2D slice series of 3D array in numpy

Question

I have a 3D array that represents density values over cartesian space. To get a 2D image I just sum over one of the axes using sum(array,2) and then use the matplotlib function imshow(array2D) to obtain the 2D image.

What I want to do is use imshow() to display only one slice of the 3D array at a time so that I can 'page' through the 3D array to see different points of the image.

The slice command is simple: array[:,:,x] but I see no way to display every slice one at a time at least. Does anyone have suggestions other than manually changing the program file each time? Can this be done interactively somehow?

Community · Accepted Answer · 2017-05-23 11:43:24Z

4

I actually wrote code to do exactly what I think you are looking for, see if this helps:

import numpy as np
import pylab

class plotter:
    def __init__(self, im, i=0):
        self.im = im
        self.i = i
        self.vmin = im.min()
        self.vmax = im.max()
        self.fig = pylab.figure()
        pylab.gray()
        self.ax = self.fig.add_subplot(111)
        self.draw()
        self.fig.canvas.mpl_connect('key_press_event',self)

    def draw(self):
        if self.im.ndim is 2:
            im = self.im
        if self.im.ndim is 3:
            im = self.im[...,self.i]
            self.ax.set_title('image {0}'.format(self.i))

        pylab.show()

        self.ax.imshow(im, vmin=self.vmin, vmax=self.vmax, interpolation=None)


    def __call__(self, event):
        old_i = self.i
        if event.key=='right':
            self.i = min(self.im.shape[2]-1, self.i+1)
        elif event.key == 'left':
            self.i = max(0, self.i-1)
        if old_i != self.i:
            self.draw()
            self.fig.canvas.draw()


def slice_show(im, i=0):
    plotter(im, i)

Just call the show function on your 3d array, i will tell it what slice to displaying. You can step through slices with arrow keys as long as you have the plot selected.

Note, this expects arrays with shape (x, y, z), you could for example get such an array from a series of 2d arrays with np.dstack((im1, im2, ...)).

See also Interactive matplotlib plot with two sliders for a code example of doing it with gui sliders

edited May 23, 2017 at 11:43

CommunityBot

11 silver badge

answered Jul 15, 2011 at 12:58

triplepoint217

4823 silver badges10 bronze badges

Sign up to request clarification or add additional context in comments.

2 Comments

Bi Rico Over a year ago

Thanks for this, I was looking for something like this too. Just fyi, every time you call imshow it stacks another image onto a pile of images, you might want to do something like self.ax.images.pop() before you do the imshow in order to avoid a memory leak.

triplepoint217 Over a year ago

hey cool, I have suspected a memory leak, I will give ax.images.pop() a try

Collectives™ on Stack Overflow

2D slice series of 3D array in numpy

1 Answer 1

2 Comments

Your Answer

Linked

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

2 Comments

Your Answer

Sign up or log in

Post as a guest

Linked

Related