From 839f4434507c7312aaa24c630dfeba8f77420d3d Mon Sep 17 00:00:00 2001 From: Mustafa Kerem Kurban Date: Mon, 4 Mar 2024 16:51:26 +0100 Subject: [PATCH 1/4] fix nodes.h5 for example 2 --- .ipynb_checkpoints/AUTHORS-checkpoint.txt | 28 ++ AUTHORS.txt | 1 + .../usecase2-checkpoint.rst | 66 ++++ .../nodes.h5-checkpoint.txt | 306 ++++++++++++++++++ .../projections.h5-checkpoint.txt | 239 ++++++++++++++ source/usecases/usecase2/nodes.h5 | Bin 25584 -> 31744 bytes source/usecases/usecase2/nodes.h5.txt | 7 + 7 files changed, 647 insertions(+) create mode 100644 .ipynb_checkpoints/AUTHORS-checkpoint.txt create mode 100644 source/.ipynb_checkpoints/usecase2-checkpoint.rst create mode 100644 source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt create mode 100644 source/usecases/usecase2/.ipynb_checkpoints/projections.h5-checkpoint.txt diff --git a/.ipynb_checkpoints/AUTHORS-checkpoint.txt b/.ipynb_checkpoints/AUTHORS-checkpoint.txt new file mode 100644 index 0000000..db55a36 --- /dev/null +++ b/.ipynb_checkpoints/AUTHORS-checkpoint.txt @@ -0,0 +1,28 @@ +Alberto Antonietti +Aleksei Sanin +Alexander Dietz +Alexandru Savulescu +Alexis Arnaudon +Andrew Hale +Ben Morrice +Ecker András +Eleftherios Zisis +Fernando Pereira +Gianluca Ficarelli +Ioannis Magkanaris +James Gonzalo King +Jean Jacquemier +Jean-Denis Courcol +Joni Herttuainen +Jorge Blanco Alonso +Kerem Kurban +King James Gonzalo +Matthias Wolf +Michael Gevaert +Mike Gevaert +Pramod Kumbhar +Sirio Bolaños Puchet +Stefano Maximiliano Antonel +Thomas Delemontex +Vishal Sood +Weina Ji diff --git a/AUTHORS.txt b/AUTHORS.txt index dbb0e0c..db55a36 100644 --- a/AUTHORS.txt +++ b/AUTHORS.txt @@ -15,6 +15,7 @@ Jean Jacquemier Jean-Denis Courcol Joni Herttuainen Jorge Blanco Alonso +Kerem Kurban King James Gonzalo Matthias Wolf Michael Gevaert diff --git a/source/.ipynb_checkpoints/usecase2-checkpoint.rst b/source/.ipynb_checkpoints/usecase2-checkpoint.rst new file mode 100644 index 0000000..d141d93 --- /dev/null +++ b/source/.ipynb_checkpoints/usecase2-checkpoint.rst @@ -0,0 +1,66 @@ +:orphan: + +usecase 2 +========= + +.. image:: _static/usecase2.svg + :align: center + +This usecase 2 is 1 population of biophysical neurons with chemical synapses between neurons of that population and 1 virtual node population projecting into the biophysical neurons. +In this usecase, virtual and biophysical nodes are in the same node files as opposed to usecase4. + +circuit configuration +--------------------- +.. include:: usecases/usecase2/circuit_sonata.json + :literal: + +node files +---------- + +biophysical nodes and virtual nodes +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. include:: usecases/usecase2/nodes.h5.txt + :literal: + +edge files +---------- + +edges between the biophysical neurons +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. include:: usecases/usecase2/edges.h5.txt + :literal: + +projections to the biophysical neurons +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. include:: usecases/usecase2/projections.h5.txt + :literal: + +reports +------- + +simulation config used (report section only) + +.. include:: usecases/usecase2/simulation_sonata.json + :literal: + +spike report +^^^^^^^^^^^^ + +.. include:: usecases/usecase2/reporting/spikes.h5.txt + :literal: + + +soma report +^^^^^^^^^^^ + +.. include:: usecases/usecase2/reporting/soma_report.h5.txt + :literal: + +compartment report +^^^^^^^^^^^^^^^^^^ + +.. include:: usecases/usecase2/reporting/compartment_report.h5.txt + :literal: diff --git a/source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt b/source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt new file mode 100644 index 0000000..36c3a9d --- /dev/null +++ b/source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt @@ -0,0 +1,306 @@ +HDF5 "./results/usecase2/nodes.h5" { +GROUP "/" { + GROUP "nodes" { + GROUP "NodeA" { + GROUP "0" { + GROUP "@library" { + DATASET "etype" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + "dNAC", "dSTUT" + } + } + DATASET "hemisphere" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + "left", "right" + } + } + DATASET "model_type" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 1 ) / ( 1 ) } + DATA { + "biophysical" + } + } + DATASET "morph_class" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + "INT", "PYR" + } + } + DATASET "mtype" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + "L4_MC", "L5_PC" + } + } + DATASET "region" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 1 ) / ( 1 ) } + DATA { + "RB" + } + } + DATASET "synapse_class" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 1 ) / ( 1 ) } + DATA { + "INH" + } + } + } + GROUP "dynamics_params" { + DATASET "AIS_scaler" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 1.75862, 1.10591 + } + } + DATASET "holding_current" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 1.58202, 1.53737 + } + } + DATASET "threshold_current" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 1.67888, 1.72063 + } + } + } + DATASET "etype" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 1, 0 + } + } + DATASET "hemisphere" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 0, 1 + } + } + DATASET "layer" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + "LA", "LB" + } + } + DATASET "minis" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 47.36, 18.6332 + } + } + DATASET "model_template" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + "hoc:cNAC_L23BTC", "hoc:cADpyr_L2TPC" + } + } + DATASET "model_type" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 0, 0 + } + } + DATASET "morph_class" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 1, 0 + } + } + DATASET "morphology" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + "C210401C", "rr110330_C3_idA" + } + } + DATASET "mtype" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 0, 1 + } + } + DATASET "orientation_w" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + -0.124826, 0.783546 + } + } + DATASET "orientation_x" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 0.927326, -0.233117 + } + } + DATASET "orientation_y" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 0.58345, 0.0577898 + } + } + DATASET "orientation_z" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 0.136089, 0.851193 + } + } + DATASET "region" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 0, 0 + } + } + DATASET "synapse_class" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 0, 0 + } + } + DATASET "x" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 97.627, 430.379 + } + } + DATASET "y" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 205.527, 89.7664 + } + } + DATASET "z" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + -152.69, 291.788 + } + } + } + DATASET "node_type_id" { + DATATYPE H5T_STD_I64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + -1, -1 + } + } + } + GROUP "VirtualPopA" { + GROUP "0" { + GROUP "@library" { + DATASET "model_type" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 1 ) / ( 1 ) } + DATA { + "virtual" + } + } + } + DATASET "model_type" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 0, 0 + } + } + DATASET "model_template" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 1 ) / ( 1 ) } + DATA { + NULL + } + } + } + DATASET "node_type_id" { + DATATYPE H5T_STD_I64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + -1, -1 + } + } + } + } +} +} diff --git a/source/usecases/usecase2/.ipynb_checkpoints/projections.h5-checkpoint.txt b/source/usecases/usecase2/.ipynb_checkpoints/projections.h5-checkpoint.txt new file mode 100644 index 0000000..456ae6e --- /dev/null +++ b/source/usecases/usecase2/.ipynb_checkpoints/projections.h5-checkpoint.txt @@ -0,0 +1,239 @@ +HDF5 "./results/usecase2/projections.h5" { +GROUP "/" { + GROUP "edges" { + GROUP "VirtualPopA__NodeA__chemical" { + GROUP "0" { + DATASET "afferent_center_x" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 81.1608, 156.339, 51.0543, 407.517 + } + } + DATASET "afferent_center_y" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 194.028, 184.127, 198.152, 17.7689 + } + } + DATASET "afferent_center_z" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + -115.748, -164.805, -134.199, 303.212 + } + } + DATASET "afferent_section_id" { + DATATYPE H5T_STD_I64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 300, 279, 311, 229 + } + } + DATASET "afferent_section_type" { + DATATYPE H5T_STD_I64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 3, 3, 3, 4 + } + } + DATASET "afferent_segment_id" { + DATATYPE H5T_STD_I64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 3, 10, 43, 10 + } + } + DATASET "afferent_segment_offset" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 0.26935, 0.218497, 0.112087, 0.309447 + } + } + DATASET "afferent_surface_x" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 80.8799, 156.261, 51.1682, 407.639 + } + } + DATASET "afferent_surface_y" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 194.007, 183.978, 198.251, 17.6852 + } + } + DATASET "afferent_surface_z" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + -115.78, -164.862, -134.155, 303.271 + } + } + DATASET "conductance" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 0.205892, 0.259128, 0.321129, 0.165976 + } + } + DATASET "conductance_scale_factor" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 0.693702, 0.579886, 0.30748, 0.455382 + } + } + DATASET "decay_time" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 1.6849, 1.57322, 1.78481, 1.85187 + } + } + DATASET "delay" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 7.4917, 8.78452, 1.02863, 0.923739 + } + } + DATASET "depression_time" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 628.848, 643.329, 675.611, 639.61 + } + } + DATASET "facilitation_time" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 22.9208, 17.7784, 22.8311, 18.6011 + } + } + DATASET "n_rrp_vesicles" { + DATATYPE H5T_STD_I64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 2, 2, 4, 1 + } + } + DATASET "spine_length" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 2498.04, 3132.25, 9654.17, 5884.69 + } + } + DATASET "syn_type_id" { + DATATYPE H5T_STD_I64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 71, 56, 24, 79 + } + } + DATASET "u_hill_coefficient" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 1.61881, 1.47487, 1.47013, 1.71607 + } + } + DATASET "u_syn" { + DATATYPE H5T_IEEE_F64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 0.52246, 0.548929, 0.50581, 0.538351 + } + } + } + DATASET "edge_type_id" { + DATATYPE H5T_STD_I64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + -1, -1, -1, -1 + } + } + GROUP "indices" { + GROUP "source_to_target" { + DATASET "node_id_to_ranges" { + DATATYPE H5T_STD_U64LE + DATASPACE SIMPLE { ( 2, 2 ) / ( 2, 2 ) } + DATA { + 0, 0, + 0, 1 + } + } + DATASET "range_to_edge_id" { + DATATYPE H5T_STD_U64LE + DATASPACE SIMPLE { ( 1, 2 ) / ( 1, 2 ) } + DATA { + 0, 4 + } + } + } + GROUP "target_to_source" { + DATASET "node_id_to_ranges" { + DATATYPE H5T_STD_U64LE + DATASPACE SIMPLE { ( 2, 2 ) / ( 2, 2 ) } + DATA { + 0, 1, + 1, 2 + } + } + DATASET "range_to_edge_id" { + DATATYPE H5T_STD_U64LE + DATASPACE SIMPLE { ( 2, 2 ) / ( 2, 2 ) } + DATA { + 0, 3, + 3, 4 + } + } + } + } + DATASET "source_node_id" { + DATATYPE H5T_STD_U64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 1, 1, 1, 1 + } + ATTRIBUTE "node_population" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SCALAR + DATA { + "VirtualPopA" + } + } + } + DATASET "target_node_id" { + DATATYPE H5T_STD_U64LE + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + 0, 0, 0, 1 + } + ATTRIBUTE "node_population" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SCALAR + DATA { + "NodeA" + } + } + } + } + } +} +} diff --git a/source/usecases/usecase2/nodes.h5 b/source/usecases/usecase2/nodes.h5 index 992666b9e351a08e27036d78c38b5d206d06c3d4..5c7df03a6dfd984f5029c57e28d0bca94e16767b 100644 GIT binary patch delta 189 zcmexxoU!2t;{**RhMJ99(;^uyCLfG6m&naeNzI8bNzE z3v9NC;$vlGp6nj4$)y36`;a_wquk^LCLEJ1;$KWQaLwBMDd8UzGb01* Date: Mon, 4 Mar 2024 16:57:50 +0100 Subject: [PATCH 2/4] fix example 4 too --- .../nodes.h5-checkpoint.txt | 2 +- source/usecases/usecase2/nodes.h5.txt | 2 +- .../virtual_nodes_A.h5-checkpoint.txt | 45 ++++++++++++++++++ .../virtual_nodes_B.h5-checkpoint.txt | 45 ++++++++++++++++++ source/usecases/usecase4/virtual_nodes_A.h5 | Bin 12360 -> 18520 bytes .../usecases/usecase4/virtual_nodes_A.h5.txt | 7 +++ source/usecases/usecase4/virtual_nodes_B.h5 | Bin 12360 -> 18520 bytes .../usecases/usecase4/virtual_nodes_B.h5.txt | 7 +++ 8 files changed, 106 insertions(+), 2 deletions(-) create mode 100644 source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_A.h5-checkpoint.txt create mode 100644 source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_B.h5-checkpoint.txt diff --git a/source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt b/source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt index 36c3a9d..1538a5c 100644 --- a/source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt +++ b/source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt @@ -289,7 +289,7 @@ GROUP "/" { DATATYPE H5T_STD_U32LE DATASPACE SIMPLE { ( 1 ) / ( 1 ) } DATA { - NULL + "NULL" } } } diff --git a/source/usecases/usecase2/nodes.h5.txt b/source/usecases/usecase2/nodes.h5.txt index 36c3a9d..1538a5c 100644 --- a/source/usecases/usecase2/nodes.h5.txt +++ b/source/usecases/usecase2/nodes.h5.txt @@ -289,7 +289,7 @@ GROUP "/" { DATATYPE H5T_STD_U32LE DATASPACE SIMPLE { ( 1 ) / ( 1 ) } DATA { - NULL + "NULL" } } } diff --git a/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_A.h5-checkpoint.txt b/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_A.h5-checkpoint.txt new file mode 100644 index 0000000..32a8c45 --- /dev/null +++ b/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_A.h5-checkpoint.txt @@ -0,0 +1,45 @@ +HDF5 "./results/usecase4/virtual_nodes_A.h5" { +GROUP "/" { + GROUP "nodes" { + GROUP "VirtualPopA" { + GROUP "0" { + GROUP "@library" { + DATASET "model_type" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 1 ) / ( 1 ) } + DATA { + "virtual" + } + } + } + DATASET "model_type" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 0, 0 + } + } + DATASET "model_template" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 1 ) / ( 1 ) } + DATA { + "NULL" + } + } + } + DATASET "node_type_id" { + DATATYPE H5T_STD_I64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + -1, -1 + } + } + } + } +} +} diff --git a/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_B.h5-checkpoint.txt b/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_B.h5-checkpoint.txt new file mode 100644 index 0000000..6cabe29 --- /dev/null +++ b/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_B.h5-checkpoint.txt @@ -0,0 +1,45 @@ +HDF5 "./results/usecase4/virtual_nodes_B.h5" { +GROUP "/" { + GROUP "nodes" { + GROUP "VirtualPopB" { + GROUP "0" { + GROUP "@library" { + DATASET "model_type" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_UTF8; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 1 ) / ( 1 ) } + DATA { + "virtual" + } + } + } + DATASET "model_type" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + 0, 0 + } + } + DATASET "model_template" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 1 ) / ( 1 ) } + DATA { + "NULL" + } + } + } + DATASET "node_type_id" { + DATATYPE H5T_STD_I64LE + DATASPACE SIMPLE { ( 2 ) / ( 2 ) } + DATA { + -1, -1 + } + } + } + } +} +} diff --git a/source/usecases/usecase4/virtual_nodes_A.h5 b/source/usecases/usecase4/virtual_nodes_A.h5 index ec4e3431d3925645e7be4176155628af3a658256..401029749573634fa21ffd74d776c85fbdf67cdb 100644 GIT binary patch delta 187 zcmX?