def test_pipeline_warpping(self):
""" Method to test the xml description to pipeline on the fly warpping.
"""
pipeline = get_process_instance("capsul.utils.test.xml_pipeline.xml")
self.assertTrue(isinstance(pipeline, Pipeline))
for node_name in ["", "p1", "p2"]:
self.assertTrue(node_name in pipeline.nodes)
def __init__(self, process, iterative_parameters):
super(ProcessIteration, self).__init__()
self.process = get_process_instance(process)
self.regular_parameters = set()
self.iterative_parameters = set(iterative_parameters)
# Check that all iterative parameters are valid process parameters
user_traits = self.process.user_traits()
for parameter in self.iterative_parameters:
if parameter not in user_traits:
raise ValueError('Cannot iterate on parameter %s '
'that is not a parameter of process %s'
% (parameter, self.process.id))
# Create iterative process parameters by copying process parameter
# and changing iterative parameters to list
for name, trait in user_traits.iteritems():
if name in iterative_parameters:
self.add_trait(name, List(trait, output=trait.output,
optional=trait.optional))
else:
self.regular_parameters.add(name)
self.add_trait(name, trait)
# copy initial value of the underlying process to self
# Note: should be this be done via a links system ?
setattr(self, name, getattr(self.process, name))
def test_simple_run(self):
""" Method to test a simple 1 cpu call with the scheduler.
"""
# Configure the environment
study_config = StudyConfig(
modules=[],
use_smart_caching=True,
output_directory=self.outdir,
number_of_cpus=1,
generate_logging=True,
use_scheduler=True)
# Create pipeline
pipeline = get_process_instance(self.pipeline_name)
pipeline.date_in_filename = True
# Set pipeline input parameters
dicom_dataset = get_sample_data("dicom")
dcmfolder = os.path.join(self.outdir, "dicom")
if not os.path.isdir(dcmfolder):
os.makedirs(dcmfolder)
shutil.copy(dicom_dataset.barre, os.path.join(dcmfolder, "heart.dcm"))
pipeline.source_dir = dcmfolder
# View pipeline
if 0:
from capsul.qt_gui.widgets import PipelineDevelopperView
from PySide import QtGui
app = QtGui.QApplication(sys.argv)
view1 = PipelineDevelopperView(pipeline)
view1.show()
app.exec_()
# Execute the pipeline in the configured study
study_config.run(pipeline)
def pilot_gdti_estimation():
"""
Generalized diffusion tensor estimation
=======================================
"""
# System import
import os
import sys
import datetime
import PySide.QtGui as QtGui
# CAPSUL import
from capsul.qt_gui.widgets import PipelineDevelopperView
from capsul.study_config.study_config import StudyConfig
from capsul.process.loader import get_process_instance
"""
Study configuration
-------------------
We first define the working directory and guarantee this folder exists on
the file system:
"""
working_dir = "/volatile/nsap/clindmri/gdti"
if not os.path.isdir(working_dir):
os.makedirs(working_dir)
"""
And then define the study configuration (here we activate the smart
caching module that will be able to remember which process has already been
processed):
"""
study_config = StudyConfig(modules=["SmartCachingConfig"],
use_smart_caching=True,
output_directory=working_dir)
# Create pipeline
start_time = datetime.datetime.now()
print "Start Pipeline Creation", start_time
pipeline = get_process_instance("clindmri.estimation.gdti.xml")
print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)
# View pipeline
if 0:
app = QtGui.QApplication(sys.argv)
view1 = PipelineDevelopperView(pipeline)
view1.show()
app.exec_()
del view1
# Set pipeline input parameters
pipeline.dfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.nii.gz"
pipeline.bvalfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.bval"
pipeline.bvecfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.bvec"
pipeline.order = 2
pipeline.odf = False
print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)
# Execute the pipeline in the configured study
study_config.run(pipeline, verbose=1)
def test_process_warpping(self):
""" Method to test the function to process on the fly warpping.
