Mailman 3 August 2018 - scikit-image

Re: [scikit-image] Error during env setup
by Sena Agezo 29 Aug '18

29 Aug '18

The pip install -e . finally worked! I ran the “make clean” first as Juan suggested and then the pip command. Mark, to answer your question, I am running it on ubuntu-16.04.5 LTS. Thanks a lot for your help. -Sena > On Aug 29, 2018, at 11:34 AM, Mark Harfouche <mark.harfouche(a)gmail.com> wrote: > > Thanks for those outputs. They were good at eliminating sources of problems. > > What Linux distribution are you using and what compilers do you have installed? > > On Wed, Aug 29, 2018 at 7:36 AM Juan Nunez-Iglesias <jni(a)fastmail.com <mailto:jni@fastmail.com>> wrote: > Hmmm. Unfortunately I have no ideas right now about what is going wrong there. One question: can you try running "make clean" and then the pip command again? Sometimes I get weird behaviour where Cython files don't get rebuilt. But other than that I have no idea. I don't see this on my Linux machine. Anyone else? > > > On Wed, Aug 29, 2018, at 11:09 PM, Sena Agezo wrote: > >> These are the outputs for pip install -e . --no-deps and build_versions.py . >> >> >> >> >> >> -Sena >> >> >> >>> On Aug 28, 2018, at 2:15 PM, Mark Harfouche <mark.harfouche(a)gmail.com <mailto:mark.harfouche@gmail.com>> wrote: >>> >>> I meant the full output of your build pip install -e . --no-deps >>> >>> >>> >>> On Tue, Aug 28, 2018 at 11:14 AM Mark Harfouche <mark.harfouche(a)gmail.com <mailto:mark.harfouche@gmail.com>> wrote: >>> Hi Sena, >>> >>> Please run >>> >>> pip install requirements-parser >>> python tools/build_versions.py >>> >>> Please provide the output of build_versions.py >>> >>> >>> Can you somehow post the full output of the command? >>> Maybe to pastebin? >>> >>> Mark >>> >>> >>> >>> On Tue, Aug 28, 2018 at 10:54 AM Sena Agezo <senaagezo(a)gmail.com <mailto:senaagezo@gmail.com>> wrote: >>> Hi Juan, >>> >>> Yes, I did install Cython first before attempting to “pip install -e .” >>> >>> -Sena >>> >>>> On Aug 27, 2018, at 8:45 PM, Juan Nunez-Iglesias <jni(a)fastmail.com <mailto:jni@fastmail.com>> wrote: >>>> >>>> Hi Sena, thanks for wanting to contribute! >>>> >>>> I believe you need install Cython first, and then it should work. Can you give that a try and report back? >>>> >>>> Juan. >>>> >>>> On Tue, Aug 28, 2018, at 7:31 AM, Sena Agezo wrote: >>>>> Hi, >>>>> >>>>> I am trying to make a contribution to the scikit-image documentation. In my attempt to setup the environment after creating it, I keep getting an error(see below). This error happens when I do "pip install -e ." in the cloned scikit-image. I’m doing this on a linux machine. >>>>> >>>>> error: Command "gcc -pthread -B /home/liulab/anaconda3/envs/skimage/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -c _extrema_cy.c -o build/temp.linux-x86_64-3.6/_extrema_cy.o -MMD -MF build/temp.linux-x86_64-3.6/_extrema_cy.o.d" failed with exit status 1 >>>>> gcc: error: _extrema_cy.c: No such file or directory >>>>> gcc: error: _extrema_cy.c: No such file or directory >>>>> >>>>> ---------------------------------------- >>>>> Command "/home/liulab/anaconda3/envs/skimage/bin/python -c "import setuptools, tokenize;__file__='/home/liulab/Documents/scikit-image/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps" failed with error code 1 in /home/liulab/Documents/scikit-image/ >>>>> >>>>> Please advise on what I should do to solve the issue and let me know if you have any questions. >>>>> >>>>> Thanks, >>>>> Sena >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> scikit-image mailing list >>>>> scikit-image(a)python.org <mailto:scikit-image@python.org> >>>>> https://mail.python.org/mailman/listinfo/scikit-image <https://mail.python.org/mailman/listinfo/scikit-image> >>>> >>>> _______________________________________________ >>>> scikit-image mailing list >>>> scikit-image(a)python.org <mailto:scikit-image@python.org> >>>> https://mail.python.org/mailman/listinfo/scikit-image <https://mail.python.org/mailman/listinfo/scikit-image> >>> >>> >>> _______________________________________________ >>> scikit-image mailing list >>> scikit-image(a)python.org <mailto:scikit-image@python.org> >>> https://mail.python.org/mailman/listinfo/scikit-image <https://mail.python.org/mailman/listinfo/scikit-image> >>> _______________________________________________ >>> scikit-image mailing list >>> scikit-image(a)python.org <mailto:scikit-image@python.org> >>> https://mail.python.org/mailman/listinfo/scikit-image <https://mail.python.org/mailman/listinfo/scikit-image> >> >> _______________________________________________ >> scikit-image mailing list >> scikit-image(a)python.org <mailto:scikit-image@python.org> >> https://mail.python.org/mailman/listinfo/scikit-image <https://mail.python.org/mailman/listinfo/scikit-image> > >> Email had 2 attachments: >> >> build_version.py_output.pdf >> 27k (application/pdf) >> Pip_install_output.pdf >> 49k (application/pdf) > > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org <mailto:scikit-image@python.org> > https://mail.python.org/mailman/listinfo/scikit-image <https://mail.python.org/mailman/listinfo/scikit-image> > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

