Utility dcm2str to apply Attributes Format Pattern to dicom file and/…

…or command line parameters #385

README.md

@@ -59,6 +59,7 @@ Utilities
 ---------
 - [dcm2dcm][]: Transcode DICOM file according the specified Transfer Syntax
 - [dcm2jpg][]: Convert DICOM image to JPEG or other image formats
+- [dcm2str][]: Apply Attributes Format Pattern to dicom file or command line parameters.
 - [dcm2xml][]: Convert DICOM file in XML presentation
 - [dcmdir][]: Dump, create or update DICOMDIR file
 - [dcmdump][]: Dump DICOM file in textual form
@@ -93,6 +94,7 @@ Utilities
 
 [dcm2dcm]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-dcm2dcm/README.md
 [dcm2jpg]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-dcm2jpg/README.md
+[dcm2str]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-dcm2str/README.md
 [dcm2xml]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-dcm2xml/README.md
 [dcmdir]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-dcmdir/README.md
 [dcmdump]: https://github.com/dcm4che/dcm4che/blob/master/dcm4che-tool/dcm4che-tool-dcmdump/README.md

dcm4che-assembly/pom.xml

@@ -270,6 +270,11 @@
       <artifactId>dcm4che-tool-dcm2json</artifactId>
       <version>${project.version}</version>
     </dependency>
+    <dependency>
+      <groupId>org.dcm4che.tool</groupId>
+      <artifactId>dcm4che-tool-dcm2str</artifactId>
+      <version>${project.version}</version>
+    </dependency>
     <dependency>
       <groupId>org.dcm4che.tool</groupId>
       <artifactId>dcm4che-tool-dcm2xml</artifactId>

dcm4che-assembly/src/bin/dcm2str

@@ -0,0 +1,56 @@
+#!/bin/sh
+# -------------------------------------------------------------------------
+# dcm2str  Launcher
+# -------------------------------------------------------------------------
+
+MAIN_CLASS=org.dcm4che3.tool.dcm2str.Dcm2Str
+MAIN_JAR=dcm4che-tool-dcm2str-${project.version}.jar
+
+DIRNAME="`dirname "$0"`"
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false;
+case "`uname`" in
+    CYGWIN*)
+        cygwin=true
+        ;;
+esac
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched
+if $cygwin ; then
+    [ -n "$DCM4CHE_HOME" ] &&
+        DCM4CHE_HOME=`cygpath --unix "$DCM4CHE_HOME"`
+    [ -n "$JAVA_HOME" ] &&
+        JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+fi
+
+# Setup DCM4CHE_HOME
+if [ "x$DCM4CHE_HOME" = "x" ]; then
+    DCM4CHE_HOME=`cd "$DIRNAME"/..; pwd`
+fi
+
+# Setup the JVM
+if [ "x$JAVA_HOME" != "x" ]; then
+    JAVA=$JAVA_HOME/bin/java
+else
+    JAVA="java"
+fi
+
+# Setup the classpath
+CP="$DCM4CHE_HOME/etc/dcm2str/"
+CP="$CP:$DCM4CHE_HOME/lib/$MAIN_JAR"
+CP="$CP:$DCM4CHE_HOME/lib/dcm4che-core-${project.version}.jar"
+CP="$CP:$DCM4CHE_HOME/lib/dcm4che-tool-common-${project.version}.jar"
+CP="$CP:$DCM4CHE_HOME/lib/slf4j-api-1.7.25.jar"
+CP="$CP:$DCM4CHE_HOME/lib/slf4j-log4j12-1.7.25.jar"
+CP="$CP:$DCM4CHE_HOME/lib/log4j-1.2.17.jar"
+CP="$CP:$DCM4CHE_HOME/lib/commons-cli-${commons-cli.version}.jar"
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin; then
+    JAVA=`cygpath --path --windows "$JAVA"`
+    CP=`cygpath --path --windows "$CP"`
+fi
+
+# Execute the JVM
+exec "$JAVA" $JAVA_OPTS -cp "$CP" $MAIN_CLASS "$@"