"""
process = get_process_instance(
"capsul.process.test.test_load_from_description.to_warp_func")
self.assertTrue(isinstance(process, Process))
for input_name in ["parameter1", "parameter2", "parameter3"]:
self.assertTrue(input_name in process.traits(output=False))
for output_name in ["output1", "output2"]:
self.assertTrue(output_name in process.traits(output=True))
process()
self.assertEqual(process.output1, 1)
self.assertEqual(process.output2, "done")
modules=["MatlabConfig", "SPMConfig", "NipypeConfig", "FSLConfig",
"FreeSurferConfig", "SmartCachingConfig"],
matlab_exec="/neurospin/local/bin/matlab",
spm_directory="/i2bm/local/spm8-6313",
use_matlab=True,
use_spm=True,
use_nipype=True,
use_smart_caching=True,
output_directory="/volatile/nsap/catalogue/spm_first_level/")
print "Done in {0} seconds".format(datetime.datetime.now() - start_time)
# Create pipeline
start_time = datetime.datetime.now()
print "Start Pipeline Creation", start_time
pipeline = get_process_instance(
"caps.nsap.functional_statistic.pipeline.spm_first_level_pipeline.xml")
print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)
# Set pipeline input parameters
start_time = datetime.datetime.now()
print "Start Parametrization", start_time
localizer_dataset = get_sample_data("localizer")
pipeline.behavioral_data = [localizer_dataset.onsets]
pipeline.fmri_sessions = [localizer_dataset.preproc_fmri]
pipeline.time_repetition = localizer_dataset.TR
pipeline.realignment_parameters = localizer_dataset.mouvment_parameters
pipeline.condition_name = "Conditions"
pipeline.onset_name = "Onsets"
pipeline.duration_name = "Durations"
pipeline.delimiter = ";"
def pilot_qa_fmri():
"""
Imports
-------
This code needs 'capsul' and 'mmutils' package in order to instanciate and
execute the pipeline and to get a toy dataset.
These packages are available in the 'neurospin' source list or in pypi.
"""
# Capsul import
from capsul.study_config.study_config import StudyConfig
from capsul.process.loader import get_process_instance
# Mmutils import
from mmutils.toy_datasets import get_sample_data
"""
Parameters
----------
The 'pipeline_name' parameter contains the location of the pipeline XML
description that will perform the DICOMs conversion, and the 'outdir' the
location of the pipeline's results: in this case a temporary directory.
"""
pipeline_name = "mmqa.fmri.fmri_quality_assurance_bbox.xml"
outdir = tempfile.mkdtemp()
"""
Capsul configuration
--------------------
A 'StudyConfig' has to be instantiated in order to execute the pipeline
properly. It enables us to define the results directory through the
'output_directory' attribute, the number of CPUs to be used through the
'number_of_cpus' attributes, and to specify that we want a log of the
processing step through the 'generate_logging'. The 'use_scheduler'
must be set to True if more than 1 CPU is used.
"""
study_config = StudyConfig(number_of_cpus=1,
generate_logging=True,
use_scheduler=True,
output_directory=outdir)
"""
Get the toy dataset
-------------------
The toy dataset is composed of a functional image that is downloaded
if it is necessary throught the 'get_sample_data' function and exported
locally.
"""
localizer_dataset = get_sample_data("localizer_extra")
"""
Pipeline definition
-------------------
The pipeline XML description is first imported throught the
'get_process_instance' method, and the resulting pipeline instance is
parametrized: in this example we decided to set the date in the converted
file name and we set two DICOM directories to be converted in Nifti
format.
"""
pipeline = get_process_instance(pipeline_name)
pipeline.image_file = localizer_dataset.fmri
pipeline.repetition_time = 2.0
pipeline.exclude_volume = []
pipeline.roi_size = 21
pipeline.score_file = os.path.join(outdir, "scores.json")
"""
Pipeline representation
-----------------------
By executing this block of code, a pipeline representation can be
displayed. This representation is composed of boxes connected to each
other.
