-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge remote-tracking branch 'origin/main' into custom-analyses
* origin/main: Add tests for Python 3.12 (#16) Remove pytest-lazy-fixture (#15) Add CLI to convert and import inferred spikes in CSV format (#14) Apply black 24.1, pin pytest<8 (#12) Install tree when building readthedocs (#11) Add a simple simulation campaign using a subsampled circuit (#10) Support relative paths in the simulation campaign config (#9)
- Loading branch information
Showing
109 changed files
with
1,702 additions
and
1,856 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -20,3 +20,5 @@ build: | |
os: ubuntu-22.04 | ||
tools: | ||
python: "3.11" | ||
apt_packages: | ||
- tree |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,34 @@ | ||
# simple configuration with extraction and analysis, and combination of parameters | ||
version: 3 | ||
simulation_campaign: ../simulation-campaign/config.json | ||
output: analysis_output | ||
analysis: | ||
spikes: | ||
extraction: | ||
report: | ||
type: spikes | ||
neuron_classes: | ||
Rt_EXC: {query: {layer: [Rt], synapse_class: [EXC]}} | ||
VPL_EXC: {query: {layer: [VPL], synapse_class: [EXC]}} | ||
Rt_INH: {query: {layer: [Rt], synapse_class: [INH]}} | ||
VPL_INH: {query: {layer: [VPL], synapse_class: [INH]}} | ||
limit: 1000 | ||
population: thalamus_neurons | ||
node_set: null | ||
windows: | ||
w1: {bounds: [20, 90], window_type: spontaneous} | ||
w2: {bounds: [10, 70], initial_offset: 10, n_trials: 3, trial_steps_value: 10} | ||
features: | ||
- type: multi | ||
groupby: [simulation_id, circuit_id, neuron_class, window] | ||
function: blueetl.external.bnac.calculate_features.calculate_features_multi | ||
params: | ||
export_all_neurons: true | ||
params_product: | ||
ratio: [0.25, 0.50, 0.75] | ||
nested_example: | ||
- params: {bin_size: 1} | ||
- params: {bin_size: 2} | ||
params_zip: | ||
param1: [10, 20] | ||
param2: [11, 21] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,44 @@ | ||
{ | ||
"version": 2, | ||
"manifest": { | ||
"$BASE_DIR": ".", | ||
"$NETWORK_NODES_DIR": "$BASE_DIR/networks/nodes", | ||
"$NETWORK_EDGES_DIR": "$BASE_DIR/networks/edges" | ||
}, | ||
"node_sets_file": "$BASE_DIR/node_sets.json", | ||
"networks": { | ||
"nodes": [ | ||
{ | ||
"nodes_file": "$NETWORK_NODES_DIR/thalamus_neurons/nodes.h5", | ||
"populations": { | ||
"thalamus_neurons": { | ||
"type": "biophysical", | ||
"biophysical_neuron_models_dir": "emodels_hoc", | ||
"alternate_morphologies": { | ||
"neurolucida-asc": "morphologies/ASC", | ||
"h5v1": "morphologies/h5v1" | ||
} | ||
} | ||
} | ||
} | ||
], | ||
"edges": [ | ||
{ | ||
"edges_file": "$NETWORK_EDGES_DIR/thalamus_neurons__thalamus_neurons__chemical/edges.h5", | ||
"populations": { | ||
"thalamus_neurons__thalamus_neurons__chemical": { | ||
"type": "chemical" | ||
} | ||
} | ||
}, | ||
{ | ||
"edges_file": "$NETWORK_EDGES_DIR/thalamus_neurons__thalamus_neurons__electrical_synapse/edges.h5", | ||
"populations": { | ||
"thalamus_neurons__thalamus_neurons__electrical_synapse": { | ||
"type": "electrical" | ||
} | ||
} | ||
} | ||
] | ||
} | ||
} |
Binary file added
BIN
+1.08 MB
doc/source/data/circuit/networks/edges/thalamus_neurons__thalamus_neurons__chemical/edges.h5
Binary file not shown.
Binary file added
BIN
+89 KB
...ta/circuit/networks/edges/thalamus_neurons__thalamus_neurons__electrical_synapse/edges.h5
Binary file not shown.
