Merge pull request #268 from dbkeator/master

fixes version of ontquery to 0.2.3.

nidm/core/BIDS_Constants.py

@@ -33,21 +33,42 @@
     "T2w" : Constants.NIDM_MRI_T2,
     "inplaneT2" : Constants.NIDM_MRI_T2,
     "bold" : Constants.NIDM_MRI_FLOW,
-    "dti" : Constants.NIDM_MRI_DIFFUSION_TENSOR
+    "dti" : Constants.NIDM_MRI_DIFFUSION_TENSOR,
+    "asl" : Constants.NIDM_MRI_ASL
 }
 #JSON file keys
 json_keys = {
     ##Image terms
     "run" : Constants.NIDM_ACQUISITION_ENTITY,
     "ImageType" : Constants.DICOM["ImageType"],
     "ManufacturerModelName" : Constants.DICOM["ManufacturerModelName"],
+    "Manufacturer" : Constants.DICOM["Manufacturer"],
     "ScanningSequence" : Constants.DICOM["ScanningSequence"],
     "SequenceVariant" : Constants.DICOM["SequenceVariant"],
     "ScanOptions" : Constants.DICOM["ScanOptions"],
     "MRAcquisitionType" : Constants.DICOM["MRAcquisitionType"],
     "SequenceName" : Constants.DICOM["SequenceName"],
     "RepetitionTime" : Constants.DICOM["RepetitionTime"],
-    "EchoTime" : Constants.DICOM["EchoTime"],
+    "RepetitionTimePreparation" : Constants.BIDS["RepetitionTimePreparation"],
+    "ArterialSpinLabelingType" : Constants.BIDS["ArterialSpinLabelingType"],
+    "PostLabelingDelay" : Constants.BIDS["PostLabelingDelay"],
+    "BackgroundSuppression" : Constants.BIDS["BackgroundSuppression"],
+    "BackgroundSuppressionPulseTime" : Constants.BIDS["BackgroundSuppressionPulseTime"],
+    "BackgroundSuppressionNumberPulses" : Constants.BIDS["BackgroundSuppressionNumberPulses"],
+    "LabelingLocationDescription" : Constants.BIDS["LabelingLocationDescription"],
+    "LookLocker" : Constants.BIDS["LookLocker"],
+    "LabelingEfficiency" : Constants.BIDS["LabelingEfficiency"],
+    "LabelingDuration" : Constants.BIDS["LabelingDuration"],
+    "LabelingPulseAverageGradient" : Constants.BIDS["LabelingPulseAverageGradient"],
+    "LabelingPulseMaximumGradient" : Constants.BIDS["LabelingPulseMaximumGradient"],
+    "LabelingPulseDuration" : Constants.BIDS["LabelingPulseDuration"],
+    "LabelingPulseFlipAngle" : Constants.BIDS["LabelingPulseFlipAngle"],
+    "LabelingPulseInterval" : Constants.BIDS["LabelingPulseInterval"],
+    "PCASLType" : Constants.BIDS["PCASLType"],
+    "M0Type" : Constants.BIDS["M0Type"],
+    "TotalAcquiredPairs" : Constants.BIDS["TotalAcquiredPairs"],
+    "VascularCrushing" : Constants.BIDS["VascularCrushing"],
+    "EchoTime" : Constants.BIDS["EchoTime"],
     "InversionTime" : Constants.DICOM["InversionTime"],
     "NumberOfAverages" : Constants.DICOM["NumberOfAverages"],
     "ImagingFrequency" : Constants.DICOM["ImagingFrequency"],
@@ -66,17 +87,19 @@
     "ProtocolName": Constants.DICOM["ProtocolName"],
     "TransmitCoilName": Constants.DICOM["TransmitCoilName"],
     "AcquisitionMatrix": Constants.DICOM["AcquisitionMatrix"],
+    "AcquisitionVoxelSize" : Constants.BIDS["AcquisitionVoxelSize"],
     "InPlanePhaseEncodingDirection": Constants.DICOM["InPlanePhaseEncodingDirection"],
-    "FlipAngle": Constants.DICOM["FlipAngle"],
+    "FlipAngle": Constants.BIDS["FlipAngle"],
     "VariableFlipAngleFlag": Constants.DICOM["VariableFlipAngleFlag"],
     "PatientPosition": Constants.DICOM["PatientPosition"],
-    "PhaseEncodingDirection": Constants.NIDM["PhaseEncodingDirection"],
-    "SliceTiming": Constants.NIDM["SliceTiming"],
-    "TotalReadoutTime" : Constants.DICOM["TotalReadoutTime"],
+    "PhaseEncodingDirection": Constants.BIDS["PhaseEncodingDirection"],
+    "SliceTiming": Constants.BIDS["SliceTiming"],
+    "TotalReadoutTime" : Constants.BIDS["TotalReadoutTime"],
     "EffectiveEchoSpacing" : Constants.NIDM["EffectiveEchoSpacing"],
     "NumberDiscardedVolumesByScanner" : Constants.NIDM["NumberDiscardedVolumesByScanner"],
     "NumberDiscardedVolumesByUser" : Constants.NIDM["NumberDiscardedVolumesByUser"],
     "DelayTime" : Constants.NIDM["DelayTime"],
+    "PulseSequenceType" : Constants.DICOM["PulseSequenceName"],
     ###Task Stuff
     "TaskName" : Constants.NIDM_MRI_FUNCTION_TASK
     # "CogAtlasID" :

