Merge pull request #25 from evanheller/master

Added .dax reader/writer plugins for ImageJ

.gitignore

@@ -8,6 +8,7 @@ build/
 *.eggs
 dist/
 .cache/
+.DS_STORE
 storm_analysis/test/output/
 *__pycache__*
 

storm_analysis/imagej_plugins/dax_file_io/Dax_Reader.java

@@ -0,0 +1,148 @@
+//ImageJ reader plugin for Zhuang lab .dax files
+//Translated from the Python versions in storm-analysis/sa_library and 
+//based on sample IJ reader/writer plugins by Albert Cardona at 
+//http://albert.rierol.net/imagej_programming_tutorials.html.
+//Evan Heller, 10/2015
+
+import java.io.*;  
+import ij.*;  
+import ij.io.*;
+import ij.plugin.PlugIn;
+import ij.plugin.FileInfoVirtualStack;
+import java.util.regex.Pattern;
+import java.util.regex.Matcher;
+
+public class Dax_Reader extends ImagePlus implements PlugIn {
+
+    public void run(String arg) {  
+        String path = getPath(arg);  
+        if (null == path) return;  
+        if (!parse(path)) return;  
+        if (null == arg || 0 == arg.trim().length()) this.show(); // was opened by direct call to the plugin  
+        // not via HandleExtraFileTypes which would  
+        // have given a non-null arg.  
+    }  
+
+    private String getPath(String arg) {  
+        if (null != arg) {  
+            if (0 == arg.indexOf("http://")  || new File(arg).exists()) return arg;  
+        }  
+        // else, ask:  
+        OpenDialog od = new OpenDialog("Choose a .dax 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();  
+    }  
+
+    private boolean parse(String path) {  
+        File mydax = new File(path);
+        String dirname = mydax.getParent();
+        String filename = mydax.getName();
+        if (dirname.length() > 0) dirname += "/";
+
+        String inf_file = dirname + filename.split("\\.")[0] + ".inf";
+
+        //Image parameters
+        int image_height = 256;
+        int image_width = 256;
+        int number_frames = 0, scalemax=0, scalemin=0;
+        boolean bigendian = false;
+        float lock_target, stage_x = 0, stage_y = 0;
+
+        //Extract the movie information from the associated inf file
+        Pattern size_re = Pattern.compile("frame dimensions = ([\\d]+) x ([\\d]+)");
+        Pattern length_re = Pattern.compile("number of frames = ([\\d]+)");
+        Pattern endian_re = Pattern.compile(" (big|little) endian");
+        Pattern stagex_re = Pattern.compile("Stage X = ([\\d\\.\\-]+)");
+        Pattern stagey_re = Pattern.compile("Stage Y = ([\\d\\.\\-]+)");
+        Pattern lock_target_re = Pattern.compile("Lock Target = ([\\d\\.\\-]+)");
+        Pattern scalemax_re = Pattern.compile("scalemax = ([\\d\\.\\-]+)");
+        Pattern scalemin_re = Pattern.compile("scalemin = ([\\d\\.\\-]+)");
+
+        try {
+            BufferedReader br = new BufferedReader(new FileReader(inf_file));
+            String line;
+            Matcher m;
+
+            while ( (line = br.readLine()) != null) {
+                m = size_re.matcher(line);
+                if (m.find()) {
+                    image_width = Integer.parseInt(m.group(1));
+                    image_height = Integer.parseInt(m.group(2));
+                }
+
+                m = length_re.matcher(line);
+                if ( m.find() ) number_frames = Integer.parseInt(m.group(1));
+
+                m = endian_re.matcher(line);
+                if ( m.find() ) { 
+                    if (m.group(1).equals("big")) bigendian = true;
+                }
+
+                m = stagex_re.matcher(line);
+                if ( m.find() ) stage_x = Float.parseFloat(m.group(1));
+
+                m = stagey_re.matcher(line);
+                if ( m.find() ) stage_y = Float.parseFloat(m.group(1));
+
+                m = lock_target_re.matcher(line);
+                if (m.find() ) lock_target = Float.parseFloat(m.group(1));
+
+                m = scalemax_re.matcher(line);
+                if (m.find() ) scalemax = Integer.parseInt(m.group(1));
+
+                m = scalemin_re.matcher(line);
+                if ( m.find() ) scalemin = Integer.parseInt(m.group(1));
+            }
+
+            br.close();
+
+        } 
+        catch (IOException e) {
+            System.err.println("Caught IOException: " + e.getMessage());
+            return false;
+        }
+
+        FileInfo fi = new FileInfo();
+        fi.fileType=2;
+        fi.fileFormat=fi.TIFF;
+        fi.directory=dirname;
+        fi.fileName=filename.split("\\.")[0] + ".dax";
+        fi.width=image_width;
+        fi.height=image_height;
+        fi.nImages=number_frames;
+        fi.gapBetweenImages = 0;
+        fi.intelByteOrder = !bigendian;
+        fi.whiteIsZero = false;
+        fi.longOffset = fi.offset = 0;
+
+        try {
+            ImagePlus imp;
+
+            //Open regular stack if small enough; otherwise, virtual
+            if (number_frames <= 500) {
+                FileOpener fo = new FileOpener(fi);  
+                imp = fo.open(false);  
+            } 
+            else {
+                FileInfoVirtualStack fv = new FileInfoVirtualStack(fi, false);
+                imp = new ImagePlus("",fv);
+            }
+
+            this.setStack(imp.getTitle(), imp.getStack());  
+            this.setCalibration(imp.getCalibration());  
+            Object obinfo = imp.getProperty("Info");  
+            if (null != obinfo) this.setProperty("Info", obinfo);  
+            this.setFileInfo(imp.getOriginalFileInfo());  
+
+        }
+        catch (Exception e) {
+            e.printStackTrace(); 
+            return false;
+        }
+
+        return true;
+    }
+}

