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##### Activity
• Jul 05 23:58
alexdesiqueira commented #6426
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• Jul 05 17:53
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• Jul 05 17:53
tlambert03 opened #6429
• Jul 05 16:52
lagru commented #6387
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FirefoxMetzger commented #877
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• Jul 04 11:24
mariosgeo commented #6320
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• Jul 04 10:59
mariosgeo commented #6320
seansabe
@seansabe
I did it but still sticking.
Juan Nunez-Iglesias
@jni
@seansabe very weird. are you installing from conda-forge or defaults?
also, are you able to conda-install other things?
seansabe
@seansabe
@jni Yes, I am using conda-forge. And I am able to install other stuff.
Mark Harfouche
@hmaarrfk
presently, the challenge is likely that scikit-image depends on matplotlib, which depends on qt
it takes time for my environment to solve
Benjamin Root
@WeatherGod
yeah, we just recently noticed some dependency issues with matplotlib+qt on conda yesterday. I don't think we figured out exactly what's wrong, but it might be qtconsole that is the root of the issues
Juan Nunez-Iglesias
@jni
@WeatherGod did something install eventually? @seansabe are you able to create a brand new environment? conda create --name skimage-test --channel=conda-forge python=3.7 scikit-image=0.14.1
Matt Wenham
@MattWenham
@jni - just looking through your revisions on my PR. What's missing from the docstring for _coprop_weights? Is it just the Returns that are missing or something more?
Matt Wenham
@MattWenham
@jni - Would you expect all my helper functions to have full docstrings? Can / how can I make them private to the texture Cython module??
Matt Wenham
@MattWenham
Ignore the 'private' bit, I've got it now...
Matt Wenham
@MattWenham
It's nearly there... could someone please investigate why one of the automated builds is failing? I don't think this has anything to do with my changes 🤔
Matt Wenham
@MattWenham
It's failing on both builds which use PIP_FLAGS="--pre" so I assume it's something to do with a pre-release version of another library.
Juan Nunez-Iglesias
@jni
@MattWenham you are correct, those are not your fault.
Ghost
@ghost~565b49ee16b6c7089cbc9b44
Hi! :) Are there any libraries to read/write binary .bmp files in Python ecosystem?
Davis Bennett
@d-v-b
Ghost
@ghost~565b49ee16b6c7089cbc9b44
@d-v-b imageio doesn't work with booleans, as far as I remember.
Davis Bennett
@d-v-b
ah sorry, i misread "binary"
Mark Harfouche
@hmaarrfk
@soupault you can try to add the functionality you need https://github.com/hmaarrfk/redpil
Juan Nunez-Iglesias
@jni
@soupault my very vague understanding of these things is that bmp is a pretty simple format. Perhaps you should extend imageio to support binary bmps? =)
Mark Harfouche
@hmaarrfk
@jni, yeah redpil does alot of reading the metadata and builds the infrastructure you would need to support these images.
I actually think I implemented reading boolean images. I have a test for it:
https://github.com/hmaarrfk/redpil/blob/master/redpil/tests/test_bmp.py#L76
The hard thing to understand is that boolean images are forced to be palletted, so even though there are only 2 possible values, those values will have RGB values assigned to them.
but the test also seems to indicated that pillow is also able to read the same image
Juan Nunez-Iglesias
@jni
@hmaarrfk why did you decide to write redpil independently rather than contribute to imageio?
Mark Harfouche
@hmaarrfk
just faster development cycle. imageio also stated that it was a frontend to other plugins
Mark Harfouche
@hmaarrfk
eventually, i guess I didn't care for a few reasons:
1. bitmaps force your data to be 4 byte aligned. Seems like an unecessary limitation for RGB or gray data.
2. imageio got the pillow settings correct so as to write images at (native?) speeds
Juan Nunez-Iglesias
@jni
@hmaarrfk what do you mean you didn't care? Are you saying the redpil bmp code is bit-rotting/unmaintained? I don't have much skin in this game, just want to get an accurate view of the image io landscape in Python
Mark Harfouche
@hmaarrfk
I think to displace Pillow would take a lot of work. Putting some experimental code in imageio would be dangerous. Originally, i thought there would be a speed advantage. And there was, but I submitted some patches to imageio that helped in that regard. Now redpil supports a different subset of bmp than Pillow so that might be a plus. There were a few examples in some BMP library that I wanted to get to really complete coverage of the BMP standard.
That is an issue I opened up in Pillow for them to expand support for bmp
Ghost
@ghost~565b49ee16b6c7089cbc9b44