nidm/core/Constants.py

@@ -383,6 +383,7 @@ def __init__(self, namespaces=None):
 NIDM_MRI_DIFFUSION_TENSOR = QualifiedName(provNamespace("nidm", NIDM),"DiffusionTensor")
 NIDM_MRI_FLOW = QualifiedName(provNamespace("nidm", NIDM),"FlowWeighted")
 NIDM_MRI_BOLD_EVENTS = QualifiedName(provNamespace("nidm", NIDM),"StimulusResponseFile")
+NIDM_MRI_ASL = QualifiedName(provNamespace("nidm",NIDM),"ArterialSpinLabeling")
 CRYPTO_SHA512  =QualifiedName(provNamespace("crypto", CRYPTO),"sha512")
 DATALAD_LOCATION = QualifiedName(provNamespace("datalad", DATALAD),"Location")
 ##############################################################################

nidm/experiment/Core.py

@@ -361,18 +361,21 @@ def serializeJSONLD(self):
 
 
 
-        #WIP: currently this creates a default JSON-LD context from Constants.py and not in the correct way from the
-        #NIDM-E OWL files that that will be the next iteration
+        # WIP: currently this creates a default JSON-LD context from Constants.py and not in the correct way from the
+        # NIDM-E OWL files that that will be the next iteration
         context1 = self.createDefaultJSONLDcontext()
-        #This part adds to the context any prefixes in an existing NIDM-E file that might have been added by a user
-        #and isn't covered by the default namespaces / constants in Constants.py
+        # This part adds to the context any prefixes in an existing NIDM-E file that might have been added by a user
+        # and isn't covered by the default namespaces / constants in Constants.py
         context2 = self.prefix_to_context()
         context = dict(context1, **context2)
 
-        #WIP: LOOK AT https://github.com/satra/nidm-jsonld
+        # WIP: LOOK AT https://github.com/satra/nidm-jsonld
         #return rdf_graph_parse.serialize(format='json-ld', context=context, indent=4).decode('ASCII')
         g=rdf_graph_parse.serialize(format='json-ld', indent=4).decode('ASCII')
+
+
         import pyld as ld
+
         return json.dumps(ld.jsonld.compact(json.loads(g), context),indent=4)
 
     def createDefaultJSONLDcontext(self):
@@ -548,6 +551,12 @@ def prefix_to_context(self):
             #context[key]['@type']='@id'
             if type(value.uri) == str:
                 context[key]= value.uri
+            # added for some weird namespaces where key is URIRef and value is Namespace
+            # seems to only apply to PROV and NIDM qualified names.
+            # has something to do with read_nidm function in Utils and add_metadata_for_subject
+            # when it comes across a NIDM or PROV term.
+            elif type(key) == URIRef:
+                continue
             else:
                 context[key]= str(value.uri)
 

nidm/experiment/Utils.py

@@ -95,6 +95,8 @@ def read_nidm(nidmDoc):
     rdf_graph = Graph()
     rdf_graph_parse = rdf_graph.parse(nidmDoc,format=util.guess_format(nidmDoc))
 
