def main():
if len(sys.argv) > 1:
nidm_original_version = sys.argv[1]
nidm_version = nidm_original_version.replace(".", "")
else:
nidm_original_version = "dev"
nidm_version = 'dev'
# Retreive owl file for NIDM-Results
if nidm_version == "dev":
owl_file = os.path.join(TERMS_FOLDER, 'nidm-experiment.owl')
import_files = glob.glob(os.path.join(NIDMPATH, "imports", '*.ttl'))
else:
owl_file = os.path.join(RELEASED_TERMS_FOLDER, \
'nidm-experiment_'+nidm_version+'.owl')
# For released version of the ontology imports are embedded
import_files = None
# check the file exists
assert os.path.exists(owl_file)
subcomponents = collections.OrderedDict()
subcomponents["Investigation"] = [NIDM['InvestigationCollection'],
NIDM['InvestigationProcess'],NIDM['Model'],
NIDM['ModelSpecification'],NIDM['Group'],
NIDM['Contrast'], NIDM['Task'],NIDM['Condition']]
subcomponents["Session"] = [NIDM['DataCollection'],NIDM['SessionAcquisition']]
subcomponents["Serie"] = [NIDM['AnatomyImagingAcquisition'],
NIDM['TaskBasedImagingAcquisition'], NIDM['AnatomicalScan'],
NIDM['FunctionalScan'], NIDM['BehaviorAndConsitionOnsets'],
NIDM['MRScanner'], NIDM['PresentationSoftware']]
subcomponents["Project"] = [NIDM['ProjectObject']]
subcomponents["Study"] = [NIDM['StudyObject']]
subcomponents["Acquisition"] = [NIDM['AcquisitionObject']]
subcomponents["Other"] = []
# Add manually used and wasDerivedFrom because these are not stored in the
# owl file (no relations yet!)
used_by = {
}
generated_by = {
}
derived_from = {
}
owlspec = OwlSpecification(owl_file, import_files, "NIDM-Experiment",
subcomponents, used_by, generated_by, derived_from,
prefix=str(NIDM))
if not nidm_version == "dev":
owlspec.text = owlspec.text.replace("(under development)", nidm_original_version)
owlspec.text = owlspec.text.replace("img/", "img/nidm-results_"+nidm_version+"/")
component_name = "nidm-experiment"
owlspec._header_footer(component=component_name, version=nidm_version)
owlspec.write_specification(component=component_name, version=nidm_version)
def main():
if len(sys.argv) > 1:
nidm_original_version = sys.argv[1]
nidm_version = nidm_original_version.replace(".", "")
else:
nidm_original_version = "dev"
nidm_version = 'dev'
# Retreive owl file for NIDM-Results
if nidm_version == "dev":
owl_file = os.path.join(TERMS_FOLDER, 'nidm-experiment.owl')
import_files = glob.glob(os.path.join(NIDMPATH, "imports", '*.ttl'))
else:
owl_file = os.path.join(RELEASED_TERMS_FOLDER, \
'nidm-experiment_'+nidm_version+'.owl')
# For released version of the ontology imports are embedded
import_files = None
# check the file exists
assert os.path.exists(owl_file)
subcomponents = collections.OrderedDict()
subcomponents["Investigation"] = [NIDM['InvestigationCollection'],
NIDM['InvestigationProcess'],NIDM['Model'],
NIDM['ModelSpecification'],NIDM['Group'],
NIDM['Contrast'], NIDM['Task'],NIDM['Condition']]
subcomponents["Session"] = [NIDM['DataCollection'],NIDM['SessionAcquisition']]
subcomponents["Serie"] = [NIDM['AnatomyImagingAcquisition'],
NIDM['TaskBasedImagingAcquisition'], NIDM['AnatomicalScan'],
NIDM['FunctionalScan'], NIDM['BehaviorAndConditionOnsets'],
NIDM['MRScanner'], NIDM['PresentationSoftware']]
subcomponents["Project"] = [NIDM['ProjectObject']]
subcomponents["Study"] = [NIDM['StudyObject']]
subcomponents["Acquisition"] = [NIDM['AcquisitionObject']]
subcomponents["Other"] = []
