Ginkgo merge requestshttps://framagit.org/cpoupon/gkg/-/merge_requests2020-06-11T14:46:17Zhttps://framagit.org/cpoupon/gkg/-/merge_requests/1Add Torch dependency2020-06-11T14:46:17ZAlexandreAdd Torch dependencyhttps://framagit.org/cpoupon/gkg/-/merge_requests/3Add real and imaginary part getters in CVector with Unit tests2021-07-23T12:04:14ZAnasAdd real and imaginary part getters in CVector with Unit tests- Adding getter functions inside "**CVector**" class to get the real part and imaginary part of a "**CVector**" instance.
- Adding validated unit tests for the methods : **GetRealPart** and **GetImagPart** of a "**CVector**". Both method...- Adding getter functions inside "**CVector**" class to get the real part and imaginary part of a "**CVector**" instance.
- Adding validated unit tests for the methods : **GetRealPart** and **GetImagPart** of a "**CVector**". Both methods return an instance of "**Vector**".https://framagit.org/cpoupon/gkg/-/merge_requests/4Multi compartment simulation2021-12-14T13:23:10ZSimon LegeayMulti compartment simulationFirst merge request for Multi compartmental simulation command branch
New features:
- gamma distribution of T1, T2, rho,
- Kraemer algorithm for volume fraction draw for N components (gels + parenchyma)
- multithreading for computatio...First merge request for Multi compartmental simulation command branch
New features:
- gamma distribution of T1, T2, rho,
- Kraemer algorithm for volume fraction draw for N components (gels + parenchyma)
- multithreading for computation,
No core function of Gkg has been modified, but as suggestions, Kraemer algorithm could be add in Numericalanalysis, and gamma distribution could be mutualised with the one in MedusaCyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/6Atoms code and inverse matrix calculation2022-01-03T14:20:56ZAnasAtoms code and inverse matrix calculationAjout de nouvelles classes: NAtom, NSphereAtom, minEllipsoidAtom. (pour New Atom, New SphereAtom et minimal Ellipsoid Atom)
Ajout de la méthode getInverseMatrix dans NumImplementationFactory ainsi que le test unitaire pour vérifier la mé...Ajout de nouvelles classes: NAtom, NSphereAtom, minEllipsoidAtom. (pour New Atom, New SphereAtom et minimal Ellipsoid Atom)
Ajout de la méthode getInverseMatrix dans NumImplementationFactory ainsi que le test unitaire pour vérifier la méthode.
La classe NAtom est abstraite pure et comporte les méthodes isInside(vector) pour vérifier si un spin est à l'intérieur d'un atome. Elle contient aussi la méthode bool collidesWith(const Atom&) ce qui permet de tester la collision entre deux atomes quelconques (sphere-sphere, ellipsoid-sphere) et potentiellement d'autres atomes de bases.
La classe minEllipsoidAtom est minimale au point de vue de la mémoire car elle a comma attribut qu'un seul vecteur de 10 valeurs. Tous les calculs sont déléguées aux constructeurs et aux méthodes.Ivy UszynskiIvy Uszynskihttps://framagit.org/cpoupon/gkg/-/merge_requests/5Timed medusa with Timer class minor updates2022-03-04T08:31:21ZAnasTimed medusa with Timer class minor updates- Adding time duration measurements for creating virtual tissue creation.
- Storage of the time durations measured in the ".medusageometry.minf" file.
- Bug fix in Timer class: duration time was underestimated.
- Minor feature added in T...- Adding time duration measurements for creating virtual tissue creation.
- Storage of the time durations measured in the ".medusageometry.minf" file.
- Bug fix in Timer class: duration time was underestimated.
- Minor feature added in Timer class : duration in **seconds** instead of milliseconds.
