add extract_edf_header stub

somnonetz · Mar 13, 2020 · 30d58c1 · 30d58c1
1 parent bff551c
commit 30d58c1
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Showing 4 changed files with 48 additions and 32 deletions.
diff --git a/resources/catalog/snet-pipeline/bin/snet-pipeline b/resources/catalog/snet-pipeline/bin/snet-pipeline
diff --git a/resources/catalog/somnonetz-pipeline/bin/extract_edf_header b/resources/catalog/somnonetz-pipeline/bin/extract_edf_header
@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+
+import argparse
+from pyxnat import Interface
+from edfrd import read_header
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-session', required=True)
+    parser.add_argument('-subject', required=True)
+    parser.add_argument('-project', required=True)
+    parser.add_argument('-xnatID')
+    parser.add_argument('-host', required=True)
+    parser.add_argument('-user', required=True)
+    parser.add_argument('-pwd', required=True)
+
+    # args = parser.parse_args()
+    # xnat = Interface(args.host, user=args.user, password=args.pwd)
+    # scan = xnat.select(f'/project/{args.project}/subject/{args.subject}/experiment/{args.session}/scan/psg')
+    # remote_edf = scan.resources().files().first()
+    # edf_path = remote_edf.get(f'./{remote_edf.label()}')
+    # header = read_header(edf_path)
+
+    # scan.insert(**{
+    #     'scans': 'snet01:psgScanData',
+    #     'snet01:psgScanData/edfversion': header.version,
+    #     'snet01:psgScanData/patientid': header.local_patient_identification,
+    #     'snet01:psgScanData/localrecordid': header.local_recording_identification,
+    #     'snet01:psgScanData/recordingstartdate': header.startdate_of_recording,
+    #     'snet01:psgScanData/recordingstarttime': header.starttime_of_recording,
+    #     'snet01:psgScanData/numberofheaderbytes': header.number_of_bytes_in_header_record,
+    #     'snet01:psgScanData/reservedheaderfield': header.reserved,
+    #     'snet01:psgScanData/numberofdatarecords': header.number_of_data_records,
+    #     # 'snet01:psgScanData/durationofdatarecordseconds': header.duration_of_a_data_record,
+    #     'snet01:psgScanData/numberofsignalsindatarecord': header.number_of_signals,
+    #     # 'snet01:psgScanData/psgdevice': '?',
+    #     # 'snet01:psgScanData/durationofrecordhours': header.duration_of_a_data_record,
+    #     # 'snet01:psgScanData/continuousdataflag': '0',
+    #     # 'snet01:psgScanData/comment': '',
+    # })
diff --git a/...snet-pipeline/resources/snet-resource.xml → ...pipeline/resources/extract_edf_header.xml b/...snet-pipeline/resources/snet-resource.xml → ...pipeline/resources/extract_edf_header.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <pip:Resource xmlns:pip="http://nrg.wustl.edu/pipeline">
-	<pip:name>snet-pipeline</pip:name>
-	<pip:location>snet-pipeline/bin</pip:location>
+	<pip:name>extract_edf_header</pip:name>
+	<pip:location>somnonetz-pipeline/bin</pip:location>
 	<pip:type>Executable</pip:type>
-	<pip:description>Executes shell script</pip:description>
+	<pip:description>Extract EDF header data and write back to xnat</pip:description>
 	<pip:input>
 		<pip:argument id="session">
 			<pip:name>session</pip:name>
@@ -21,10 +21,6 @@
 			<pip:name>xnatID</pip:name>
 			<pip:description>XNAT Session ID</pip:description>
 		</pip:argument>
-		<pip:argument id="algorithm">
-			<pip:name>algorithm</pip:name>
-			<pip:description>algorithm to be applied</pip:description>
-		</pip:argument>
 		<pip:argument id="host">
 			<pip:name>host</pip:name>
 			<pip:description>XNAT Host</pip:description>

diff --git a/...s/catalog/snet-pipeline/snet-pipeline.xml → ...somnonetz-pipeline/somnonetz-pipeline.xml b/...s/catalog/snet-pipeline/snet-pipeline.xml → ...somnonetz-pipeline/somnonetz-pipeline.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <Pipeline xmlns="http://nrg.wustl.edu/pipeline" xmlns:xi="http://www.w3.org/2001/XInclude" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:nrgString="java:org.nrg.pipeline.utils.StringUtils" xsi:schemaLocation="http://nrg.wustl.edu/pipeline ..\schema\pipeline.xsd">
-	<name>snet-pipeline</name>
-	<location>snet-pipeline</location>
-	<description>Execution of polysomnography analysis tools</description>
+	<name>somnonetz-pipeline</name>
+	<location>somnonetz-pipeline</location>
+	<description>Pipeline for use with snet-plugin</description>
 	<documentation>
 		<input-parameters>
 			<parameter>
@@ -33,20 +33,6 @@
 				</values>
 				<description>The XNAT session ID</description>
 			</parameter>
-			<parameter>
-				<name>algorithm</name>
-				<values>
-					<csv>sn_getEDFHeaderdata</csv>
-				</values>
-				<description>method for </description>
-			</parameter>
-			<parameter>
-				<name>notify</name>
-				<values>
-					<csv>0</csv>
-				</values>
-				<description>Set the value to 1 if you want the pipeline to notify the user when complete. 0 otherwise</description>
-			</parameter>
 		</input-parameters>
 	</documentation>
 	<parameters>
@@ -58,8 +44,8 @@
         </parameter>
 	</parameters>
 	<steps>
-		<step id="0" description="Execute shell script" workdirectory="^/Pipeline/parameters/parameter[name='workdir']/values/unique/text()^">
-			<resource name="snet-resource.xml" location="snet-pipeline/resources">				
+		<step id="0" description="Extract EDF header data and write back to xnat" workdirectory="^/Pipeline/parameters/parameter[name='workdir']/values/unique/text()^">
+			<resource name="extract_edf_header.xml" location="somnonetz-pipeline/resources">				
 				<argument id="session">
 					<value>^/Pipeline/parameters/parameter[name='sessionLabel']/values/unique/text()^</value>
 				</argument>
@@ -72,9 +58,6 @@
 				<argument id="xnatID">
 					<value>^/Pipeline/parameters/parameter[name='xnatID']/values/unique/text()^</value>
 				</argument>
-				<argument id="algorithm">
-					<value>^/Pipeline/parameters/parameter[name='algorithm']/values/unique/text()^</value>
-				</argument>
 				<argument id="host">
 					<value>^if (count(/Pipeline/parameters/parameter[name='aliasHost']/values) > 0) then /Pipeline/parameters/parameter[name='aliasHost']/values/unique/text() else /Pipeline/parameters/parameter[name='host']/values/unique/text()^</value>
 				</argument>