[scikit-image] pixel value changes during reading image and showing images using skimage and matplotlib

[Thomas Caswell]

plt.imread falls back to PIL/pillow for tiff reading which does not always
handle high-bit depth tiffs well.  I (as a lead mpl dev) would discourage
`plt.imread` for 'production' use, there are many better options out there
(ex skimage, http://imageio.github.io/ ,
http://soft-matter.github.io/pims/v0.3.3/  ,
http://imread.readthedocs.io/en/latest/  ).

Tom

On Sun, Dec 11, 2016 at 2:04 PM wine lover <winecoding at gmail.com> wrote:

> Hi Imanol,
>
> It works fine now, thanks for your suggestions.
>
> Regarding the second part of my question. If I read the image using
> matlibplot instead of skimage,
> i.e.,  output=plt.imread(os.path.join(image_path,raw_image_name))
>
> I found that the pixel values of output were all changed, and they becomes
> either 255. or 0. which causes the image shown as all black. What are the
> possible reasons for plt.imread. Thanks.
>
> Yuanyuan
>
> On Sun, Dec 11, 2016 at 4:54 AM, Imanol Luengo <
> imanol.luengo at nottingham.ac.uk> wrote:
>
> Dear Yuanyuan,
>
> The reason why you are looking at a *color* image is due to the colormaps:
>
> http://matplotlib.org/users/colormaps.html
>
> The default colormap (to map from numbers to colors) is not grayscale, as
> matplotlib is not primarly focus on images, and grayscale is not an
> *adequate* colormap to represent other types of plots.
>
> To properly visualize your image specify a colormap to the plot function:
>
>      plt.imshow(output, 'gray')
>
> Cheers,
>
> Imanol
>
> On 11/12/16 06:46, wine lover wrote:
>
> Dear All,
>
> I have a tif images, its type is float32, shape is (128*128) (a grayscale
> image). All the pixel values are of range [0.0, 1.0]
>
>  I am trying to read it using skimage and show it on screen using
> matplotlib.
>
> from skimage import ioimport matplotlib.pyplot as plt
> output=io.imread(os.path.join(image_path,raw_image_name))print(output.dtype)print(output.shape)print(output.max())print(output.min())
> plt.imshow(output)
> plt.show()
>
> The output image looks like color image instead of gray image as shown
> originally. I attached the screenshot as the capture-1.jpg.
>
> However, when I read the image using matplotlib instead,i.e.,
> output=plt.imread(os.path.join(image_path,raw_image_name)). I found that
> pixel value will become 255 and 0. The dtype is still float32. But when I
> print output, the pixel values are either 0. or 255.
>
> The output image will become black as shown in the second image
> (capture-2.jpg). I am confused how does this work? My guess is that there
> are some dtype changes happening during the reading image and showing
> image,
>
>
> Thanks,
>
> Yuanyuan
>
>
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