spam issueshttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues2022-12-14T11:24:05+01:00https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/35Nice documentation2022-12-14T11:24:05+01:00Emmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frNice documentationParameters and Returns keywords are not working (example: https://ttk.gricad-pages.univ-grenoble-alpes.fr/RandomWaffle/measures.html#measures.covariance.compute)
It would be nice to have something like that https://docs.scipy.org/doc/n...Parameters and Returns keywords are not working (example: https://ttk.gricad-pages.univ-grenoble-alpes.fr/RandomWaffle/measures.html#measures.covariance.compute)
It would be nice to have something like that https://docs.scipy.org/doc/numpy/reference/generated/numpy.core.defchararray.translate.html#numpy.core.defchararray.translate
Is it possible to change sphinx options to have nicer documentation ?Rémi CailletaudRémi Cailletaudhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/43Tifffile needs c file2022-12-14T11:24:05+01:00Rémi CailletaudTifffile needs c filetiffile needs a c file to compile _tifffile, it's not in the pip packagetiffile needs a c file to compile _tifffile, it's not in the pip packageEmmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frEmmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/45Simple get started guide2022-12-14T11:24:05+01:00Emmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frSimple get started guideWe need to think about a simple **get started** guide on the web site with info about :
* [ ] introduction on the differents tools
* [x] install (virtualenv, git clone)
* [ ] use (source virtualenv, use a script)
* [ ] read the doc
* [ ...We need to think about a simple **get started** guide on the web site with info about :
* [ ] introduction on the differents tools
* [x] install (virtualenv, git clone)
* [ ] use (source virtualenv, use a script)
* [ ] read the doc
* [ ] how to contribute (branch, pull requests)https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/2python doc-string2022-12-14T11:24:01+01:00Emmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frpython doc-stringhttp://sametmax.com/les-docstrings/http://sametmax.com/les-docstrings/Emmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frEmmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/74Shell setup2022-12-14T11:23:59+01:00EXT Takashi MatsushimaShell setupRecommended setup:
.bashrc:
`
export spam=$HOME/bin/spam
alias activateSpam='source $spam/venv/bin/activate'
alias startSpam='cd $spam && activateSpam && ipython --profile=spam'
alias updateSpam='cd $spam && activateSpam && git pull &&...Recommended setup:
.bashrc:
`
export spam=$HOME/bin/spam
alias activateSpam='source $spam/venv/bin/activate'
alias startSpam='cd $spam && activateSpam && ipython --profile=spam'
alias updateSpam='cd $spam && activateSpam && git pull && python setup.py install'
`
.ipython/profile_spam/startup/startup.py
`
import numpy
import scipy.ndimage
import scipy.spatial
import tifffile
import matplotlib.pyplot as plt
import spam.DIC.correlate as corr
import spam.DIC.transformationOperator as transf
import spam.label.toolkit as ltk
`
agreed?https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/215update image correlation tutorials so as to be compatible with the new scripts2021-10-01T14:37:06+02:00Olga Stamatiupdate image correlation tutorials so as to be compatible with the new scriptshttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/212documentation: remove mpi from anaconda docs2021-06-22T19:03:35+02:00Edward Andòdocumentation: remove mpi from anaconda docsit's no longer neededit's no longer neededhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/170Script documentation: return status for ddic2020-09-25T13:50:12+02:00Edward AndòScript documentation: return status for ddicfor example -5 is not glt but margin alignmentfor example -5 is not glt but margin alignmenthttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/173Paper: Review 22020-07-08T15:09:08+02:00Edward AndòPaper: Review 2* [x] Write something about speed (DIC and label)
* [x] Input data format? Admittedly this is only explicit in the script help + how to make a 3D tiff
* [ ] Website: I would appreciate it if the authors could point out key parameters tha...* [x] Write something about speed (DIC and label)
* [x] Input data format? Admittedly this is only explicit in the script help + how to make a 3D tiff
* [ ] Website: I would appreciate it if the authors could point out key parameters that can be twisted for different purposes along with the examples. Or even better organizing parameter twisting as a separate part of the tutorial.
