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abria / TeraStitcher

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
http://abria.github.io/TeraStitcher/
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Minor wiki issue: the paraconverter.pyc is missing form dropbox #42

Open luofang34 opened 5 years ago

luofang34 commented 5 years ago

From the wiki page of Multi CPU parallelization, the linked file of paraconverter.pyc is currently unavailable from Dropbox. Though user could found still find a paraconverter.py elsewhere, it seems that's an outdated version.

iannellog commented 5 years ago

I have tried to download the Paraconverter script from https://github.com/abria/TeraStitcher/wiki/Multi-CPU-parallelization-using-MPI-and-Python-scripts (it is actually named Paraconverter2.3.2,py) and I was able to do that. Also the link you report in your mail works. It is likely that was a temporary unavailability from dropbox. Now it seems all ok. Let me know if yo have still problems (if you send me your email I can send it directly since GitHub does not allow to send attachments in replies) Best.

-- Giulio

Il giorno ven 21 dic 2018 alle ore 20:39 Fang Luo notifications@github.com ha scritto:

From the wiki page of Multi CPU parallelization https://github.com/abria/TeraStitcher/wiki/Multi-CPU-parallelization-using-MPI-and-Python-scripts, the linked file https://www.dropbox.com/s/865g7duwf2wl1hd/Paraconverter2.3.2.pyc?dl=1 of paraconverter.pyc is currently unavailable from Dropbox. Though user could found still find a paraconverter.py elsewhere, it seems that's an outdated version.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/abria/TeraStitcher/issues/42, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1pznxFflv2TC3YZ80qQgCwexz1SGks5u7TjQgaJpZM4Ze5g6 .

--

Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ

luofang34 commented 5 years ago

Thanks for your quick reply！However I retried the link and still unable to access the Dropbox file. So I've sent an Email to request a copy of paraconverter2.3.2.py. My email address is luofang@shanghaitech.edu.cn

Thanks again

Fang Luo

iannellog commented 5 years ago

Dear Linus, form your mail I uderstand that you tried to launch a script named Parastitcher3.2.0.py. Actually since we have made available the precompiled .pyc version only, you have to simply launch Parastitcher3.2.0.pyc instead of Parastitcher3.2.0.py. The link to download it is here

https://github.com/abria/TeraStitcher/wiki/Multi-CPU-parallelization-using-MPI-and-Python-scripts#download

If that is the problem, this way you should have solved the issue.

However, I add some more information that can be useful to you.

First, as you have probably noticed there are two tools ( https://github.com/abria/TeraStitcher/wiki/Multi-CPU-parallelization-using-MPI-and-Python-scripts#download ):

Second, if you are interested in both Parastitcher and Paraconverter, you should consider that the use is similar but the demo of Paraconverter ( https://github.com/abria/TeraStitcher/wiki/Multi-CPU-parallelization-using-MPI-and-Python-scripts#demo-of-paraconverter) is not updated.

For testing Parastitcher follow the instructions at link:

https://github.com/abria/TeraStitcher/wiki/Demo-and-batch-scripts#use-python-mpi-and-gpus

For testing Paraconverter you should follow a similar procedure (you can use either the same dataset of Parastitcher to merge an unstitched image, or any other already merged image you have providing that it is an allowed format), but have a look to section 3.2 of the TeraTools Guide to appreciate the differences.

I hope this helps, but do not hesitate to write me again if something goes wrong.

I also inform you that a new paper about TeraStitcher is going to be published on Frontiers in Neuroinformatics whose subject is precisely stitching parallelization (the abstract here: https://www.frontiersin.org/articles/10.3389/fninf.2019.00041/abstract). Please cite this paper in the future if you use our tools.

Best regards.

-- Giulio

Il giorno sab 25 mag 2019 alle ore 13:57 Linus Manubens-Gil < notifications@github.com> ha scritto:

Hello,

First of all thank you very much for this very nice piece of software.

I am trying to follow your Parastitcher demo using Windows. It seems it misses a Parastitcher3.py file. Given that the provided Parastitcher3.2.0.pyc is precompiled I could not think of any way to overcome the problem. I searched for a Parastitcher3.py in your repository but I couldn't find anything.

