回复:Re: Medial axis skeletonization length
you can also try sknw
----- 原始邮件 ----- 发件人: Leena Choureyleenagour@gmail.com 收件人: Mailing list for scikit-image (http://scikit-image.org)scikit-image@python.org 主题: [scikit-image] Re: Medial axis skeletonization length 日期: 2018-11-30 09:10
hi tried installing skan, successful install, but getting error while using : --------------------------------------------------------------- from skan import csr Traceback (most recent call last): File "<input>", line 1, in <module> File "/home/etu/.eclipse/org.eclipse.platform_3.8_155965261/plugins/org.python.pydev_4.5.5.201603221110/pysrc/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/skan/__init__.py", line 1, in <module> from .csr import skeleton_to_csgraph, branch_statistics, summarise File "/home/etu/.eclipse/org.eclipse.platform_3.8_155965261/plugins/org.python.pydev_4.5.5.201603221110/pysrc/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/skan/csr.py", line 164 junction_centroids, *, spacing=1): ^ SyntaxError: invalid syntax
On Thu, Nov 29, 2018 at 6:20 AM Juan Nunez-Iglesias jni@fastmail.com wrote:
Hi Stefanie, Jean-Patrick, et al,
I invite you to look at my Skan (skeleton analysis) package. Docs here: https://jni.github.io/skan/ Paper here: https://peerj.com/articles/4312/ (the supplemental info mentions some of the edge cases we’ve taken care of.)
Skan is installable with "pip install skan" or "conda install -c conda-forge skan”.
I’m working on a new higher level Skeleton class, but it’s a WIP and you’ll need to install from source: https://github.com/jni/skan/blob/5c0d23e5b1eab2fb06b25ff599e98eaa11d621e6/sk... (Not that that’s a big deal since the lib is pure Python.)
Comments, suggestions, and contributions are all welcome!
Juan.
On 29 Nov 2018, at 8:37 am, Jean-Patrick Pommier jeanpatrick.pommier@gmail.com wrote: I tried this : https://dip4fish.blogspot.com/2014/05/construct-graph-from-skeleton-image-of...
Le mer. 28 nov. 2018 à 19:59, Stefanie Lück luecks@gmail.com a écrit :
Dear all,
I have a question I use the medial axis skeletonization implementation of scikit-image. Is it possible to get the length of the medial axis and the number of branches growing from the medial axis?
Thank you very much in advance Stefanie
_______________________________________________ scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
Leena,
You should use Python 3.6 or later. Skan does not support Python 2.7.
As mentioned by Stéfan, at this point, if you have further questions, we should probably move away from the scikit-image mailing list and to the skan issue tracker. github.com/jni/skan
On Fri, Nov 30, 2018, at 1:53 PM, imagepy@sina.com wrote:
you can also try sknw
----- 原始邮件 ----- 发件人: Leena Choureyleenagour@gmail.com 收件人: Mailing list for scikit-image (http://scikit-image.org)scikit-image@python.org 主题: [scikit-image] Re: Medial axis skeletonization length 日期: 2018-11-30 09:10
hi tried installing skan, successful install, but getting error while using :
from skan import csr Traceback (most recent call last): File "<input>", line 1, in <module> File "/home/etu/.eclipse/org.eclipse.platform_3.8_155965261/plugins/org.python.pydev_4.5.5.201603221110/pysrc/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/skan/__init__.py", line 1, in <module> from .csr import skeleton_to_csgraph, branch_statistics, summarise File "/home/etu/.eclipse/org.eclipse.platform_3.8_155965261/plugins/org.python.pydev_4.5.5.201603221110/pysrc/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/skan/csr.py", line 164 junction_centroids, *, spacing=1): ^ SyntaxError: invalid syntax
On Thu, Nov 29, 2018 at 6:20 AM Juan Nunez-Iglesias jni@fastmail.com wrote:
Hi Stefanie, Jean-Patrick, et al,
I invite you to look at my Skan (skeleton analysis) package. Docs here: https://jni.github.io/skan/ Paper here: https://peerj.com/articles/4312/ (the supplemental info mentions some of the edge cases we’ve taken care of.)
Skan is installable with "pip install skan" or "conda install -c conda-forge skan”.
I’m working on a new higher level Skeleton class, but it’s a WIP and you’ll need to install from source: https://github.com/jni/skan/blob/5c0d23e5b1eab2fb06b25ff599e98eaa11d621e6/sk... (Not that that’s a big deal since the lib is pure Python.)
