[scikit-image] Image intensity measure.regionprops

Hi scikit-image users/devs, I'm using skimage.measure.regionprops and I'm little bit confused about a result I get with it. I'm working with a zstack of a microscopy image that I have segmented/label and I'm trying to get the mean intensity of the labeled region: region_props =

Re: [scikit-image] Numba on pypi

On 13 July 2017 22:30:03 Nadav Horesh wrote: I'd make numba dependency optional, since keeping llvm and llvmlite versions in sync requires special attention (at least with the Linux distros I used), what makes numba availability below 100%. I don't think we need to

Re: [scikit-image] Numba on pypi

I'd make numba dependency optional, since keeping llvm and llvmlite versions in sync requires special attention (at least with the Linux distros I used), what makes numba availability below 100%. Nadav. On Jul 14, 2017 5:23 AM, "Gregory Lee" wrote: > I am also +1 on

Re: [scikit-image] Numba on pypi

I am also +1 on allowing numba code in scikit-image. I have tended to prefer Cython in the past, but it has been a while since I looked at numba and it seems it has come a long way in recent years. Juan's blog post and the simple example you provided are great examples of relevant use cases.

Re: [scikit-image] 回复：Re: 回复： Numba on pypi

What I find numba brings to the table is a significantly more expressive and easier to maintain code base. Essentially writing basic bare bones loops often are easiest to JIT. They are then easier to debug, and faster to iterate on thanks to removing the compilation step. I haven't checked

Re: [scikit-image] Memory consumption of measure.label (compared to matlab)

On Thu, Jul 13, 2017, at 04:21, Martin Fleck wrote: > Indeed, this could be the complete problem already! For the analysis I use a > binary image - so only one bit per pixel. FWIW, binary images are stored as ubyte, so 1 *byte* per pixel. > Greg: Regarding your PR and my analysis: My analysis

Re: [scikit-image] 回复：Re: 回复： Numba on pypi

On Thu, Jul 13, 2017, at 03:04, imag...@sina.com wrote: > May I start a new topic thread? with the test image, and my numba code. Yes, please. Stéfan ___ scikit-image mailing list scikit-image@python.org

Re: [scikit-image] Memory consumption of measure.label (compared to matlab)

Hi again, attached is a file "matlab_memory_info" and again the same "skiamge_memory_profiler.out" that I showed before. in the matlab_memory_info file, I added for every matlab call the equivalent that I do in skimage. I don't think it will be needed - the attached files should be enough - but

Re: [scikit-image] Memory consumption of measure.label (compared to matlab)

Hi again, here you can download a minimal example: https://drive.google.com/open?id=0BzmlODsuIIz0elpIcU1kdmpNTlE (download button is the arrow on the top right) In order to run it and get the memory_profiler output you have to install memory_profiler e.g. with pip3 install memory_profiler and

Re: [scikit-image] Memory consumption of measure.label (compared to matlab)

Hi Juan, hi Greg, quoting Greg: > I think the main reason for the increased memory usage is that the output type of the label function is int64 while your input is most likely uint8. Indeed, this could be the complete problem already! For the analysis I use a binary image - so only one bit per

Re: [scikit-image] 回复： Numba on pypi

Hi Thomas On Thu, Jul 13, 2017, at 01:04, Thomas Walter via scikit-image wrote: > A question to Stéfan: would this mean that you would remove all cython code > from scikit-image or would numba just be another option? I think we'd probably keep both around; one of the advantages of this

Re: [scikit-image] 回复： Numba on pypi

Hi YXDragon, just a word on some aspect you mention: > the local_max has not a tolerance, so the result is too massy, then do a watershed end with too many fragments..., The definition that underlies this function is: "A local maximum is a region of constant grey level strictly greater than

Re: [scikit-image] Numba on pypi

On Thu, Jul 13, 2017 at 6:16 PM, Stefan van der Walt wrote: > Hi everyone, > > As many of you know, speed has been a point of contention in > scikit-image for a long time. We've made a very deliberate decision to > focus on writing high-level, understandable code (via

[scikit-image] 回复： Numba on pypi

Hi Stéfan: I appreciate Numba. for sometimes, we must do a 'for' in our python code, but just a 'for' with a 'if', It is fussy to compile a so/dll or write cython. Numba is very portable, and can run anywhere, just need to install numba and llvmlite. (That means our package could be a