Merge pull request #39 from INM-6/master

created VERSION_LOG.md to record all changes made in every release version
INM-6 · Sep 20, 2023 · be361ff · be361ff
2 parents 0839edb + d8a0f5f
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diff --git a/.gitignore b/.gitignore
@@ -21,3 +21,5 @@ figures/Schmidt2018/.ipynb_checkpoints/*
 figures/Schmidt2018_dyn/.ipynb_checkpoints/*
 
 multiarea_model/.ipynb_checkpoints/*
+
+multiarea_model/data_multiarea/.ipynb_checkpoints/*
diff --git a/VERSION_LOG.md b/VERSION_LOG.md
@@ -0,0 +1,41 @@
+## MAM v1.1.0
+
+### New Features:
+
+* Documentation Enhancements:
+  * Streamlined README.md with a Try It On EBRAINS button and step-by-step user instructions.
+  * Removed "Testing on EBRAINS" section for clarity.
+
+* Parameter Tuning Improvements:
+  * Segregated parameters in down-scale multi-area mode into Parameters to Tune and Default Parameters.
+  * Introduced exposure of four user-friendly parameters, while retaining others for internal tuning.
+
+* Visualization Augmentations:
+  * Introduced Extract and Visualize Interareal Connectivity to display area-level relative connectivity via heatmaps.
+  * Added Simulation Results Visualization section with separate code modules in “./figures/MAM2EBRAINS”.
+  * Enriched visualization with three new plots detailing instantaneous firing rate, resting state, and time-averaged population rates.
+  * Refined representation of resting state plots inspired from Schmidt M et al. (2018), allowing users flexible area selection, altered synchrony representation, and a focus on binned spike histograms.
+
+### Enhancements:
+
+* Notebook Refinements:
+  * Overhauled Jupyter Notebook structure with an accessible table of contents for user navigation.
+  * Enhanced parameter descriptions for both exposed and default sets.
+  * Incorporated model overview and concise description of the down-scaled multi-area model.
+  * Cross-referenced relevant publication figures for user benefit.
+
+### Code Optimizations:
+
+* Minimized irrelevant print statements in codebase for clearer user outputs.
+* Updated .gitignore to exclude checkpoint files.
+
+### Bug Fixes:
+
+* Resolved file path separator issue in ./multiarea_model/data_multiarea/SLN_logdensities.R.
+* Addressed datatype concerns in ./multiarea-model/analysis.py for array initialization.
+
+## MAM v1.0.0
+
+### Bug Fixes:
+
+* Rectified incorrect NEST logo URL in README.md.
diff --git a/multi-area-model.ipynb b/multi-area-model.ipynb
@@ -509,7 +509,7 @@
      "output_type": "stream",
      "text": [
       "Initializing network from dictionary.\n",
-      "RAND_DATA_LABEL 7110\n"
+      "RAND_DATA_LABEL 7968\n"
      ]
     },
     {
@@ -591,72 +591,72 @@
      "text": [
       "Prepared simulation in 0.00 seconds.\n",
       "Rank 0: created area V1 with 0 local nodes\n",
-      "Memory after V1 : 1515.14 MB\n",
+      "Memory after V1 : 1516.25 MB\n",
       "Rank 0: created area V2 with 0 local nodes\n",
-      "Memory after V2 : 1541.85 MB\n",
+      "Memory after V2 : 1542.84 MB\n",
       "Rank 0: created area VP with 0 local nodes\n",
-      "Memory after VP : 1571.02 MB\n",
+      "Memory after VP : 1572.02 MB\n",
       "Rank 0: created area V3 with 0 local nodes\n",
-      "Memory after V3 : 1599.30 MB\n",
+      "Memory after V3 : 1600.25 MB\n",
       "Rank 0: created area V3A with 0 local nodes\n",
-      "Memory after V3A : 1619.24 MB\n",
+      "Memory after V3A : 1620.27 MB\n",
       "Rank 0: created area MT with 0 local nodes\n",
-      "Memory after MT : 1644.78 MB\n",
+      "Memory after MT : 1645.80 MB\n",
       "Rank 0: created area V4t with 0 local nodes\n",
-      "Memory after V4t : 1669.75 MB\n",
+      "Memory after V4t : 1670.73 MB\n",
       "Rank 0: created area V4 with 0 local nodes\n",
-      "Memory after V4 : 1696.68 MB\n",
+      "Memory after V4 : 1697.67 MB\n",
       "Rank 0: created area VOT with 0 local nodes\n",
