Can now perform compression and decompression on same imzML file

AlanRace · Jan 14, 2019 · cfdd075 · cfdd075
1 parent 1eeb17b
commit cfdd075
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Showing 4 changed files with 24 additions and 4 deletions.
diff --git a/.gitignore b/.gitignore
@@ -38,3 +38,7 @@ jimzMLConverter/src/main/assembly/
 jimzMLConverter/\.idea/
 
 jimzMLConverter/jimzMLConverter\.iml
+
+\.idea/
+
+jimzMLConverter/Ontologies/
diff --git a/jimzMLConverter/pom.xml b/jimzMLConverter/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>com.alanmrace</groupId>
     <artifactId>jimzMLConverter</artifactId>
-    <version>1.0-SNAPSHOT</version>
+    <version>1.0.1</version>
     <packaging>jar</packaging>
 
 
@@ -168,8 +168,8 @@
     <dependencies>
         <dependency>
             <groupId>${project.groupId}</groupId>
-            <artifactId>jimzMLParser</artifactId>
-            <version>${project.version}</version>
+            <artifactId>jimzmlparser</artifactId>
+            <version>1.0.4</version>
         </dependency>
         <dependency>
             <groupId>junit</groupId>
@@ -211,6 +211,12 @@
             <artifactId>slf4j-log4j12</artifactId>
             <version>1.7.13</version>
         </dependency>
+        <dependency>
+            <groupId>org.jetbrains</groupId>
+            <artifactId>annotations</artifactId>
+            <version>13.0</version>
+            <scope>compile</scope>
+        </dependency>
 
         <!-- END FOR HDF5 -->
 

diff --git a/jimzMLConverter/src/main/java/com/alanmrace/jimzmlconverter/ImzMLToImzMLConverter.java b/jimzMLConverter/src/main/java/com/alanmrace/jimzmlconverter/ImzMLToImzMLConverter.java
@@ -170,6 +170,8 @@ public void convert() throws ConversionException {
             for (int fileIndex = 0; fileIndex < inputFilenames.length; fileIndex++) {
                 String imzMLFilename = inputFilenames[fileIndex];
 
+                Logger.getLogger(MzMLToImzMLConverter.class.getName()).log(Level.INFO, "Processing " + imzMLFilename);
+
                 try {
                     ImzML currentimzML = ImzMLHandler.parseimzML(imzMLFilename);
 
@@ -213,6 +215,10 @@ public void convert() throws ConversionException {
                             binaryDataArray.removeChildrenOfCVParam(BinaryDataArray.COMPRESSION_TYPE_ID, false);
                             binaryDataArray.removeChildrenOfCVParam(BinaryDataArray.BINARY_DATA_TYPE_ID, false);
 
+                            // TODO: ONLY HERE BECAUSE OF 3D DATA FROM SCILS LAB - need a better way to do this otherwise this will
+                            // cause all RPGs to be removed which may not be desirable
+                            binaryDataArray.removeAllReferenceableParamGroupRefs();
+
                             if (binaryDataArray.ismzArray()) {
                                 binaryDataArray.addReferenceableParamGroupRef(new ReferenceableParamGroupRef(rpgmzArray));
                                 binaryDataArray.removeCVParam(BinaryDataArray.MZ_ARRAY_ID);

diff --git a/jimzMLConverter/src/main/java/com/alanmrace/jimzmlconverter/MainCommand.java b/jimzMLConverter/src/main/java/com/alanmrace/jimzmlconverter/MainCommand.java
@@ -215,7 +215,7 @@ public void convert(String parsedCommand) {
 
                     String[] inputFilenames;
 
-                    if (extension.equals("grd") || extension.equals("mzML"))
+                    if (extension.equals("grd") || extension.equals("mzML") || extension.equals("imzML"))
                         inputFilenames = new String[] {fileName};
                     else if(currentFile.isDirectory() && !fileName.endsWith(".raw")) {
                         inputFilenames = currentFile.list();
@@ -346,6 +346,8 @@ else if(currentFile.isDirectory() && !fileName.endsWith(".raw")) {
 
                                     converter = null;
                                 }
+                            } else {
+                                converter = new ImzMLToImzMLConverter(outputPath, inputFilenames);
                             }
                         }
 
@@ -439,6 +441,8 @@ else if(currentFile.isDirectory() && !fileName.endsWith(".raw")) {
                                     ((ImzMLConverter) converter).setPixelLocations(locations);
                                     ((ImzMLConverter) converter).setOutputFilename(outputPath + "_" + splitIndex);
                                 }
+
+                                logger.log(Level.INFO, MessageFormat.format("Converting using {0} compression for m/z array", ((ImzMLConverter)converter).mzArrayCompressionType));
                             }
                         }