#1307 : dcm4che utilities : Fix issues and improve documentation for …

…several dcm4che tools
dcm4che · Apr 3, 2023 · a50891d · a50891d
1 parent 27ee3ac
commit a50891d
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diff --git a/README.md b/README.md
@@ -92,6 +92,7 @@ Utilities
 - [deidentify][]: De-identify one or several DICOM files
 - [emf2sf][]: Convert DICOM Enhanced Multi-frame image to legacy DICOM Single-frame images
 - [findscu][]: Invoke DICOM C-FIND Query Request
+- [fixlo2un][]: Fixes length of private tags truncated to 2 bytes on conversion from implicit VR to explicit VR Transfer Syntax
 - [getscu][]: Invoke DICOM C-GET Retrieve Request
 - [hl72xml][]: Convert HL7 v2.x message in XML presentation
 - [hl7pdq][]: Query HL7 v2.x Patient Demographics Supplier
@@ -101,6 +102,8 @@ Utilities
 - [ianscp][]: DICOM Instance Availability Notification receiver 
 - [ianscu][]: Send DICOM Instance Availability Notification
 - [jpg2dcm][]: Convert JPEG images or MPEG videos in DICOM files
+- [json2dcm][]: Converts JSON file to DICOM file
+- [json2index][]: Creates search index for UI configuration from JSON schema files
 - [json2props][]: Convert Archive configuration schema JSON files to key/value properties files and vice versa
 - [json2rst][]: Generate ReStructuredText files from Archive configuration schema JSON files
 - [maskpxdata][]: Mask information burned into the Pixel Data
@@ -118,6 +121,7 @@ Utilities
 - [swappxdata][]: Swaps bytes of uncompressed pixel data in DICOM files
 - [syslog][]: Send Syslog messages via TCP/TLS or UDP to a Syslog Receiver
 - [syslogd][]: Receives RFC 5424 Syslog messages via TCP/TLS or UDP
+- [tpl2xml][]: Converts private dictionaries present in template file(s) to xml file(s).
 - [upsscu][]: Invokes services of Unified Procedure Step Service Class
 - [wadors][]: Wado RS Client Simulator 
 - [wadows][]: Wado WS Client Simulator 
@@ -141,6 +145,7 @@ Utilities
 [deidentify]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-deidentify/README.md
 [emf2sf]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-emf2sf/README.md
 [findscu]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-findscu/README.md
+[fixlo2un]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-fixlo2un/README.md
 [getscu]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-getscu/README.md
 [hl72xml]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-hl72xml/README.md
 [hl7pdq]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-hl7pdq/README.md
@@ -150,6 +155,8 @@ Utilities
 [ianscp]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-ianscp/README.md
 [ianscu]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-ianscu/README.md
 [jpg2dcm]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-jpg2dcm/README.md
+[json2dcm]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-json2dcm/README.md
+[json2index]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-json2index/README.md
 [json2props]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-json2props/README.md
 [json2rst]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-json2rst/README.md
 [maskpxdata]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-maskpxdata/README.md
@@ -167,6 +174,7 @@ Utilities
 [swappxdata]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-swappxdata/README.md
 [syslog]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-syslog/README.md
 [syslogd]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-syslogd/README.md
+[tpl2xml]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-tpl2xml/README.md
 [upsscu]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-upsscu/README.md
 [wadors]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-wadors/README.md
 [wadows]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-wadows/README.md

diff --git a/dcm4che-assembly/src/bin/fixlo2un b/dcm4che-assembly/src/bin/fixlo2un
@@ -38,6 +38,8 @@ fi
 
 # Setup the classpath
 CP="$DCM4CHE_HOME/lib/$MAIN_JAR"
+CP="$CP:$DCM4CHE_HOME/lib/dcm4che-tool-common-${project.version}.jar"
+CP="$CP:$DCM4CHE_HOME/lib/commons-cli-${commons-cli.version}.jar"
 
 # For Cygwin, switch paths to Windows format before running java
 if $cygwin; then

diff --git a/dcm4che-assembly/src/bin/fixlo2un.bat b/dcm4che-assembly/src/bin/fixlo2un.bat
@@ -41,5 +41,7 @@ set JAVA=%JAVA_HOME%\bin\java
 :SKIP_SET_JAVA_HOME
 
 set CP=%DCM4CHE_HOME%\lib\%MAIN_JAR%
+set CP=%CP%;%DCM4CHE_HOME%\lib\dcm4che-tool-common-${project.version}.jar
+set CP=%CP%;%DCM4CHE_HOME%\lib\commons-cli-${commons-cli.version}.jar
 