Comments, suggestions, and contributions are all welcome!
Juan.
On 29 Nov 2018, at 8:37 am, Jean-Patrick Pommier jeanpatrick.pommier@gmail.com wrote: I tried this : https://dip4fish.blogspot.com/2014/05/construct-graph-from-skeleton-image-of...
Le mer. 28 nov. 2018 à 19:59, Stefanie Lück luecks@gmail.com a écrit :
Dear all,
I have a question I use the medial axis skeletonization implementation of scikit-image. Is it possible to get the length of the medial axis and the number of branches growing from the medial axis?
Thank you very much in advance Stefanie
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
-- http://dip4fish.blogspot.fr/ Dedicated to Digital Image Processing for FISH, QFISH and other things about the telomeres.
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org 来自新浪邮箱触屏版
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Thanks, I'll check it out.
On Fri, Nov 30, 2018 at 8:26 AM Juan Nunez-Iglesias jni@fastmail.com wrote:
Leena,
You should use Python 3.6 or later. Skan does not support Python 2.7.
As mentioned by Stéfan, at this point, if you have further questions, we should probably move away from the scikit-image mailing list and to the skan issue tracker. github.com/jni/skan
On Fri, Nov 30, 2018, at 1:53 PM, imagepy@sina.com wrote:
you can also try sknw
----- 原始邮件 ----- 发件人: Leena Choureyleenagour@gmail.com 收件人: Mailing list for scikit-image (http://scikit-image.org)< scikit-image@python.org> 主题: [scikit-image] Re: Medial axis skeletonization length 日期: 2018-11-30 09:10
hi tried installing skan, successful install, but getting error while using :
from skan import csr Traceback (most recent call last): File "<input>", line 1, in <module>
File "/home/etu/.eclipse/org.eclipse.platform_3.8_155965261/plugins/org.python.pydev_4.5.5.201603221110/pysrc/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/skan/__init__.py", line 1, in <module> from .csr import skeleton_to_csgraph, branch_statistics, summarise
File "/home/etu/.eclipse/org.eclipse.platform_3.8_155965261/plugins/org.python.pydev_4.5.5.201603221110/pysrc/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/skan/csr.py", line 164 junction_centroids, *, spacing=1): ^ SyntaxError: invalid syntax
On Thu, Nov 29, 2018 at 6:20 AM Juan Nunez-Iglesias <jni@fastmail.com
wrote:
Hi Stefanie, Jean-Patrick, et al,
I invite you to look at my Skan (skeleton analysis) package. Docs here: https://jni.github.io/skan/ Paper here: https://peerj.com/articles/4312/
(the supplemental info mentions some of the edge cases we’ve taken care of.)
Skan is installable with "pip install skan" or "conda install -c conda-forge skan”.
I’m working on a new higher level Skeleton class, but it’s a WIP and you’ll need to install from source:
https://github.com/jni/skan/blob/5c0d23e5b1eab2fb06b25ff599e98eaa11d621e6/sk... (Not that that’s a big deal since the lib is pure Python.)
Comments, suggestions, and contributions are all welcome!
Juan.
On 29 Nov 2018, at 8:37 am, Jean-Patrick Pommier < jeanpatrick.pommier@gmail.com> wrote: I tried this : https://dip4fish.blogspot.com/2014/05/construct-graph-from-skeleton-image-of...
Le mer. 28 nov. 2018 à 19:59, Stefanie Lück luecks@gmail.com a écrit :
Dear all,
I have a question I use the medial axis skeletonization implementation of scikit-image. Is it possible to get the length of the medial axis and the number of branches growing from the medial axis?
Thank you very much in advance Stefanie
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
-- http://dip4fish.blogspot.fr/
Dedicated to Digital Image Processing for FISH, QFISH and other things about the telomeres.
