group_connectivity_pipeline
from nipype.workflows.dmri.connectivity.group_connectivity import (
from niflow.nipype1.workflows.dmri.mrtrix.group_connectivity import create_group_connectivity_pipeline
from niflow.nipype1.workflows.dmri.connectivity.group_connectivity import (
create_merge_network_results_by_group_workflow,
create_merge_group_network_results_workflow,
create_average_networks_by_group_workflow)
Expand Down
18 changes: 16 additions & 2 deletions package/niflow/nipype1/examples/dmri_preprocessing.py
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Expand Up @@ -32,13 +32,13 @@
from nipype.interfaces import ants
"""
Load specific nipype's workflows for preprocessing of dMRI data:
:class:`nipype.workflows.dmri.preprocess.epi.all_peb_pipeline`,
:class:`niflow.nipype1.workflows.dmri.preprocess.epi.all_peb_pipeline`,
as data include a *b0* volume with reverse encoding direction
(*P>>>A*, or *y*), in contrast with the general acquisition encoding
that is *A>>>P* or *-y* (in RAS systems).
"""

from nipype.workflows.dmri.fsl.artifacts import all_fsl_pipeline, remove_bias
from niflow.nipype1.workflows.dmri.fsl.artifacts import all_fsl_pipeline, remove_bias
"""
Map field names into individual subject runs
"""
Expand Down Expand Up @@ -130,6 +130,7 @@
"""

bias = remove_bias()

"""
Connect nodes in workflow
=========================
Expand All @@ -148,10 +149,23 @@
(prep, bias, [('outputnode.out_file', 'inputnode.in_file'),
('outputnode.out_mask', 'inputnode.in_mask')]),
(datasource, bias, [('bvals', 'inputnode.in_bval')])])

"""
Run the workflow as command line executable
"""

if __name__ == '__main__':
wf.run()
wf.write_graph()

"""
References
----------

.. [Jeurissen2014] Jeurissen et al., Multi-tissue constrained spherical deconvolution
for improved analysis of multi-shell diffusion MRI data.
NeuroImage 103:411--426. 2014.
doi:`10.1016/j.neuroimage.2014.07.061
<https://doi.org/10.1016/j.neuroimage.2014.07.061>`__.

"""
4 changes: 2 additions & 2 deletions package/niflow/nipype1/examples/dmri_tbss_nki.py
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Expand Up @@ -10,8 +10,8 @@

"""

from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
from nipype.workflows.dmri.fsl.tbss import create_tbss_non_FA, create_tbss_all
from niflow.nipype1.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
from niflow.nipype1.workflows.dmri.fsl.tbss import create_tbss_non_FA, create_tbss_all
"""
Tell python where to find the appropriate functions.
"""
Expand Down
3 changes: 1 addition & 2 deletions package/niflow/nipype1/examples/fmri_ants_openfmri.py
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Expand Up @@ -38,10 +38,9 @@
from nipype.interfaces.io import FreeSurferSource
import nipype.interfaces.utility as niu
from nipype.interfaces.utility import Merge, IdentityInterface
from nipype.workflows.fmri.fsl import (create_featreg_preproc,
from niflow.nipype1.workflows.fmri.fsl import (create_featreg_preproc,
create_modelfit_workflow,
create_fixed_effects_flow)
from nipype.utils import NUMPY_MMAP

config.enable_provenance()
version = 0
Expand Down
3 changes: 1 addition & 2 deletions package/niflow/nipype1/examples/fmri_fsl.py
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Expand Up @@ -101,11 +101,10 @@ def pickfirst(files):

def getmiddlevolume(func):
from nibabel import load
from nipype.utils import NUMPY_MMAP
funcfile = func
if isinstance(func, list):
funcfile = func[0]
_, _, _, timepoints = load(funcfile, mmap=NUMPY_MMAP).shape
_, _, _, timepoints = load(funcfile).shape
return int(timepoints / 2) - 1


Expand Down
2 changes: 1 addition & 1 deletion package/niflow/nipype1/examples/fmri_fsl_feeds.py
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Expand Up @@ -22,7 +22,7 @@
from nipype.interfaces import fsl # fsl
from nipype.pipeline import engine as pe # pypeline engine
from nipype.algorithms import modelgen as model # model generation
from nipype.workflows.fmri.fsl import (
from niflow.nipype1.workflows.fmri.fsl import (
create_featreg_preproc, create_modelfit_workflow, create_reg_workflow)
from nipype.interfaces.base import Bunch
"""
Expand Down
2 changes: 1 addition & 1 deletion package/niflow/nipype1/examples/fmri_fsl_reuse.py
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Expand Up @@ -28,7 +28,7 @@
import nipype.algorithms.modelgen as model # model generation
import nipype.algorithms.rapidart as ra # artifact detection

from nipype.workflows.fmri.fsl import (create_featreg_preproc,
from niflow.nipype1.workflows.fmri.fsl import (create_featreg_preproc,
create_modelfit_workflow,
create_fixed_effects_flow)
"""
Expand Down
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