Merge pull request #5 from mdoube/testing

Add opener API to Read_Stratec_File

src/org/doube/bonej/pqct/Read_Stratec_File.java

@@ -31,33 +31,51 @@
 public class Read_Stratec_File extends ImagePlus implements PlugIn {
 	//Global variables
 	//Stratec header stuff
-	public byte[] PName = new byte[40]; //
-	public String PatName;
-	public long PatNo;
-	public int PatMeasNo;
-	public long PatBirth; //
-	public long MeasDate; //
-	public double VoxelSize; //
-	public int PicX0; //
-	public int PicY0; //
-	public int PicMatrixX; //
-	public int PicMatrixY; //
-	public byte[] MInfo = new byte[324]; //
-	public String MeasInfo;
-	public byte[] Dev = new byte[13];
-	public String Device;
-	public byte[] PID = new byte[13];
-	public String PatID;
-	public double ObjLen; //
-	public short[] data;
-	public short min,max;
-	public String fileName;
-	public String properties;
+	private byte[] PName = new byte[40]; //
+	private String PatName;
+	private long PatNo;
+	private int PatMeasNo;
+	private long PatBirth; //
+	private long MeasDate; //
+	private double VoxelSize; //
+	private int PicX0; //
+	private int PicY0; //
+	private int PicMatrixX; //
+	private int PicMatrixY; //
+	private byte[] MInfo = new byte[324]; //
+	private String MeasInfo;
+	private byte[] Dev = new byte[13];
+	private String Device;
+	private byte[] PID = new byte[13];
+	private String PatID;
+	private double ObjLen; //
+	private String fileName;
+	private String properties;
 
 	public Read_Stratec_File() { //Constructor
 		//this = null;
 	}
 
+	/**
+	 * Opens a Stratec pQCT file
+	 * 
+	 * @param path full path to the file
+	 * @return ImagePlus containing the calibrated pQCT image
+	 * @throws IllegalArgumentException if the path is null or the file is not normal
+	 */
+	public ImagePlus open(String path) throws IllegalArgumentException {
+		if (path == null)
+			throw new IllegalArgumentException("Path cannot be null");
+		File theFile = new File(path);
+		if (!theFile.isFile())
+			throw new IllegalArgumentException("Path is not a normal file");
+		String directory = theFile.getParent()+"/";
+		fileName = theFile.getName();
+		read(directory);
+		fileInfo();
+		return this;
+	}
+
 	//Overriding the abstract runnable run method. Apparently plugins run in threads
 	public void run(String arg) { 
 		String directory;
@@ -73,6 +91,15 @@ public void run(String arg) {
 		}
 		if (fileName==null) return;
 		read(directory);
+		fileInfo();
+		if (arg.isEmpty() && this.getHeight()>0){
+			this.show();
+			return;
+		}
+		if (this.getHeight()<1) return;
+	}
+
+	private void fileInfo() {
 		FileInfo fi = this.getFileInfo(); 
 		fi.pixelWidth = VoxelSize;
 		fi.pixelHeight = VoxelSize;
@@ -81,14 +108,9 @@ public void run(String arg) {
 		fi.info		= properties;
 		fi.fileType = ij.io.FileInfo.GRAY16_SIGNED;	//
         this.setFileInfo(fi);
-		if (arg.isEmpty() && this.getHeight()>0){
-			this.show();
-			return;
-		}
-		if (this.getHeight()<1) return;
 	}
-	
-	public void read(String directory){
+
+	private void read(String directory){
 		File fileIn = new File(directory+fileName);
 		long fileLength = fileIn.length();
 		try{BufferedInputStream inputStream = new BufferedInputStream(new FileInputStream(fileIn));
@@ -135,7 +157,7 @@ public void read(String directory){
 		}
 	}
 
-	public void readHeader(byte[] fileData){
+	private void readHeader(byte[] fileData){
 		byte stringLength;
 		int offset =12;
 		VoxelSize = Double.longBitsToDouble((long) ( ((long) (fileData[offset+7] & 0xFF))<<56 | ((long) (fileData[offset+6] & 0xFF))<<48 | ((long) (fileData[offset+5] & 0xFF))<<40 | ((long) (fileData[offset+4] & 0xFF))<<32 | ((long) (fileData[offset+3] & 0xFF))<<24 | ((long) (fileData[offset+2] & 0xFF))<<16 | ((long) (fileData[offset+1] & 0xFF))<<8 | ((long) (fileData[offset+0] & 0xFF))<<0));
@@ -188,7 +210,7 @@ public void readHeader(byte[] fileData){
 		PicMatrixY = ((int) ((int) (fileData[offset+1] & 0xFF)) <<8 | ((int) (fileData[offset+0] & 0xFF)));
 	}
 
-	public void setProperties(){
+	private void setProperties(){
 		String[] propertyNames = {"File Name","Pixel Spacing","ObjLen","MeasInfo","Acquisition Date",
 									"Device","PatMeasNo","PatNo","Patient's Birth Date","Patient's Name",
 									"Patient ID","PicX0","PicY0",