Mri Viewer

---

show code

collapse code

'''This is a simple mri viewer the mri is read using the img module with the read function
   from mri import img
   nim=img.read()'
   import numpy
   t=viewmri.plotit(numpy.flipud(nim.data))'''
 
import numpy
from numpy import shape
from pylab import figure, show, connect, disconnect, cm, axis, subplots_adjust
 
##from mri import img
##nim=img.read()
##x=nim.data.transpose()
 
class IndexTracker:
    def __init__(self, data, ax1, ax2, ax3):
        self.ax1 = ax1
        ax1.set_title('Sagital')
        self.ax2 = ax2
        ax2.set_title('Coronal')
        self.ax3 = ax3
        ax3.set_title('Axial')
 
        self.data = data
        rows,cols,self.slices1 = data.shape
        rows,self.slices2,cols = data.shape
        self.slices3,rows,cols = data.shape
 
        self.ind1 = self.slices1/2
        self.ind2 = self.slices2/2
        self.ind3 = self.slices3/2
 
        self.im1 = ax1.imshow(self.data[:,:,self.ind1], cmap=cm.gray)
        self.im2 = ax2.imshow(self.data[:,self.ind2,:], cmap=cm.gray)
        self.im3 = ax3.imshow(self.data[self.ind3,:,:], cmap=cm.gray)
 
        self.update1()
 
    def onscroll(self, event):
        if event.inaxes == self.ax1:
            if event.button=='up':
                self.ind1 = numpy.clip(self.ind1+1, 0, self.slices1-1)
            else:
                self.ind1 = numpy.clip(self.ind1-1, 0, self.slices1-1)
 
            self.update()
##            self.im1.set_data(self.data[:,:,self.ind1])   
##            self.im1.axes.figure.canvas.draw()
 
        if event.inaxes == self.ax2:
            if event.button=='up':
                self.ind2 = numpy.clip(self.ind2+1, 0, self.slices2-1)
            else:
                self.ind2 = numpy.clip(self.ind2-1, 0, self.slices2-1)
 
            self.update()
##            self.im2.set_data(self.data[:,self.ind2,:])   
##            self.im2.axes.figure.canvas.draw()
 
        if event.inaxes == self.ax3:
            if event.button=='up':
                self.ind3 = numpy.clip(self.ind3+1, 0, self.slices3-1)
            else:
                self.ind3 = numpy.clip(self.ind3-1, 0, self.slices3-1)
 
            self.update()
##            self.im3.set_data(self.data[self.ind3,:,:])   
##            self.im3.axes.figure.canvas.draw()
 
    def update(self):
        self.update1();self.update2();self.update3()
 
    def update1(self):
        self.im1.set_data(self.data[:,:,self.ind1])   
        self.im1.axes.figure.canvas.draw()
##        self.ax1.axhline(y=self.ind1, xmin=0, xmax=1)
##        axvline(x=.5, ymin=0, ymax=1)
    def update2(self):
        self.im2.set_data(self.data[:,self.ind2,:])   
        self.im2.axes.figure.canvas.draw()
    def update3(self):
        self.im3.set_data(self.data[self.ind3,:,:])   
        self.im3.axes.figure.canvas.draw()
 
    def click(self,event):
        print 'you clicked', event.xdata, event.ydata
##        print 'you pressed button ', event.button
##        print 'your on slice ', self.ind1, event.inaxes
        self.events=event        
 
        if event.inaxes == self.ax1:
##            print 'you clicked on image 1'
            self.ind2=int(event.xdata)
            self.ind3=int(event.ydata)
            print 'slice ', self.ind3
            self.update()
        if event.inaxes == self.ax2:
##            print 'you clicked on image 2'
            self.ind1=int(event.xdata)
            self.ind3=int(event.ydata)
            print 'slice ', self.ind1
            self.update()
        if event.inaxes == self.ax3:
##            print 'you clicked on image 3'
            self.ind1=int(event.xdata)
            self.ind2=int(event.ydata)
            print 'slice ', self.ind2
            self.update()
 
        return event
 
def plotit(data):
    "mri=img.decimate(nim, 5)"
    "ex. slice.plot(mri)"
    fig = figure()
    subplots_adjust(left=0, bottom=0,right=1, top=.85,wspace=.1, hspace=.1)
 
    ax1 = fig.add_subplot(221);axis('off')
    ax2 = fig.add_subplot(222);axis('off')
    ax3 = fig.add_subplot(223);axis('off')
    tracker = IndexTracker(data, ax1, ax2, ax3)
    fig.canvas.mpl_connect('scroll_event', tracker.onscroll)
    connect('button_press_event', tracker.click)
    show()
    return tracker

show howto

collapse howto

This is a simple mri viewer the mri is read using the img module with the read function
from mri import img
nim=img.read()'
data=nim.data()'
t=viewmri.plotit(numpy.flipud(nim.data))'''

---

---