# Add manually used and wasDerivedFrom because these are not stored in the
# owl file (no relations yet!)
used_by = {
}
generated_by = {
}
derived_from = {
}
owlspec = OwlSpecification(owl_file, import_files, "NIDM-Experiment",
subcomponents, used_by, generated_by, derived_from,
prefix=str(NIDM))
if not nidm_version == "dev":
owlspec.text = owlspec.text.replace("(under development)", nidm_original_version)
owlspec.text = owlspec.text.replace("img/", "img/nidm-results_"+nidm_version+"/")
component_name = "nidm-experiment"
owlspec._header_footer(component=component_name, version=nidm_version)
owlspec.write_specification(component=component_name, version=nidm_version)
def main():
if len(sys.argv) > 1:
nidm_original_version = sys.argv[1]
nidm_version = nidm_original_version.replace(".", "")
else:
nidm_original_version = "dev"
nidm_version = 'dev'
# Retreive owl file for NIDM-Results
if nidm_version == "dev":
owl_file = os.path.join(TERMS_FOLDER, 'nidm-experiment.owl')
import_files = glob.glob(
os.path.join(NIDM_EXPE_PATH, "imports", '*.ttl'))
else:
owl_file = os.path.join(RELEASED_TERMS_FOLDER, \
'nidm-experiment_'+nidm_version+'.owl')
# For released version of the ontology imports are embedded
import_files = None
# check the file exists
assert os.path.exists(owl_file)
subcomponents = collections.OrderedDict()
subcomponents['Project'] = [
NIDM['CoInvestigator'], NIDM['Gender'], NIDM['Group'],
NIDM['ModelDesigner'], NIDM['ModelSpecification'],
NIDM['PrincipalInvestigator'], NIDM['Project'], NIDM['Protocol'],
NIDM['ResearchAssistant'], NIDM['SpecifiedPlan'], NIDM['Subject']
]
subcomponents['Acquisition'] = [
NIDM['Acquisition'], NIDM['AcquisitionDeviceOperator'],
NIDM['AcquisitionMethod'], NIDM['AcquisitionModality'],
NIDM['AcquisitionObject'], NIDM['AcquisitionObjectQuality'],
NIDM['BehavioralInstrument'], NIDM['AuxiliaryFile'],
NIDM['AuxiliaryFileCollection'], NIDM['DemographicsInstrument'],
NIDM['ImageContrastType'], NIDM['ImageDataReconstruction'],
NIDM['ImageUsageType'], NIDM['InformedConsentInstrument'],
NIDM['InstrumentAdministrator'], NIDM['InstrumentUsageType'],
NIDM['PerformedPlan'], NIDM['PresentationSoftware'],
NIDM['ProcessedAcquisitionObject'], NIDM['RawAcquisitionObject'],
NIDM['ReconstructedAcquisitionObject'], NIDM['Session'],
NIDM['SessionObject'], NIDM['StimulusPresentationFile'],
NIDM['StimulusResponseFile'], NIDM['Task']
]
subcomponents['Magnetic Resonance Imaging'] = [
NIDM['Anatomical'], NIDM['ArterialSpinLabeling'], NIDM['Cartesian'],
NIDM['DICOMTagCollection'], NIDM['DiffusionTensor'],
NIDM['DiffusionWeighted'], NIDM['DynamicContrastEnhanced'],
NIDM['DynamicSusceptibilityContrast'], NIDM['EchoPlanar'],
NIDM['FlowWeighted'], NIDM['Functional'], NIDM['ImageContrastType'],
NIDM['ImageDataReconstruction'], NIDM['ImageUsageType'],
NIDM['Inside-outSpiral'], NIDM['MagneticResonanceImaging'],
NIDM['NuclearMagneticResonanceSpectroscopy'],
NIDM['NuclearMagneticResonanceSpectroscopicImaging'],
NIDM['Outside-inSpiral'], NIDM['ParallelImaging'],
NIDM['ProtonDensityWeighted'], NIDM['PulseSequence'],
NIDM['QuantitativeSusceptibilityMapping'], NIDM['Rectilinear'],
NIDM['SimultaneousMultisliceMethod'], NIDM['Structural'],
NIDM['SusceptibilityWeighted'], NIDM['SusceptibilityWeightedImaging'],
NIDM['T1Weighted'], NIDM['T2StarWeighted'], NIDM['T2Weighted'],
NIDM['b-ValueFile'], NIDM['b-VectorFile'],
NIDM['k-spaceTraversalScheme'], NIDM['NIDM_0000152'],
NIDM['NIDM_0000153'], NIDM['NIDM_0000154'], NIDM['NIDM_0000155']
]
subcomponents['Electrophysiology'] = [
NIDM['Amperometry'], NIDM['CurrentClamp'],
NIDM['Electroencephalography'], NIDM['Electrocorticography'],
NIDM['ElectrophysiologyRecording'],
NIDM['ExtracellularElectrophysiologyRecording'],
NIDM['FieldPotential'],
NIDM['IntracellularElectrophysiologyRecording'],
NIDM['Magnetoencephalography'], NIDM['MultiUnitReccording'],
NIDM['SharpElectrode'], NIDM['SingleUnitReccording'],
NIDM['PatchClamp'], NIDM['VoltageClamp']
]
subcomponents['Devices'] = [
NIDM['CurrentAmplifier'], NIDM['SignalGenerator'],
NIDM['StimulusGenerator'], NIDM['StimulusIsolator'],
NIDM['VoltageAmplifier'], NIDM['EyeTrackingDevice'],
NIDM['HeartRateMonitor'], NIDM['Electrode'],
NIDM['ElectroencephalographyAcquisitionDevice'],
NIDM['MagneticResonanceImagingScanner'],
NIDM['PositronEmissionTomographyScanner'],
NIDM['SinglePhotonEmissionComputedTomographyScanner'],
NIDM['MagnetoencephalographyAcquisitionDevice'],
NIDM['MultielectrodeArray'], NIDM['Attenuator'],
NIDM['RespirationRateMonitor'], NIDM['SignalFilter']
]
subcomponents['Positron Emission Tomography'] = [
NIDM['PositronEmissionTomography']
]
subcomponents['X-ray Computed Tomography'] = [
NIDM['X-rayComputedTomography']
]
subcomponents["Other"] = []