 "%JAVA%" %JAVA_OPTS% -cp "%CP%" %MAIN_CLASS% %ARGS%
diff --git a/dcm4che-assembly/src/bin/json2index b/dcm4che-assembly/src/bin/json2index
@@ -38,6 +38,8 @@ fi
 
 # Setup the classpath
 CP="$DCM4CHE_HOME/lib/$MAIN_JAR"
+CP="$CP:$DCM4CHE_HOME/lib/dcm4che-tool-common-${project.version}.jar"
+CP="$CP:$DCM4CHE_HOME/lib/commons-cli-${commons-cli.version}.jar"
 CP="$CP:$DCM4CHE_HOME/lib/jakarta.json-${jakarta.json.version}.jar"
 
 # For Cygwin, switch paths to Windows format before running java

diff --git a/dcm4che-assembly/src/bin/json2index.bat b/dcm4che-assembly/src/bin/json2index.bat
@@ -41,6 +41,8 @@ set JAVA=%JAVA_HOME%\bin\java
 :SKIP_SET_JAVA_HOME
 
 set CP=%DCM4CHE_HOME%\lib\%MAIN_JAR%
+set CP=%CP%;%DCM4CHE_HOME%\lib\dcm4che-tool-common-${project.version}.jar
+set CP=%CP%;%DCM4CHE_HOME%\lib\commons-cli-${commons-cli.version}.jar
 set CP=%CP%;%DCM4CHE_HOME%\lib\jakarta.json-${jakarta.json.version}.jar
 
 "%JAVA%" %JAVA_OPTS% -cp "%CP%" %MAIN_CLASS% %ARGS%
diff --git a/dcm4che-assembly/src/bin/json2props b/dcm4che-assembly/src/bin/json2props
@@ -38,6 +38,8 @@ fi
 
 # Setup the classpath
 CP="$DCM4CHE_HOME/lib/$MAIN_JAR"
+CP="$CP:$DCM4CHE_HOME/lib/dcm4che-tool-common-${project.version}.jar"
+CP="$CP:$DCM4CHE_HOME/lib/commons-cli-${commons-cli.version}.jar"
 CP="$CP:$DCM4CHE_HOME/lib/jakarta.json-${jakarta.json.version}.jar"
 
 # For Cygwin, switch paths to Windows format before running java

diff --git a/dcm4che-assembly/src/bin/json2props.bat b/dcm4che-assembly/src/bin/json2props.bat
@@ -41,6 +41,8 @@ set JAVA=%JAVA_HOME%\bin\java
 :SKIP_SET_JAVA_HOME
 
 set CP=%DCM4CHE_HOME%\lib\%MAIN_JAR%
+set CP=%CP%;%DCM4CHE_HOME%\lib\dcm4che-tool-common-${project.version}.jar
+set CP=%CP%;%DCM4CHE_HOME%\lib\commons-cli-${commons-cli.version}.jar
 set CP=%CP%;%DCM4CHE_HOME%\lib\jakarta.json-${jakarta.json.version}.jar
 
 "%JAVA%" %JAVA_OPTS% -cp "%CP%" %MAIN_CLASS% %ARGS%
diff --git a/dcm4che-assembly/src/bin/json2rst b/dcm4che-assembly/src/bin/json2rst
@@ -38,6 +38,8 @@ fi
 
 # Setup the classpath
 CP="$DCM4CHE_HOME/lib/$MAIN_JAR"
+CP="$CP:$DCM4CHE_HOME/lib/dcm4che-tool-common-${project.version}.jar"
+CP="$CP:$DCM4CHE_HOME/lib/commons-cli-${commons-cli.version}.jar"
 CP="$CP:$DCM4CHE_HOME/lib/jakarta.json-${jakarta.json.version}.jar"
 