![.medusageometry.minf file](/uploads/7dbb67599f9fcea861cb52bfef86e65e/Screenshot_from_2021-09-21_10-40-49.png)Cyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/8Paving command2022-03-04T15:45:12ZSimon LegeayPaving commandImportant points:
- Addition of the package Metis, set with `find_package( Metis QUIET )` (maybe should be REQUIRED),
- Addition of MaskPartitioning that handles building of the graph, given a particular neighborhood, and Metis computati...Important points:
- Addition of the package Metis, set with `find_package( Metis QUIET )` (maybe should be REQUIRED),
- Addition of MaskPartitioning that handles building of the graph, given a particular neighborhood, and Metis computation
- Addition of DwiNodePavingCommand (incomplete for the moment), that loads a neighborhood and apply Metis partitioning on the input mask,Cyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/9Improving Virtual_Tissue.cxx by adding a Sphere Atom count threshold.2022-03-14T16:00:32ZBrulléImproving Virtual_Tissue.cxx by adding a Sphere Atom count threshold.Staying under this threshold guarantee us to not be out of memory during the following stage of the simulation.Staying under this threshold guarantee us to not be out of memory during the following stage of the simulation.https://framagit.org/cpoupon/gkg/-/merge_requests/7RMI SEQUENCES Updates2022-03-14T16:01:13ZBrulléRMI SEQUENCES Updatesadding :
-gkg-simulation-mri-sequence/TrapezoidGradientPulse.h
-gkg-simulation-mri-sequence/TrapezoidGradientPulse.cxx
-Trapezoid COSINE OGSE waveform in OGSE Sequences
-Trapezoid SINE OGSE waveform in OGSE Sequences
-Update the Cmakeadding :
-gkg-simulation-mri-sequence/TrapezoidGradientPulse.h
-gkg-simulation-mri-sequence/TrapezoidGradientPulse.cxx
-Trapezoid COSINE OGSE waveform in OGSE Sequences
-Trapezoid SINE OGSE waveform in OGSE Sequences
-Update the CmakeCyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/10Update on virtual tissue (exceed sphere atom count)2022-03-16T08:28:59ZBrulléUpdate on virtual tissue (exceed sphere atom count)Improving the generation of simulation by preventing a number of sphere too high.Improving the generation of simulation by preventing a number of sphere too high.https://framagit.org/cpoupon/gkg/-/merge_requests/11New functionalities for node paving command2022-03-23T15:03:28ZSimon LegeayNew functionalities for node paving command- geodesic distance with dijkstra algorihtm
- new type of neighborhood
- clean DwiNodePavingCommand- geodesic distance with dijkstra algorihtm
- new type of neighborhood
- clean DwiNodePavingCommandCyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/14Replace GliaPopulation.cxx2022-04-13T07:07:33ZBrulléReplace GliaPopulation.cxx[Glial_Bad_Init](/uploads/3e0b3c7ca6fa342b923490e18166764a/Glial_Bad_Init)
[Glial_Good_Init](/uploads/0e5db582e569030e50f3db9c3bda5521/Glial_Good_Init)
Adding one line on the glial population file to initiate a different center for di...[Glial_Bad_Init](/uploads/3e0b3c7ca6fa342b923490e18166764a/Glial_Bad_Init)
[Glial_Good_Init](/uploads/0e5db582e569030e50f3db9c3bda5521/Glial_Good_Init)
Adding one line on the glial population file to initiate a different center for different glials populations.https://framagit.org/cpoupon/gkg/-/merge_requests/17Kokkos remove overlapp modifications2022-04-13T07:21:23ZBrulléKokkos remove overlapp modificationshttps://framagit.org/cpoupon/gkg/-/merge_requests/18Minor fixes: eigenvalue test condition and last parameter value2022-04-14T12:37:36ZAnasMinor fixes: eigenvalue test condition and last parameter value- Changing the test condition for the ellipsoidMatrix eigenvalues (if one of the eigvalues is negative).
- Removing a *2 factor to the ellipsoid's last parameter (parameter[9] initialisation from compressed matrix).- Changing the test condition for the ellipsoidMatrix eigenvalues (if one of the eigvalues is negative).
- Removing a *2 factor to the ellipsoid's last parameter (parameter[9] initialisation from compressed matrix).Cyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/12Json template for simulation2022-04-15T07:51:42ZBrulléJson template for simulationProviding a set of different JSON for launching simulations ( 1 Fiber population, 2 Fiber populations, 3 Fiber populations, 1 Fiber + 1 Astro populations and 2 Fiber + 1 Astro + 1 Oligo populations ).
The JSON files are completed by the ...Providing a set of different JSON for launching simulations ( 1 Fiber population, 2 Fiber populations, 3 Fiber populations, 1 Fiber + 1 Astro populations and 2 Fiber + 1 Astro + 1 Oligo populations ).
The JSON files are completed by the result of a simulation ( .raw file ) the meta data ( .minf ) and the terminal output during the process.
After trying the different populations simulations few issues must be remembered :
- Astrocytes ans oligodendrocytes somas are distributed with the same coordinates ( it must be link to an error of ramdom seed reset)
- Does the process of the glials cell count in the population fraction volume ?
- The beading doesnt work
- The myelin sheath works weirdly, it make appears huge somas at the top and bottom of the fibers ( maybe a simple Json calibration issue ).
All these issues might be fixed trough a future incoming merge request.https://framagit.org/cpoupon/gkg/-/merge_requests/19Removing from previous Fiber.cxx the method "add tortuosity" because it is...2022-04-25T13:39:59ZBrulléRemoving from previous Fiber.cxx the method "add tortuosity" because it is...Adding the tortuosity is now done in " Fiber Population " and parallelized.
For large simulation, after experimentation, the time dedicated to the tortuosity formation is exponentially improved, but for small simulation the classic way c...Adding the tortuosity is now done in " Fiber Population " and parallelized.
For large simulation, after experimentation, the time dedicated to the tortuosity formation is exponentially improved, but for small simulation the classic way can be better.
If this upgrade is merge we can parallelize tortuosity for glial cells aswell.https://framagit.org/cpoupon/gkg/-/merge_requests/13Mpi test2022-04-25T14:55:08ZSimon LegeayMpi testCyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/20Extraction method on cartesian field2022-04-25T17:20:24ZSimon LegeayExtraction method on cartesian fieldCyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/15Node data distribution2022-04-25T17:20:45ZSimon LegeayNode data distributionCyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/21Pli dmri global tractography2022-04-28T12:00:31ZSimon LegeayPli dmri global tractographyhttps://framagit.org/cpoupon/gkg/-/merge_requests/22global tracto directory added2022-04-28T12:04:36ZSimon Legeayglobal tracto directory added