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Re: [scikit-image] Error during env setup
by Mark Harfouche 29 Aug '18

29 Aug '18

Thanks for those outputs. They were good at eliminating sources of problems. What Linux distribution are you using and what compilers do you have installed? On Wed, Aug 29, 2018 at 7:36 AM Juan Nunez-Iglesias <jni(a)fastmail.com> wrote: > Hmmm. Unfortunately I have no ideas right now about what is going wrong > there. One question: can you try running "make clean" and then the pip > command again? Sometimes I get weird behaviour where Cython files don't get > rebuilt. But other than that I have no idea. I don't see this on my Linux > machine. Anyone else? > > > On Wed, Aug 29, 2018, at 11:09 PM, Sena Agezo wrote: > > These are the outputs for pip install -e . --no-deps and build_versions.py > . > > > > > > -Sena > > > > On Aug 28, 2018, at 2:15 PM, Mark Harfouche <mark.harfouche(a)gmail.com> > wrote: > > I meant the full output of your build pip install -e . --no-deps > > > On Tue, Aug 28, 2018 at 11:14 AM Mark Harfouche <mark.harfouche(a)gmail.com> > wrote: > > Hi Sena, > > Please run > > pip install requirements-parser > python tools/build_versions.py > > Please provide the output of build_versions.py > > Can you somehow post the full output of the command? > Maybe to pastebin? > > Mark > > > On Tue, Aug 28, 2018 at 10:54 AM Sena Agezo <senaagezo(a)gmail.com> wrote: > > Hi Juan, > > Yes, I did install Cython first before attempting to “pip install -e .” > > -Sena > > On Aug 27, 2018, at 8:45 PM, Juan Nunez-Iglesias <jni(a)fastmail.com> wrote: > > Hi Sena, thanks for wanting to contribute! > > I believe you need install Cython first, and then it should work. Can you > give that a try and report back? > > Juan. > > On Tue, Aug 28, 2018, at 7:31 AM, Sena Agezo wrote: > > Hi, > > I am trying to make a contribution to the scikit-image documentation. In > my attempt to setup the environment after creating it, I keep getting an > error(see below). This error happens when I do "pip install -e ." in the > cloned scikit-image. I’m doing this on a linux machine. > > *error: Command "gcc -pthread -B > /home/liulab/anaconda3/envs/skimage/compiler_compat -Wl,--sysroot=/ > -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC > -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include > -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include > -I/home/liulab/anaconda3/envs/skimage/include/python3.6m > -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -c _extrema_cy.c > -o build/temp.linux-x86_64-3.6/_extrema_cy.o -MMD -MF > build/temp.linux-x86_64-3.6/_extrema_cy.o.d" failed with exit status 1* > * gcc: error: _extrema_cy.c: No such file or directory* > * gcc: error: _extrema_cy.c: No such file or directory* > > * ----------------------------------------* > *Command "/home/liulab/anaconda3/envs/skimage/bin/python -c "import > setuptools, > tokenize;__file__='/home/liulab/Documents/scikit-image/setup.py';f=getattr(tokenize, > 'open', open)(__file__);code=f.read().replace('\r\n', > '\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps" > failed with error code 1 in /home/liulab/Documents/scikit-image/* > > Please advise on what I should do to solve the issue and let me know if > you have any questions. > > Thanks, > Sena > > > > > *_______________________________________________* > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image > > > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image > > > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image > > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image > > *_______________________________________________* > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image > > Email had 2 attachments: > > - build_version.py_output.pdf > 27k (application/pdf) > - Pip_install_output.pdf > 49k (application/pdf) > > > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image >