"""
if 0:
from capsul.qt_gui.widgets import PipelineDevelopperView
from PySide import QtGui
app = QtGui.QApplication(sys.argv)
view1 = PipelineDevelopperView(pipeline)
view1.show()
app.exec_()
"""
Pipeline execution
------------------
Finally the pipeline is eecuted in the defined 'study_config'.
"""
study_config.run(pipeline)
"""
Access the result
-----------------
Display the computed scores
"""
scores_file = pipeline.scores_file
with open(scores_file, "r") as _file:
scores = json.load(_file)
for key, value in scores.iteritems():
print "{0} = {1}".format(key, value)
def pilot_qa_fmri():
"""
Imports
-------
This code needs 'capsul' and 'mmutils' package in order to instanciate and
execute the pipeline and to get a toy dataset.
These packages are available in the 'neurospin' source list or in pypi.
"""
# Capsul import
from capsul.study_config.study_config import StudyConfig
from capsul.process.loader import get_process_instance
# Mmutils import
from mmutils.toy_datasets import get_sample_data
"""
Parameters
----------
The 'pipeline_name' parameter contains the location of the pipeline XML
description that will perform the DICOMs conversion, and the 'outdir' the
location of the pipeline's results: in this case a temporary directory.
"""
pipeline_name = "mmqa.fmri.fmri_quality_assurance_bbox.xml"
outdir = tempfile.mkdtemp()
"""
Capsul configuration
--------------------
A 'StudyConfig' has to be instantiated in order to execute the pipeline
properly. It enables us to define the results directory through the
'output_directory' attribute, the number of CPUs to be used through the
'number_of_cpus' attributes, and to specify that we want a log of the
processing step through the 'generate_logging'. The 'use_scheduler'
must be set to True if more than 1 CPU is used.
"""
study_config = StudyConfig(
number_of_cpus=1,
generate_logging=True,
use_scheduler=True,
output_directory=outdir)
"""
Get the toy dataset
-------------------
The toy dataset is composed of a functional image that is downloaded
if it is necessary throught the 'get_sample_data' function and exported
locally.
"""
localizer_dataset = get_sample_data("localizer_extra")
"""
Pipeline definition
-------------------
The pipeline XML description is first imported throught the
'get_process_instance' method, and the resulting pipeline instance is
parametrized: in this example we decided to set the date in the converted
file name and we set two DICOM directories to be converted in Nifti
format.
"""
pipeline = get_process_instance(pipeline_name)
pipeline.image_file = localizer_dataset.fmri
pipeline.repetition_time = 2.0
pipeline.exclude_volume = []
pipeline.roi_size = 21
pipeline.score_file = os.path.join(outdir, "scores.json")
"""
Pipeline representation
-----------------------
By executing this block of code, a pipeline representation can be
displayed. This representation is composed of boxes connected to each
other.
"""
if 0:
from capsul.qt_gui.widgets import PipelineDevelopperView
from PySide import QtGui
app = QtGui.QApplication(sys.argv)
view1 = PipelineDevelopperView(pipeline)
view1.show()
app.exec_()
"""
Pipeline execution
------------------
Finally the pipeline is eecuted in the defined 'study_config'.
