How to use cmap function efficiently in python?

Asked May 26 '17 at 06:20

Active May 26 '17 at 08:42

Viewed 120 times

I am trying this below code to find the bacteria in the image. but the cmap function is not doing anything in the image.

Am i missing anything in the code? Why the cmap is not working? I am getting the original image even after applying cmap.

can i know the reason for this?

import scipy.ndimage 
import skimage.io
from matplotlib import cm as cm
import numpy as np
from matplotlib import pyplot as plt
im_phase = skimage.io.imread('ecoli_phase.tif')
skimage.io.imshow(im_phase / im_phase.max())
fig, ax = plt.subplots(2, 2, figsize=(12,10))
ax[0,0].imshow(im_phase, cmap=plt.cm.gray)
ax[0,1].imshow(im_phase, cmap=plt.cm.RdBu_r)
ax[1,0].imshow(im_phase, cmap=plt.cm.YlGnBu_r)
ax[1,1].imshow(im_phase, cmap=plt.cm.copper)

asked May 26 '17 at 06:20

meena udayasankar

Is your image a grey-scale image? The documentation states that pseudo-color does not work on rgb images. – Thomas Kühn May 26 '17 at 06:25
1

@GergesDib I was too slow :D – Thomas Kühn May 26 '17 at 06:26
@meena Use skimage.color.rgb2gray to use cmap – Gerges May 26 '17 at 06:27
Please also have a look at the relevant [documentation page](https://matplotlib.org/users/image_tutorial.html) – Thomas Kühn May 26 '17 at 06:28
@Gerges Dib . Thanks .. my img is rgb. now i converted that to gray scale. its working now. – meena udayasankar May 26 '17 at 06:43
and I am trying to plot the image in four graph using subplot. (i.e) ax[0,0].imshow.. but its not plotting the gray. what i have to include? – meena udayasankar May 26 '17 at 06:45
@meena can you update your question with the gray scale conversion and clearly state where the problem is now? Once that's done the question could be reopened. – ImportanceOfBeingErnest May 26 '17 at 10:17

How to use cmap function efficiently in python?

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