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Re: [scikit-image] Error during env setup
by Sena Agezo 29 Aug '18

29 Aug '18

These are the outputs for pip install -e . --no-deps and build_versions.py . -Sena > On Aug 28, 2018, at 2:15 PM, Mark Harfouche <mark.harfouche(a)gmail.com> wrote: > > I meant the full output of your build pip install -e . --no-deps > > > On Tue, Aug 28, 2018 at 11:14 AM Mark Harfouche <mark.harfouche(a)gmail.com <mailto:mark.harfouche@gmail.com>> wrote: > Hi Sena, > > Please run > > pip install requirements-parser > python tools/build_versions.py > Please provide the output of build_versions.py > > Can you somehow post the full output of the command? > Maybe to pastebin? > > Mark > > > On Tue, Aug 28, 2018 at 10:54 AM Sena Agezo <senaagezo(a)gmail.com <mailto:senaagezo@gmail.com>> wrote: > Hi Juan, > > Yes, I did install Cython first before attempting to “pip install -e .” > > -Sena > >> On Aug 27, 2018, at 8:45 PM, Juan Nunez-Iglesias <jni(a)fastmail.com <mailto:jni@fastmail.com>> wrote: >> >> Hi Sena, thanks for wanting to contribute! >> >> I believe you need install Cython first, and then it should work. Can you give that a try and report back? >> >> Juan. >> >> On Tue, Aug 28, 2018, at 7:31 AM, Sena Agezo wrote: >>> Hi, >>> >>> I am trying to make a contribution to the scikit-image documentation. In my attempt to setup the environment after creating it, I keep getting an error(see below). This error happens when I do "pip install -e ." in the cloned scikit-image. I’m doing this on a linux machine. >>> >>> error: Command "gcc -pthread -B /home/liulab/anaconda3/envs/skimage/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -c _extrema_cy.c -o build/temp.linux-x86_64-3.6/_extrema_cy.o -MMD -MF build/temp.linux-x86_64-3.6/_extrema_cy.o.d" failed with exit status 1 >>> gcc: error: _extrema_cy.c: No such file or directory >>> gcc: error: _extrema_cy.c: No such file or directory >>> >>> ---------------------------------------- >>> Command "/home/liulab/anaconda3/envs/skimage/bin/python -c "import setuptools, tokenize;__file__='/home/liulab/Documents/scikit-image/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps" failed with error code 1 in /home/liulab/Documents/scikit-image/ >>> >>> Please advise on what I should do to solve the issue and let me know if you have any questions. >>> >>> Thanks, >>> Sena >>> >>> >>> >>> >>> _______________________________________________ >>> scikit-image mailing list >>> scikit-image(a)python.org <mailto:scikit-image@python.org> >>> https://mail.python.org/mailman/listinfo/scikit-image <https://mail.python.org/mailman/listinfo/scikit-image> >> >> _______________________________________________ >> scikit-image mailing list >> scikit-image(a)python.org <mailto:scikit-image@python.org> >> https://mail.python.org/mailman/listinfo/scikit-image <https://mail.python.org/mailman/listinfo/scikit-image> > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org <mailto:scikit-image@python.org> > https://mail.python.org/mailman/listinfo/scikit-image <https://mail.python.org/mailman/listinfo/scikit-image> > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

