[Issue 843] Moved vertex type map to vertices; split printParameters by model by CodersRepo · Pull Request #936 · UWB-Biocomputing/Graphitti

CodersRepo · 2026-05-08T19:25:18Z

…eters by model

Closes #843

Description

Moved per-vertex types out of Layout; register history in AllVertices subclasses.
LayoutNeuro owns neuro lists and logging; Layout911 owns role index lists.
Update call sites (connections, recorders, GPU ConnGrowth).

Checklist (Mandatory for new features)

Added Documentation
Added Unit Tests

Testing (Mandatory for all changes)

GPU Test: test-medium-connected.xml Passed
GPU Test: test-large-long.xml Passed

…eters by model

Copilot

Pull request overview

This PR refactors per-vertex type ownership from Layout into AllVertices, and adjusts recorder/history registration and layout parameter printing to be model-specific (Neuro vs NG911). The changes touch initialization, connection growth (GPU), recorders, and NG911 connection editing.

Changes:

Moved vertexTypeMap_ from Layout to AllVertices (including recorder registration + cereal serialization).
Updated Neuro/NG911 call sites (vertices, connections, inputs, recorders, GPU code) to read/write types via layout.getVertices().vertexTypeMap_.
Added model-specific cached index lists in LayoutNeuro/Layout911 and reworked LayoutNeuro::printParameters() accordingly.

Reviewed changes

Copilot reviewed 17 out of 18 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
Simulator/Vertices/NG911/All911Vertices.cpp	Updates NG911 vertex logic to use vertex types via `Layout::getVertices()`; ensures history registration chains to base.
Simulator/Vertices/Neuro/AllSpikingNeurons.cpp	Calls base `AllVertices::registerHistoryVariables()` so vertex types are recorded.
Simulator/Vertices/Neuro/AllIZHNeurons.cpp	Switches excitatory/inhibitory checks to the new vertex type storage.
Simulator/Vertices/Neuro/AllIFNeurons.cpp	Switches neuron-type dispatch + error logging to the new vertex type storage.
Simulator/Vertices/AllVertices.h	Adds `vertexTypeMap_` to vertices; changes `registerHistoryVariables()` to a virtual base implementation; updates serialization.
Simulator/Vertices/AllVertices.cpp	Initializes and registers `vertexTypeMap_` with the recorder.
Simulator/Utils/Inputs/SInputPoisson.cpp	Uses the moved vertex type map when selecting edge types.
Simulator/Recorders/NG911/Xml911Recorder.cpp	Reads vertex types from `layout.getVertices()` during save.
Simulator/Layouts/NG911/Layout911.h	Adds NG911 role index lists/count owned by the NG911 layout.
Simulator/Layouts/NG911/Layout911.cpp	Populates vertex types via vertices; adds role lists; updates `edgType` to use new storage.
Simulator/Layouts/Neuro/LayoutNeuro.h	Adds cached neuron index lists and serializes them.
Simulator/Layouts/Neuro/LayoutNeuro.cpp	Prints model-specific layout parameters using cached lists; updates type map generation and starter tracking.
Simulator/Layouts/Layout.h	Makes `printParameters()` pure-virtual (model-specific only); removes layout-owned type map serialization.
Simulator/Layouts/Layout.cpp	Removes layout history registration for vertex types; initializes vertex types via vertices.
Simulator/Connections/NG911/Connections911.cpp	Updates NG911 connection-editing logic to mutate vertex types via vertices.
Simulator/Connections/Neuro/ConnGrowth_d.cpp	Copies neuron type map to device using the new vertices-owned storage.
.gitignore	Ignores additional Debug log filename patterns.

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Pull request overview

Copilot reviewed 16 out of 17 changed files in this pull request and generated 2 comments.