"""
study_config.run(pipeline)
"""
Access the result
-----------------
Display the computed scores
"""
scores_file = pipeline.scores_file
with open(scores_file, "r") as _file:
scores = json.load(_file)
for key, value in scores.iteritems():
print "{0} = {1}".format(key, value)
# Configure the environment
start_time = datetime.datetime.now()
print "Start Configuration", start_time
study_config = StudyConfig(
modules=["SmartCachingConfig"],
use_smart_caching=True,
output_directory="/volatile/nsap/catalogue/quality_assurance/")
print "Done in {0} seconds".format(datetime.datetime.now() - start_time)
# Create pipeline
start_time = datetime.datetime.now()
print "Start Pipeline Creation", start_time
pipeline = get_process_instance("mmqa.fmri.fmri_quality_assurance.xml")
print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)
# Set pipeline input parameters
start_time = datetime.datetime.now()
print "Start Parametrization", start_time
localizer_dataset = get_sample_data("localizer")
pipeline.image_file = localizer_dataset.fmri
pipeline.repetition_time = localizer_dataset.TR
print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)
# View pipeline
app = QtGui.QApplication(sys.argv)
view1 = PipelineDevelopperView(pipeline)
study_config = StudyConfig(
modules=["SmartCachingConfig"],
# matlab_exec="/neurospin/local/bin/matlab",
# spm_directory="/i2bm/local/spm8-6313",
# use_matlab=True,
# use_spm=True,
# use_nipype=True,
use_smart_caching=False,
output_directory="/volatile/nsap/frouin/my_caps_bank")
print "Done in {0} seconds".format(datetime.datetime.now() - start_time)
# Create pipeline
start_time = datetime.datetime.now()
print "Start Pipeline Creation", start_time
pipeline = get_process_instance("my_caps_bank.baby.two_nodes_pipeline.xml")
print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)
# View pipeline
#app = QtGui.QApplication(sys.argv)
#view1 = PipelineDevelopperView(pipeline)
#view1.show()
#app.exec_()
#del view1
# Set pipeline input parameters
#start_time = datetime.datetime.now()
#print "Start Parametrization", start_time
pipeline.thefilein = '/tmp/clone/tuyaux/data/toto.txt.gz'
#pipeline.offset = -1000
def pilot_dcm2nii():
"""
Imports
-------
This code needs 'capsul' and 'mmutils' package in order to instanciate and
execute the pipeline and to get a toy dataset.
These packages are available in the 'neurospin' source list or in pypi.
"""
import os
import sys
import shutil
import tempfile
from capsul.study_config.study_config import StudyConfig
from capsul.process.loader import get_process_instance
from mmutils.toy_datasets import get_sample_data
"""
Parameters
----------
The 'pipeline_name' parameter contains the location of the pipeline XML
description that will perform the DICOMs conversion, and the 'outdir' the
location of the pipeline's results: in this case a temporary directory.
"""
pipeline_name = "dcmio.dcmconverter.dcm_to_nii.xml"
outdir = tempfile.mkdtemp()
"""
Capsul configuration
--------------------
A 'StudyConfig' has to be instantiated in order to execute the pipeline
properly. It enables us to define the results directory through the
'output_directory' attribute, the number of CPUs to be used through the
'number_of_cpus' attributes, and to specify that we want a log of the
processing step through the 'generate_logging'. The 'use_scheduler'
must be set to True if more than 1 CPU is used.
"""
study_config = StudyConfig(
modules=[],
output_directory=outdir,
number_of_cpus=1,
generate_logging=True,
use_scheduler=True)
"""
Get the toy dataset
-------------------
The toy dataset is composed of a 3D heart dicom image that is downloaded
if it is necessary throught the 'get_sample_data' function and exported
locally in a 'heart.dcm' file.
"""
dicom_dataset = get_sample_data("dicom")
dcmfolder = os.path.join(outdir, "dicom")
if not os.path.isdir(dcmfolder):
os.makedirs(dcmfolder)
shutil.copy(dicom_dataset.barre, os.path.join(dcmfolder, "heart.dcm"))
"""
Pipeline definition
-------------------
The pipeline XML description is first imported throught the
'get_process_instance' method, and the resulting pipeline instance is
parametrized: in this example we decided to set the date in the converted
file name and we set two DICOM directories to be converted in Nifti
format.
"""
pipeline = get_process_instance(pipeline_name)
pipeline.date_in_filename = True
pipeline.dicom_directories = [dcmfolder, dcmfolder]
pipeline.additional_informations = [[("Provided by", "Neurospin@2015")],
[("Provided by", "Neurospin@2015"),
("TR", "1500")]]
pipeline.dcm_tags = [("TR", [("0x0018", "0x0080")]),
("TE", [("0x0018", "0x0081")])]
"""
Pipeline representation
-----------------------
By executing this block of code, a pipeline representation can be
displayed. This representation is composed of boxes connected to each
other.
