[scikit-image] 回复： Python 3 transition

[imagepy]

Just my own opinion. we can give up python2.x  -- YXDragon
- 原始邮件 -
发件人：Stefan van der Walt 
收件人：scikit-image@python.org
主题：[scikit-image] Python 3 transition
日期：2017年11月11日 14点34分

Hi, everyone
I'd like to make a 4th attempt to determine our transition pathway to
Python 3.  The last thread is here:
https://mail.python.org/pipermail/scikit-image/2017-July/005304.html
I would like to propose that the next version, 0.14 (scheduled for March
of next year), becomes the last targeted for Python 2.  It will also be
an LTS (Long Time Support), which means we will backport serious fixes
for a period of one year.  0.15 will then target Python >= 3.5 only
(sorry, no f-strings yet!).
Let me know your thoughts.
Stéfan
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[scikit-image] 回复：Re: my watershed

[imagepy]

add one:if scikit-image can implements a ridge filter. just like watershed 
mixed with the skeleton. make all region a same label, then do level loop, just 
stop when one pixel left. It's usful in geography and hydrology analysis.
- 原始邮件 -
发件人：Juan Nunez-Iglesias 
收件人：scikit-image , imag...@sina.com,  
"Mailing_list_for_scikit-image_(http://scikit-image.org)" 

主题：Re: [scikit-image] my watershed
日期：2017年09月21日 13点48分




Hi Yan,


Thanks for this. Simple functions are very good for one’s own images, as well 
as to understand an algorithm, but for a widely used library like scikit-image, 
flexibility and robustness are least as important as speed. In skimage, we aim 
to support floating point input images, for which your code won’t work. There 
is a lot of thought into edge cases going into the skimage implementation, 
which unfortunately could have an effect on performance. The question we need 
to solve isn’t “can we make a super-fast watershed implementation”, but, “can 
we make a flexible and robust implementation that is also fast?” Using Numba is 
certainly not off-limits, but any candidate implementation should at a minimum 
pass the skimage test suite.


I once tried a level-by-level implementation of watershed, by the way. It has a 
fatal flaw, which is that valleys with no markers will never get labeled. 
Here’s a test case that works with skimage but fails in your implementation. 
(Note also that your implementation overwrites the seeds image, which is pretty 
crazy. =)


Thanks again!


Juan.



In [44]: import watershed
In [45]: from skimage import morphology
In [46]: import numpy as np
In [47]: image = np.array([1, 0, 1, 0, 1, 0, 1], dtype=np.uint8)
In [48]: seeds = np.array([0, 1, 0, 0, 0, 2, 0])
In [49]: morphology.watershed(image, seeds)
Out[49]: array([1, 1, 1, 1, 2, 2, 2], dtype=int32)
In [50]: watershed.watershed(image, seeds)
Out[50]: array([0, 0, 0, 0, 0, 0, 0])
In [51]: seeds
Out[51]: array([0, 0, 0, 0, 0, 0, 0])




On 12 Sep 2017, 6:34 AM +1000, imag...@sina.com, wrote:


Hi:
Now It supports nd. but less of test. this image, skimage cost 20s, mine less 
than 1s.
It is wrriten with numba in 90 lines. did not support compactness, but it's 
simple, and fast.


YXDragon
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[scikit-image] 回复：Re: 转发：some question about_h_minma_(need_a_paremeter,_and_can_run_faster)

[imagepy]

sorry! Perhaps I wrote mixed and disorderly, I want to say, I had improve or 
wrote some function, I want to contribute them when we support numba.
- 原始邮件 -
发件人：Stefan van der Walt <stef...@berkeley.edu>
收件人：scikit-image@python.org
主题：Re: [scikit-image] 转发：some question 
about_h_minma_(need_a_paremeter,_and_can_run_faster)
日期：2017年09月10日 11点29分




Hi, YXDragon



On Fri, Sep 8, 2017, at 21:25, imag...@sina.com wrote:

So I wrote h_minma/maxma and watershed myself (as a sub package of my project 
imagepy). My watershed now only support 2D, But the h_minma now is OK, works on 
nd. I had test one image:

   scikit-image's h_minma runs in 15s, and mine runs in 0.3s, 45times.




I tested on my machine and can confirm the slowness.  Would you be willing to 
help profile the code, to find out why it is so slow?