# Add manually used and wasDerivedFrom because these are not stored in the
# owl file (no relations yet!)
used_by = {}
generated_by = {}
derived_from = {}
owlspec = OwlSpecification(owl_file,
import_files,
"NIDM-Experiment",
subcomponents,
used_by,
generated_by,
derived_from,
prefix=str(NIDM))
if not nidm_version == "dev":
owlspec.text = owlspec.text.replace("(under development)",
nidm_original_version)
owlspec.text = owlspec.text.replace(
"img/", "img/nidm-results_" + nidm_version + "/")
component_name = "nidm-experiment"
owlspec._header_footer(component=component_name, version=nidm_version)
owlspec.write_specification(component=component_name, version=nidm_version)
def main(nidm_original_version):
nidm_version = nidm_original_version.replace(".", "")
# Retreive owl file for NIDM-Results
if nidm_version == "dev":
owl_file = os.path.join(TERMS_FOLDER, 'nidm-results.owl')
import_files = glob.glob(os.path.join(NIDMPATH, "imports", '*.ttl'))
else:
owl_file = os.path.join(RELEASED_TERMS_FOLDER,
'nidm-results_' + nidm_version + '.owl')
# For released version of the ontology imports are embedded
import_files = None
# check the file exists
assert os.path.exists(owl_file)
components = collections.OrderedDict()
components["General"] = [NIDM_MAP]
components["Parameters estimation"] = [
NIDM_DATA, NIDM_ERROR_MODEL, NIDM_DESIGN_MATRIX,
NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_PARAMETER_ESTIMATE_MAP,
NIDM_GRAND_MEAN_MAP, NIDM_RESIDUAL_MEAN_SQUARES_MAP,
NIDM_MASK_MAP, NIDM_RESELS_PER_VOXEL_MAP]
components["Contrast estimation"] = [
NIDM_CONTRAST_ESTIMATION,
STATO_CONTRAST_WEIGHT_MATRIX, NIDM_CONTRAST_MAP, NIDM_STATISTIC_MAP,
NIDM_CONTRAST_STANDARD_ERROR_MAP]
components["Inference"] = [
NIDM_INFERENCE, NIDM_HEIGHT_THRESHOLD, NIDM_EXTENT_THRESHOLD,
NIDM_EXCURSION_SET_MAP, NIDM_CLUSTER_LABELS_MAP,
NIDM_SEARCH_SPACE_MASK_MAP,
NIDM_SIGNIFICANT_CLUSTER, NIDM_PEAK, NIDM_COORDINATE,
NIDM_CONJUNCTION_INFERENCE, NIDM_CLUSTER_DEFINITION_CRITERIA,
NIDM_DISPLAY_MASK_MAP, NIDM_PEAK_DEFINITION_CRITERIA]
if nidm_version == 'dev':
# For the developement version only list all terms that were not
# referred to in other components
components["Other"] = []
# Add manually used and wasDerivedFrom because these are not stored in the
# owl file
used_by = {
NIDM_DATA: [NIDM_MODEL_PARAMETERS_ESTIMATION],
NIDM_ERROR_MODEL: [NIDM_MODEL_PARAMETERS_ESTIMATION],
NIDM_DESIGN_MATRIX: [NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_CONTRAST_ESTIMATION],
NIDM_PARAMETER_ESTIMATE_MAP: [NIDM_CONTRAST_ESTIMATION],
NIDM_RESIDUAL_MEAN_SQUARES_MAP: [NIDM_CONTRAST_ESTIMATION],
NIDM_MASK_MAP: [NIDM_CONTRAST_ESTIMATION,
NIDM_MODEL_PARAMETERS_ESTIMATION],
STATO_CONTRAST_WEIGHT_MATRIX: [NIDM_CONTRAST_ESTIMATION],
NIDM_CONTRAST_MAP: [NIDM_INFERENCE],
NIDM_STATISTIC_MAP: [NIDM_INFERENCE],
NIDM_CLUSTER_DEFINITION_CRITERIA: [NIDM_INFERENCE],
NIDM_DISPLAY_MASK_MAP: [NIDM_INFERENCE],
NIDM_PEAK_DEFINITION_CRITERIA: [NIDM_INFERENCE],
NIDM_RESELS_PER_VOXEL_MAP: [NIDM_INFERENCE]
}
generated_by = {
