Merge pull request #414 from Hjorthmedh/dev

Minor bug fixes
Hjorthmedh · Mar 20, 2024 · 95c559d · 95c559d
2 parents 7a950ed + 53050f6
commit 95c559d
Show file tree

Hide file tree

Showing 28 changed files with 7,991 additions and 162 deletions.
diff --git a/examples/Parkinson/parkinsonGenerateNetwork_DIFFERENT_NETWORKS.sh b/examples/Parkinson/parkinsonGenerateNetwork_DIFFERENT_NETWORKS.sh
@@ -9,7 +9,7 @@ simNamePart=10k_20211105-tune-FS-v1
 #cellspecDir=data/parkinson-2021-01-07
 #cellspecDir=../snudda/data/parkinson-2021-03-19
 #cellspecDir=../../BasalGangliaData/Parkinson.OLD
-export PD_DATA_DIR="../../BasalGangliaData/Parkinson/20211105"
+export PD_DATA_DIR="../../../BasalGangliaData/Parkinson/20221213"
 
 ipcluster start --profile=$IPYTHON_PROFILE --ip=127.0.0.1&
 sleep 20
@@ -20,7 +20,6 @@ sleep 20
 simName=networks/pd0_$simNamePart
 
 export SNUDDA_DATA="$PD_DATA_DIR/PD0"
-# export SNUDDA_DATA="../../BasalGangliaData/Parkinson/20211105/PD0"
 echo "Setting SNUDDA_DATA to $SNUDDA_DATA"
 
 # Note that we need to start ipcluster after the SNUDDA_DATA environment
@@ -36,26 +35,26 @@ python3 ../snudda/analyse/analyse_striatum.py $simName/network-synapses.hdf5
 
 ####################
 
-simName=networks/pd1_$simNamePart
+if false; then
 
-export SNUDDA_DATA="$PD_DATA_DIR/PD1"
-# export SNUDDA_DATA="../../BasalGangliaData/Parkinson/20211105/PD1"
-echo "Setting SNUDDA_DATA to $SNUDDA_DATA"
+  simName=networks/pd1_$simNamePart
 
-snudda init $simName --size $numNeurons --overwrite --connectionFile $SNUDDA_DATA/connectivity/network-config-PD.json
-snudda place $simName --parallel
-snudda detect $simName --parallel
-snudda prune $simName --parallel
+  export SNUDDA_DATA="$PD_DATA_DIR/PD1"
+  echo "Setting SNUDDA_DATA to $SNUDDA_DATA"
 
-python3 ../snudda/analyse/analyse_striatum.py $simName/network-synapses.hdf5
+  snudda init $simName --size $numNeurons --overwrite --connectionFile $SNUDDA_DATA/connectivity/network-config-PD.json
+  snudda place $simName --parallel
+  snudda detect $simName --parallel
+  snudda prune $simName --parallel
 
+  python3 ../snudda/analyse/analyse_striatum.py $simName/network-synapses.hdf5
+fi
 
 ####################
 
 simName=networks/pd2_$simNamePart
 
 export SNUDDA_DATA="$PD_DATA_DIR/PD2"
-# export SNUDDA_DATA="../../BasalGangliaData/Parkinson/20211105/PD2"
 echo "Setting SNUDDA_DATA to $SNUDDA_DATA"
 
 snudda init $simName --size $numNeurons --overwrite --connectionFile $SNUDDA_DATA/connectivity/network-config-PD.json
@@ -68,18 +67,19 @@ python3 ../snudda/analyse/analyse_striatum.py $simName/network-synapses.hdf5
 
 #####################
 
-simName=networks/pd3_$simNamePart
+if false; then
 
-export SNUDDA_DATA="$PD_DATA_DIR/PD3"
-# export SNUDDA_DATA="../../BasalGangliaData/Parkinson/20211105/PD3"
-echo "Setting SNUDDA_DATA to $SNUDDA_DATA"
+  simName=networks/pd3_$simNamePart
 
-snudda init $simName --size $numNeurons --overwrite --connectionFile $SNUDDA_DATA/connectivity/network-config-PD.json
-snudda place $simName --parallel
-snudda detect $simName --parallel
-snudda prune $simName --parallel
+  export SNUDDA_DATA="$PD_DATA_DIR/PD3"
+  echo "Setting SNUDDA_DATA to $SNUDDA_DATA"
 
-python3 ../snudda/analyse/analyse_striatum.py $simName/network-synapses.hdf5
+  snudda init $simName --size $numNeurons --overwrite --connectionFile $SNUDDA_DATA/connectivity/network-config-PD.json
+  snudda place $simName --parallel
+  snudda detect $simName --parallel
+  snudda prune $simName --parallel
 
+  python3 ../snudda/analyse/analyse_striatum.py $simName/network-synapses.hdf5
 
+fi
 
diff --git a/examples/notebooks/Parkinson/ExportNetwork.ipynb b/examples/notebooks/Parkinson/ExportNetwork.ipynb