 # For Cygwin, switch paths to Windows format before running java

diff --git a/dcm4che-assembly/src/bin/json2rst.bat b/dcm4che-assembly/src/bin/json2rst.bat
@@ -41,6 +41,8 @@ set JAVA=%JAVA_HOME%\bin\java
 :SKIP_SET_JAVA_HOME
 
 set CP=%DCM4CHE_HOME%\lib\%MAIN_JAR%
+set CP=%CP%;%DCM4CHE_HOME%\lib\dcm4che-tool-common-${project.version}.jar
+set CP=%CP%;%DCM4CHE_HOME%\lib\commons-cli-${commons-cli.version}.jar
 set CP=%CP%;%DCM4CHE_HOME%\lib\jakarta.json-${jakarta.json.version}.jar
 
 "%JAVA%" %JAVA_OPTS% -cp "%CP%" %MAIN_CLASS% %ARGS%
diff --git a/dcm4che-assembly/src/bin/planarconfig b/dcm4che-assembly/src/bin/planarconfig
@@ -39,8 +39,10 @@ fi
 # Setup the classpath
 CP="$DCM4CHE_HOME/etc/planarconfig/"
 CP="$CP:$DCM4CHE_HOME/lib/$MAIN_JAR"
+CP="$CP:$DCM4CHE_HOME/lib/commons-cli-${commons-cli.version}.jar"
 CP="$CP:$DCM4CHE_HOME/lib/dcm4che-core-${project.version}.jar"
 CP="$CP:$DCM4CHE_HOME/lib/dcm4che-image-${project.version}.jar"
+CP="$CP:$DCM4CHE_HOME/lib/dcm4che-tool-common-${project.version}.jar"
 CP="$CP:$DCM4CHE_HOME/lib/slf4j-api-${slf4j.version}.jar"
 CP="$CP:$DCM4CHE_HOME/lib/logback-core-${logback.version}.jar"
 CP="$CP:$DCM4CHE_HOME/lib/logback-classic-${logback.version}.jar"

diff --git a/dcm4che-assembly/src/bin/planarconfig.bat b/dcm4che-assembly/src/bin/planarconfig.bat
@@ -42,8 +42,10 @@ set JAVA=%JAVA_HOME%\bin\java
 
 set CP=%DCM4CHE_HOME%\etc\planarconfig\
 set CP=%CP%;%DCM4CHE_HOME%\lib\%MAIN_JAR%
+set CP=%CP%;%DCM4CHE_HOME%\lib\commons-cli-${commons-cli.version}.jar
 set CP=%CP%;%DCM4CHE_HOME%\lib\dcm4che-core-${project.version}.jar
 set CP=%CP%;%DCM4CHE_HOME%\lib\dcm4che-image-${project.version}.jar
+set CP=%CP%;%DCM4CHE_HOME%\lib\dcm4che-tool-common-${project.version}.jar
 set CP=%CP%;%DCM4CHE_HOME%\lib\slf4j-api-${slf4j.version}.jar
 set CP=%CP%;%DCM4CHE_HOME%\lib\logback-core-${logback.version}.jar
 set CP=%CP%;%DCM4CHE_HOME%\lib\logback-classic-${logback.version}.jar