NIDM_PARAMETER_ESTIMATE_MAP: NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_RESIDUAL_MEAN_SQUARES_MAP: NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_RESELS_PER_VOXEL_MAP: NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_MASK_MAP: NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_CONTRAST_MAP: NIDM_CONTRAST_ESTIMATION,
NIDM_STATISTIC_MAP: NIDM_CONTRAST_ESTIMATION,
NIDM_CONTRAST_STANDARD_ERROR_MAP: NIDM_CONTRAST_ESTIMATION,
}
derived_from = {
NIDM_SIGNIFICANT_CLUSTER: NIDM_EXCURSION_SET_MAP,
NIDM_PEAK: NIDM_SIGNIFICANT_CLUSTER,
NIDM_CLUSTER_CENTER_OF_GRAVITY: NIDM_SIGNIFICANT_CLUSTER
}
if nidm_version == "020":
# nidm namespaces were defined under incf.org (instead of purl)
NIDM_INCF = Namespace('http://www.incf.org/ns/nidash/nidm#')
SPM_INCF = Namespace('http://www.incf.org/ns/nidash/spm#')
FSL_INCF = Namespace('http://www.incf.org/ns/nidash/fsl#')
# The following classes were named differently in 0.2.0
renaming = [(NIDM_EXCURSION_SET_MAP, NIDM_INCF['ExcursionSet']),
(NIDM_SEARCH_SPACE_MASK_MAP, NIDM_INCF['SearchSpaceMap']),
(NIDM_SIGNIFICANT_CLUSTER, NIDM_INCF['Cluster']),
(NIDM_ERROR_MODEL, NIDM_INCF['NoiseModel']),
(NIDM_CONTRAST_ESTIMATION,
NIDM_INCF['ContrastEstimation']),
(NIDM_CONTRAST_MAP, NIDM_INCF['ContrastMap']),
(NIDM_MAP, NIDM_INCF['Map']),
(NIDM_DATA, NIDM_INCF['Data']),
(NIDM_DESIGN_MATRIX, NIDM_INCF['DesignMatrix']),
(NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_INCF['ModelParametersEstimation']),
(NIDM_GRAND_MEAN_MAP, NIDM_INCF['GrandMeanMap']),
(NIDM_RESIDUAL_MEAN_SQUARES_MAP,
NIDM_INCF['ResidualMeanSquaresMap']),
(NIDM_MASK_MAP, NIDM_INCF['MaskMap']),
(STATO_CONTRAST_WEIGHT_MATRIX,
NIDM_INCF['ContrastWeights']),
(NIDM_STATISTIC_MAP, NIDM_INCF['StatisticMap']),
(NIDM_CONTRAST_STANDARD_ERROR_MAP,
NIDM_INCF['ContrastStandardErrorMap']),
(NIDM_INFERENCE, NIDM_INCF['Inference']),
(NIDM_HEIGHT_THRESHOLD, NIDM_INCF['HeightThreshold']),
(NIDM_EXTENT_THRESHOLD, NIDM_INCF['ExtentThreshold']),
(NIDM_PEAK, NIDM_INCF['Peak']),
(NIDM_CLUSTER_LABELS_MAP, NIDM_INCF['ClusterLabelsMap']),
(NIDM_COORDINATE, NIDM_INCF['Coordinate']),
(NIDM_PARAMETER_ESTIMATE_MAP,
NIDM_INCF['ParameterEstimateMap']),
(NIDM_RESELS_PER_VOXEL_MAP,
SPM_INCF['ReselsPerVoxelMap']),
(NIDM_CLUSTER_CENTER_OF_GRAVITY,
FSL_INCF['CenterOfGravity'])]
# MaskMap was sometimes called CustomMaskMap (when isUserDefined=true)
components["Parameters estimation"].append(NIDM_INCF['CustomMaskMap'])
# The following classes were not represented in 0.2.0
components["Inference"].remove(NIDM_CLUSTER_DEFINITION_CRITERIA)
components["Inference"].remove(NIDM_PEAK_DEFINITION_CRITERIA)
components["Inference"].remove(NIDM_DISPLAY_MASK_MAP)
components["Inference"].remove(NIDM_CONJUNCTION_INFERENCE)
# The following classes were represented in another component in 0.2.0
components["Parameters estimation"].remove(NIDM_RESELS_PER_VOXEL_MAP)
del used_by[NIDM_CLUSTER_DEFINITION_CRITERIA]
del used_by[NIDM_PEAK_DEFINITION_CRITERIA]
del used_by[NIDM_DISPLAY_MASK_MAP]
# SPM and FSL software were described using software-specific terms
components["SPM-specific Concepts"] = [
NIDM_INCF['SPM'], SPM_INCF['ReselsPerVoxelMap']]