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Re: [scikit-image] Error during env setup
by Mark Harfouche 28 Aug '18

28 Aug '18

I meant the full output of your build pip install -e . --no-deps On Tue, Aug 28, 2018 at 11:14 AM Mark Harfouche <mark.harfouche(a)gmail.com> wrote: > Hi Sena, > > Please run > > pip install requirements-parser > python tools/build_versions.py > > Please provide the output of build_versions.py > > Can you somehow post the full output of the command? > Maybe to pastebin? > > Mark > > On Tue, Aug 28, 2018 at 10:54 AM Sena Agezo <senaagezo(a)gmail.com> wrote: > >> Hi Juan, >> >> Yes, I did install Cython first before attempting to “pip install -e .” >> >> -Sena >> >> On Aug 27, 2018, at 8:45 PM, Juan Nunez-Iglesias <jni(a)fastmail.com> >> wrote: >> >> Hi Sena, thanks for wanting to contribute! >> >> I believe you need install Cython first, and then it should work. Can you >> give that a try and report back? >> >> Juan. >> >> On Tue, Aug 28, 2018, at 7:31 AM, Sena Agezo wrote: >> >> Hi, >> >> I am trying to make a contribution to the scikit-image documentation. In >> my attempt to setup the environment after creating it, I keep getting an >> error(see below). This error happens when I do "pip install -e ." in the >> cloned scikit-image. I’m doing this on a linux machine. >> >> *error: Command "gcc -pthread -B >> /home/liulab/anaconda3/envs/skimage/compiler_compat -Wl,--sysroot=/ >> -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC >> -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include >> -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include >> -I/home/liulab/anaconda3/envs/skimage/include/python3.6m >> -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -c _extrema_cy.c >> -o build/temp.linux-x86_64-3.6/_extrema_cy.o -MMD -MF >> build/temp.linux-x86_64-3.6/_extrema_cy.o.d" failed with exit status 1* >> * gcc: error: _extrema_cy.c: No such file or directory* >> * gcc: error: _extrema_cy.c: No such file or directory* >> >> * ----------------------------------------* >> *Command "/home/liulab/anaconda3/envs/skimage/bin/python -c "import >> setuptools, >> tokenize;__file__='/home/liulab/Documents/scikit-image/setup.py';f=getattr(tokenize, >> 'open', open)(__file__);code=f.read().replace('\r\n', >> '\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps" >> failed with error code 1 in /home/liulab/Documents/scikit-image/* >> >> Please advise on what I should do to solve the issue and let me know if >> you have any questions. >> >> Thanks, >> Sena >> >> >> >> >> *_______________________________________________* >> scikit-image mailing list >> scikit-image(a)python.org >> https://mail.python.org/mailman/listinfo/scikit-image >> >> >> _______________________________________________ >> scikit-image mailing list >> scikit-image(a)python.org >> https://mail.python.org/mailman/listinfo/scikit-image >> >> >> _______________________________________________ >> scikit-image mailing list >> scikit-image(a)python.org >> https://mail.python.org/mailman/listinfo/scikit-image >> >

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Re: [scikit-image] Error during env setup
by Sena Agezo 28 Aug '18