@soupault my very vague understanding of these things is that bmp is a pretty simple format. Perhaps you should extend imageio to support binary bmps? =)

I'll consider this :). Need some sample data first...

@hmaarrfk thanks for your link. Looks like a nice place to contribute experimental code :).
Ghost
@ghost~565b49ee16b6c7089cbc9b44
Have you seen this early-alpha GitHub Workflow thing - https://user-images.githubusercontent.com/527589/46967252-9d15c200-d075-11e8-886f-19af1cf545fd.gif ? Perhaps, we should think about moving our infra (CI backend, releasing, ASV hooks, etc) to this platform once it's made public.
Kira Evans
@kne42
whoah that looks super cool!
E | M
@ewuramaminka

I have loaded CT dicom images. I want to segment the tissue within the CT. E.g. I want to determine there is 30% soft tissue 45% bone tissue, 20% air etc ... based on hounsefield units.

Anyone an expert in biomedical image analysis with scikit image?
Any useful libraries?

Looking for help. Thanks ☺️

Curtis Rueden
@ctrueden
@ewuramaminka I would encourage you to start a thread on https://forum.image.sc with an example of your images, and tagged with scikit-image.
E | M
@ewuramaminka
@ctrueden sure. Doing this now. Thanks
E | M
@ewuramaminka
for a frame of image slices --> fig, axes=plt.subplots(nrows=2, ncols=36) how can I maximize the frame ? I have tried ==> mng = plt.get_current_fig_manager()
mng.resize(*mng.window.maxsize()) but i get AttributeError: 'FigureManagerBase' object has no attribute 'window'. please assist.
Mark Harfouche
@hmaarrfk
you want to maximize the window?
E | M
@ewuramaminka

Yes. Because i made over 70 subplots and figure is so small as shown in console

Can my subplot frame be created in a window which can be maximized ?

Mark Harfouche
@hmaarrfk
making 70 subplots seems like a bad idea, do you have a 20k screen that is 60 inches wide?
Kevin Mader
@kmader
@ewuramaminka for processing medical CT images using skimage, a great starting resource is the Data Science Bowl 2017 with a large number of Jupyter Notebooks (called Kaggle Kernels) on how to preprocess the data, segment lungs, and ultimately train models: https://www.kaggle.com/gzuidhof/full-preprocessing-tutorial and https://www.kaggle.com/ankasor/improved-lung-segmentation-using-watershed are a good start. They also deal directly with the DICOM data and show how that can be opened, rescaled, etc. The kernels page is here: https://www.kaggle.com/c/data-science-bowl-2017/kernels and the competition also has a large number of discussions which can provide useful starting points.
E | M
@ewuramaminka
@kmader thanks a lot!
Tanim Islam
@tanimislam
Hi all, can scikit-image save an $M \times N$ integer numpy array into a 16-bit grayscale image?
Juan Nunez-Iglesias
@jni
yep, if you do from skimage import io; io.imsave('filename.png', arr.astype(np.uint16)), it should work. I'm assuming of course that you don't have any integers larger than 65535
Tanim Islam
@tanimislam
thanks @jni
and yes, no integers larger than 65535 (numpy array represents 16-bit grayscale data)
Stefan van der Walt
@stefanv

Hi everyone; we're going to try something new for the chat forum. Please direct your browsers to:

https://skimage.zulipchat.com

(or download the app)

We'll try this forum for a few weeks to see how it goes!