Showing an image with pylab.imshow()

Question

I'm relatively new to all this and I started the tutorial on image analysis here. When trying to perform the `pylab.imshow(dna)` step it returns the following error: ``` In [10]: pylab.imshow(dna) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) in () ----> 1 pylab.imshow(dna) /usr/lib/pymodules/python2.7/matplotlib/pyplot.pyc in imshow(X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, hold, **kwargs) 2375 ax.hold(hold) 2376 try: -> 2377 ret = ax.imshow(X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs) 2378 draw_if_interactive() 2379 finally: /usr/lib/pymodules/python2.7/matplotlib/axes.pyc in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resa…

Accepted Answer

it's just what the image is saved as in dna = mahotas.imread('dna.jpeg') type(dna) gives numpy.ndarray and dna.shape gives (1024, 1344, 1)

This is the problem, if you pass a 3D `ndarray`, it expects that you will have 3 or 4 planes (RGB or RGBA) (Read the code on line 410 in the last frame of the stack trace).

You just need to get rid of the extra dimension using

```
dna = dna.squeeze()
```

or

```
imshow(dna.squeeze())
```

To see what `squeeze` is doing, see the following example:

```
a = np.arange(25).reshape(5, 5, 1)
print a.shape # (5, 5, 1)
b = a.squeeze()
print b.shape # (5, 5)
```

Showing an image with pylab.imshow()

Solution

Problem