Best regards

Stéfan






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[scikit-image] 回复：Re: Release date for 0.14

[imagepy]

Hi Juan:What do you mean "undoing the speed regression of watershed"?  I found 
watershed run very slowly with large image,  and I am writting one with numba.  
 YXDragon
- 原始邮件 -
发件人：Juan Nunez-Iglesias 
收件人：scikit-image List Mailing ,  
"Mailing_list_for_scikit-image_(http://scikit-image.org)" 

主题：Re: [scikit-image] Release date for 0.14
日期：2017年09月01日 21点48分




Hi Egor,


Thanks for your support! I would prefer Nov 15 because I know for a fact that I 
will struggle to finish some of the major PRs that I need to get in before 
0.14, including undoing the speed regression of watershed, and nd moments. (For 
the first one I don’t even know where to start currently.)


Juan.



On 1 Sep 2017, 12:31 PM +0300, Egor Panfilov , wrote:


Dear all,


I propose to set a release date for scikit-image 0.14 on the mid of October 
(15th should do). Also, I'd volunteer to be a release manager for the release.
Please, let me know if you agree. If so, I kindly ask you to take a deep breath 
and try to review some of the scheduled PRs in the coming month.


Thanks in advance, and have a nice we!



Regards,
Egor Panfilov

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[scikit-image] 回复： Numba on pypi

[imagepy]

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 light-weight library, undepended 
any native so/dll)
  As I metioned befor, many scikit-image's algrisms are not exquisite 
enough(just my own opinion),  the mid_axi function results too many branch 
and sometimes with hols,the local_max has not a tolerance, so the 
result is too massy, then do a watershed end with too many fragments...,  
and how to build a graph from the skeleton, then do a network analysis.
I want to do a contribute to scikit-image, But after some effort, I give up, I 
prefor to write a dynamic lib rather then Cython. In the end, I wrote them in 
Numba. So I appreciate to use Numba.
BestYXDragon
- 原始邮件 -
发件人：Stefan van der Walt 
收件人：scikit-image@python.org
主题：[scikit-image] Numba on pypi
日期：2017年07月13日 14点17分

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 Python and
Cython): both to lower the barrier to entry for newcomers, and to lessen
the burden on maintainers.  But execution time comparisons, vs OpenCV
e.g., left much to be desired.
I think we have hit a turning point in the road.  Binary wheels for
Numba (actually, llvmlite) were recently uploaded to PyPi, making this
technology available to users on both pip and conda installations.  The
importance of this release on pypi should not be dismissed, and I am
grateful to the numba team and Continuum for making that decision.
So, how does that impact scikit-image?  Well, imagine we choose to
optimize various procedures via numba (see Juan's blog post for exactly
how impactful this can be:
https://ilovesymposia.com/2017/03/15/prettier-lowlevelcallables-with-numba-jit-and-decorators/).
The only question we have to answer (from a survival point of view)
needs to be: if, somehow, something happens to numba, will an
alternative will be available at that time?  Looking at the Python JIT
landscape (which is very active), and the current state of numba
development, I think this is likely.  And, if we choose to use numba, of
course we'll help to keep it healthy, as far as we can.
I'd love to hear your thoughts.  I, for one, am excited about the
prospect of writing kernels as simply as:
>>> @jit_filter_function
... def fmin(values):
... result = np.inf
... for v in values:
... if v < result:
... result = v
... return result
>>> ndi.generic_filter(image, fmin, footprint=fp)
Best regards
Stéfan
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[scikit-image] 回复：Re: building scikit-image plugin and tool set.

[imagepy]

Hi Stefan and Dongyao:I think the most difference between camera image, 
semiconductor industry and biology is the image format, and some specific 
algrism, As a plugin system, we just need to build general environment, 
supporting Numpy(uint8, int16, float32, float64), and some common mark(lookup 
table, scale ruler). about the difference, Developer in different fields can 
wrote their own reader plugins(such as pydicom).bwt:I do not appreciate 
integrate ui and plugins in scikit-image, scikit-image should be pure a 
processing library.
About the ui, wxPhoenix has support Py2, Py3, on Win, Mac ,Linux. You can 
find Linux whl here and will be avalible in pypi soon. (In fact I had tested 
ImagePy on win, mac, linux with py2/py3) I think QT and WX are both OK, but wx 
is more light weighted (just 10M on win), It is friendly for user to download.
I also agree with That web is the best choice. But I have no energy to do 
it myself, I am not good at web, js, I just see the image show and parameter 
adjust in Jupyter's demo (but the most difficult is to edit the roi line, 
curve, circle, and polygon, edit the node, sometimes with holes). I would be 
very happy If I can get contact with their developer!
BestYXDragon
- 原始邮件 -
发件人：Dongyao Li <lidongyao...@gmail.com>
收件人："Mailing list for scikit-image (http://scikit-image.org)" 
<scikit-image@python.org>
主题：Re: [scikit-image] building scikit-image plugin and tool set.
日期：2017年07月01日 03点40分