storm_analysis/imagej_plugins/dax_file_io/Dax_Writer.java

@@ -0,0 +1,78 @@
+//ImageJ writer plugin for Zhuang lab .dax files
+//Translated from the Python versions in storm-analysis/sa_library and 
+//based on sample IJ reader/writer plugins by Albert Cardona at 
+//http://albert.rierol.net/imagej_programming_tutorials.html.
+//Evan Heller, 10/2015
+
+import java.io.*;  
+import ij.*;  
+import ij.io.*;
+import ij.plugin.PlugIn;
+import ij.process.ImageProcessor;
+import ij.process.ImageConverter;
+
+public class Dax_Writer implements PlugIn {  
+
+    public void run(String arg) {  
+        ImagePlus imp = WindowManager.getCurrentImage();  
+        if (null == imp) return;  
+        SaveDialog sd = new SaveDialog("Save Dax", "untitled", null);  
+        String dir = sd.getDirectory();  
+        if (null == dir) return; // user canceled dialog  
+        dir = dir.replace('\\', '/'); // Windows safe  
+        if (!dir.endsWith("/")) dir += "/";  
+        saveDax(imp, dir + sd.getFileName());  
+    }  
+
+    static public void saveDax(ImagePlus imp, String path) {  
+        File file = new File(path);  
+        DataOutputStream dos = null;  
+
+        try {  
+            dos = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(file)));  
+
+            // read data:  
+            FileInfo fi = imp.getFileInfo(); 
+            String inf_file = path.split("\\.")[0] + ".inf";
+
+            FileWriter fw = new FileWriter(inf_file); 
+
+            //Write a rudimentary .inf file 
+            fw.write("binning = 1 x 1\n");
+            fw.write("data type = 16 bit integers (binary, big endian)\n");
+            fw.write("frame dimensions = " + fi.width + " x " + fi.height + "\n");
+            fw.write("number of frames = " + fi.nImages + "\n");
+            fw.write("Lock Target = 0.0\n");
+            fw.write("x_start = 1\n");
+            fw.write("x_end = " + fi.width + "\n");
+            fw.write("y_start = 1\n");
+            fw.write("y_end = " + fi.height + "\n");
+            fw.flush();
+            fw.close();
+
+            ImageProcessor ip;
+
+            //Covert to 16-bit grayscale for writing to .dax
+            if (imp.getBitDepth() != 16) {
+                ImageConverter ic = new ImageConverter(imp);
+                ic.convertToGray16();
+            }
+
+            //Write the data to file
+            for (int i=0; i<imp.getNSlices(); i++) {  
+                imp.setSlice(i);
+                ip= imp.getProcessor(); //Get ip of current slice
+                short[] px = (short[])ip.getPixels();
+
+                for (int j=0; j<px.length; j++) 
+                    dos.writeShort(px[j]);
+
+            }  
+            dos.flush();  
+            dos.close(); 
+
+        } catch (Exception e) {  
+            e.printStackTrace();  
+        } 
+    }  
+}