From 056367b1359dcaf2e43d64181b2f3b59c37d5ba1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20Haberth=C3=BCr?= <email@davidhaberthuer.ch>
Date: Mon, 2 Feb 2015 15:36:39 +0100
Subject: [PATCH] Adding Fiji plugin, source code and README

---
 ImageJ/DMP_Reader.class           | Bin 0 -> 2975 bytes
 ImageJ/DMP_Reader.java            | 109 ++++++++++++++++++++++++++++++
 ImageJ/HandleExtraFileTypes.class | Bin 0 -> 10037 bytes
 ImageJ/README.md                  |   4 ++
 4 files changed, 113 insertions(+)
 create mode 100644 ImageJ/DMP_Reader.class
 create mode 100644 ImageJ/DMP_Reader.java
 create mode 100644 ImageJ/HandleExtraFileTypes.class
 create mode 100644 ImageJ/README.md

diff --git a/ImageJ/DMP_Reader.class b/ImageJ/DMP_Reader.class
new file mode 100644
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diff --git a/ImageJ/DMP_Reader.java b/ImageJ/DMP_Reader.java
new file mode 100644
index 0000000..cd419c3
--- /dev/null
+++ b/ImageJ/DMP_Reader.java
@@ -0,0 +1,109 @@
+import ij.plugin.*;
+import java.awt.*;
+import java.io.*;
+import ij.*;
+import ij.io.*;
+import ij.process.*;
+import ij.measure.*;
+
+/**	Opens and displays DMP images.                                  */
+/** Adapted from a plugin called PDS_Reader.java from Mike Martin.  */
+/**     21-SEP-2010  bernd.pinzer@psi.ch                            */
+public class DMP_Reader extends ImagePlus implements PlugIn {
+
+	private static final String TITLE = "DMP Reader";
+	private String directory, fileName;
+	private DataInputStream f;
+	private StringBuffer info = new StringBuffer(512);
+	private double bscale, bzero;
+	String keyword, value, line = "", sampleType, encodingType="",mapScale="";
+	private int recordBytes,bitsPerPixel;
+
+	public void run(String arg) {
+                String path = getPath(arg);
+                int islash = path.lastIndexOf('/');  
+                directory = path.substring(0, islash+1);  
+                fileName = path.substring(islash+1);  
+		if (fileName==null)
+			return;
+		IJ.showStatus("Opening: " + directory + fileName);
+		FileInfo fi = null;
+		try {
+			fi = getInfo();
+		} catch (IOException e) {
+			IJ.showMessage(TITLE, ""+e);
+			return;
+		}
+		if (fi!=null && fi.width>0 && fi.height>0) {
+			FileOpener fo = new FileOpener(fi);
+			ImagePlus imp = fo.open(false);
+			ImageProcessor ip = imp.getProcessor();
+			setProcessor(fileName, ip);
+			if (arg.equals("")) show();
+		} //else 
+			//IJ.error("This does not appear to be a PDS file.");
+		IJ.showStatus("");
+	}
+
+
+
+
+
+	
+	FileInfo getInfo() throws IOException {
+		FileInfo fi = new FileInfo();
+		fi.fileName = fileName;
+		fi.directory = directory;
+		fi.width = 0;
+		fi.height = 0;
+		fi.offset = 6;
+		
+		//BufferedReader f = new BufferedReader(new FileReader(directory+fileName));
+                InputStream is = new FileInputStream(directory+fileName);
+                byte[] buf = new byte[6];  // we're about to read the first 6 bytes
+                is.read(buf, 0, 6);
+                //one reason I hate java: there's no such thing as a uint16 data
+                //type. To work around this, we have to do some gymnastics:
+                int firstByte = 0;
+                int secondByte = 0;
+                firstByte  = (0x000000FF & ((int)buf[0]));
+                secondByte = (0x000000FF & ((int)buf[1]));
+                fi.width = (secondByte << 8 | firstByte);
+                // because I never could remember that even a single day, here
+                // are some explanations: 
+                // first we are promoting a signed byte to an int, which
+                // results in bits 8 through 31 set to 1 if the number happens
+                // to be larger than 127. the bitwise and with 0x000000FF wipes
+                // out all but the first 8 bits.
+                // The last line deals with endianness: the binary file is
+                // little endian, while java is in general big endian.
+                //System.out.println(fi.width);
+		
+                firstByte  = (0x000000FF & ((int)buf[2]));
+                secondByte = (0x000000FF & ((int)buf[3]));
+                fi.height = (secondByte << 8 | firstByte);
+                //System.out.println(fi.height);
+
+                fi.fileType = FileInfo.GRAY32_FLOAT;
+                fi.intelByteOrder = true;
+
+    		fi.valueUnit = "gray value";
+		return fi;
+	} // setting the FileInfo  
+
+
+
+        private String getPath(String arg) {  
+          if (null != arg) {  
+            if (new File(arg).exists()) return arg;  
+          }  
+          // else, ask:  
+          OpenDialog od = new OpenDialog("Choose a .DMP file", null);  
+          String dir = od.getDirectory();  
+          if (null == dir) return null; // dialog was canceled          
+          dir = dir.replace('\\', '/'); // Windows safe  
+          if (!dir.endsWith("/")) dir += "/";  
+          return dir + od.getFileName();  
+        }  
+
+} // end of DMP reader class
diff --git a/ImageJ/HandleExtraFileTypes.class b/ImageJ/HandleExtraFileTypes.class
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diff --git a/ImageJ/README.md b/ImageJ/README.md
new file mode 100644
index 0000000..a8ffee9
--- /dev/null
+++ b/ImageJ/README.md
@@ -0,0 +1,4 @@
+# Reading TOMCAT DMP files with ImageJ/Fiji
+
+Drop the file DMP_Reader.class (source code in DMP_Reader.java) into the plugins directory (or any subfolder therein).
+Make sure you also drop the file HandleExtraFileTypes.class to the plugins directory (and only there!) to enable the reader in the 'open' dialog.