Hi YXDragon and Stefan:
I am a process engineer in semiconductor industry. I wrote a SEM/STEM/TEM 
analysis software with UI based on scikit-image, pyqt, and others, using the 
concept of plugins. I agree with Stefan's point that there is a market for 
this. However my experience is that the images from scientific instruments like 
SEM/STEM/TEM/MRI are quite different with images from cameras. And people in 
semiconductor industry and people working on biology have very different needs. 
I feel like the focus right now is mostly on the biology community.
I am very happy to hear that we can possibly build a web-based UI for image 
analysis now. It will integrate the image analysis and further data analysis 
greatly, which is the our future direction. It would be great if scikit-image 
could include some demo of it in the future, just like the "viewer" package 
skimage has right now.
Best,Dongyao

On Fri, Jun 30, 2017 at 10:48 AM, Stefan van der Walt <stef...@berkeley.edu> 
wrote:





Hi, YXDragon



On Fri, Jun 30, 2017, at 01:46, imag...@sina.com wrote:

 Now I think It is time to build a project named skimg-plgs. And I had 
wrote some presentative demo with friendly interact. these demo are all from 
the gallery, (interactive snake contours, interactive watershed...) I want to 
build a full plugin system and tool set covering scikit-image's every module. 
Then we can build a large user community like ImageJ, not only programers but 
also the doctors and biologists.



Given the immense success of projects such as ImageJ, and based on feedback 
I've received from practitioners in microscopy, there is certainly a market for 
a GUI built on top of scikit-image.



I don't personally have the time to contribute to such an effort at the moment 
(my focus is probably best spent keeping skimage on track!), but I am 
appreciative of the work you are doing, and encourage you to continue.



I may have mentioned this to you before, but I am not sure about the long-term 
viability of WXPython.  I heard that they have a Phoenix rewrite underway, but 
looking at the latest PyPI release 
(https://pypi.python.org/pypi/wxPython/4.0.0a1) they also only support Windows 
and MacOS.



With a Jupyter Lab release imminent, I would strongly consider using the web as 
UI, and building components that integrate with that project.  I can put you in 
contact with their developers, if you like.



Best regards

Stéfan






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[scikit-image] 回复:Re: 回复: Need help to get graph from image

[imagepy]

I has build the networt, look tips 2. imagepy is not a function library, but a 
interactive framework witch can wrap numpy, scipy, scikitimage, opencv as a 
friendly.software.  by another, please donot save picture as jpg. the dct 
transform may destroy the high frequent information.


来自我的新浪邮箱android客户端


 原始邮件 

发件人:Leena Chourey
时间:2017年5月18日 13:30(星期四)
收件人:imag...@sina.com
Mailing list for scikit-image (http://scikit-image.org)
主题:Re: [scikit-image] 回复: Need help to get graph from image
Thanks YXDragon for quick reply. Yes I have tried skeletonisation but hanged 
for further processing. hope the links u have sent will help to resolve.Wow.. 
great. that is exactly I need and done partially. Can u pls explain the 
1.jpg--->2.jpg--->3.jpg. I want exactly the same 3.jpg (junction points). Can i 
call imagepy in my python script and get the o/p of it for further 
processing?Is it possible to convert directly image to graph data structure?
On Thu, May 18, 2017 at 10:42 AM,  <imag...@sina.com> wrote:
1. you can do a skeleton, then use a np.ones((3,3)) to convolve. then 3 means 
junction, one means termin. 2 means path.2. trace from a termin. iterate all 
the pixel > 0. and add node if != 2!
some tips:1. if you do skeleton straightly, you will get some small branch, you 
can remove them by graph analysis. but I have a tip, you can do a gauss blur, 
then threshold again. this will smooth the binary image.2. trace the path is 
not very simple, you need care many detail... you can look mine.3. the 
scikit-images skeleton method prefers to generate branch (sometimes we 
want, but here we need not), you can look here.
you can have a try my project imagery do some test. which can wrap scikit-image 
like photoshop!(but I do not know if scikit-image has a method to build the 
skeleton)
My English is solo, forgive me. 
    YXDragon - 
ImagePy来自我的新浪邮箱android客户端 原始邮件 
发件人:Leena Chourey时间:2017年5月18日 
12:05(星期四)收件人:scikit-image@python.org主题:[scikit-image] Need help to get graph 
from imageDear All,I need to convert shape based image(graph_search2.jpg) into 
graph and then graph data structure. I have tried to filter the image and then 
with threshold, contour based approach access shapes(nodes), lines(edges) and 
arrows. but facing difficulty in getting relation b/w nodes and edges. Please 
help to find interest point(interest_points.jpg) and relation in node n 
edges.-- Thanks & Regards, -धन्यवादLeena Chourey , लीना चौरे C-DAC Mumbai 
सी-डैक, मुम्बई ___scikit-image 
mailing 
listscikit-image@python.orghttps://mail.python.org/mailman/listinfo/scikit-image


