spam issueshttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues2018-02-11T21:12:43+01:00https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/33Cleaning kalisphera2018-02-11T21:12:43+01:00Rémi CailletaudCleaning kalispheraWe should clean kalisphera, shouldn't we only keep Kalibrary directories ?
The setup now installs randomwaffle.kalibraryWe should clean kalisphera, shouldn't we only keep Kalibrary directories ?
The setup now installs randomwaffle.kalibraryhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/36Naming Convention2022-12-14T11:24:04+01:00Emmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frNaming ConventionWe have to agree on a way of naming convention... at least for the module and function names.
And make all the changes. I like camel case with first letter in lowercase.
* [ ] `FirstCamelCase`
* [x] `otherCamelCase`
* [ ] `Wh@tTh3fUcK`
...We have to agree on a way of naming convention... at least for the module and function names.
And make all the changes. I like camel case with first letter in lowercase.
* [ ] `FirstCamelCase`
* [x] `otherCamelCase`
* [ ] `Wh@tTh3fUcK`
* [ ] `boring_underscores`https://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/87Merge getContactPoints and _getContactPairs in spam.label.contact2021-10-25T21:48:52+02:00Edward AndòMerge getContactPoints and _getContactPairs in spam.label.contactthey almost do the same thing...they almost do the same thing...Gustavo Pinzongustavo.pinzon@3sr-grenoble.frGustavo Pinzongustavo.pinzon@3sr-grenoble.frhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/124zoom direction in computePhi is not consistent with scipy.ndimage.zoom2022-12-14T11:24:01+01:00Edward Andòzoom direction in computePhi is not consistent with scipy.ndimage.zoomflip it, it will make more sense for `spam-ereg` tooflip it, it will make more sense for `spam-ereg` tooEdward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/140Homogenise "SubPixReturnStat" named outputs2020-03-15T14:14:01+01:00Edward AndòHomogenise "SubPixReturnStat" named outputsbetween dict returns, TSV and VTKbetween dict returns, TSV and VTKOlga StamatiOlga Stamatihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/148Non-general files in root2022-12-14T11:23:59+01:00Edward AndòNon-general files in rootThe files
.atomignore
.build-tools.cson
.install.bash
seem quite user-specific: if so suggest to add them to .gitignore but not keep them in repositoryThe files
.atomignore
.build-tools.cson
.install.bash
seem quite user-specific: if so suggest to add them to .gitignore but not keep them in repositoryEmmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frEmmanuel Roubinemmanuel.roubin@univ-grenoble-alpes.frhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/152spam-mmr-graphical: make consistent with spam.DIC.register2020-06-14T15:13:11+02:00Edward Andòspam-mmr-graphical: make consistent with spam.DIC.registerPerhaps it would be better for everyone to deform image 2 as well as updating a single Phi that includes the initial "eye" guess
* [x] Reinstate returnStatus updating as per multiModalRegistration()
* [x] Input TSV Phi guess is now the ...Perhaps it would be better for everyone to deform image 2 as well as updating a single Phi that includes the initial "eye" guess
* [x] Reinstate returnStatus updating as per multiModalRegistration()
* [x] Input TSV Phi guess is now the wrong way around
* [x] Reinstate crop in FinalStepAlessandro TengattiniAlessandro Tengattinihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/153spam-mmr wishlist2022-12-14T11:47:34+01:00Edward Andòspam-mmr wishlist* [x] In the joint histogram fitting, the height of the gaussian fit is currently named (global) "Phi", which is confusing
* [x] Tutorial (in progress)
* [x] Function documentation in correlateGM.py for `gaussianMixtureParameters()`
* [x...* [x] In the joint histogram fitting, the height of the gaussian fit is currently named (global) "Phi", which is confusing
* [x] Tutorial (in progress)
* [x] Function documentation in correlateGM.py for `gaussianMixtureParameters()`
* [x] Function documentation in correlateGM.py for `phaseDiagram()`
* [x] Be explicit about where gradients are calculated and whether they are updated or not
* [x] Verbose mode for `gaussianMixtureParameters()`
* [ ] Add spam-mmr script test.