components["FSL-specific Concepts"] = [
NIDM_INCF['FSL'], FSL_INCF['CenterOfGravity']]
# Add manually used and wasDerivedFrom because these are not stored in
# the owl file
used_by[NIDM_INCF['CustomMaskMap']] = [
NIDM_INCF['ModelParametersEstimation']]
used_by[NIDM_MASK_MAP] = [NIDM_CONTRAST_ESTIMATION]
# In version 0.2.0 "ErrorModel" was called "NoiseModel"
components, used_by, generated_by, derived_from = _replace_term_by(
renaming, components, used_by, generated_by, derived_from)
owlspec = OwlSpecification(
owl_file, import_files, "NIDM-Results",
components, used_by, generated_by, derived_from, prefix=str(NIDM))
owlspec._header_footer(component="nidm-results", version=nidm_version)
if not nidm_version == "dev":
if nidm_version == "110":
# Previous version
owlspec.text = owlspec.text.replace(
"nidm-results_020.html", "nidm-results_100.html")
elif nidm_version == "020":
# Previous version
owlspec.text = owlspec.text.replace(
"nidm-results_020.html", "nidm-results_010.html")
owlspec.text = dev_to_release(owlspec.text, nidm_original_version)
owlspec.write_specification(component="nidm-results", version=nidm_version)
def main(nidm_original_version):
nidm_version = nidm_original_version.replace(".", "")
# Retreive owl file for NIDM-Results
if nidm_version == "dev":
owl_file = os.path.join(TERMS_FOLDER, 'nidm-results.owl')
import_files = glob.glob(os.path.join(NIDMPATH, "imports", '*.ttl'))
else:
owl_file = os.path.join(RELEASED_TERMS_FOLDER,
'nidm-results_' + nidm_version + '.owl')
# For released version of the ontology imports are embedded
import_files = None
# check the file exists
assert os.path.exists(owl_file)
components = collections.OrderedDict()
components["General"] = [
NIDM_RESULTS, NIDM_MAP, NIDM_COORDINATE_SPACE, SPM_SOFTWARE,
FSL_SOFTWARE
]
components["Parameters estimation"] = [
NIDM_MODEL_PARAMETERS_ESTIMATION, NIDM_DATA, NIDM_DESIGN_MATRIX,
NIDM_ERROR_MODEL, NIDM_GRAND_MEAN_MAP, NIDM_MASK_MAP,
NIDM_PARAMETER_ESTIMATE_MAP, NIDM_RESELS_PER_VOXEL_MAP,
NIDM_RESIDUAL_MEAN_SQUARES_MAP
]
components["Contrast estimation"] = [
NIDM_CONTRAST_ESTIMATION, STATO_CONTRAST_WEIGHT_MATRIX,
NIDM_CONTRAST_MAP, NIDM_CONTRAST_STANDARD_ERROR_MAP,
NIDM_CONTRAST_EXPLAINED_MEAN_SQUARE_MAP, NIDM_STATISTIC_MAP
]
components["Inference"] = [
NIDM_INFERENCE, NIDM_CLUSTER_DEFINITION_CRITERIA,
NIDM_CLUSTER_LABELS_MAP, NIDM_COORDINATE, NIDM_DISPLAY_MASK_MAP,
NIDM_EXCURSION_SET_MAP, NIDM_EXTENT_THRESHOLD, NIDM_HEIGHT_THRESHOLD,
NIDM_PEAK, NIDM_PEAK_DEFINITION_CRITERIA, NIDM_SEARCH_SPACE_MASK_MAP,
NIDM_SUPRA_THRESHOLD_CLUSTER
]
if nidm_version == 'dev':
# For the developement version only list all terms that were not
# referred to in other components
components["Other"] = []
# Add manually used and wasDerivedFrom because these are not stored in the
# owl file
used_by = {
NIDM_DATA: [NIDM_MODEL_PARAMETERS_ESTIMATION],
NIDM_ERROR_MODEL: [NIDM_MODEL_PARAMETERS_ESTIMATION],
NIDM_DESIGN_MATRIX:
[NIDM_MODEL_PARAMETERS_ESTIMATION, NIDM_CONTRAST_ESTIMATION],
NIDM_PARAMETER_ESTIMATE_MAP: [NIDM_CONTRAST_ESTIMATION],
NIDM_RESIDUAL_MEAN_SQUARES_MAP: [NIDM_CONTRAST_ESTIMATION],