"""
if 0:
from capsul.qt_gui.widgets import PipelineDevelopperView
from PySide import QtGui
app = QtGui.QApplication(sys.argv)
view1 = PipelineDevelopperView(pipeline)
view1.show()
app.exec_()
"""
Pipeline execution
------------------
Finally the pipeline is eecuted in the defined 'study_config'.
"""
study_config.run(pipeline)
"""
Access the result
-----------------
The 'nibabel' package is used to load the generated images. We display the
numpy array shape and the stored repetiton and echo times: in order
to load the 'descrip' image field we use the 'json' package.
"""
import json
import copy
import nibabel
generated_images = pipeline.filled_converted_files
for fnames in generated_images:
print(">>>", fnames, "...")
im = nibabel.load(fnames[0])
print("shape=", im.get_data().shape)
header = im.get_header()
a = str(header["descrip"])
a = a.strip()
description = json.loads(copy.deepcopy(a))
print("TE=", description["TE"])
print("TR=", description["TR"])
print("Provided by=", description["Provided by"])
def pilot_dcm2nii():
"""
Imports
-------
This code needs 'capsul' and 'mmutils' package in order to instanciate and
execute the pipeline and to get a toy dataset.
These packages are available in the 'neurospin' source list or in pypi.
"""
import os
import sys
import shutil
import tempfile
from capsul.study_config.study_config import StudyConfig
from capsul.process.loader import get_process_instance
from mmutils.toy_datasets import get_sample_data
"""
Parameters
----------
The 'pipeline_name' parameter contains the location of the pipeline XML
description that will perform the DICOMs conversion, and the 'outdir' the
location of the pipeline's results: in this case a temporary directory.
"""
pipeline_name = "dcmio.dcmconverter.dcm_to_nii.xml"
outdir = tempfile.mkdtemp()
"""
Capsul configuration
--------------------
A 'StudyConfig' has to be instantiated in order to execute the pipeline
properly. It enables us to define the results directory through the
'output_directory' attribute, the number of CPUs to be used through the
'number_of_cpus' attributes, and to specify that we want a log of the
processing step through the 'generate_logging'. The 'use_scheduler'
must be set to True if more than 1 CPU is used.
"""
study_config = StudyConfig(modules=[],
output_directory=outdir,
number_of_cpus=1,
generate_logging=True,
use_scheduler=True)
"""
Get the toy dataset
-------------------
The toy dataset is composed of a 3D heart dicom image that is downloaded
if it is necessary throught the 'get_sample_data' function and exported
locally in a 'heart.dcm' file.
"""
dicom_dataset = get_sample_data("dicom")
dcmfolder = os.path.join(outdir, "dicom")
if not os.path.isdir(dcmfolder):
os.makedirs(dcmfolder)
shutil.copy(dicom_dataset.barre, os.path.join(dcmfolder, "heart.dcm"))
"""
Pipeline definition
-------------------
The pipeline XML description is first imported throught the
'get_process_instance' method, and the resulting pipeline instance is
parametrized: in this example we decided to set the date in the converted
file name and we set two DICOM directories to be converted in Nifti
format.
"""
pipeline = get_process_instance(pipeline_name)
pipeline.date_in_filename = True
pipeline.dicom_directories = [dcmfolder, dcmfolder]
pipeline.additional_informations = [[("Provided by", "Neurospin@2015")],
[("Provided by", "Neurospin@2015"),
("TR", "1500")]]
pipeline.dcm_tags = [("TR", [("0x0018", "0x0080")]),
("TE", [("0x0018", "0x0081")])]
"""
Pipeline representation
-----------------------
By executing this block of code, a pipeline representation can be
displayed. This representation is composed of boxes connected to each
other.
"""
if 0:
from capsul.qt_gui.widgets import PipelineDevelopperView
from PySide import QtGui
app = QtGui.QApplication(sys.argv)
view1 = PipelineDevelopperView(pipeline)
view1.show()
app.exec_()
"""
Pipeline execution
------------------
Finally the pipeline is eecuted in the defined 'study_config'.