28 Aug '18

Hi Juan, Yes, I did install Cython first before attempting to “pip install -e .” -Sena > On Aug 27, 2018, at 8:45 PM, Juan Nunez-Iglesias <jni(a)fastmail.com> wrote: > > Hi Sena, thanks for wanting to contribute! > > I believe you need install Cython first, and then it should work. Can you give that a try and report back? > > Juan. > > On Tue, Aug 28, 2018, at 7:31 AM, Sena Agezo wrote: >> Hi, >> >> I am trying to make a contribution to the scikit-image documentation. In my attempt to setup the environment after creating it, I keep getting an error(see below). This error happens when I do "pip install -e ." in the cloned scikit-image. I’m doing this on a linux machine. >> >> error: Command "gcc -pthread -B /home/liulab/anaconda3/envs/skimage/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -c _extrema_cy.c -o build/temp.linux-x86_64-3.6/_extrema_cy.o -MMD -MF build/temp.linux-x86_64-3.6/_extrema_cy.o.d" failed with exit status 1 >> gcc: error: _extrema_cy.c: No such file or directory >> gcc: error: _extrema_cy.c: No such file or directory >> >> ---------------------------------------- >> Command "/home/liulab/anaconda3/envs/skimage/bin/python -c "import setuptools, tokenize;__file__='/home/liulab/Documents/scikit-image/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps" failed with error code 1 in /home/liulab/Documents/scikit-image/ >> >> Please advise on what I should do to solve the issue and let me know if you have any questions. >> >> Thanks, >> Sena >> >> >> >> >> _______________________________________________ >> scikit-image mailing list >> scikit-image(a)python.org <mailto:scikit-image@python.org> >> https://mail.python.org/mailman/listinfo/scikit-image <https://mail.python.org/mailman/listinfo/scikit-image> > > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org <mailto:scikit-image@python.org> > https://mail.python.org/mailman/listinfo/scikit-image <https://mail.python.org/mailman/listinfo/scikit-image>

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Error during env setup
by Sena Agezo 27 Aug '18

27 Aug '18

Hi, I am trying to make a contribution to the scikit-image documentation. In my attempt to setup the environment after creating it, I keep getting an error(see below). This error happens when I do "pip install -e ." in the cloned scikit-image. I’m doing this on a linux machine. error: Command "gcc -pthread -B /home/liulab/anaconda3/envs/skimage/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include -I/tmp/pip-build-env-29p1x6uy/lib/python3.6/site-packages/numpy/core/include -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -I/home/liulab/anaconda3/envs/skimage/include/python3.6m -c _extrema_cy.c -o build/temp.linux-x86_64-3.6/_extrema_cy.o -MMD -MF build/temp.linux-x86_64-3.6/_extrema_cy.o.d" failed with exit status 1 gcc: error: _extrema_cy.c: No such file or directory gcc: error: _extrema_cy.c: No such file or directory ---------------------------------------- Command "/home/liulab/anaconda3/envs/skimage/bin/python -c "import setuptools, tokenize;__file__='/home/liulab/Documents/scikit-image/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" develop --no-deps" failed with error code 1 in /home/liulab/Documents/scikit-image/ Please advise on what I should do to solve the issue and let me know if you have any questions. Thanks, Sena

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interactive segment function in skimage 0.14
by imagepy＠sina.com 26 Aug '18

26 Aug '18

I found there are several interactive segment method in 0.14 version here. These method are very useful in many case, But they need a interactive enviroment to make the initial seed/rectangle/contours. So I would integrade these method in ImagePy, I will tell you when it is completed. YXDragon

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Re: [scikit-image] Help with skimage.graph MCP
by Ömer Özak 17 Aug '18

