Reinitializing python matplotlib module - reset button

Question

I have a short matplotlib module where I do some basic image analysis, delete slices, register, sum and save. However, I would like to add a reset button to re-initialise the module, putting the image data back to its initial state.

Basically, if I have a list of 2D images which make up a dynamic data set. I want to be able to delete frames, register the images and finally create a summed image. To do this I manipulate the list raw_dicom_stack. However, if something goes wrong I would like another button reset which resets raw_dicom_stack and restarts the class with the original data. I copy the contents of raw_dicom_stack to reset_stack early on and to reset I try:

I have tried:

def reset(self, event):
    self.__init__(self.reset_stack, self.nframes, self.ds)

but this crashes the module and I get no error message. Where am I going wrong?

def main():
    root = Tk()
    root.withdraw()
    #Default DMSA image directory
    IMAGE_DIR = '/home/nm/Python/DMSA/dmsa_examples/dynamics/'
    filename = tkFileDialog.askopenfilename(parent=root,initialdir=IMAGE_DIR, title='Select dicom image')
    if filename == '':
        quit()

    ds = dicom.read_file(filename)
    pix = ds.pixel_array
    #find out size of pixel array
    #print 'dicom image has x,y,z dimensions %d,%d,%d' %(int(pix.shape[0]), int(pix.shape[1]), int(pix.shape[2]))
    raw_dicom_stack = []

    for x in range(pix.shape[0]/2):
        raw_dicom_stack.append(pix[x,:,:])


    nframes = pix.shape[0]/2;
    # Visualize it
    viewer = VolumeViewer(raw_dicom_stack, nframes, ds)
    viewer.show()

class VolumeViewer(object):
    def __init__(self, raw_dicom_stack, nframes, ds):

        self.raw_dicom_stack = raw_dicom_stack
        self.nframes = nframes
        self.summed_image = np.zeros((self.raw_dicom_stack[0].shape[0],self.raw_dicom_stack[0].shape[1]))
        self.frame = 0
        self.frames_delete = 0
        self.ds = ds
        self.reset_stack = raw_dicom_stack


        # Plot the first slice of the image
        self.fig, self.ax = plt.subplots()
        self.im = self.ax.imshow(np.array(raw_dicom_stack[0]), cmap = cm.gray)


    def update(self, value):
        self.frame = int(self.nframes * value)
        # Update the image data
        dat = np.array(self.raw_dicom_stack[self.frame])
        self.im.set_data(dat)
        self.im.set_clim([dat.min(), dat.max()])
        # Redraw the plot
        self.fig.canvas.draw()      

    def add(self,event):
        if self.query_add == True:
            print "Image series has already summed"
        else:
            for x in range(self.nframes):
                self.summed_image += self.raw_dicom_stack[x]
            del self.raw_dicom_stack[:]
            self.raw_dicom_stack.append(self.summed_image[:,:])
            self.nframes = len(self.raw_dicom_stack)

            # Update the image data
            dat = np.array(self.raw_dicom_stack[0])
            self.im.set_data(dat)
            self.slider.reset()
            self.im.set_clim([dat.min(), dat.max()])
            # Redraw the plot
            self.fig.canvas.draw()

            self.query_add = True
            #rezero summed_image
            #summed_image = np.zeros((self.summed_image.shape[0],self.summed_image.shape[1]))


    def show(self):
        plt.show()

    def reset(self, event):

        #self.summed_image = np.zeros((self.raw_dicom_stack[0].shape[0],self.raw_dicom_stack[0].shape[1]))
        #self.query_register = False
        #self.query_add = False
        self.__init__(self.reset_stack, self.nframes, self.ds)

    def quit(self,event):
        quit()

if __name__ == '__main__':
    main()

Also is it possible that you provide a minimal example that illustrates the problem, running that code is a bit difficult not having all the dependencies on hand — Matti Lyra
– Matti Lyra, Commented Feb 1, 2013 at 15:43
@MattiLyra I get no error message. I have reworded my question and also removed much of the code unrelated to the problem, hopefully it makes a little more sense now — moadeep
– moadeep, Commented Feb 1, 2013 at 15:55

Matti Lyra · Accepted Answer · 2013-02-01 16:12:41Z

1

Running the following code with Python 2.7.3 works perfectly fine

import numpy as np

class VolumeViewer(object):
    def __init__(self, raw_dicom_stack, nframes, ds):

        self.raw_dicom_stack = raw_dicom_stack
        self.nframes = nframes
        self.summed_image = np.zeros((self.raw_dicom_stack[0].shape[0],self.raw_dicom_stack[0].shape[1]))
        self.frame = 0
        self.frames_delete = 0
        self.ds = ds
        self.reset_stack = raw_dicom_stack


        # Plot the first slice of the image
        self.fig, self.ax = plt.subplots()
        self.im = self.ax.imshow(np.array(raw_dicom_stack[0]), cmap = cm.gray)


    def update(self, value):
        self.frame = int(self.nframes * value)
        # Update the image data
        dat = np.array(self.raw_dicom_stack[self.frame])
        self.im.set_data(dat)
        self.im.set_clim([dat.min(), dat.max()])
        # Redraw the plot
        self.fig.canvas.draw()      

    def add(self,event):
        if self.query_add == True:
            print "Image series has already summed"
        else:
            for x in range(self.nframes):
                self.summed_image += self.raw_dicom_stack[x]
            del self.raw_dicom_stack[:]
            self.raw_dicom_stack.append(self.summed_image[:,:])
            self.nframes = len(self.raw_dicom_stack)

            # Update the image data
            dat = np.array(self.raw_dicom_stack[0])
            self.im.set_data(dat)
            self.slider.reset()
            self.im.set_clim([dat.min(), dat.max()])
            # Redraw the plot
            self.fig.canvas.draw()

            self.query_add = True
            #rezero summed_image
            #summed_image = np.zeros((self.summed_image.shape[0],self.summed_image.shape[1]))


    def show(self):
        plt.show()

    def reset(self, event):

        #self.summed_image = np.zeros((self.raw_dicom_stack[0].shape[0],self.raw_dicom_stack[0].shape[1]))
        #self.query_register = False
        #self.query_add = False
        self.__init__(self.reset_stack, self.nframes, self.ds)

    def quit(self,event):
        quit()

if __name__ == '__main__':
    viewer = VolumeViewer(np.zeros((2,10,10)), 4, None)
    viewer.reset()

answered Feb 1, 2013 at 16:12

Matti Lyra

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3 Comments

moadeep Over a year ago

@MattLyra - I get the same problem with the program hanging. Is there a better way to restart the class when the button is selected

Matti Lyra Over a year ago

Well you can always try separating the code from __init__ into reset, but I don't think that's going to help as it's probably not calling __init__ that fails but something with the actual re initialisation. Have you stepped through the init code in the debugger to see where it hangs?

moadeep Over a year ago

Problem solved. It was related to the way I was copying raw_dicom_stack

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