+
+
     # add known CDE graphs
     #rdf_graph_parse = rdf_graph.parse
 
@@ -137,6 +139,7 @@ def read_nidm(nidmDoc):
         add_metadata_for_subject (rdf_graph_parse,proj_id,project.graph.namespaces,project)
 
 
+
     #Query graph for sessions, instantiate session objects, and add to project._session list
     #Get subject URI for sessions
     for s in rdf_graph_parse.subjects(predicate=RDF.type,object=URIRef(Constants.NIDM_SESSION.uri)):
@@ -153,7 +156,6 @@ def read_nidm(nidmDoc):
         #add session to project
         project.add_sessions(session)
 
-
         #now get remaining metadata in session object and add to session
         #Cycle through Session metadata adding to prov graph
         add_metadata_for_subject (rdf_graph_parse,s,project.graph.namespaces,session)
@@ -325,6 +327,7 @@ def read_nidm(nidmDoc):
         add_metadata_for_subject(rdf_graph_parse, row['uuid'], project.graph.namespaces, derivobj)
 
 
+
     return(project)
 
 
@@ -390,9 +393,9 @@ def add_metadata_for_subject (rdf_graph,subject_uri,namespaces,nidm_obj):
                     # automatically by provDocument so they aren't accessible via the namespaces list
                     # so we check explicitly here
                     if ((obj_nm == str(Constants.PROV))):
-                        nidm_obj.add_attributes({predicate: pm.QualifiedName(Constants.PROV,obj_term)})
+                        nidm_obj.add_attributes({predicate: QualifiedName(Constants.PROV[obj_term])})
                     elif ((obj_nm == str(Constants.NIDM))):
-                        nidm_obj.add_attributes({predicate: pm.QualifiedName(Constants.NIDM,obj_term)})
+                        nidm_obj.add_attributes({predicate: QualifiedName(Constants.NIDM[obj_term])})
                     else:
                         found_uri = find_in_namespaces(search_uri=URIRef(obj_nm),namespaces=namespaces)
                         # if obj_nm is not in namespaces then it must just be part of some URI in the triple

nidm/experiment/tools/bidsmri2nidm.py

@@ -27,7 +27,7 @@
 # **************************************************************************************
 
 import sys, getopt, os
-
+import bids
 from nidm.experiment import Project,Session,MRAcquisition,AcquisitionObject,DemographicsObject, AssessmentAcquisition, \
     AssessmentObject,MRObject,Acquisition
 from nidm.core import BIDS_Constants,Constants
@@ -44,7 +44,7 @@
 import csv
 import glob
 from argparse import ArgumentParser
-from bids import BIDSLayout
+
 #  Python program to find SHA256 hash string of a file
 import hashlib
 from io import StringIO
@@ -395,6 +395,69 @@ def addimagingsessions(bids_layout,subject_id,session,participant, directory,img
                     else:
                         acq_obj.add_attributes({BIDS_Constants.json_keys[key]:dataset[key]})
 