+aAN}F1P!JLkBwS!yo?r;J9*6|bMsSDbK*- zco~@|^Gj=TX+Xt23?^=rn`|NdVRL}Y4`F6T2G+^e{IZh^WV|FjEFfwGph{s>$L2zT oT6S|5AU^`C1Z0c5v%e46HmG`-%^-Ck;1}xS1EeDb1Pvw+gN<5oyo?%?J9*7H7#Sd7vZJ*8!~>k0Kk&-&GBQo(m)4w|ApK$D L0gcT8GCza?@Cp%W diff --git a/source/usecases/usecase4/virtual_nodes_A.h5.txt b/source/usecases/usecase4/virtual_nodes_A.h5.txt index 456f7cd..32a8c45 100644 --- a/source/usecases/usecase4/virtual_nodes_A.h5.txt +++ b/source/usecases/usecase4/virtual_nodes_A.h5.txt @@ -24,6 +24,13 @@ GROUP "/" { 0, 0 } } + DATASET "model_template" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 1 ) / ( 1 ) } + DATA { + "NULL" + } + } } DATASET "node_type_id" { DATATYPE H5T_STD_I64LE diff --git a/source/usecases/usecase4/virtual_nodes_B.h5 b/source/usecases/usecase4/virtual_nodes_B.h5 index b1444359cfc849a1a141004e7a190683f5f49191..e3c7d791c5c6968309a347245abed1e5c24ccbbc 100644 GIT binary patch delta 187 zcmX?+aAN}F1P!JLkBwS!yo?r;J9*6|bMsSDbK*- zco~@|^Gj=TX+Xt23?^=rn`|NdVRL}Y4`F6T2G+^e{IZh^WV|FjEFfwGph{s>$L2zT oT6S|5AU^`C1Z0c5v%e46HmG`-%^-Ck;1}xS1EeDb1Pvw+gN<5oyo?%?J9*7H7#Sd7vZJ*8!~>k0Kk&-&GBQo(m)4w|ApK$D L0gcT8GCza?@Cp%W diff --git a/source/usecases/usecase4/virtual_nodes_B.h5.txt b/source/usecases/usecase4/virtual_nodes_B.h5.txt index f9d22ca..6cabe29 100644 --- a/source/usecases/usecase4/virtual_nodes_B.h5.txt +++ b/source/usecases/usecase4/virtual_nodes_B.h5.txt @@ -24,6 +24,13 @@ GROUP "/" { 0, 0 } } + DATASET "model_template" { + DATATYPE H5T_STD_U32LE + DATASPACE SIMPLE { ( 1 ) / ( 1 ) } + DATA { + "NULL" + } + } } DATASET "node_type_id" { DATATYPE H5T_STD_I64LE From 44d77947d3ff59a27fd6fd0c78705669bb43809b Mon Sep 17 00:00:00 2001 From: Mustafa Kerem Kurban Date: Mon, 4 Mar 2024 16:58:59 +0100 Subject: [PATCH 3/4] rm ipynb_checkpoints --- .ipynb_checkpoints/AUTHORS-checkpoint.txt | 28 ----------------------- 1 file changed, 28 deletions(-) delete mode 100644 .ipynb_checkpoints/AUTHORS-checkpoint.txt diff --git a/.ipynb_checkpoints/AUTHORS-checkpoint.txt b/.ipynb_checkpoints/AUTHORS-checkpoint.txt deleted file mode 100644 index db55a36..0000000 --- a/.ipynb_checkpoints/AUTHORS-checkpoint.txt +++ /dev/null @@ -1,28 +0,0 @@ -Alberto Antonietti -Aleksei Sanin -Alexander Dietz -Alexandru Savulescu -Alexis Arnaudon -Andrew Hale -Ben Morrice -Ecker András -Eleftherios Zisis -Fernando Pereira -Gianluca Ficarelli -Ioannis Magkanaris -James Gonzalo King -Jean Jacquemier -Jean-Denis Courcol -Joni Herttuainen -Jorge Blanco Alonso -Kerem Kurban -King James Gonzalo -Matthias Wolf -Michael Gevaert -Mike Gevaert -Pramod Kumbhar -Sirio Bolaños Puchet -Stefano Maximiliano Antonel -Thomas Delemontex -Vishal Sood -Weina Ji From 20742f211e3b0136bf954cb4aeae44266b70c69e Mon Sep 17 00:00:00 2001 From: Mustafa Kerem Kurban Date: Mon, 4 Mar 2024 17:00:45 +0100 Subject: [PATCH 4/4] rm extra checkpoints --- .../usecase2-checkpoint.rst | 66 ---- .../nodes.h5-checkpoint.txt | 306 ------------------ .../projections.h5-checkpoint.txt | 239 -------------- .../virtual_nodes_A.h5-checkpoint.txt | 45 --- .../virtual_nodes_B.h5-checkpoint.txt | 45 --- 5 files changed, 701 deletions(-) delete mode 100644 source/.ipynb_checkpoints/usecase2-checkpoint.rst delete mode 100644 source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt delete mode 100644 source/usecases/usecase2/.ipynb_checkpoints/projections.h5-checkpoint.txt delete mode 100644 source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_A.h5-checkpoint.txt delete mode 100644 source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_B.h5-checkpoint.txt diff --git a/source/.ipynb_checkpoints/usecase2-checkpoint.rst b/source/.ipynb_checkpoints/usecase2-checkpoint.rst deleted file mode 100644 index d141d93..0000000 --- a/source/.ipynb_checkpoints/usecase2-checkpoint.rst +++ /dev/null @@ -1,66 +0,0 @@ -:orphan: - -usecase 2 -========= - -.. image:: _static/usecase2.svg - :align: center - -This usecase 2 is 1 population of biophysical neurons with chemical synapses between neurons of that population and 1 virtual node population projecting into the biophysical neurons. -In this usecase, virtual and biophysical nodes are in the same node files as opposed to usecase4. - -circuit configuration ---------------------- -.. include:: usecases/usecase2/circuit_sonata.json - :literal: - -node files ----------- - -biophysical nodes and virtual nodes -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -.. include:: usecases/usecase2/nodes.h5.txt - :literal: - -edge files ----------- - -edges between the biophysical neurons -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -.. include:: usecases/usecase2/edges.h5.txt - :literal: - -projections to the biophysical neurons -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -.. include:: usecases/usecase2/projections.h5.txt - :literal: - -reports -------- - -simulation config used (report section only) - -.. include:: usecases/usecase2/simulation_sonata.json - :literal: - -spike report -^^^^^^^^^^^^ - -.. include:: usecases/usecase2/reporting/spikes.h5.txt - :literal: - - -soma report -^^^^^^^^^^^ - -.. include:: usecases/usecase2/reporting/soma_report.h5.txt - :literal: - -compartment report -^^^^^^^^^^^^^^^^^^ - -.. include:: usecases/usecase2/reporting/compartment_report.h5.txt - :literal: diff --git a/source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt b/source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt deleted file mode 100644 index 1538a5c..0000000 --- a/source/usecases/usecase2/.ipynb_checkpoints/nodes.h5-checkpoint.txt +++ /dev/null @@ -1,306 +0,0 @@ -HDF5 "./results/usecase2/nodes.h5" { -GROUP "/" { - GROUP "nodes" { - GROUP "NodeA" { - GROUP "0" { - GROUP "@library" { - DATASET "etype" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - "dNAC", "dSTUT" - } - } - DATASET "hemisphere" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - "left", "right" - } - } - DATASET "model_type" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 1 ) / ( 1 ) } - DATA { - "biophysical" - } - } - DATASET "morph_class" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - "INT", "PYR" - } - } - DATASET "mtype" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - "L4_MC", "L5_PC" - } - } - DATASET "region" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 1 ) / ( 1 ) } - DATA { - "RB" - } - } - DATASET "synapse_class" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 1 ) / ( 1 ) } - DATA { - "INH" - } - } - } - GROUP "dynamics_params" { - DATASET "AIS_scaler" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 1.75862, 1.10591 - } - } - DATASET "holding_current" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 1.58202, 1.53737 - } - } - DATASET "threshold_current" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 1.67888, 1.72063 - } - } - } - DATASET "etype" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 1, 0 - } - } - DATASET "hemisphere" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 0, 1 - } - } - DATASET "layer" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - "LA", "LB" - } - } - DATASET "minis" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 47.36, 18.6332 - } - } - DATASET "model_template" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - "hoc:cNAC_L23BTC", "hoc:cADpyr_L2TPC" - } - } - DATASET "model_type" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 0, 0 - } - } - DATASET "morph_class" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 1, 0 - } - } - DATASET "morphology" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - "C210401C", "rr110330_C3_idA" - } - } - DATASET "mtype" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 0, 1 - } - } - DATASET "orientation_w" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - -0.124826, 0.783546 - } - } - DATASET "orientation_x" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 0.927326, -0.233117 - } - } - DATASET "orientation_y" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 0.58345, 0.0577898 - } - } - DATASET "orientation_z" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 0.136089, 0.851193 - } - } - DATASET "region" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 0, 0 - } - } - DATASET "synapse_class" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 0, 0 - } - } - DATASET "x" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 97.627, 430.379 - } - } - DATASET "y" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 205.527, 89.7664 - } - } - DATASET "z" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - -152.69, 291.788 - } - } - } - DATASET "node_type_id" { - DATATYPE H5T_STD_I64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - -1, -1 - } - } - } - GROUP "VirtualPopA" { - GROUP "0" { - GROUP "@library" { - DATASET "model_type" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 1 ) / ( 1 ) } - DATA { - "virtual" - } - } - } - DATASET "model_type" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 0, 0 - } - } - DATASET "model_template" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 1 ) / ( 1 ) } - DATA { - "NULL" - } - } - } - DATASET "node_type_id" { - DATATYPE H5T_STD_I64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - -1, -1 - } - } - } - } -} -} diff --git a/source/usecases/usecase2/.ipynb_checkpoints/projections.h5-checkpoint.txt b/source/usecases/usecase2/.ipynb_checkpoints/projections.h5-checkpoint.txt deleted file mode 100644 index 456ae6e..0000000 --- a/source/usecases/usecase2/.ipynb_checkpoints/projections.h5-checkpoint.txt +++ /dev/null @@ -1,239 +0,0 @@ -HDF5 "./results/usecase2/projections.h5" { -GROUP "/" { - GROUP "edges" { - GROUP "VirtualPopA__NodeA__chemical" { - GROUP "0" { - DATASET "afferent_center_x" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 81.1608, 156.339, 51.0543, 407.517 - } - } - DATASET "afferent_center_y" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 194.028, 184.127, 198.152, 17.7689 - } - } - DATASET "afferent_center_z" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - -115.748, -164.805, -134.199, 303.212 - } - } - DATASET "afferent_section_id" { - DATATYPE H5T_STD_I64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 300, 279, 311, 229 - } - } - DATASET "afferent_section_type" { - DATATYPE H5T_STD_I64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 3, 3, 3, 4 - } - } - DATASET "afferent_segment_id" { - DATATYPE H5T_STD_I64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 3, 10, 43, 10 - } - } - DATASET "afferent_segment_offset" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 0.26935, 0.218497, 0.112087, 0.309447 - } - } - DATASET "afferent_surface_x" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 80.8799, 156.261, 51.1682, 407.639 - } - } - DATASET "afferent_surface_y" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 194.007, 183.978, 198.251, 17.6852 - } - } - DATASET "afferent_surface_z" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - -115.78, -164.862, -134.155, 303.271 - } - } - DATASET "conductance" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 0.205892, 0.259128, 0.321129, 0.165976 - } - } - DATASET "conductance_scale_factor" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 0.693702, 0.579886, 0.30748, 0.455382 - } - } - DATASET "decay_time" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 1.6849, 1.57322, 1.78481, 1.85187 - } - } - DATASET "delay" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 7.4917, 8.78452, 1.02863, 0.923739 - } - } - DATASET "depression_time" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 628.848, 643.329, 675.611, 639.61 - } - } - DATASET "facilitation_time" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 22.9208, 17.7784, 22.8311, 18.6011 - } - } - DATASET "n_rrp_vesicles" { - DATATYPE H5T_STD_I64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 2, 2, 4, 1 - } - } - DATASET "spine_length" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 2498.04, 3132.25, 9654.17, 5884.69 - } - } - DATASET "syn_type_id" { - DATATYPE H5T_STD_I64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 71, 56, 24, 79 - } - } - DATASET "u_hill_coefficient" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 1.61881, 1.47487, 1.47013, 1.71607 - } - } - DATASET "u_syn" { - DATATYPE H5T_IEEE_F64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 0.52246, 0.548929, 0.50581, 0.538351 - } - } - } - DATASET "edge_type_id" { - DATATYPE H5T_STD_I64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - -1, -1, -1, -1 - } - } - GROUP "indices" { - GROUP "source_to_target" { - DATASET "node_id_to_ranges" { - DATATYPE H5T_STD_U64LE - DATASPACE SIMPLE { ( 2, 2 ) / ( 2, 2 ) } - DATA { - 0, 0, - 0, 1 - } - } - DATASET "range_to_edge_id" { - DATATYPE H5T_STD_U64LE - DATASPACE SIMPLE { ( 1, 2 ) / ( 1, 2 ) } - DATA { - 0, 4 - } - } - } - GROUP "target_to_source" { - DATASET "node_id_to_ranges" { - DATATYPE H5T_STD_U64LE - DATASPACE SIMPLE { ( 2, 2 ) / ( 2, 2 ) } - DATA { - 0, 1, - 1, 2 - } - } - DATASET "range_to_edge_id" { - DATATYPE H5T_STD_U64LE - DATASPACE SIMPLE { ( 2, 2 ) / ( 2, 2 ) } - DATA { - 0, 3, - 3, 4 - } - } - } - } - DATASET "source_node_id" { - DATATYPE H5T_STD_U64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 1, 1, 1, 1 - } - ATTRIBUTE "node_population" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SCALAR - DATA { - "VirtualPopA" - } - } - } - DATASET "target_node_id" { - DATATYPE H5T_STD_U64LE - DATASPACE SIMPLE { ( 4 ) / ( 4 ) } - DATA { - 0, 0, 0, 1 - } - ATTRIBUTE "node_population" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SCALAR - DATA { - "NodeA" - } - } - } - } - } -} -} diff --git a/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_A.h5-checkpoint.txt b/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_A.h5-checkpoint.txt deleted file mode 100644 index 32a8c45..0000000 --- a/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_A.h5-checkpoint.txt +++ /dev/null @@ -1,45 +0,0 @@ -HDF5 "./results/usecase4/virtual_nodes_A.h5" { -GROUP "/" { - GROUP "nodes" { - GROUP "VirtualPopA" { - GROUP "0" { - GROUP "@library" { - DATASET "model_type" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 1 ) / ( 1 ) } - DATA { - "virtual" - } - } - } - DATASET "model_type" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 0, 0 - } - } - DATASET "model_template" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 1 ) / ( 1 ) } - DATA { - "NULL" - } - } - } - DATASET "node_type_id" { - DATATYPE H5T_STD_I64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - -1, -1 - } - } - } - } -} -} diff --git a/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_B.h5-checkpoint.txt b/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_B.h5-checkpoint.txt deleted file mode 100644 index 6cabe29..0000000 --- a/source/usecases/usecase4/.ipynb_checkpoints/virtual_nodes_B.h5-checkpoint.txt +++ /dev/null @@ -1,45 +0,0 @@ -HDF5 "./results/usecase4/virtual_nodes_B.h5" { -GROUP "/" { - GROUP "nodes" { - GROUP "VirtualPopB" { - GROUP "0" { - GROUP "@library" { - DATASET "model_type" { - DATATYPE H5T_STRING { - STRSIZE H5T_VARIABLE; - STRPAD H5T_STR_NULLTERM; - CSET H5T_CSET_UTF8; - CTYPE H5T_C_S1; - } - DATASPACE SIMPLE { ( 1 ) / ( 1 ) } - DATA { - "virtual" - } - } - } - DATASET "model_type" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - 0, 0 - } - } - DATASET "model_template" { - DATATYPE H5T_STD_U32LE - DATASPACE SIMPLE { ( 1 ) / ( 1 ) } - DATA { - "NULL" - } - } - } - DATASET "node_type_id" { - DATATYPE H5T_STD_I64LE - DATASPACE SIMPLE { ( 2 ) / ( 2 ) } - DATA { - -1, -1 - } - } - } - } -} -}