diff --git a/dcm4che-tool/dcm4che-tool-fixlo2un/README.md b/dcm4che-tool/dcm4che-tool-fixlo2un/README.md
@@ -1,23 +1,30 @@
-```console
-$ fixlo2un 
-Usage: fixlo2un SOURCE DEST
-       fixlo2un SOURCE... DIRECTORY
-```
-```console
-$ fixlo2un corrupted.dcm fixed.dcm
+````
+usage: fixlo2un SOURCE DEST
+or fixlo2un SOURCE... DIRECTORY
+
+Utility to fix length of private (gggg,00ee) elements truncated to 2 bytes
+on conversion from implicit VR to explicit VR Transfer Syntax
+-
+Options:
+ -h,--help      display this help and exit
+ -V,--version   output version information and exit
+-
+Example: fixlo2un corrupted.dcm fixed.dcm
 corrupted.dcm -> fixed.dcm
-  2008: (0043,0042) LO #66 -> UN #4718658
-  4720674: (0045,0044) LO #68 -> UN #4390980
-  9111662: (0047,0047) LO #70 -> UN #4522054
-  24709496: (004D,004B) LO #76 -> UN #4849740
-  29559244: (004F,004F) LO #78 -> UN #5111886
-  34671138: (0053,0052) LO #82 -> UN #5242962
-  39914108: (0055,0054) LO #84 -> UN #5439572
-  45353688: (0057,0057) LO #86 -> UN #5570646
-  50924342: (0059,0059) LO #88 -> UN #5701720
-  68357220: (005D,005C) LO #92 -> UN #6029404
-  74386632: (005D,005D) LO #94 -> UN #6094942
-  80481582: (005F,005F) LO #96 -> UN #6226016
-  86707606: (0061,005F) LO #96 -> UN #6226016
-  92933630: (0065,006C) LO #126 -> UN #9371774
-```
+=> Results in
+2008: (0043,0042) LO #66 -> UN #4718658
+4720674: (0045,0044) LO #68 -> UN #4390980
+9111662: (0047,0047) LO #70 -> UN #4522054
+24709496: (004D,004B) LO #76 -> UN #4849740
+29559244: (004F,004F) LO #78 -> UN #5111886
+34671138: (0053,0052) LO #82 -> UN #5242962
+39914108: (0055,0054) LO #84 -> UN #5439572
+45353688: (0057,0057) LO #86 -> UN #5570646
+50924342: (0059,0059) LO #88 -> UN #5701720
+68357220: (005D,005C) LO #92 -> UN #6029404
+74386632: (005D,005D) LO #94 -> UN #6094942
+80481582: (005F,005F) LO #96 -> UN #6226016
+86707606: (0061,005F) LO #96 -> UN #6226016
+92933630: (0065,006C) LO #126 -> UN #9371774
+-
+````
diff --git a/dcm4che-tool/dcm4che-tool-fixlo2un/pom.xml b/dcm4che-tool/dcm4che-tool-fixlo2un/pom.xml
@@ -52,5 +52,12 @@
 
   <artifactId>dcm4che-tool-fixlo2un</artifactId>
 
+  <dependencies>
+    <dependency>
+      <groupId>org.dcm4che.tool</groupId>
+      <artifactId>dcm4che-tool-common</artifactId>
+      <version>${project.version}</version>
+    </dependency>
+  </dependencies>
 
 </project>
diff --git a/dcm4che-tool/dcm4che-tool-fixlo2un/src/main/java/org/dcm4che3/tool/fixlo2un/FixLO2UN.java b/dcm4che-tool/dcm4che-tool-fixlo2un/src/main/java/org/dcm4che3/tool/fixlo2un/FixLO2UN.java
@@ -41,6 +41,11 @@
 
 package org.dcm4che3.tool.fixlo2un;
 
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.dcm4che3.tool.common.CLIUtils;
+
 import java.io.IOException;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
@@ -49,13 +54,16 @@
 import java.nio.file.*;
 import java.nio.file.attribute.BasicFileAttributes;
 import java.util.EnumSet;
+import java.util.List;
+import java.util.ResourceBundle;
 
 /**
  * @author Gunter Zeilinger <gunterze@gmail.com>
  * @since May 2019
  */
 public class FixLO2UN extends SimpleFileVisitor<Path> {
 
+    private static final ResourceBundle rb = ResourceBundle.getBundle("org.dcm4che3.tool.fixlo2un.messages");
     private final ByteBuffer buffer = ByteBuffer.wrap(new byte[] { 0x55, 0x4e, 0, 0, 0, 0, 0, 0 })
             .order(ByteOrder.LITTLE_ENDIAN);
     private final Path srcPath;
@@ -68,21 +76,35 @@ private FixLO2UN(Path srcPath, Path destPath, Dest dest) {
         this.dest = dest;
     }
 