Comments suppressed due to low confidence (1)

Simulator/Layouts/NG911/Layout911.cpp:163

Same issue as above for the responder->CALR case: the condition checks FIRE/EMS against destVertex instead of srcVertex. As written, FIRE/EMS responders won’t be classified as responder sources here. Adjust the predicate to test vtypes[srcVertex] for LAW/FIRE/EMS and vtypes[destVertex] for CALR.

   else if ((vtypes[srcVertex] == vertexType::LAW || vtypes[destVertex] == vertexType::FIRE
             || vtypes[destVertex] == vertexType::EMS)
            && vtypes[destVertex] == vertexType::CALR)
      return edgeType::RC;

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Pull request overview

Copilot reviewed 16 out of 17 changed files in this pull request and generated 1 comment.

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

stiber · 2026-05-18T20:43:02Z

-/// Prints out all parameters to logging file. Registered to OperationManager as Operation::printParameters
-void Layout::printParameters() const
-{
-   GraphManager<NeuralVertexProperties>::VertexIterator vi, vi_end;
-   GraphManager<NeuralVertexProperties> &gm = GraphManager<NeuralVertexProperties>::getInstance();
-   stringstream output;
-   output << "\nLAYOUT PARAMETERS" << endl;
-   output << "\tEndogenously active neuron positions: ";
-
-   for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
-      assert(*vi < numVertices_);
-      if (gm[*vi].active) {
-         output << *vi << " ";
-      }
-   }
-   output << endl;
-
-   output << "\tInhibitory neuron positions: ";
-
-   for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
-      assert(*vi < numVertices_);
-      if (gm[*vi].type == "INH") {
-         output << *vi << " ";
-      }
-   }
-   output << endl;
-
-   LOG4CPLUS_DEBUG(fileLogger_, output.str());
-}


Was this replaced by simpler code in LayourNeuro.cpp?

stiber

I have one question, but this is mergeable unless that question raises a problem.

refactor(layout): moved vertex type map to vertices; split printParam…

bb46edd

…eters by model

CodersRepo requested a review from Copilot May 8, 2026 19:25

Copilot started reviewing on behalf of CodersRepo May 8, 2026 19:26 View session

Dhruva Vatsal Pyapali added 2 commits May 8, 2026 12:29

Fixed Clang Formatting

75b8797

Fixed Clang pt 2

b439583

Copilot AI reviewed May 8, 2026

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Fixed CMakeLists.txt (set gpu to no default)

286715f

CodersRepo self-assigned this May 8, 2026

CodersRepo requested a review from Copilot May 8, 2026 20:37

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CodersRepo requested a review from Copilot May 13, 2026 00:10

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Comment thread Simulator/Layouts/NG911/Layout911.cpp Outdated

Comment thread Simulator/Vertices/AllVertices.h Outdated

Dhruva Vatsal Pyapali and others added 2 commits May 12, 2026 17:29

Fix Layout911::edgType responder checks to use srcVertex for FIRE/EMS

2b3890e

Potential fix for pull request finding

1793292

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

CodersRepo requested a review from Copilot May 13, 2026 00:56

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CodersRepo requested a review from Copilot May 14, 2026 18:07

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Comment thread Simulator/Utils/Inputs/SInputPoisson.cpp Outdated

Potential fix for pull request finding

51d0c03

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

CodersRepo requested a review from stiber May 15, 2026 05:25

stiber reviewed May 18, 2026

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stiber approved these changes May 18, 2026

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[Issue 843] Moved vertex type map to vertices; split printParameters by model#936

[Issue 843] Moved vertex type map to vertices; split printParameters by model#936
CodersRepo wants to merge 7 commits into
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issue-843-Move-better-vertex-classes-attributes--from-layout-classes

CodersRepo commented May 8, 2026 •

edited

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stiber May 18, 2026

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CodersRepo commented May 8, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Description

Checklist (Mandatory for new features)

Testing (Mandatory for all changes)

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stiber May 18, 2026

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CodersRepo commented May 8, 2026 •

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