dcm4che-assembly/src/bin/dcm2str.bat

@@ -0,0 +1,52 @@
+@echo off
+rem -------------------------------------------------------------------------
+rem dcm2str  Launcher
+rem -------------------------------------------------------------------------
+
+if not "%ECHO%" == ""  echo %ECHO%
+if "%OS%" == "Windows_NT"  setlocal
+
+set MAIN_CLASS=org.dcm4che3.tool.dcm2str.Dcm2Str
+set MAIN_JAR=dcm4che-tool-dcm2str-${project.version}.jar
+
+set DIRNAME=.\
+if "%OS%" == "Windows_NT" set DIRNAME=%~dp0%
+
+rem Read all command line arguments
+
+set ARGS=
+:loop
+if [%1] == [] goto end
+        set ARGS=%ARGS% %1
+        shift
+        goto loop
+:end
+
+if not "%DCM4CHE_HOME%" == "" goto HAVE_DCM4CHE_HOME
+
+set DCM4CHE_HOME=%DIRNAME%..
+
+:HAVE_DCM4CHE_HOME
+
+if not "%JAVA_HOME%" == "" goto HAVE_JAVA_HOME
+
+set JAVA=java
+
+goto SKIP_SET_JAVA_HOME
+
+:HAVE_JAVA_HOME
+
+set JAVA=%JAVA_HOME%\bin\java
+
+:SKIP_SET_JAVA_HOME
+
+set CP=%DCM4CHE_HOME%\etc\dcm2str\
+set CP=%CP%;%DCM4CHE_HOME%\lib\%MAIN_JAR%
+set CP=%CP%;%DCM4CHE_HOME%\lib\dcm4che-core-${project.version}.jar
+set CP=%CP%;%DCM4CHE_HOME%\lib\dcm4che-tool-common-${project.version}.jar
+set CP=%CP%;%DCM4CHE_HOME%\lib\slf4j-api-1.7.25.jar
+set CP=%CP%;%DCM4CHE_HOME%\lib\slf4j-log4j12-1.7.25.jar
+set CP=%CP%;%DCM4CHE_HOME%\lib\log4j-1.2.17.jar
+set CP=%CP%;%DCM4CHE_HOME%\lib\commons-cli-${commons-cli.version}.jar
+
+"%JAVA%" %JAVA_OPTS% -cp "%CP%" %MAIN_CLASS% %ARGS%

dcm4che-assembly/src/etc/dcm2str/log4j.properties

@@ -0,0 +1,5 @@
+log4j.rootLogger=INFO, stdout
+
+log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+log4j.appender.stdout.layout.ConversionPattern=%d{ABSOLUTE} %-5p - %m\n

dcm4che-assembly/src/main/assembly/bin.xml

@@ -139,6 +139,7 @@
         <include>org.dcm4che.tool:dcm4che-tool-dcm2dcm</include>
         <include>org.dcm4che.tool:dcm4che-tool-dcm2jpg</include>
         <include>org.dcm4che.tool:dcm4che-tool-dcm2json</include>
+        <include>org.dcm4che.tool:dcm4che-tool-dcm2str</include>
         <include>org.dcm4che.tool:dcm4che-tool-dcm2xml</include>
         <include>org.dcm4che.tool:dcm4che-tool-dcmdir</include>
         <include>org.dcm4che.tool:dcm4che-tool-dcmldap</include>

