Classes
class	ClassicGlow
	Plugin implementing the classic glow/hot LUT which seems to be missing from ImageJ. More...
class	LoadTestData
	Plugin class to load the standard test data from the JAR file. More...
class	JNIUserInterface
	3B User interface for the Java plugin. More...
class	SPair
	Utility class to hold a pair of strings. More...
class	Util
	Utility calss to hold a number of handy static functions. More...
class	three_B
	ImageJ plugin class. More...
class	AdvancedDialog
	Control panel which basically presents the .cfg file in a large edit box along with additional necessary things (frame range and pixel size). More...
class	ThreeBDialog
	Dialog box for starting 3B The dialog highlights bad things in red. More...
class	Spot
	Basic spot class, simply contains coordinates. More...
class	SomethingChanges
	Listener class which triggers a complete redraw. More...
class	FloatSliderWithBox
	This class makes a floating point slider bar with an edit box next to it for more precision. More...
class	CloseButtonListener
	Close button issues a window close event. More...
class	StopButtonListener
	Stop 3B thread. More...
class	ExportButtonListener
	Listener for the export button. More...
class	EControlPanel
	Control panel for running 3B plugin and providing interactive update. More...
class	ThreeBRunner
	This class deals with running the actual 3B code It should be run in a separate thread It will make calls back to a viewer, and accepts termination calls as well. More...
class	ThreeBHelp
	3B plugin cclass to bring up a basic help window. More...
class	ThreeBLoader
	Plugin class to load up an old 3B run. More...
Functions
string	get_string (JNIEnv *env, jstring js)
Image< jbyte >	get_local_copy_of_image (JNIEnv *env, jbyteArray data, int rows, int cols)
Image< float >	get_local_copy_of_image (JNIEnv *env, jfloatArray data, int rows, int cols)
JNIEXPORT void JNICALL	Java_ThreeBRunner_call (JNIEnv *env, jobject jthis, jstring cfg, jobjectArray images, jbyteArray mask_data, jint n_images, jint rows, jint cols, jstring file)
static SPair	Util::getFileName (String t)

Function Documentation

string get_string	(	JNIEnv *	env,
		jstring	js
	)

Get a local C++ copy of a java string.

Definition at line 122 of file multispot5_jni.cc.

Referenced by Java_ThreeBRunner_call().

{
    const char* str;

    //Covert the config into a string
    str = env->GetStringUTFChars(js, NULL);

    string stdstring(str);
    env->ReleaseStringUTFChars(js, str);


    return stdstring;
}

Image<jbyte> get_local_copy_of_image	(	JNIEnv *	env,
		jbyteArray	data,
		int	rows,
		int	cols
	)

Get a local C++ copy of an image from a jbyteArray coming from the guts of ImageJ.

Definition at line 138 of file multispot5_jni.cc.

Referenced by Java_ThreeBRunner_call().

{
    //This takes a copy of the pixels (perhaps)
    jbyte* pix = env->GetByteArrayElements(data, NULL);

    BasicImage<jbyte> pix_im(pix, ImageRef(cols, rows));

    Image<jbyte> im;
    im.copy_from(pix_im);
    
    //This frees the pixels if copied, or releases a reference
    env->ReleaseByteArrayElements(data,pix, JNI_ABORT);
    
    return im;
}

Image<float> get_local_copy_of_image	(	JNIEnv *	env,
		jfloatArray	data,
		int	rows,
		int	cols
	)

Get a local C++ copy of an image from a jfloatArray coming from the guts of ImageJ.

Definition at line 156 of file multispot5_jni.cc.