NIDM_MASK_MAP:
[NIDM_CONTRAST_ESTIMATION, NIDM_MODEL_PARAMETERS_ESTIMATION],
STATO_CONTRAST_WEIGHT_MATRIX: [NIDM_CONTRAST_ESTIMATION],
NIDM_CONTRAST_MAP: [NIDM_INFERENCE],
NIDM_STATISTIC_MAP: [NIDM_INFERENCE],
NIDM_CLUSTER_DEFINITION_CRITERIA: [NIDM_INFERENCE],
NIDM_DISPLAY_MASK_MAP: [NIDM_INFERENCE],
NIDM_PEAK_DEFINITION_CRITERIA: [NIDM_INFERENCE],
NIDM_RESELS_PER_VOXEL_MAP: [NIDM_INFERENCE]
}
generated_by = {
NIDM_PARAMETER_ESTIMATE_MAP: NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_RESIDUAL_MEAN_SQUARES_MAP: NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_RESELS_PER_VOXEL_MAP: NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_MASK_MAP: NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_CONTRAST_MAP: NIDM_CONTRAST_ESTIMATION,
NIDM_STATISTIC_MAP: NIDM_CONTRAST_ESTIMATION,
NIDM_CONTRAST_EXPLAINED_MEAN_SQUARE_MAP: NIDM_CONTRAST_ESTIMATION,
NIDM_CONTRAST_STANDARD_ERROR_MAP: NIDM_CONTRAST_ESTIMATION,
NIDM_GRAND_MEAN_MAP: NIDM_MODEL_PARAMETERS_ESTIMATION,
}
derived_from = {
NIDM_SUPRA_THRESHOLD_CLUSTER: NIDM_EXCURSION_SET_MAP,
NIDM_PEAK: NIDM_SUPRA_THRESHOLD_CLUSTER,
NIDM_CLUSTER_CENTER_OF_GRAVITY: NIDM_SUPRA_THRESHOLD_CLUSTER
}
if nidm_version == "020":
# nidm namespaces were defined under incf.org (instead of purl)
NIDM_INCF = Namespace('http://www.incf.org/ns/nidash/nidm#')
SPM_INCF = Namespace('http://www.incf.org/ns/nidash/spm#')
FSL_INCF = Namespace('http://www.incf.org/ns/nidash/fsl#')
# The following classes were named differently in 0.2.0
renaming = [
(NIDM_EXCURSION_SET_MAP, NIDM_INCF['ExcursionSet']),
(NIDM_SEARCH_SPACE_MASK_MAP, NIDM_INCF['SearchSpaceMap']),
(NIDM_SUPRA_THRESHOLD_CLUSTER, NIDM_INCF['Cluster']),
(NIDM_ERROR_MODEL, NIDM_INCF['NoiseModel']),
(NIDM_CONTRAST_ESTIMATION, NIDM_INCF['ContrastEstimation']),
(NIDM_CONTRAST_MAP, NIDM_INCF['ContrastMap']),
(NIDM_MAP, NIDM_INCF['Map']), (NIDM_DATA, NIDM_INCF['Data']),
(NIDM_DESIGN_MATRIX, NIDM_INCF['DesignMatrix']),
(NIDM_MODEL_PARAMETERS_ESTIMATION,
NIDM_INCF['ModelParametersEstimation']),
(NIDM_GRAND_MEAN_MAP, NIDM_INCF['GrandMeanMap']),
(NIDM_RESIDUAL_MEAN_SQUARES_MAP,
NIDM_INCF['ResidualMeanSquaresMap']),
(NIDM_MASK_MAP, NIDM_INCF['MaskMap']),
(STATO_CONTRAST_WEIGHT_MATRIX, NIDM_INCF['ContrastWeights']),
(NIDM_STATISTIC_MAP, NIDM_INCF['StatisticMap']),
(NIDM_CONTRAST_STANDARD_ERROR_MAP,
NIDM_INCF['ContrastStandardErrorMap']),
(NIDM_INFERENCE, NIDM_INCF['Inference']),
(NIDM_HEIGHT_THRESHOLD, NIDM_INCF['HeightThreshold']),
(NIDM_EXTENT_THRESHOLD, NIDM_INCF['ExtentThreshold']),
(NIDM_PEAK, NIDM_INCF['Peak']),
(NIDM_CLUSTER_LABELS_MAP, NIDM_INCF['ClusterLabelsMap']),
(NIDM_COORDINATE, NIDM_INCF['Coordinate']),
(NIDM_PARAMETER_ESTIMATE_MAP, NIDM_INCF['ParameterEstimateMap']),
(NIDM_RESELS_PER_VOXEL_MAP, SPM_INCF['ReselsPerVoxelMap']),
(NIDM_CLUSTER_CENTER_OF_GRAVITY, FSL_INCF['CenterOfGravity'])
]
# MaskMap was sometimes called CustomMaskMap (when isUserDefined=true)
components["Parameters estimation"].append(NIDM_INCF['CustomMaskMap'])
# The following classes were not represented in 0.2.0
components["Inference"].remove(NIDM_CLUSTER_DEFINITION_CRITERIA)
