Merge pull request #401 from seanhatton/fmriprep

Added thickness and surface area switches
incf-nidash · Jun 4, 2024 · 6423c93 · 6423c93
2 parents 669f75a + 78edd22
commit 6423c93
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Showing 2 changed files with 92 additions and 7 deletions.
diff --git a/src/nidm/experiment/Query.py b/src/nidm/experiment/Query.py
@@ -1133,14 +1133,7 @@ def GetBrainVolumes(nidm_file_list):
         prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
         prefix prov: <http://www.w3.org/ns/prov#>
         prefix ndar: <https://ndar.nih.gov/api/datadictionary/v2/dataelement/>
-        prefix fsl: <http://purl.org/nidash/fsl#>
         prefix nidm: <http://purl.org/nidash/nidm#>
-        prefix onli: <http://neurolog.unice.fr/ontoneurolog/v3.0/instrument.owl#>
-        prefix freesurfer: <https://surfer.nmr.mgh.harvard.edu/>
-        prefix dx: <http://ncitt.ncit.nih.gov/Diagnosis>
-        prefix ants: <http://stnava.github.io/ANTs/>
-        prefix dct: <http://purl.org/dc/terms/>
-        prefix dctypes: <http://purl.org/dc/dcmitype/>
         prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
         select distinct ?ID ?tool ?softwareLabel ?federatedLabel ?laterality ?volume
@@ -1163,10 +1156,72 @@ def GetBrainVolumes(nidm_file_list):
 
             }
             """
+    df = sparql_query_nidm(nidm_file_list.split(","), query, output_file=None)
+    return df
+
+def GetBrainThickness(nidm_file_list):
+    query = """
+        # This query simply returns the brain thickness data without dependencies on other demographics/assessment measures.
+
+        prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+        prefix prov: <http://www.w3.org/ns/prov#>
+        prefix ndar: <https://ndar.nih.gov/api/datadictionary/v2/dataelement/>
+        prefix nidm: <http://purl.org/nidash/nidm#>
+        prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+        select distinct ?ID ?tool ?softwareLabel ?federatedLabel ?laterality ?volume
+        where {
+                ?tool_act a prov:Activity ;
+                            prov:qualifiedAssociation [prov:agent [nidm:NIDM_0000164 ?tool]] .
+                        ?tool_act prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] .
+                        ?tool_entity prov:wasGeneratedBy ?tool_act ;
+                                ?measure ?volume .
+
+                                ?tool_entity prov:wasGeneratedBy ?tool_act ;
+                                        ?measure ?volume .
+
+                                        ?measure a/rdfs:subClassOf* nidm:DataElement ;
+                                                 rdfs:label ?softwareLabel;
+                                                 nidm:measureOf <http://uri.interlex.org/base/ilx_0111689> .
+                                        OPTIONAL {?measure nidm:isAbout ?federatedLabel }.
+                                        OPTIONAL {?measure nidm:hasLaterality ?laterality }.
 
+            }
+            """
     df = sparql_query_nidm(nidm_file_list.split(","), query, output_file=None)
     return df
 
+def GetBrainSurfaceArea(nidm_file_list):
+    query = """
+        # This query simply returns the brain surface area data without dependencies on other demographics/assessment measures.
+
+        prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+        prefix prov: <http://www.w3.org/ns/prov#>
+        prefix ndar: <https://ndar.nih.gov/api/datadictionary/v2/dataelement/>
+        prefix nidm: <http://purl.org/nidash/nidm#>
+        prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+        select distinct ?ID ?tool ?softwareLabel ?federatedLabel ?laterality ?volume
+        where {
+                ?tool_act a prov:Activity ;
+                            prov:qualifiedAssociation [prov:agent [nidm:NIDM_0000164 ?tool]] .
+                        ?tool_act prov:qualifiedAssociation [prov:agent [ndar:src_subject_id ?ID]] .
+                        ?tool_entity prov:wasGeneratedBy ?tool_act ;
+                                ?measure ?volume .
+
+                                ?tool_entity prov:wasGeneratedBy ?tool_act ;
+                                        ?measure ?volume .
+
+                                        ?measure a/rdfs:subClassOf* nidm:DataElement ;
+                                                rdfs:label ?softwareLabel;
+                                                nidm:measureOf <http://purl.obolibrary.org/obo/PATO_0001323> .
+                                        OPTIONAL {?measure nidm:isAbout ?federatedLabel }.
+                                        OPTIONAL {?measure nidm:hasLaterality ?laterality }.
+
+            }
+            """
+    df = sparql_query_nidm(nidm_file_list.split(","), query, output_file=None)
+    return df
 
 def expandNIDMAbbreviation(shortKey) -> str:
     """

diff --git a/src/nidm/experiment/tools/nidm_query.py b/src/nidm/experiment/tools/nidm_query.py
@@ -10,6 +10,8 @@
 from nidm.experiment.Query import (
     GetBrainVolumeDataElements,
     GetBrainVolumes,
+    GetBrainThickness,
+    GetBrainSurfaceArea,
     GetDataElements,
     GetInstrumentVariables,
     GetParticipantIDs,
@@ -81,6 +83,18 @@
     is_flag=True,
     help="Parameter, if set, will return all brain volume data elements and values along with participant IDs in NIDM file",
 )
+@optgroup.option(
+    "--get_brainthickness",
+    "-bt",
+    is_flag=True,
+    help="Parameter, if set, will return all brain thickness data elements and values along with participant IDs in NIDM file",
+)
+@optgroup.option(
+    "--get_brainsurfacearea",
+    "-bsa",
+    is_flag=True,
+    help="Parameter, if set, will return all brain surface area data elements and values along with participant IDs in NIDM file",
+)
 @optgroup.option(
     "--get_fields",
     "-gf",
@@ -122,6 +136,8 @@ def query(
     get_instrument_vars,
     get_dataelements,
     get_brainvols,
+    get_brainthickness,
+    get_brainsurfacearea,
     get_dataelements_brainvols,
     get_fields,
     uri,
@@ -266,6 +282,20 @@ def query(
             brainvol.to_csv(output_file)
         else:
             print(brainvol.to_string())
+    elif get_brainthickness:
+        brainthx = GetBrainThickness(nidm_file_list=nidm_file_list)
+        # if output file parameter specified
+        if output_file is not None:
+            brainthx.to_csv(output_file)
+        else:
+            print(brainvol.to_string())
+    elif get_brainsurfacearea:
+        brainsurfacearea = GetBrainSurfaceArea(nidm_file_list=nidm_file_list)
+        # if output file parameter specified
+        if output_file is not None:
+            brainsurfacearea.to_csv(output_file)
+        else:
+            print(brainvol.to_string())            
     elif query_file:
         df = sparql_query_nidm(nidm_file_list.split(","), query_file, output_file)