* [x] Make print in iteration in `multimodalRegistration()` the same (with pbar) as `register()` (line ~490)
* [x] Add -tsv output to `spam-mmr` script
* [x] Fix up the tremendously broken mmr example [here](https://ttk.gricad-pages.univ-grenoble-alpes.fr/spam/spam_examples/DIC/plot_multiModalRegistration.html#sphx-glr-spam-examples-dic-plot-multimodalregistration-py)v1Alessandro TengattiniAlessandro Tengattinihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/155olga: duplicate BCtoDVC in optionsParser2020-06-04T12:07:34+02:00Edward Andòolga: duplicate BCtoDVC in optionsParserone has to goone has to goOlga StamatiOlga Stamatihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/156move `DEM_to_kalisphera_adapter.py` from scripts and covert it into an example2020-06-08T09:50:02+02:00Olga Stamatimove `DEM_to_kalisphera_adapter.py` from scripts and covert it into an exampleOlga StamatiOlga Stamatihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/161read and write stretch tensor U as a symmetric tensor2020-06-29T09:39:17+02:00Olga Stamatiread and write stretch tensor U as a symmetric tensor* [x] `spam-regularStrain`
* [x] `spam-discreteStrain`
* [x] `spam.helpers.tsvio.writeStrainTSV()`
* [x] `spam.helpers.tsvio.readStrainTSV()`* [x] `spam-regularStrain`
* [x] `spam-discreteStrain`
* [x] `spam.helpers.tsvio.writeStrainTSV()`
* [x] `spam.helpers.tsvio.readStrainTSV()`Olga StamatiOlga Stamatihttps://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/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/168RS in VTK from spam-ddic2020-06-26T12:31:54+02:00Edward AndòRS in VTK from spam-ddicRS and not returnStatus?RS and not returnStatus?Edward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/174in spam-ldic save displacements as point data and not as cell data2020-10-06T18:48:55+02:00Olga Stamatiin spam-ldic save displacements as point data and not as cell dataOlga StamatiOlga Stamatihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/179forgotten F11, F12 etc in `spam.deformation.correctPhiField()`2020-09-02T14:12:24+02:00Olga Stamatiforgotten F11, F12 etc in `spam.deformation.correctPhiField()`Olga StamatiOlga Stamatihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/189spam-regularStrain change output file name Q8 -> Q4 in 2D mode2020-11-16T13:46:03+01:00Edward Andòspam-regularStrain change output file name Q8 -> Q4 in 2D modehttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/196from nlenoir: remove save final Phi TSV button at the end of MMR graphical2021-04-09T11:23:51+02:00Edward Andòfrom nlenoir: remove save final Phi TSV button at the end of MMR graphical...just save it automatically like all the other files...just save it automatically like all the other filesAlessandro TengattiniAlessandro Tengattinihttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/205spam.DIC.applyPhi() PhiPoint option should be renamed to PhiCentre2021-05-20T17:42:15+02:00Edward Andòspam.DIC.applyPhi() PhiPoint option should be renamed to PhiCentrePhiCentre is consistent with deformation.computePhiPhiCentre is consistent with deformation.computePhiEdward AndòEdward Andòhttps://gricad-gitlab.univ-grenoble-alpes.fr/ttk/spam/-/issues/208Remove functions now existing in numpy.scipy2022-02-16T10:46:03+01:00Edward AndòRemove functions now existing in numpy.scipyRecent scipy.ndimage work is great:
- applyPhi: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.affine_transform.html
- rotations: https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.transform.Rotatio...Recent scipy.ndimage work is great:
- applyPhi: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.affine_transform.html
- rotations: https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.transform.Rotation.html
- applyPhiField? https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.geometric_transform.html#scipy.ndimage.geometric_transformEdward AndòEdward Andòhttps://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/217create a general tsv/vtk/tiff writer for all spam scripts2021-10-12T13:42:26+02:00Olga Stamaticreate a general tsv/vtk/tiff writer for all spam scriptscurrently similar lines of code appear in the end of each scriptcurrently similar lines of code appear in the end of each script