components["Inference"].remove(NIDM_PEAK_DEFINITION_CRITERIA)
components["Inference"].remove(NIDM_DISPLAY_MASK_MAP)
components["Inference"].remove(NIDM_CONJUNCTION_INFERENCE)
# The following classes were represented in another component in 0.2.0
components["Parameters estimation"].remove(NIDM_RESELS_PER_VOXEL_MAP)
del used_by[NIDM_CLUSTER_DEFINITION_CRITERIA]
del used_by[NIDM_PEAK_DEFINITION_CRITERIA]
del used_by[NIDM_DISPLAY_MASK_MAP]
# SPM and FSL software were described using software-specific terms
components["SPM-specific Concepts"] = [
NIDM_INCF['SPM'], SPM_INCF['ReselsPerVoxelMap']
]
components["FSL-specific Concepts"] = [
NIDM_INCF['FSL'], FSL_INCF['CenterOfGravity']
]
# Add manually used and wasDerivedFrom because these are not stored in
# the owl file
used_by[NIDM_INCF['CustomMaskMap']] = [
NIDM_INCF['ModelParametersEstimation']
]
used_by[NIDM_MASK_MAP] = [NIDM_CONTRAST_ESTIMATION]
# In version 0.2.0 "ErrorModel" was called "NoiseModel"
components, used_by, generated_by, derived_from = _replace_term_by(
renaming, components, used_by, generated_by, derived_from)
commentable = False
if nidm_version == "dev":
commentable = True
intro = ""
if nidm_version == "dev":
intro = """
<p>This section introduces neuroimaging results concepts with \
definitions and illustrative examples.</p>
"""
owlspec = OwlSpecification(owl_file,
import_files,
"NIDM-Results",
components,
used_by,
generated_by,
derived_from,
prefix=str(NIDM),
commentable=commentable,
intro=intro)
owlspec._header_footer(component="nidm-results", version=nidm_version)
if not nidm_version == "dev":
if nidm_version == "110":
# Previous version
owlspec.text = owlspec.text.replace("nidm-results_020.html",
"nidm-results_100.html")
elif nidm_version == "020":
# Previous version
owlspec.text = owlspec.text.replace("nidm-results_020.html",
"nidm-results_010.html")
owlspec.text = dev_to_release(owlspec.text, nidm_original_version)
owlspec.write_specification(component="nidm-results", version=nidm_version)
def main():
if len(sys.argv) > 1:
nidm_original_version = sys.argv[1]
nidm_version = nidm_original_version.replace(".", "")
else:
nidm_original_version = "dev"
nidm_version = 'dev'
# Retreive owl file for NIDM-Results
if nidm_version == "dev":
owl_file = os.path.join(TERMS_FOLDER, 'nidm-experiment.owl')
import_files = glob.glob(os.path.join(NIDM_EXPE_PATH, "imports", '*.ttl'))
else:
owl_file = os.path.join(RELEASED_TERMS_FOLDER, \
'nidm-experiment_'+nidm_version+'.owl')
# For released version of the ontology imports are embedded
import_files = None
# check the file exists
assert os.path.exists(owl_file)
subcomponents = collections.OrderedDict()
subcomponents['Project'] = [
NIDM['CoInvestigator'], NIDM['Gender'],NIDM['Group'], NIDM['ModelDesigner'], NIDM['ModelSpecification'],
NIDM['PrincipalInvestigator'], NIDM['Project'], NIDM['Protocol'], NIDM['ResearchAssistant'],
NIDM['SpecifiedPlan'], NIDM['Subject']
]
subcomponents['Acquisition'] = [
NIDM['Acquisition'],NIDM['AcquisitionDeviceOperator'],NIDM['AcquisitionMethod'],NIDM['AcquisitionModality'],