dcm4che-tool/dcm4che-tool-dcm2str/README.md

@@ -0,0 +1,51 @@
+    usage: dcm2str -p PATTERN <file(s)|directory(ies)> -s
+                   <[seq/]attr=value>...
+
+    Apply Attributes Format Pattern either to one or more DICOM files and/or
+    DICOM file(s) in one or more directories. If individual attributes are
+    specified, the attributes of the DICOM file(s) shall be overwritten by the
+    specified attributes before the Attributes Format Pattern is applied.
+    -
+    Options:
+     -h,--help               display this help and exit
+     -p <arg>                Specify Attributes Format Pattern to be applied.
+     -s <[seq/]attr=value>   Specify attributes added to the object(s). It can
+                             be specified by keyword or tag (in hex), e.g.
+                             StudyInstanceUID=1.2.3 or 0020000D=1.2.3.
+                             Attributes in nested Datasets can be specified by
+                             including the keyword/tag value of the sequence
+                             attribute, e.g. 00400275/00400009 for Scheduled
+                             Procedure Step ID in the Request Attributes
+                             Sequence.
+     -V,--version            output version information and exit
+
+    Examples:
+    => dcm2str -p {0020000D,hash}/{0020000E,hash}/{00080018,hash}/{rnd}
+    image.dcm
+    Apply Attributes Format Pattern to the specified DICOM file.
+
+    => dcm2str -p {0020000D,hash}/{0020000E,hash}/{00080018,hash}/{rnd}
+    image.dcm -sStudyInstanceUID=1.2.3 -sSeriesInstanceUID=1.2.3.4
+    -sSOPInstanceUID=1.2.3.4.5
+    Overwrite attributes of the specified DICOM file with specified DICOM
+    attributes and then apply Attributes Format Pattern to the specified DICOM
+    file.
+
+    => dcm2str -p {0020000D,hash}/{0020000E,hash}/{00080018,hash}/{rnd}
+    image.dcm /path-to-other-DICOM-files-directory -sStudyInstanceUID=1.2.3
+    -sSeriesInstanceUID=1.2.3.4 -sSOPInstanceUID=1.2.3.4.5
+    Overwrite attributes of the specified DICOM file and of other DICOM files
+    in the directory with the specified DICOM attributes and only then apply
+    Attributes Format Pattern to DICOM file and to other DICOM files in the
+    directory.
+
+    => dcm2str -p {0020000D,hash}/{0020000E,hash}/{00080018,hash}/{rnd}
+    image.dcm /path-to-other-DICOM-files-directory
+    Apply Attributes Format Pattern to the specified DICOM file and also to
+    the other DICOM files in the specified directory.
+
+    => dcm2str -p {0020000D,hash}/{0020000E,hash}/{00080018,hash}/{rnd}
+    -sStudyInstanceUID=1.2.3 -sSeriesInstanceUID=1.2.3.4
+    -sSOPInstanceUID=1.2.3.4.5
+    Apply Attributes Format Pattern to DICOM attributes passed as command line
+    parameters.

dcm4che-tool/dcm4che-tool-dcm2str/pom.xml

@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <parent>
+        <artifactId>dcm4che-tool</artifactId>
+        <groupId>org.dcm4che.tool</groupId>
+        <version>5.15.1</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+
+    <artifactId>dcm4che-tool-dcm2str</artifactId>
+    <name>dcm4che-tool-dcm2str</name>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.dcm4che</groupId>
+            <artifactId>dcm4che-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-log4j12</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.dcm4che.tool</groupId>
+            <artifactId>dcm4che-tool-common</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+
+</project>

dcm4che-tool/dcm4che-tool-dcm2str/src/main/java/org/dcm4che3/tool/dcm2str/Dcm2Str.java