-      "Memory after VOT : 1721.41 MB\n",
+      "Memory after VOT : 1722.37 MB\n",
       "Rank 0: created area MSTd with 0 local nodes\n",
-      "Memory after MSTd : 1741.30 MB\n",
+      "Memory after MSTd : 1742.29 MB\n",
       "Rank 0: created area PIP with 0 local nodes\n",
-      "Memory after PIP : 1762.64 MB\n",
+      "Memory after PIP : 1763.63 MB\n",
       "Rank 0: created area PO with 0 local nodes\n",
-      "Memory after PO : 1784.18 MB\n",
+      "Memory after PO : 1785.13 MB\n",
       "Rank 0: created area DP with 0 local nodes\n",
-      "Memory after DP : 1804.32 MB\n",
+      "Memory after DP : 1805.43 MB\n",
       "Rank 0: created area MIP with 0 local nodes\n",
-      "Memory after MIP : 1825.89 MB\n",
+      "Memory after MIP : 1826.88 MB\n",
       "Rank 0: created area MDP with 0 local nodes\n",
-      "Memory after MDP : 1847.39 MB\n",
+      "Memory after MDP : 1848.38 MB\n",
       "Rank 0: created area VIP with 0 local nodes\n",
-      "Memory after VIP : 1869.36 MB\n",
+      "Memory after VIP : 1870.34 MB\n",
       "Rank 0: created area LIP with 0 local nodes\n",
-      "Memory after LIP : 1893.33 MB\n",
+      "Memory after LIP : 1894.24 MB\n",
       "Rank 0: created area PITv with 0 local nodes\n",
-      "Memory after PITv : 1918.53 MB\n",
+      "Memory after PITv : 1919.55 MB\n",
       "Rank 0: created area PITd with 0 local nodes\n",
-      "Memory after PITd : 1943.70 MB\n",
+      "Memory after PITd : 1944.77 MB\n",
       "Rank 0: created area MSTl with 0 local nodes\n",
-      "Memory after MSTl : 1965.03 MB\n",
+      "Memory after MSTl : 1965.95 MB\n",
       "Rank 0: created area CITv with 0 local nodes\n",
-      "Memory after CITv : 1983.83 MB\n",
+      "Memory after CITv : 1984.88 MB\n",
       "Rank 0: created area CITd with 0 local nodes\n",
-      "Memory after CITd : 2003.14 MB\n",
+      "Memory after CITd : 2004.21 MB\n",
       "Rank 0: created area FEF with 0 local nodes\n",
-      "Memory after FEF : 2024.65 MB\n",
+      "Memory after FEF : 2025.55 MB\n",
       "Rank 0: created area TF with 0 local nodes\n",
-      "Memory after TF : 2040.28 MB\n",
+      "Memory after TF : 2041.22 MB\n",
       "Rank 0: created area AITv with 0 local nodes\n",
-      "Memory after AITv : 2062.86 MB\n",
+      "Memory after AITv : 2063.93 MB\n",
       "Rank 0: created area FST with 0 local nodes\n",
-      "Memory after FST : 2079.55 MB\n",
+      "Memory after FST : 2080.65 MB\n",
       "Rank 0: created area 7a with 0 local nodes\n",
-      "Memory after 7a : 2100.87 MB\n",
+      "Memory after 7a : 2101.82 MB\n",
       "Rank 0: created area STPp with 0 local nodes\n",
-      "Memory after STPp : 2119.46 MB\n",
+      "Memory after STPp : 2120.56 MB\n",
       "Rank 0: created area STPa with 0 local nodes\n",
-      "Memory after STPa : 2138.71 MB\n",
+      "Memory after STPa : 2139.57 MB\n",
       "Rank 0: created area 46 with 0 local nodes\n",
-      "Memory after 46 : 2154.03 MB\n",
+      "Memory after 46 : 2155.02 MB\n",
       "Rank 0: created area AITd with 0 local nodes\n",
-      "Memory after AITd : 2176.71 MB\n",
+      "Memory after AITd : 2177.61 MB\n",
       "Rank 0: created area TH with 0 local nodes\n",
-      "Memory after TH : 2189.28 MB\n",
-      "Created areas and internal connections in 2.05 seconds.\n",
-      "Created cortico-cortical connections in 20.48 seconds.\n",
-      "Simulated network in 71.65 seconds.\n"
+      "Memory after TH : 2190.27 MB\n",
+      "Created areas and internal connections in 2.20 seconds.\n",
+      "Created cortico-cortical connections in 20.14 seconds.\n",
+      "Simulated network in 77.14 seconds.\n"
      ]
     }
    ],
Original file line number	Diff line number	Diff line change
Expand Up		@@ -21,3 +21,5 @@ figures/Schmidt2018/.ipynb_checkpoints/*
		figures/Schmidt2018_dyn/.ipynb_checkpoints/*

		multiarea_model/.ipynb_checkpoints/*

		multiarea_model/data_multiarea/.ipynb_checkpoints/*