* [ ] Website: I would appreciate it if the 'tools provided' part can be separated out as itself in the main list (right now it is under intro). It would be easier for users to find and search.
* [x] Another point relates to the paper. It would be great if links to 'tools provided' (or even 'Gallery of examples' could be provided there for each function toolkits. This would give the users an easier way to get to know the functions more straightforwardly and in more detail if they want to.
* [x] Figure numbers in reference section in Paper
* [x] A little unrelated, but add CMV's citation and capabilitiesOlga StamatiOlga Stamatihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/169option "binningLabelled=1" not commented in mergeReguarAndDiscrete2020-06-26T12:31:55+02:00Edward Andòoption "binningLabelled=1" not commented in mergeReguarAndDiscretejust describe itjust describe itEdward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/166Paper: Review 1: Paper fixes2020-06-26T11:22:46+02:00Edward AndòPaper: Review 1: Paper fixesFor @jwbuurlage's review comments regarding paper
* [x] I think the summary could benefit from giving some simple examples, in simple words, of 3D image measurement tasks that the software can perform.
* [x] State of the field: Yes, but...For @jwbuurlage's review comments regarding paper
* [x] I think the summary could benefit from giving some simple examples, in simple words, of 3D image measurement tasks that the software can perform.
* [x] State of the field: Yes, but the section is short, and would benefit from one or two sentences about each software package and what the functionality overlap is between them and spam.
* [x] Reread: My main critique is that the language is too colloquial in a number of places.
* [x] There are some inconsistencies with font usage: some software packages are written using a monospace font, and some are not. I would indeed write NumPy over numpy, and some official spellings of software packages are all lowercase which complicates matters. However, why are sphinx and unittest monospace, but tifffile and meshio are not? I would double check all official spellings of packages, for example it is Git not git.
* [x] Some of the links are not permalinks, and this is even sometimes explicitely marked as such ('currently available at').
* [x] Add muDIC to other software available and (freckles?)Edward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/165Paper: Review 1: technical issues2020-06-23T18:50:05+02:00Edward AndòPaper: Review 1: technical issuesFor @jwbuurlage's review comments not regarding paper
* [x] install docs: integrate his working fedora instructions
* [x] install docs: add a Other Linux Distributions with list of dependencies to avoid Ubuntu install reverse engineering...For @jwbuurlage's review comments not regarding paper
* [x] install docs: integrate his working fedora instructions
* [x] install docs: add a Other Linux Distributions with list of dependencies to avoid Ubuntu install reverse engineering
* [x] intro: say more about what it actually does here: https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/intro.html
* [ ] investigate meta-package to slim down dependencies (this would work for R, CGAL, ...)
* [x] upload datasets onto Zenodo for tutorials
* [x] issues/support make it clear that now you can (and should) create an issue on gitlab
* [x] update tutorials with links to Zenodo datasetsEdward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/164Update conventions2020-06-15T14:37:03+02:00Edward AndòUpdate conventionsWrite about Phi always im1 -> im2Write about Phi always im1 -> im2Edward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/133doc: explain radii in spam-discreteStrains2019-09-13T20:47:20+02:00Edward Andòdoc: explain radii in spam-discreteStrainsEdward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/123add orientations to label toolkit tutorial2019-06-18T14:43:43+02:00Edward Andòadd orientations to label toolkit tutorialEdward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/82snippets2018-07-14T18:53:08+02:00Emmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frsnippetsCan we make something cool out of them ?
Like that ?
https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/snippets/40Can we make something cool out of them ?
Like that ?
https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/snippets/40https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/34Pipeline error and doc2017-09-27T20:55:52+02:00Emmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frPipeline error and docSince the pipeline for `pages` is nearly systematically failing (which is not our fault) we can't have an up to date documentation...
What can we do about it ?Since the pipeline for `pages` is nearly systematically failing (which is not our fault) we can't have an up to date documentation...
What can we do about it ?https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/18Data too big2017-09-11T21:56:18+02:00Edward AndòData too bigToo big `/data` folder -- downloading branch from Crete is not easy!Too big `/data` folder -- downloading branch from Crete is not easy!Rémi CailletaudRémi Cailletaud