Marcel, Would you be able to attach one of your images for me to test against? Regards, Steve On Wednesday, February 4, 2015 at 9:22:44 AM UTC-6, Marcel Gutsche wrote:

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

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.

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:

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

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 2015-02-06 3:21 GMT+01:00 Juan Nunez-Iglesias <jni.soma@gmail.com>:

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

On Fri, Feb 6, 2015 at 1:19 PM, Steven Silvester < steven.silvester@gmail.com> wrote:

...

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:

...

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

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