From ac0ba0eab14f3840b2609d85f70901d72855c0ed Mon Sep 17 00:00:00 2001 From: Johannes Hjorth Date: Mon, 30 Sep 2024 14:39:56 +0200 Subject: [PATCH] Update version --- .../StriatumExample/CreateStriatum.ipynb | 1083 ++++++++++++++++- snudda/__init__.py | 2 +- 2 files changed, 1082 insertions(+), 3 deletions(-) diff --git a/examples/notebooks/StriatumExample/CreateStriatum.ipynb b/examples/notebooks/StriatumExample/CreateStriatum.ipynb index 502f1a592..e781fba74 100644 --- a/examples/notebooks/StriatumExample/CreateStriatum.ipynb +++ b/examples/notebooks/StriatumExample/CreateStriatum.ipynb @@ -285,10 +285,1089 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "id": "800e4d0c-c334-4751-8a36-32c031240fd7", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Placing neurons\n", + "Network path: networks/striatum1000\n", + "Reading SNUDDA_DATA=/home/hjorth/HBP/BasalGangliaData/data from networks/striatum1000/network-config.json\n", + "\u001b[1;33m[Open3D WARNING] [RemoveNonManifoldEdges] This mesh contains triangle uvs that are not handled in this function\u001b[0;m\n", + "Generating 280255 points for /home/hjorth/HBP/BasalGangliaData/data/meshes/Striatum-dorsal-left-hemisphere.obj\n", + "Filtering, keeping inside points: 82279 / 268076\n", + "neuron_name = 'dSPN_0', num = 120, neuron_path = '$SNUDDA_DATA/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026'\n", + "neuron_name = 'dSPN_1', num = 118, neuron_path = '$SNUDDA_DATA/neurons/striatum/dspn/str-dspn-e150917_c10_D1-mWT-P270-20-v20211026'\n", + "neuron_name = 'dSPN_2', num = 119, neuron_path = '$SNUDDA_DATA/neurons/striatum/dspn/str-dspn-e150917_c6_D1-m21-6-DE-v20211028'\n", + "neuron_name = 'dSPN_3', num = 118, neuron_path = '$SNUDDA_DATA/neurons/striatum/dspn/str-dspn-e150917_c9_D1-mWT-1215MSN03-v20211026'\n", + "neuron_name = 'iSPN_0', num = 118, neuron_path = '$SNUDDA_DATA/neurons/striatum/ispn/str-ispn-e150908_c4_D2-m51-5-DE-v20211026'\n", + "neuron_name = 'iSPN_1', num = 119, neuron_path = '$SNUDDA_DATA/neurons/striatum/ispn/str-ispn-e150917_c11_D2-mWT-MSN1-v20211026'\n", + "neuron_name = 'iSPN_2', num = 118, neuron_path = '$SNUDDA_DATA/neurons/striatum/ispn/str-ispn-e151123_c1_D2-mWT-P270-09-v20211026'\n", + "neuron_name = 'iSPN_3', num = 120, neuron_path = '$SNUDDA_DATA/neurons/striatum/ispn/str-ispn-e160118_c10_D2-m46-3-DE-v20211026'\n", + "neuron_name = 'FS_0', num = 3, neuron_path = '$SNUDDA_DATA/neurons/striatum/fs/str-fs-e160628_FS2-mMTC180800A-IDB-v20210210'\n", + "neuron_name = 'FS_1', num = 3, neuron_path = '$SNUDDA_DATA/neurons/striatum/fs/str-fs-e161024_FS16-mDR-rat-Mar-13-08-1-536-R-v20210210'\n", + "neuron_name = 'FS_2', num = 3, neuron_path = '$SNUDDA_DATA/neurons/striatum/fs/str-fs-e161205_FS1-mBE104E-v20210209'\n", + "neuron_name = 'FS_3', num = 4, neuron_path = '$SNUDDA_DATA/neurons/striatum/fs/str-fs-e161205_FS1-mMTC180800A-IDB-v20210210'\n", + "neuron_name = 'ChIN_0', num = 11, neuron_path = '$SNUDDA_DATA/neurons/striatum/chin/str-chin-e170614_cell6-m17JUL301751_170614_no6_MD_cell_1_x63-v20190710'\n", + "neuron_name = 'LTS_0', num = 4, neuron_path = '$SNUDDA_DATA/neurons/striatum/lts/LTS_180118_morp_9862_updated_20210301'\n", + "neuron_name = 'LTS_1', num = 3, neuron_path = '$SNUDDA_DATA/neurons/striatum/lts/LTS_180118_morp_9862_updated_April2022'\n", + "stop_parallel disabled, to keep pool running.\n", + "\n", + "Execution time: 2.2s\n", + "Touch detection\n", + "Network path: networks/striatum1000\n", + "Reading SNUDDA_DATA=/home/hjorth/HBP/BasalGangliaData/data from networks/striatum1000/network-config.json\n", + "No d_view specified, running distribute neurons in serial\n", + "Traceback (most recent call last):\n", + " File \"/home/hjorth/HBP/Snudda/snudda/neurons/morphology_data.py\", line 483, in load_cache\n", + " raise ValueError(f\"Cache mismatch. Different paths:\\nRequested: {self.swc_file}\\nCached: {data['swc_file']}\")\n", + "ValueError: Cache mismatch. Different paths:\n", + "Requested: /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/morphology/WT-0728MSN01-cor-rep-ax-res3-var7.swc\n", + "Cached: ../../../BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/morphology/WT-0728MSN01-cor-rep-ax-res3-var7.swc\n", + "\n", + "Failed to load cache from /home/hjorth/HBP/BasalGangliaData/data/neurons/striatum/dspn/str-dspn-e150602_c1_D1-mWT-0728MSN01-v20211026/morphology/WT-0728MSN01-cor-rep-ax-res3-var7.swc-cache.pickle\n", + "Processing hyper voxel : 798/3600 (34 neurons)\n", + "Processing hyper voxel : 784/3600 (32 neurons)\n", + "Processing hyper voxel : 846/3600 (31 neurons)\n", + "Processing hyper voxel : 1250/3600 (29 neurons)\n", + "Processing hyper voxel : 559/3600 (29 neurons)\n", + "Processing hyper voxel : 741/3600 (27 neurons)\n", + "Processing hyper voxel : 1191/3600 (27 neurons)\n", + "Processing hyper voxel : 830/3600 (27 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"Processing hyper voxel : 903/3600 (1 neurons)\n", + "Processing hyper voxel : 902/3600 (1 neurons)\n", + "Processing hyper voxel : 1001/3600 (1 neurons)\n", + "Processing hyper voxel : 3295/3600 (1 neurons)\n", + "Reading SNUDDA_DATA=/home/hjorth/HBP/BasalGangliaData/data from networks/striatum1000/network-config.json\n", + "stop_parallel disabled, to keep pool running.\n", + "\n", + "Execution time: 93.6s\n", + "Prune synapses\n", + "Network path: networks/striatum1000\n", + "No file networks/striatum1000/pruning_merge_info.json\n", + "Read 19138 out of total 19138 synapses\n", + "stop_parallel disabled, to keep pool running.\n", + "\n", + "Execution time: 97.7s\n" + ] + } + ], "source": [ "snd.create_network()" ] diff --git a/snudda/__init__.py b/snudda/__init__.py index 3479630f2..d40eaedec 100644 --- a/snudda/__init__.py +++ b/snudda/__init__.py @@ -1,6 +1,6 @@ from .core import Snudda -__version__ = "2.1.2" +__version__ = "2.1.3" from .init import SnuddaInit from .place import SnuddaPlace