NIDM['AcquisitionObject'], NIDM['AcquisitionObjectQuality'],NIDM['BehavioralInstrument'],
NIDM['AuxiliaryFile'], NIDM['AuxiliaryFileCollection'],
NIDM['ClinicalInstrument'], NIDM['DemographicsInstrument'],
NIDM['ImageContrastType'], NIDM['ImageDataReconstruction'],
NIDM['ImageUsageType'],NIDM['InformedConsentInstrument'],NIDM['InstrumentAdministrator'],
NIDM['InstrumentUsageType'],
NIDM['PerformedPlan'],NIDM['PresentationSoftware'],NIDM['ProcessedAcquisitionObject'],
NIDM['RawAcquisitionObject'],NIDM['ReconstructedAcquisitionObject'], NIDM['Session'],
NIDM['SessionObject'],NIDM['StimulusPresentationFile'], NIDM['StimulusResponseFile'],NIDM['Task']
]
subcomponents['Magnetic Resonance Imaging'] = [
NIDM['Anatomical'], NIDM['ArterialSpinLabeling'],NIDM['Cartesian'],
NIDM['DICOMTagCollection'], NIDM['DiffusionTensor'],NIDM['DiffusionWeighted'],
NIDM['DynamicContrastEnhanced'], NIDM['DynamicSusceptibilityContrast'],
NIDM['EchoPlanar'], NIDM['FlowWeighted'],NIDM['Functional'],NIDM['ImageContrastType'],
NIDM['ImageDataReconstruction'], NIDM['ImageUsageType'], NIDM['Inside-outSpiral'],
NIDM['MagneticResonanceImaging'],NIDM['NuclearMagneticResonanceSpectroscopy'],
NIDM['NuclearMagneticResonanceSpectroscopicImaging'],NIDM['Outside-inSpiral'], NIDM['ParallelImaging'],
NIDM['ProtonDensityWeighted'],NIDM['PulseSequence'],NIDM['QuantitativeSusceptibilityMapping'],
NIDM['Rectilinear'],NIDM['SimultaneousMultisliceMethod'],
NIDM['Structural'],
NIDM['SusceptibilityWeighted'],NIDM['SusceptibilityWeightedImaging'],
NIDM['T1Weighted'], NIDM['T2StarWeighted'], NIDM['T2Weighted'],NIDM['b-ValueFile'],
NIDM['b-VectorFile'], NIDM['k-spaceTraversalScheme'], NIDM['NIDM_0000152'], NIDM['NIDM_0000153'],
NIDM['NIDM_0000154'], NIDM['NIDM_0000155']
]
subcomponents['Electrophysiology'] = [
NIDM['Amperometry'], NIDM['CurrentClamp'],
NIDM['Electroencephalography'], NIDM['Electrocorticography'],NIDM['ElectrophysiologyRecording'],
NIDM['ExtracellularElectrophysiologyRecording'],NIDM['FieldPotential'],
NIDM['IntracellularElectrophysiologyRecording'],NIDM['Magnetoencephalography'],
NIDM['MultiUnitReccording'], NIDM['SharpElectrode'], NIDM['SingleUnitReccording'],
NIDM['PatchClamp'], NIDM['VoltageClamp']
]
subcomponents['Positron Emission Tomography'] = [NIDM['PositronEmissionTomography']]
subcomponents['X-ray Computed Tomography'] = [NIDM['X-rayComputedTomography']]
subcomponents["Other"] = []
# Add manually used and wasDerivedFrom because these are not stored in the
# owl file (no relations yet!)
used_by = {
}
generated_by = {
}
derived_from = {
}
owlspec = OwlSpecification(owl_file, import_files, "NIDM-Experiment",
subcomponents, used_by, generated_by, derived_from,
prefix=str(NIDM))
if not nidm_version == "dev":
owlspec.text = owlspec.text.replace("(under development)", nidm_original_version)
owlspec.text = owlspec.text.replace("img/", "img/nidm-results_"+nidm_version+"/")
component_name = "nidm-experiment"
owlspec._header_footer(component=component_name, version=nidm_version)
owlspec.write_specification(component=component_name, version=nidm_version)