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-- 
Thanks & Regards, -धन्यवादLeena Chourey , लीना चौरे C-DAC Mumbai सी-डैक, मुम्बई 



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[scikit-image] build topograph network from skeleton

[imagepy]

 Hi everyone:I saw the newest version, require the networkx module. I find 
some function to find shortest path from image. But I want to know if there is 
a method to build a network from a skeleton image(2D/3D with arcs and nodes). I 
wrote one, but in python. it runs very slowly...
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[scikit-image] 回复： Reg: Working to create an ROI interactively and then find contours.

[imagepy]

It can wrap any function based on numpy, (spicy, scikit-image, opencv, itk 
...). This framework can generate interactive dialog automatically acrroding 
your function's parameter. and support roi, mask, undo. You just need to care 
your function! It can run on win, Mac, linux under py2.7 or py3x now! (I just 
make a framework like ImageJ, but more flexable)
- 原始邮件 -
发件人：Jesu Kiran Spurgen 
收件人：scikit-image@python.org
主题：[scikit-image] Reg: Working to create an ROI interactively and then find 
contours.
日期：2017年05月15日 17点48分

Dear Experts,
I have been able to successfully find the contours on an entire image.  
However,I am more interested to define an ROI interactively and then find 
thecontours for it, whilst preserving the other parts of the image without 
anycontour-finding.
 This is what I'd like to do:
* Create the ROI interactively for the input image* Find contours 
on that ROI (without cropping the ROI away from the rest of image)* 
Other parts (which are not in the ROI) should remain untouched. 

Link1: The link I used to find the interactive rectangle is:
http://stackoverflow.com/questions/21696097/how-can-i-make-a-draggable-adjustable-roi-in-opencv-python/21696862#21696862

To find contours, I use OpenCV. 

Any suggestions/help/code would be great! Thanks,
P.S: Sorry for these questions, but I would be ever grateful for a gentle and 
kind reply. I am new to OpenCV and SciKit, hence this question. Many thanks!
Looking forward for your kind response. Please kindly let me know if I could 
provide with more information.
Best Regards,Kiran

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[scikit-image] 回复: Reg: Working to create an ROI interactively and then find contours.

[imagepy]

https://github.com/yxdragon/imagepy


my project. have a look. make scikitimage like photoshop!


 原始邮件 

发件人:Jesu Kiran Spurgen
时间:2017年5月15日 17:48(星期一)
收件人:scikit-image@python.org
主题:[scikit-image] Reg: Working to create an ROI interactively and then find 
contours.
Dear Experts,
I have been able to successfully find the contours on an entire image.  
However,I am more interested to define an ROI interactively and then find 
thecontours for it, whilst preserving the other parts of the image without 
anycontour-finding.
 This is what Id like to do:
    * Create the ROI interactively for the input image        * Find contours 
on that ROI (without cropping the ROI away from the rest of image)        * 
Other parts (which are not in the ROI) should remain untouched. 

Link1: The link I used to find the interactive rectangle is:
http://stackoverflow.com/questions/21696097/how-can-i-make-a-draggable-adjustable-roi-in-opencv-python/21696862#21696862

To find contours, I use OpenCV. 

Any suggestions/help/code would be great! Thanks,
P.S: Sorry for these questions, but I would be ever grateful for a gentle and 
kind reply. I am new to OpenCV and SciKit, hence this question. Many thanks!
Looking forward for your kind response. Please kindly let me know if I could 
provide with more information.
Best Regards,Kiran

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