17 Aug '18

Hi Zach, Thanks for the answer. I had added the find_costs_gis() function to see if the subclass was not using the new edge_maps. I actually thought the code was using the edge maps to figure out the neighborhood for each cell, so that is why I went this route. It seems I have misunderstood the code completely, especially since I'm not familiar heaps. I'll take another try and let you know if and when I fail/succeed. Best, Ömer Sent from my mobile Please excuse any typos > On Aug 17, 2018, at 2:32 AM, Zach Pincus <zpincus(a)gmail.com> wrote: > > Hello Ömer, > > Your subclass will have to have some special-case logic in > find_costs() to actually handle wrapping the index around when it > needs to go off the left or right sides of the array. Right now all > your code does is remove the warning flags that the edge map provides > to prevent this from happening, but it doesn't seem to actually do > anything to implement wraparound. > > Currently, your subclass re-implements find_costs() as > find_costs_gis(), but no actual code is different between those two > methods! And in any case, you should probably just override > find_costs() rather than make a special new method find_costs_gis(). > (This made it all a little confusing to figure out what you were > actually doing in the code.) > > I'm actually a little surprised your code isn't giving you a segfault, > because if the edge-map flags are disabled without handling index > wraparound, the costs-tracing will happily head right out of the > array's memory and into wherever else. > > If you're not comfortable with numpy array striding and dealing with > flat indices into nd-arrays (both of which are heavily used here), > this might be a little tricky. But the basic gist of what you should > do is not monkey with the edge map. Instead, in the loop in > find_costs() that sets the use_offset flag, you might want to see if > the edge map says you'll be stepping over the left or right edge. If > so, set some special flag that you will then use to switch between the > standard index-finding: > new_index = index + flat_offsets[i] > and something you'll have to implement that deals with the wraparound correctly. > > Does this help? > Zach > >> On Wed, Aug 15, 2018 at 5:21 PM, Ömer Özak <omer.ozak(a)gmail.com> wrote: >> HI all, >> >> I am trying to add another MCP subclass to use with GIS data in the graph >> submodule in skimage. In particular, I'd like to allow the left and right >> borders of the cost np.array to be connected, i.e. to be neighbors. I >> thought it would suffice to change what are considered edges...so I created >> new functions to assign edges as should be required for this case (I think), >> but I get the same results as MCP_Geometric (which makes me think the >> computation is not taking this into account or I am missing some other >> required change). Could you help me figure this out? >> >> Here’s an example of what I’d like the subclass to do >> >> import skimage.graph.mcp as mcp >> np.random.seed(0) >> a = np.ones((5, 5), dtype=np.float32) >> a[0:, 1] = -1 >> a >> ''' >> array([[ 1., -1., 1., 1., 1.], >> [ 1., -1., 1., 1., 1.], >> [ 1., -1., 1., 1., 1.], >> [ 1., -1., 1., 1., 1.], >> [ 1., -1., 1., 1., 1.]], dtype=float32) >> ''' >> >> # First column is not connected with columns 3+ under Geometric (as >> expected) >> m = mcp.MCP_Geometric(a, fully_connected=True) >> costs, traceback = m.find_costs([(1, 4)]) >> costs >> ''' >> array([[ inf, inf, 2.41421356, 1.41421356, 1. ], >> [ inf, inf, 2. , 1. , 0. ], >> [ inf, inf, 2.41421356, 1.41421356, 1. ], >> [ inf, inf, 2.82842712, 2.41421356, 2. ], >> [ inf, inf, 3.82842712, 3.41421356, 3. ]]) >> ''' >> >> # For GIS should be different >> m = mcp.MCP_GIS(a, fully_connected=True) >> costs, traceback = m.find_costs([(1, 4)]) >> costs >> ''' >> Curently >> array([[ inf, inf, 2.41421356, 1.41421356, 1. ], >> [ inf, inf, 2. , 1. , 0. ], >> [ inf, inf, 2.41421356, 1.41421356, 1. ], >> [ inf, inf, 2.82842712, 2.41421356, 2. ], >> [ inf, inf, 3.82842712, 3.41421356, 3. ]]) >> >> Expected (correct one) >> >> array([[ 1.41421356, inf, 2.41421356, 1.41421356, 1. ], >> [ 1. , inf, 2. , 1. , 0. ], >> [ 1.41421356, inf, 2.41421356, 1.41421356, 1. ], >> [ 2.41421356, inf, 2.82842712, 2.41421356, 2. ], >> [ 3.41421356, inf, 3.82842712, 3.41421356, 3. ]]) >> ''' >> >> My code is in >> https://github.com/ozak/scikit-image/blob/GIS/skimage/graph/_mcp.pyx >> >> I’d appreciate any help or pointers you can give. >> >> Cheers, >> >> Ömer >> >> _______________________________________________ >> scikit-image mailing list >> scikit-image(a)python.org >> https://mail.python.org/mailman/listinfo/scikit-image >> > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

