Merge pull request #9 from MaastrichtU-CDS/release/0.3

Release/0.3
MaastrichtU-CDS · Oct 6, 2023 · 155f5a4 · 155f5a4
2 parents 17f022d + c42dfea
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diff --git a/README.md b/README.md
@@ -38,10 +38,27 @@ Usage: ldcm-parse [OPTIONS] DICOM_INPUT_FOLDER
 
 Options:
   -o, --ontology-file TEXT  Location of ontology file to use for override.
+  -fp, --file-persistent    Store file path while parsing metadata.
   --help                    Show this message and exit.
 ```
 
 The output is saved in linkeddicom.ttl in the DICOM_INPUT_FOLDER. This data can be used by importing it into an RDF endpoint (such as Apache Jena or GraphDB).
+**If you want to use the files afterwards to calculate DVH parameters, you need to include the -fp option.**
+
+### Calculating DVH curves locally
+
+Based on the previous parsing (`ldcm-parse`) you can calculate DVH curve results and store them in a JSON-LD file (per RTSTRUCT-RTDOSE combination). Currently, the combination is being calculated following the references in the DICOM file:
+
+- RTDOSE references to RTPlan
+- RTPlan references to RTStruct
+
+A copy of this help is presented below:
+```
+Usage: ldcm-calc-dvh [OPTIONS] LDCM_RDF_LOCATION OUTPUT_LOCATION
+
+Options:
+  --help  Show this message and exit.
+```
 
 ### DICOM SCP service
 This tool can be used if you want to start a DICOM SCP service which supports C-STORE commands.
@@ -56,10 +73,12 @@ Usage: ldcm-scp [OPTIONS] PORT
   the analysis is triggered in a separate thread.
 
 Options:
-  -o, --ontology-file TEXT    Location of ontology file to use for override.
-  -s, --sparql-endpoint TEXT  SPARQL endpoint URL to post the resulting
-                              triples towards
-  --help                      Show this message and exit.
+  -o, --ontology-file TEXT       Location of ontology file to use for
+                                 override.
+  -s, --sparql-endpoint TEXT     SPARQL endpoint URL to post the resulting
+                                 triples towards
+  -dvh, --dose-volume-histogram  Compute and store DVH for all available structures.
+  --help                         Show this message and exit.
 ```
 
 By default, the UUID for the DICOM association is used as filename for the created local turtle file.

diff --git a/examples/queries/README.md b/examples/queries/README.md
@@ -3,4 +3,11 @@
 The following example queries are listed below:
 
