add SRAnonTool

SMI · Dec 2, 2023 · 82bae06 · 82bae06
1 parent b695888
commit 82bae06
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Showing 3 changed files with 26 additions and 9 deletions.
diff --git a/README.md b/README.md
@@ -18,17 +18,19 @@ Required arguments:
 -   `-a` / `--anon-script`: Path to a CTP DICOM anonymizer script file. Samples
     can be found
     [here](https://github.com/johnperry/CTP/tree/master/source/files/profiles/dicom)
+-   `-s` / `--sr-anon-tool`: Path to the
+    [SRAnonTool](https://github.com/SMI/SmiServices/tree/master/src/applications/SRAnonTool)
 
 To anonymise a single file:
 
 ```console
-$ java -jar <jar> -a <anon-script> <src-file> <anon-file>
+$ java -jar <jar> -a <anon-script> -s <sr-anon-tool> <src-file> <anon-file>
 ```
 
 To anonymise multiple files:
 
 ```console
-$ java -jar <jar> -a <anon-script> (<src-file>:<anon-file>)...
+$ java -jar <jar> -a <anon-script> -s <sr-anon-tool> (<src-file>:<anon-file>)...
 ```
 
 ## Development

diff --git a/src/main/java/uk/ac/ed/epcc/ctp_anon_cli/Program.java b/src/main/java/uk/ac/ed/epcc/ctp_anon_cli/Program.java
@@ -27,6 +27,17 @@ public static void main(String[] args) throws ParseException {
       .build();
     options.addOption(option);
 
+    option =
+      Option
+        .builder("s")
+        .argName("file")
+        .hasArg()
+        .longOpt("sr-anon-tool")
+        .desc("SR anonymisation tool")
+        .required()
+        .build();
+    options.addOption(option);
+
     CommandLineParser parser = new DefaultParser();
     CommandLine cli = null;
     try {
@@ -42,7 +53,12 @@ public static void main(String[] args) throws ParseException {
     );
 
     if (!anonScriptFile.isFile()) throw new IllegalArgumentException(
-      "Cannot find anonymisation script file: " + anonScriptFile.getPath()
+      "Cannot find anonymisation script file"
+    );
+
+    File srAnonTool = new File(Paths.get(cli.getOptionValue("s")).toString());
+    if (!srAnonTool.isFile()) throw new IllegalArgumentException(
+      "Cannot find SRAnonTool"
     );
 
     List<String> files = cli.getArgList();
@@ -58,7 +74,6 @@ public static void main(String[] args) throws ParseException {
       System.exit(1);
     }
 
-    // TODO SRAnon
     SmiCtpProcessor anonymizer = new SmiCtpProcessor(
       anonScriptFile,
       null,
@@ -67,7 +82,7 @@ public static void main(String[] args) throws ParseException {
       false,
       false,
       null,
-      null
+      srAnonTool
     );
 
     int rc = 0;

diff --git a/src/main/java/uk/ac/ed/epcc/ctp_anon_cli/SmiCtpProcessor.java b/src/main/java/uk/ac/ed/epcc/ctp_anon_cli/SmiCtpProcessor.java
@@ -25,7 +25,7 @@ public class SmiCtpProcessor {
   private boolean _recompress;
   private boolean _setBIRElement;
   private boolean _testmode;
-  private String _SRAnonTool;
+  private File _srAnonTool;
 
   private PixelScript _pixelScript;
 
@@ -41,13 +41,13 @@ public SmiCtpProcessor(
     boolean setBIRElement,
     boolean testmode,
     String check,
-    String SRAnonTool
+    File srAnonTool
   ) {
     _decompress = decompress;
     _recompress = recompress;
     _setBIRElement = setBIRElement;
     _testmode = testmode;
-    _SRAnonTool = SRAnonTool;
+    _srAnonTool = srAnonTool;
 
     if (pixelAnonScriptFile != null) {
       _pixelScript = new PixelScript(pixelAnonScriptFile);
@@ -132,7 +132,7 @@ public void anonymizeImpl(File inFile, File outFile) throws Exception {
     if (!isSR) return;
 
     String commandArray[] = {
-      _SRAnonTool,
+      _srAnonTool.getAbsolutePath(),
       "-i",
       origFile.getAbsolutePath(),
       "-o",