@@ -0,0 +1,146 @@
+/* ***** BEGIN LICENSE BLOCK *****
+ * Version: MPL 1.1/GPL 2.0/LGPL 2.1
+ *
+ * The contents of this file are subject to the Mozilla Public License Version
+ * 1.1 (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ * http://www.mozilla.org/MPL/
+ *
+ * Software distributed under the License is distributed on an "AS IS" basis,
+ * WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
+ * for the specific language governing rights and limitations under the
+ * License.
+ *
+ * The Original Code is part of dcm4che, an implementation of DICOM(TM) in
+ * Java(TM), hosted at https://github.com/dcm4che.
+ *
+ * The Initial Developer of the Original Code is
+ * J4Care.
+ * Portions created by the Initial Developer are Copyright (C) 2015-2019
+ * the Initial Developer. All Rights Reserved.
+ *
+ * Contributor(s):
+ * See @authors listed below
+ *
+ * Alternatively, the contents of this file may be used under the terms of
+ * either the GNU General Public License Version 2 or later (the "GPL"), or
+ * the GNU Lesser General Public License Version 2.1 or later (the "LGPL"),
+ * in which case the provisions of the GPL or the LGPL are applicable instead
+ * of those above. If you wish to allow use of your version of this file only
+ * under the terms of either the GPL or the LGPL, and not to allow others to
+ * use your version of this file under the terms of the MPL, indicate your
+ * decision by deleting the provisions above and replace them with the notice
+ * and other provisions required by the GPL or the LGPL. If you do not delete
+ * the provisions above, a recipient may use your version of this file under
+ * the terms of any one of the MPL, the GPL or the LGPL.
+ *
+ * ***** END LICENSE BLOCK ***** */
+
+package org.dcm4che3.tool.dcm2str;
+
+import org.apache.commons.cli.*;
+import org.dcm4che3.data.Attributes;
+import org.dcm4che3.io.DicomInputStream;
+import org.dcm4che3.tool.common.CLIUtils;
+import org.dcm4che3.util.AttributesFormat;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.file.*;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.text.MessageFormat;
+import java.util.EnumSet;
+import java.util.List;
+import java.util.ResourceBundle;
+
+/**
+ * @author Vrinda Nayak <vrinda.nayak@j4care.com>
+ * @since Jan 2019
+ */
+public class Dcm2Str {
+    private static final Logger LOG = LoggerFactory.getLogger(Dcm2Str.class);
+    private static final ResourceBundle rb = ResourceBundle.getBundle("org.dcm4che3.tool.dcm2str.messages");
+    private static String pattern;
+    private static String[] uidOptVals;
+    private static List<String> pathNames;
+
+    public static void main(String[] args) {
+        try {
+            CommandLine cl = parseComandLine(args);
+            init(cl);
+            dcm2str();
+        } catch (ParseException e) {
+            System.err.println("dcm2str: " + e.getMessage());
+            System.err.println(rb.getString("try"));
+            System.exit(2);
+        } catch (Exception e) {
+            System.err.println("dcm2str: " + e.getMessage());
+            e.printStackTrace();
+            System.exit(2);
+        }
+    }
+
+    private static CommandLine parseComandLine(String[] args) throws ParseException {
+        Options opts = new Options();
+        CLIUtils.addCommonOptions(opts);
+        opts.addOption(Option.builder("p")
+                .hasArg()
+                .desc(rb.getString("pattern"))
+                .build());
+        opts.addOption(Option.builder("s")
+                .hasArgs()
+                .argName("[seq/]attr=value")
+                .valueSeparator('=')
+                .desc(rb.getString("str"))
+                .build());
+        return CLIUtils.parseComandLine(args, opts, rb, Dcm2Str.class);
+    }
+
+    private static void init(CommandLine cl) throws Exception {
+        if ((pattern = cl.getOptionValue("p")) == null)
+            throw new MissingOptionException("Missing Attributes Format pattern");
+
+        uidOptVals = cl.getOptionValues("s");
+        pathNames = cl.getArgList();
+    }
+
+    private static void dcm2str() throws IOException {
+        for (String pathName : pathNames) {
+            Path path = Paths.get(pathName);
+            if (Files.isDirectory(path)) {
+                try {
+                    Files.walkFileTree(path, EnumSet.of(FileVisitOption.FOLLOW_LINKS), Integer.MAX_VALUE,
+                            new SimpleFileVisitor<Path>() {
+                                @Override
+                                public FileVisitResult visitFile(Path filePath, BasicFileAttributes attrs1) throws IOException {
+                                    convert(filePath);
+                                    return FileVisitResult.CONTINUE;
+                                }
+                            });
+                } catch (IOException e) {
+                    LOG.warn(e.getMessage());
+                }
+            } else
+                convert(path);
+        }
+        if (pathNames.isEmpty())
+            convert(null);
+    }
+
+    private static void convert(Path path) throws IOException {
+        Attributes attrs = toAttributes(path);
+        CLIUtils.addAttributes(attrs, uidOptVals);
+        System.out.println(MessageFormat.format(
+                rb.getString("converted"),
+                path != null ? path : "",
+                new AttributesFormat(pattern).format(attrs)));
+    }
+
+    private static Attributes toAttributes(Path path) throws IOException {
+        return path != null
+                ? new DicomInputStream(new FileInputStream(path.toFile())).readDataset(-1, -1)
+                : new Attributes();
+    }
+}