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,149 @@ | ||
{ | ||
"Mosaic": [ | ||
"All" | ||
], | ||
"All": [ | ||
"thalamus_neurons" | ||
], | ||
"thalamus_neurons": { | ||
"population": "thalamus_neurons" | ||
}, | ||
"thalamus_neurons": { | ||
"population": "thalamus_neurons" | ||
}, | ||
"Excitatory": { | ||
"synapse_class": "EXC" | ||
}, | ||
"Inhibitory": { | ||
"synapse_class": "INH" | ||
}, | ||
"Rt_RC": { | ||
"mtype": "Rt_RC" | ||
}, | ||
"VPL_IN": { | ||
"mtype": "VPL_IN" | ||
}, | ||
"VPL_TC": { | ||
"mtype": "VPL_TC" | ||
}, | ||
"bAC_IN": { | ||
"etype": "bAC_IN" | ||
}, | ||
"cAD_noscltb": { | ||
"etype": "cAD_noscltb" | ||
}, | ||
"cNAD_noscltb": { | ||
"etype": "cNAD_noscltb" | ||
}, | ||
"dAD_ltb": { | ||
"etype": "dAD_ltb" | ||
}, | ||
"dNAD_ltb": { | ||
"etype": "dNAD_ltb" | ||
}, | ||
"mc0;Rt": { | ||
"region": "mc0;Rt" | ||
}, | ||
"mc0;VPL": { | ||
"region": "mc0;VPL" | ||
}, | ||
"mc1;Rt": { | ||
"region": "mc1;Rt" | ||
}, | ||
"mc1;VPL": { | ||
"region": "mc1;VPL" | ||
}, | ||
"mc2;Rt": { | ||
"region": "mc2;Rt" | ||
}, | ||
"mc2;VPL": { | ||
"region": "mc2;VPL" | ||
}, | ||
"mc3;Rt": { | ||
"region": "mc3;Rt" | ||
}, | ||
"mc3;VPL": { | ||
"region": "mc3;VPL" | ||
}, | ||
"mc4;Rt": { | ||
"region": "mc4;Rt" | ||
}, | ||
"mc4;VPL": { | ||
"region": "mc4;VPL" | ||
}, | ||
"mc5;Rt": { | ||
"region": "mc5;Rt" | ||
}, | ||
"mc5;VPL": { | ||
"region": "mc5;VPL" | ||
}, | ||
"mc6;Rt": { | ||
"region": "mc6;Rt" | ||
}, | ||
"mc6;VPL": { | ||
"region": "mc6;VPL" | ||
}, | ||
"IN": { | ||
"mtype": { | ||
"$regex": ".*IN" | ||
}, | ||
"region": { | ||
"$regex": ".*" | ||
} | ||
}, | ||
"TC": { | ||
"mtype": { | ||
"$regex": ".*TC" | ||
}, | ||
"region": { | ||
"$regex": ".*" | ||
} | ||
}, | ||
"mc0_Column": { | ||
"region": { | ||
"$regex": "mc0.*" | ||
} | ||
}, | ||
"mc1_Column": { | ||
"region": { | ||
"$regex": "mc1.*" | ||
} | ||
}, | ||
"mc2_Column": { | ||
"region": { | ||
"$regex": "mc2.*" | ||
} | ||
}, | ||
"mc3_Column": { | ||
"region": { | ||
"$regex": "mc3.*" | ||
} | ||
}, | ||
"mc4_Column": { | ||
"region": { | ||
"$regex": "mc4.*" | ||
} | ||
}, | ||
"mc5_Column": { | ||
"region": { | ||
"$regex": "mc5.*" | ||
} | ||
}, | ||
"mc6_Column": { | ||
"region": { | ||
"$regex": "mc6.*" | ||
} | ||
}, | ||
"gapjunctions": [ | ||
"thalamus_neurons" | ||
], | ||
"gap-junctions": [ | ||
"gapjunctions" | ||
], | ||
"ML_afferents": { | ||
"population": "MedialLemniscus_projections" | ||
}, | ||
"CT_afferents": { | ||
"population": "CorticoThalamic_projections" | ||
} | ||
} |
2 changes: 2 additions & 0 deletions
2
doc/source/data/simulation-campaign/0/reporting/populations_offset.dat
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,2 @@ | ||
::0:: | ||
thalamus_neurons::0::thalamus_neurons |
Binary file not shown.
Oops, something went wrong.