-    public static void main(String[] args) throws IOException {
-        if (args.length < 2) {
-            System.out.println("Usage: fixlo2un SOURCE DEST");
-            System.out.println("       fixlo2un SOURCE... DIRECTORY");
-            System.exit(-1);
-        }
-        Path destPath = Paths.get(args[args.length - 1]);
-        if (!Files.isDirectory(destPath) && (args.length > 2 || !Files.isRegularFile(Paths.get(args[0])))) {
-            System.out.printf("target '%s' is not a directory%n", destPath);
-            System.exit(-1);
-        }
-        Dest dest = Dest.of(destPath);
-        for (int i = 0; i < args.length - 1; i++) {
-            Path srcPath = Paths.get(args[i]);
-            Files.walkFileTree(srcPath, new FixLO2UN(srcPath, destPath, dest));
+    private static CommandLine parseCommandLine(String[] args)
+            throws ParseException {
+        Options opts = new Options();
+        CLIUtils.addCommonOptions(opts);
+        return CLIUtils.parseComandLine(args, opts, rb, FixLO2UN.class);
+    }
+
+    public static void main(String[] args) {
+        try {
+            CommandLine cl = parseCommandLine(args);
+            List<String> argList = cl.getArgList();
+            Path destPath = Paths.get(argList.get(argList.size() - 1));
+            if (!Files.isDirectory(destPath) && (argList.size() > 2 || !Files.isRegularFile(Paths.get(argList.get(0))))) {
+                System.out.printf("target '%s' is not a directory%n", destPath);
+                System.exit(-1);
+            }
+            Dest dest = Dest.of(destPath);
+            for (int i = 0; i < argList.size() - 1; i++) {
+                Path srcPath = Paths.get(argList.get(i));
+                Files.walkFileTree(srcPath, new FixLO2UN(srcPath, destPath, dest));
+            }
+        } catch (ParseException e) {
+            System.err.println("json2rst: " + e.getMessage());
+            System.err.println(rb.getString("try"));
+            System.exit(2);
+        } catch (Exception e) {
+            System.err.println("json2rst: " + e.getMessage());
+            e.printStackTrace();
+            System.exit(2);
         }
     }
 

diff --git a/...l/dcm4che-tool-fixlo2un/src/main/resources/org/dcm4che3/tool/fixlo2un/messages.properties b/...l/dcm4che-tool-fixlo2un/src/main/resources/org/dcm4che3/tool/fixlo2un/messages.properties
@@ -0,0 +1,25 @@
+usage=fixlo2un SOURCE DEST\n\
+   or fixlo2un SOURCE... DIRECTORY
+try=Try `fixlo2un --help' for more information.
+description=\n\
+Utility to fix length of private (gggg,00ee) elements truncated to 2 bytes on conversion from implicit VR to explicit VR \
+Transfer Syntax \n\-\n\
+Options:
+example=-\n\
+Example: fixlo2un corrupted.dcm fixed.dcm \n\
+corrupted.dcm -> fixed.dcm \n\
+=> Results in \n\
+2008: (0043,0042) LO #66 -> UN #4718658 \n\
+4720674: (0045,0044) LO #68 -> UN #4390980 \n\
+9111662: (0047,0047) LO #70 -> UN #4522054 \n\
+24709496: (004D,004B) LO #76 -> UN #4849740 \n\
+29559244: (004F,004F) LO #78 -> UN #5111886 \n\
+34671138: (0053,0052) LO #82 -> UN #5242962 \n\
+39914108: (0055,0054) LO #84 -> UN #5439572 \n\
+45353688: (0057,0057) LO #86 -> UN #5570646 \n\
+50924342: (0059,0059) LO #88 -> UN #5701720 \n\
+68357220: (005D,005C) LO #92 -> UN #6029404 \n\
+74386632: (005D,005D) LO #94 -> UN #6094942 \n\
+80481582: (005F,005F) LO #96 -> UN #6226016 \n\
+86707606: (0061,005F) LO #96 -> UN #6226016 \n\
+92933630: (0065,006C) LO #126 -> UN #9371774 \n\-\n\ 
diff --git a/dcm4che-tool/dcm4che-tool-json2index/README.md b/dcm4che-tool/dcm4che-tool-json2index/README.md
@@ -0,0 +1,16 @@
+````
+usage: json2index <schema-dir>
+
+Utility to create search index for UI configuration from JSON schema files
+
+-
+Options:
+ -h,--help      display this help and exit
+ -V,--version   output version information and exit
+-
+Example: json2index /work/dcm4chee-arc-lang/src/main/webapp/assets/schema
+=> Shows attribute names and their descriptions in schema json files
+present in specified directory. Also shows the parent of each of the
+schemas, if any.
+-
+````
diff --git a/dcm4che-tool/dcm4che-tool-json2index/pom.xml b/dcm4che-tool/dcm4che-tool-json2index/pom.xml
@@ -54,6 +54,11 @@
       <groupId>org.glassfish</groupId>
       <artifactId>jakarta.json</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.dcm4che.tool</groupId>
+      <artifactId>dcm4che-tool-common</artifactId>
+      <version>${project.version}</version>
+    </dependency>
   </dependencies>
 
 </project>