"""
study_config.run(pipeline)
"""
Access the result
-----------------
The 'nibabel' package is used to load the generated images. We display the
numpy array shape and the stored repetiton and echo times: in order
to load the 'descrip' image field we use the 'json' package.
"""
import json
import copy
import nibabel
generated_images = pipeline.filled_converted_files
for fnames in generated_images:
print(">>>", fnames, "...")
im = nibabel.load(fnames[0])
print("shape=", im.get_data().shape)
header = im.get_header()
a = str(header["descrip"])
a = a.strip()
description = json.loads(copy.deepcopy(a))
print("TE=", description["TE"])
print("TR=", description["TR"])
print("Provided by=", description["Provided by"])
def pilot_gdti_estimation():
"""
Generalized diffusion tensor estimation
=======================================
"""
# System import
import os
import sys
import datetime
import PySide.QtGui as QtGui
# CAPSUL import
from capsul.qt_gui.widgets import PipelineDevelopperView
from capsul.study_config.study_config import StudyConfig
from capsul.process.loader import get_process_instance
"""
Study configuration
-------------------
We first define the working directory and guarantee this folder exists on
the file system:
"""
working_dir = "/volatile/nsap/clindmri/gdti"
if not os.path.isdir(working_dir):
os.makedirs(working_dir)
"""
And then define the study configuration (here we activate the smart
caching module that will be able to remember which process has already been
processed):
"""
study_config = StudyConfig(
modules=["SmartCachingConfig"],
use_smart_caching=True,
output_directory=working_dir)
# Create pipeline
start_time = datetime.datetime.now()
print "Start Pipeline Creation", start_time
pipeline = get_process_instance("clindmri.estimation.gdti.xml")
print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)
# View pipeline
if 0:
app = QtGui.QApplication(sys.argv)
view1 = PipelineDevelopperView(pipeline)
view1.show()
app.exec_()
del view1
# Set pipeline input parameters
pipeline.dfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.nii.gz"
pipeline.bvalfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.bval"
pipeline.bvecfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.bvec"
pipeline.order = 2
pipeline.odf = False
print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)
# Execute the pipeline in the configured study
study_config.run(pipeline, verbose=1)
def pilot_fsl_preproc():
"""
FSL preprocessings
==================
"""
# System import
import os
import sys
import datetime
import PySide.QtGui as QtGui
# CAPSUL import
from capsul.qt_gui.widgets import PipelineDevelopperView
from capsul.study_config.study_config import StudyConfig
from capsul.process.loader import get_process_instance
"""
Study configuration
-------------------
We first define the working directory and guarantee this folder exists on
the file system:
"""
working_dir = "/volatile/nsap/clindmri/fslpreproc"
if not os.path.isdir(working_dir):
os.makedirs(working_dir)
"""
And then define the study configuration (here we activate the smart
caching module that will be able to remember which process has already been
processed):
"""
study_config = StudyConfig(
modules=["SmartCachingConfig", "FSLConfig", "MatlabConfig",
"SPMConfig", "NipypeConfig"],
use_smart_caching=True,
fsl_config="/etc/fsl/4.1/fsl.sh",
use_fsl=True,
output_directory=working_dir)
# Create pipeline
start_time = datetime.datetime.now()
print "Start Pipeline Creation", start_time
pipeline = get_process_instance("clindmri.preproc.fsl_preproc.xml")
print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)
# View pipeline
if 0:
app = QtGui.QApplication(sys.argv)
view1 = PipelineDevelopperView(pipeline)
view1.show()
app.exec_()
del view1
# Set pipeline input parameters
pipeline.dfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.nii.gz"
pipeline.bvalfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.bval"
pipeline.bvecfile = "/volatile/imagen/dmritest/000000022453/DTI/000000022453s011a1001.bvec"
print "Done in {0} seconds.".format(datetime.datetime.now() - start_time)
#print pipeline.nodes["eddy"].process._nipype_interface.inputs
print pipeline.nodes["eddy"].process._nipype_interface.cmdline
# Execute the pipeline in the configured study
study_config.run(pipeline, verbose=1)