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Help with skimage.graph MCP
by Ömer Özak 17 Aug '18

17 Aug '18

HI all, I am trying to add another MCP subclass to use with GIS data in the graph submodule in skimage. In particular, I'd like to allow the left and right borders of the cost np.array to be connected, i.e. to be neighbors. I thought it would suffice to change what are considered edges...so I created new functions to assign edges as should be required for this case (I think), but I get the same results as MCP_Geometric (which makes me think the computation is not taking this into account or I am missing some other required change). Could you help me figure this out? Here’s an example of what I’d like the subclass to do import skimage.graph.mcp as mcp np.random.seed(0) a = np.ones((5, 5), dtype=np.float32) a[0:, 1] = -1 a ''' array([[ 1., -1., 1., 1., 1.], [ 1., -1., 1., 1., 1.], [ 1., -1., 1., 1., 1.], [ 1., -1., 1., 1., 1.], [ 1., -1., 1., 1., 1.]], dtype=float32) ''' # First column is not connected with columns 3+ under Geometric (as expected) m = mcp.MCP_Geometric(a, fully_connected=True) costs, traceback = m.find_costs([(1, 4)]) costs ''' array([[ inf, inf, 2.41421356, 1.41421356, 1. ], [ inf, inf, 2. , 1. , 0. ], [ inf, inf, 2.41421356, 1.41421356, 1. ], [ inf, inf, 2.82842712, 2.41421356, 2. ], [ inf, inf, 3.82842712, 3.41421356, 3. ]]) ''' # For GIS should be different m = mcp.MCP_GIS(a, fully_connected=True) costs, traceback = m.find_costs([(1, 4)]) costs ''' Curently array([[ inf, inf, 2.41421356, 1.41421356, 1. ], [ inf, inf, 2. , 1. , 0. ], [ inf, inf, 2.41421356, 1.41421356, 1. ], [ inf, inf, 2.82842712, 2.41421356, 2. ], [ inf, inf, 3.82842712, 3.41421356, 3. ]]) Expected (correct one) array([[ 1.41421356, inf, 2.41421356, 1.41421356, 1. ], [ 1. , inf, 2. , 1. , 0. ], [ 1.41421356, inf, 2.41421356, 1.41421356, 1. ], [ 2.41421356, inf, 2.82842712, 2.41421356, 2. ], [ 3.41421356, inf, 3.82842712, 3.41421356, 3. ]]) ''' My code is in https://github.com/ozak/scikit-image/blob/GIS/skimage/graph/_mcp.pyx I’d appreciate any help or pointers you can give. Cheers, Ömer

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+1 for releasing 0.14.1
by Mark Harfouche 09 Aug '18

09 Aug '18

Hey all, I know Jua expressed some interest for releasing 0.14.1. I just wanted to chime in and support his desire to do this. I am getting bit by a few numpy 1.15 warnings (from an other library) that annoyed me so much that I had to add ``` import warnings warnings.filterwarnings('ignore', 'Using a non-tuple sequence for multidimensional') ``` to my personal working module so as to ignore those warnings for good. I suspect others might be driven to do the same. Since scikit-image has fixed these warnings, it would be good to give users an option to upgrade and get rid of the warnings that come from our library. Mark

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