[image: image] https://user-images.githubusercontent.com/16608242/58368926-d0fe7300-7ef3-11e9-877e-13f154f0dec8.png

Am I missing something in the guide or should I also request the file to be sent to my e-mail address? (linus.manubens@crg.eu)

Thank you very much in advance! Linus Manubens-Gil

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/abria/TeraStitcher/issues/42?email_source=notifications&email_token=ACDW7VTALCWYNHYQM7626RLPXESSJA5CNFSM4GL3TA5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWHQMCA#issuecomment-495912456, or mute the thread https://github.com/notifications/unsubscribe-auth/ACDW7VRF4HVK2GRKG4TGESTPXESSJANCNFSM4GL3TA5A .

--

Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ

iannellog commented 5 years ago

Dear Giulio (and Alessandro),

Thanks again for you great software.

Apologies, I posted the issue in GitHub and later noticed that my issue was that I was trying to use mpich2 instead of Microsoft mpi as you suggest in your documentation.

The software runs incredibly smoothly.

A apologies for taking your time without a real reason, And thank you very much for your fast response!

Best! Linus Manubens-Gil

On May 26, 2019 3:45 PM, Giulio Iannello g.iannello@unicampus.it wrote: Dear Linus, form your mail I uderstand that you tried to launch a script named Parastitcher3.2.0.pyhttp://Parastitcher3.2.0.py. Actually since we have made available the precompiled .pyc version only, you have to simply launch Parastitcher3.2.0.pyc instead of Parastitcher3.2.0.pyhttp://Parastitcher3.2.0.py. The link to download it is here

https://github.com/abria/TeraStitcher/wiki/Multi-CPU-parallelization-using-MPI-and-Python-scripts#download

If that is the problem, this way you should have solved the issue.

However, I add some more information that can be useful to you.

First, as you have probably noticed there are two tools (https://github.com/abria/TeraStitcher/wiki/Multi-CPU-parallelization-using-MPI-and-Python-scripts#download):

Second, if you are interested in both Parastitcher and Paraconverter, you should consider that the use is similar but the demo of Paraconverter (https://github.com/abria/TeraStitcher/wiki/Multi-CPU-parallelization-using-MPI-and-Python-scripts#demo-of-paraconverter) is not updated.

For testing Parastitcher follow the instructions at link:

https://github.com/abria/TeraStitcher/wiki/Demo-and-batch-scripts#use-python-mpi-and-gpus

For testing Paraconverter you should follow a similar procedure (you can use either the same dataset of Parastitcher to merge an unstitched image, or any other already merged image you have providing that it is an allowed format), but have a look to section 3.2 of the TeraTools Guide to appreciate the differences.

I hope this helps, but do not hesitate to write me again if something goes wrong.

I also inform you that a new paper about TeraStitcher is going to be published on Frontiers in Neuroinformatics whose subject is precisely stitching parallelization (the abstract here: https://www.frontiersin.org/articles/10.3389/fninf.2019.00041/abstract). Please cite this paper in the future if you use our tools.

Best regards.

-- Giulio

Il giorno sab 25 mag 2019 alle ore 13:57 Linus Manubens-Gil notifications@github.com<mailto:notifications@github.com> ha scritto:

Hello,

First of all thank you very much for this very nice piece of software.

I am trying to follow your Parastitcher demo using Windows. It seems it misses a Parastitcher3.py file. Given that the provided Parastitcher3.2.0.pyc is precompiled I could not think of any way to overcome the problem. I searched for a Parastitcher3.py in your repository but I couldn't find anything.

[image]https://user-images.githubusercontent.com/16608242/58368926-d0fe7300-7ef3-11e9-877e-13f154f0dec8.png

Am I missing something in the guide or should I also request the file to be sent to my e-mail address? (linus.manubens@crg.eumailto:linus.manubens@crg.eu)

Thank you very much in advance! Linus Manubens-Gil

- You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/abria/TeraStitcher/issues/42?email_source=notifications&email_token=ACDW7VTALCWYNHYQM7626RLPXESSJA5CNFSM4GL3TA5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODWHQMCA#issuecomment-495912456, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ACDW7VRF4HVK2GRKG4TGESTPXESSJANCNFSM4GL3TA5A.

--

Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.itmailto:g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