 * **[RTSTRUCT.sparql](RTSTRUCT.sparql)** Find the structure names for all patients in various RTSTRUCT files
-* **[RTSTRUCT_CT.sparql](RTSTRUCT_CT.sparql)** Similar as `RTSTRUCT.sparql` however now with the referenced CT information
+* **[RTSTRUCT_CT.sparql](RTSTRUCT_CT.sparql)** Similar as `RTSTRUCT.sparql` however now with the referenced CT information
+* **[RT_package.sparql](RT_package.sparql)** Query which fetches the RT Dose -> Plan -> Structure -> CT (series) reference
+
+## Specific DVH queries
+* **[dose_overview.sparql](dose_overview.sparql)** Query the general/generic dose information
+* **[dvh_curve.sparql](dvh_curve.sparql)** Give a DVH curve points for a specific structure
+* **[dvh_d_point.sparql](dvh_d_point.sparql)** Query a specific DVH-d point (d30)
+* **[dvh_v_point.sparql](dvh_v_point.sparql)** Query a specific DVH-v point (v10)
diff --git a/examples/queries/RT_package.sparql b/examples/queries/RT_package.sparql
@@ -0,0 +1,34 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX ldcm: <https://johanvansoest.nl/ontologies/LinkedDicom/>
+
+select * 
+where { 
+	?rtDose rdf:type ldcm:Radiotherapy_Dose_Object;
+         ldcm:T300C0002 [
+	        ldcm:has_sequence_item [
+        		ldcm:R00081155 ?rtPlan;
+    		];
+	    ].
+
+    ?rtPlan rdf:type ldcm:Radiotherapy_Plan_Object;
+    	ldcm:T300C0060 [
+	        ldcm:has_sequence_item [
+        		ldcm:R00081155 ?rtStruct;
+    		];
+	    ].
+
+    ?rtStruct rdf:type ldcm:Radiotherapy_Structure_Object;
+    	ldcm:T30060010 [
+        	ldcm:has_sequence_item [
+		        ldcm:T30060012 [
+			        ldcm:has_sequence_item [
+        				ldcm:T30060014 [
+					        ldcm:has_sequence_item [
+        						ldcm:R0020000E ?ctSeries;
+						    ];
+					    ];
+				    ];
+			    ];
+    		];
+    	].
+}
diff --git a/examples/queries/dose_overview.sparql b/examples/queries/dose_overview.sparql
@@ -0,0 +1,19 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX schema: <https://schema.org/>
+prefix ldcm-dvh: <https://johanvansoest.nl/ontologies/LinkedDicom-dvh/>
+PREFIX ou: <http://purl.obolibrary.org/obo/UO_>
+
+select ?calculation_job ?softwareUsed ?dateTime ?structureName ?sRGB ?minDose ?meanDose ?maxDose ?volumeCC
+where { 
+	?calculation_job rdf:type ldcm-dvh:CalculationResult;
+    	ldcm-dvh:containsStructureDose ?structureDose;
+     	schema:SoftwareApplication ?softwareUsed;
+      	schema:dateCreated ?dateTime.
+
+    ?structureDose ldcm-dvh:structureName ?structureName;
+		<https://www.wikidata.org/wiki/Q284140> ?sRGB;
+		ldcm-dvh:min [ schema:value ?minDose; ];
+		ldcm-dvh:mean [ schema:value ?meanDose; ];
+		ldcm-dvh:max [ schema:value ?maxDose; ];
+		ldcm-dvh:volume [ schema:value ?volumeCC; rdf:type ou:0000097; ];
+}
diff --git a/examples/queries/dvh_curve.sparql b/examples/queries/dvh_curve.sparql
@@ -0,0 +1,19 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX schema: <https://schema.org/>
+prefix ldcm-dvh: <https://johanvansoest.nl/ontologies/LinkedDicom-dvh/>
+PREFIX ou: <http://purl.obolibrary.org/obo/UO_>
+
+select *
+where { 
+	?calculation_job rdf:type ldcm-dvh:CalculationResult;
+    	ldcm-dvh:containsStructureDose ?structureDose.
+
+    ?structureDose ldcm-dvh:structureName "Lung_L";
+        <https://www.wikidata.org/wiki/Q284140> ?sRGB;
+    	ldcm-dvh:dvh_curve ?curve.
+    ?curve ldcm-dvh:dvh_point [
+    	ldcm-dvh:dvh_d_point ?d_value;
+     	ldcm-dvh:dvh_v_point ?v_value;
+	];
+}
+ORDER BY ?d_value
diff --git a/examples/queries/dvh_d_point.sparql b/examples/queries/dvh_d_point.sparql
@@ -0,0 +1,24 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX schema: <https://schema.org/>
+prefix ldcm-dvh: <https://johanvansoest.nl/ontologies/LinkedDicom-dvh/>
+PREFIX ou: <http://purl.obolibrary.org/obo/UO_>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+select ?calculation_job (xsd:int(round(avg(?v_value))) as ?v)
+where {
+    BIND(xsd:double(30) AS ?d_point).
+    BIND(xsd:double(0.01) AS ?tolerance).
+    BIND("Heart" AS ?structureName)
+
+	?calculation_job rdf:type ldcm-dvh:CalculationResult;
+    	ldcm-dvh:containsStructureDose ?structureDose.
+
+    ?structureDose ldcm-dvh:structureName ?structureName;
+    	ldcm-dvh:dvh_curve ?curve.
+    ?curve ldcm-dvh:dvh_point [
+    	ldcm-dvh:dvh_d_point ?d_value;
+     	ldcm-dvh:dvh_v_point ?v_value;
+	];
+  filter ((?d_value > (?d_point - ?tolerance)) && (?d_value < (?d_point + ?tolerance)))
+}
+GROUP BY ?calculation_job
diff --git a/examples/queries/dvh_v_point.sparql b/examples/queries/dvh_v_point.sparql
@@ -0,0 +1,24 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX schema: <https://schema.org/>
+prefix ldcm-dvh: <https://johanvansoest.nl/ontologies/LinkedDicom-dvh/>
+PREFIX ou: <http://purl.obolibrary.org/obo/UO_>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+select ?calculation_job ((round(avg(?d_value*10))/10) as ?d)
+where {
+    BIND(xsd:double(10) AS ?v_point).
+    BIND(xsd:double(0.1) AS ?tolerance).
+    BIND("Heart" AS ?structureName)
+
+	?calculation_job rdf:type ldcm-dvh:CalculationResult;
+    	ldcm-dvh:containsStructureDose ?structureDose.
+
+    ?structureDose ldcm-dvh:structureName ?structureName;
+    	ldcm-dvh:dvh_curve ?curve.
+    ?curve ldcm-dvh:dvh_point [
+    	ldcm-dvh:dvh_d_point ?d_value;
+     	ldcm-dvh:dvh_v_point ?v_value;
+	];
+  filter ((?v_value > (?v_point - ?tolerance)) && (?v_value < (?v_point + ?tolerance)))
+}
+GROUP BY ?calculation_job