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
来自新浪邮箱触屏版 _______________________________________________ scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
Installed python 3.6, installed skan successfully (from https://jni.github.io/skan/install.html). I have both(python 2.7.4 & python 3.6 ) on linux. On command run $ skan-gui gives error: =============================================== Traceback (most recent call last): File "/usr/local/bin/skan-gui", line 11, in <module> load_entry_point('skan==0.7.1', 'console_scripts', 'skan-gui')() File "/home/leenac/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 487, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/home/leenac/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2728, in load_entry_point return ep.load() File "/home/leenac/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2346, in load return self.resolve() File "/home/leenac/.local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2352, in resolve module = __import__(self.module_name, fromlist=['__name__'], level=0) File "/home/leenac/.local/lib/python2.7/site-packages/skan/__init__.py", line 1, in <module> from .csr import skeleton_to_csgraph, branch_statistics, summarise File "/home/leenac/.local/lib/python2.7/site-packages/skan/csr.py", line 164 junction_centroids, *, spacing=1): ^ SyntaxError: invalid syntax ======================================================
On Thu, Dec 6, 2018 at 10:44 AM Leena Chourey leenagour@gmail.com wrote:
Thanks, I'll check it out.
On Fri, Nov 30, 2018 at 8:26 AM Juan Nunez-Iglesias jni@fastmail.com wrote:
Leena,
You should use Python 3.6 or later. Skan does not support Python 2.7.
As mentioned by Stéfan, at this point, if you have further questions, we should probably move away from the scikit-image mailing list and to the skan issue tracker. github.com/jni/skan
On Fri, Nov 30, 2018, at 1:53 PM, imagepy@sina.com wrote:
you can also try sknw
----- 原始邮件 ----- 发件人: Leena Choureyleenagour@gmail.com 收件人: Mailing list for scikit-image (http://scikit-image.org)< scikit-image@python.org> 主题: [scikit-image] Re: Medial axis skeletonization length 日期: 2018-11-30 09:10
hi tried installing skan, successful install, but getting error while using :
from skan import csr Traceback (most recent call last): File "<input>", line 1, in <module>
File "/home/etu/.eclipse/org.eclipse.platform_3.8_155965261/plugins/org.python.pydev_4.5.5.201603221110/pysrc/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/skan/__init__.py", line 1, in <module> from .csr import skeleton_to_csgraph, branch_statistics, summarise
File "/home/etu/.eclipse/org.eclipse.platform_3.8_155965261/plugins/org.python.pydev_4.5.5.201603221110/pysrc/_pydev_bundle/pydev_import_hook.py", line 21, in do_import module = self._system_import(name, *args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/skan/csr.py", line 164 junction_centroids, *, spacing=1): ^ SyntaxError: invalid syntax
On Thu, Nov 29, 2018 at 6:20 AM Juan Nunez-Iglesias <jni@fastmail.com
wrote:
Hi Stefanie, Jean-Patrick, et al,
I invite you to look at my Skan (skeleton analysis) package. Docs here: https://jni.github.io/skan/ Paper here: https://peerj.com/articles/4312/
(the supplemental info mentions some of the edge cases we’ve taken care of.)
Skan is installable with "pip install skan" or "conda install -c conda-forge skan”.
I’m working on a new higher level Skeleton class, but it’s a WIP and you’ll need to install from source:
https://github.com/jni/skan/blob/5c0d23e5b1eab2fb06b25ff599e98eaa11d621e6/sk... (Not that that’s a big deal since the lib is pure Python.)
Comments, suggestions, and contributions are all welcome!
Juan.
On 29 Nov 2018, at 8:37 am, Jean-Patrick Pommier < jeanpatrick.pommier@gmail.com> wrote: I tried this : https://dip4fish.blogspot.com/2014/05/construct-graph-from-skeleton-image-of...
Le mer. 28 nov. 2018 à 19:59, Stefanie Lück luecks@gmail.com a écrit :
Dear all,
I have a question I use the medial axis skeletonization implementation of scikit-image. Is it possible to get the length of the medial axis and the number of branches growing from the medial axis?
Thank you very much in advance Stefanie
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
-- http://dip4fish.blogspot.fr/
Dedicated to Digital Image Processing for FISH, QFISH and other things about the telomeres.
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
来自新浪邮箱触屏版 _______________________________________________ scikit-image mailing list -- scikit-image@python.org To unsubscribe send an email to scikit-image-leave@python.org
Hi Leena,
On Tue, 11 Dec 2018 15:32:58 +0530, Leena Chourey wrote:
Installed python 3.6, installed skan successfully (from https://jni.github.io/skan/install.html). I have both(python 2.7.4 & python 3.6 ) on linux. On command run $ skan-gui gives error:
Please post this information to the relevant forum.
Thanks, Stéfan
participants (4)
-
imagepy＠sina.com -
Juan Nunez-Iglesias -
Leena Chourey -
Stefan van der Walt