Transparent output

[Marcel Gutsche]

Hi all, 

I'm not sure if it is a bug, or whether I've just overlooked something obvious, but the internet did not offer much regarding this issue. I try to get slices from an image cube which consists of several images s = 1,...,n with the same dimensions. My new slice should have the width of the original images and the height of the number of images. Here is the code to do this: 

from skimage.io import ImageCollection, imsave

from os.path import join

import numpy as np

def main(dir):

   ic = ImageCollection( join(dir, '*.png' ) )

   row = 0  

   img = np.empty((len(ic), ic[0].shape[1], ic[0].shape[2]  ) )        

   for s in range(len(ic)):    

       img[s,...] = ic[s][row,...]

#   fname = 'new_{0:03d}.jpg'.format(v) # -> wrong colors

   fname = 'new_{0:03d}.png'.format(v)  # -> output image is transparent
       imsave(fname, img)

The problem is that the output images are all transparent. My input files are .png images with an alpha channel. I have also checked the values of the alpha channel of the output which are all set to 255, which, at least to my knowledge, should set the opacity to 100%. 

Regards, 

Marcel

[Steven Silvester]

Marcel,

Would you be able to attach one of your images for me to test against?


Regards,

Steve

[Juan Nunez-Iglesias]

Marcel,

What about slicing out the alpha channel?

Also, depending on memory considerations, you might try ic.concatenate(), which was my very first contribution to scikit-image! =D

Juan.

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[Marcel Gutsche]

Hi folks, 

thanks for the quick reply. Removing the alpha channel worked. I also added one of my images as a reference for testing, why it does not work when alpha channels are provided. Also concatenate_images works well, thanks for the hint Juan. I haven't tested it for speed, but it is way more readable. 

One quick question to google-groups: Is it possible to answer using my email client? 

Marcel.

[Stéfan van der Walt]

On Thu, Feb 5, 2015 at 1:20 AM, Marcel Gutsche <marcel....@gmail.com> wrote:
> One quick question to google-groups: Is it possible to answer using my email
> client?

Yes, that is the way most of us do it, I think. You can adjust your
mail delivery settings at

https://groups.google.com/group/scikit-image

Stéfan

[Steven Silvester]

Marcel,

When you say the output image was transparent, you mean it was all white?  I believe what happened is your call to `np.empty` creates a floating point array, which skimage expects to be in the range [0, 1], but your data is in the range [0, 255].  If you used `dtype=np.uint8` in your `np.empty` call, I suspect it would work.

Regards,

Steve


On Wednesday, February 4, 2015 at 9:22:44 AM UTC-6, Marcel Gutsche wrote:

[Juan Nunez-Iglesias]

Steve, that is a *great* catch!!! =D

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[Marcel Gutsche]

Steve, 

the output image was really transparent, i.e. my image viewer showed a grey white checker pattern to indicate transparency. My actual implementation based on the Juan's hint regarding skimage.io.concatenate_images circumvents this issues by not creating an empty array in the first place, and by discarding the alpha channel. 

Regards,

Marcel

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