+        # DBK added for ASL support 3/16/21
+        # WIP: Waiting for pybids > 0.12.4 to support perfusion scans
+        elif file_tpl.entities['datatype'] == 'perf':
+            acq_obj = MRObject(acq)
+            # add image contrast type
+            if file_tpl.entities['suffix'] in BIDS_Constants.scans:
+                acq_obj.add_attributes(
+                    {Constants.NIDM_IMAGE_CONTRAST_TYPE: BIDS_Constants.scans[file_tpl.entities['suffix']]})
+            else:
+                logging.info(
+                    "WARNING: No matching image contrast type found in BIDS_Constants.py for %s" % file_tpl.entities[
+                        'suffix'])
+            # add image usage type
+            if file_tpl.entities['datatype'] in BIDS_Constants.scans:
+                acq_obj.add_attributes({Constants.NIDM_IMAGE_USAGE_TYPE: BIDS_Constants.scans["asl"]})
+            else:
+                logging.info(
+                        "WARNING: No matching image usage type found in BIDS_Constants.py for %s" % file_tpl.entities[
+                            'datatype'])
+            # make relative link to
+            acq_obj.add_attributes(
+                    {Constants.NIDM_FILENAME: getRelPathToBIDS(join(file_tpl.dirname, file_tpl.filename), directory)})
+            # add sha512 sum
+            if isfile(join(directory, file_tpl.dirname, file_tpl.filename)):
+                acq_obj.add_attributes(
+                        {Constants.CRYPTO_SHA512: getsha512(join(directory, file_tpl.dirname, file_tpl.filename))})
+            else:
+                logging.info(
+                        "WARNING file %s doesn't exist! No SHA512 sum stored in NIDM files..." % join(directory,
+                                                                                                      file_tpl.dirname,
+                                                                                                      file_tpl.filename))
+
+            # add git-annex/datalad info if exists
+            num_sources = addGitAnnexSources(obj=acq_obj, filepath=join(file_tpl.dirname, file_tpl.filename),
+                                                 bids_root=directory)
+
+            if num_sources == 0:
+                acq_obj.add_attributes(
+                        {Constants.PROV['Location']: "file:/" + join(file_tpl.dirname, file_tpl.filename)})
+
+            if 'run' in file_tpl.entities:
+                acq_obj.add_attributes({BIDS_Constants.json_keys["run"]: file_tpl.run})
+
+            # get associated JSON file if exists
+            json_data = (bids_layout.get(suffix=file_tpl.entities['suffix'], subject=subject_id))[0].metadata
+
+            if len(json_data.info) > 0:
+                for key in json_data.info.items():
+                    if key in BIDS_Constants.json_keys:
+                        if type(json_data.info[key]) is list:
+                            acq_obj.add_attributes({BIDS_Constants.json_keys[key.replace(" ", "_")]: ''.join(
+                                    str(e) for e in json_data.info[key])})
+                        else:
+                            acq_obj.add_attributes(
+                                    {BIDS_Constants.json_keys[key.replace(" ", "_")]: json_data.info[key]})
+
+            # check if separate M0 scan exists, if so add location and filename
+            # WIP, waiting for pybids > 0.12.4 to support...
+
+        # WIP support B0 maps...waiting for pybids > 0.12.4
+        # elif file_tpl.entities['datatype'] == 'fmap':
+
+
         elif file_tpl.entities['datatype'] == 'dwi':
             #do stuff with with dwi scans...
             acq_obj = MRObject(acq)
@@ -516,7 +579,8 @@ def bidsmri2project(directory, args):
 
 
     # get BIDS layout
-    bids_layout = BIDSLayout(directory)
+    bids.config.set_option('extension_initial_dot', True)
+    bids_layout = bids.BIDSLayout(directory)
 
 
     # create empty dictinary for sessions where key is subject id and used later to link scans to same session as demographics

nidm/version.py

@@ -4,7 +4,7 @@
 # Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z"
 _version_major = 3
 _version_minor = 7 
-_version_micro = '4'  # use '' for first of series, number for 1 and above
+_version_micro = '6'  # use '' for first of series, number for 1 and above
 _version_extra = ''
 # _version_extra = ''  # Uncomment this for full releases
 
@@ -56,6 +56,6 @@
 MICRO = _version_micro
 VERSION = __version__
 INSTALL_REQUIRES = ["prov", "graphviz", "pydotplus", "pydot", "validators", "requests", "rapidfuzz", "pygithub",
-                    "pandas", "pybids>=0.12.0", "duecredit", "pytest", "graphviz", "click", "rdflib-jsonld",
-                    "pyld", "rdflib", "datalad", "ontquery>=0.2.3", "orthauth>=0.0.12","tabulate", "joblib", "cognitiveatlas", "numpy>=1.16.5", "etelemetry","click-option-group"]
+                    "pandas", "pybids>=0.12.4", "duecredit", "pytest", "graphviz", "click", "rdflib-jsonld",
+                    "pyld", "rdflib", "datalad", "ontquery==0.2.3", "orthauth>=0.0.12","tabulate", "joblib", "cognitiveatlas", "numpy>=1.16.5", "etelemetry","click-option-group"]
 SCRIPTS = ["bin/nidm_query", "bin/bidsmri2nidm", "bin/csv2nidm","bin/nidm_utils"]