{
    //This takes a copy of the pixels (perhaps)
    float* pix = env->GetFloatArrayElements(data, NULL);

    BasicImage<float> pix_im(pix, ImageRef(cols, rows));

    Image<float> im;
    im.copy_from(pix_im);
    
    //This frees the pixels if copied, or releases a reference
    env->ReleaseFloatArrayElements(data,pix, JNI_ABORT);
    
    return im;
}

JNIEXPORT void JNICALL Java_ThreeBRunner_call	(	JNIEnv *	env,
		jobject	jthis,
		jstring	cfg,
		jobjectArray	images,
		jbyteArray	mask_data,
		jint	n_images,
		jint	rows,
		jint	cols,
		jstring	file
	)

Run the 3B code.

Definition at line 176 of file multispot5_jni.cc.

References JNIUserInterface::fatal(), get_local_copy_of_image(), get_string(), null_graphics(), and JNIUserInterface::send_message().

{
    istringstream config(get_string(env, cfg));
    GUI.ParseStream(config);

    JNIUserInterface ui(env, jthis);
    ui.send_message("Initializing...");
    
    string filename = get_string(env, file);

    //Attmpt to open the file
    ofstream save_spots;
    save_spots.open(filename.c_str());
    int err = errno;

    if(!save_spots.good())
    {
        ui.fatal("failed to open " + filename + ": " + strerror(err));
        return;
    }

    vector<ImageRef> maskir;
    Image<double> maskd;
    {
        Image<jbyte> mask = get_local_copy_of_image(env, mask_data, rows, cols);
        maskd = convert_image(mask);
        for(ImageRef p(-1, 0); p.next(mask.size()); )
            if(mask[p])
                maskir.push_back(p);
    }   


    vector<Image<float> > ims;

    for(int i=0; i < n_images; i++)
    {
        jfloatArray f = static_cast<jfloatArray>(env->GetObjectArrayElement(images, i));
        ims.push_back(preprocess_image(get_local_copy_of_image(env, f, rows, cols)));
        env->DeleteLocalRef(f);
    }

    double mean, variance;
    tie(mean, variance) = mean_and_variance(ims);

    for(unsigned int i=0; i < ims.size(); i++)
            transform(ims[i].begin(), ims[i].end(), ims[i].begin(), bind1st(multiplies<double>(), 1/ sqrt(variance)));
     
    tie(mean, variance) = mean_and_variance(ims);

    //A sanity check.
    cerr << "Rescaled:\n";
    cerr << "mean = " << mean << endl;
    cerr << "std  = " << sqrt(variance) << endl;
    cerr << "Version 1.1" << endl;


    auto_ptr<FitSpotsGraphics> gr = null_graphics();

    place_and_fit_spots(ims, maskir, maskd, save_spots, *gr, ui);
}

static SPair Util::getFileName ( String t ) [inline, static, package]

The a file name for saving and complete path using ImageJ's file open dialog.

Kep re-querying user if the file will be overwritten. Windows already provides the query built in.

Parameters:

t	Initial file name

Returns:: filename and full path

Definition at line 80 of file three_B.java.

References SPair::a, and SPair::b.

Referenced by three_B::run().

    {
        //Get a filename to save as, with appropriate warnings for 
        //overwriting files.
        String fname, fullname;
        while(true)
        {
            SaveDialog save = new SaveDialog("Save 3B output", t, ".txt");
            fname = save.getFileName();

            fullname = save.getDirectory() + File.separator + fname;

            if(fname == null)
                break;

            File test = new File(fullname);
            //Windows' open dialog seems to do overwrite confirmation automatically,
            //so there is no need to do it here.
            if(!ij.IJ.isWindows() && test.exists())
            {
                GenericDialog g = new GenericDialog("Overwrite file?");
                g.addMessage("The file \"" + fname + "\" already exists. Continue and overwrite?");
                g.enableYesNoCancel("Yes", "No");
                g.showDialog();

                if(g.wasOKed())
                    break;
                else if(g.wasCanceled())
                {
                    fname = null;
                    break;
                }
            }
            else
                break;
        }

        SPair r = new SPair();
        r.a = fname;
        r.b = fullname;
        return r;
    }

Classes

Functions

Function Documentation