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Update Trodes notebook, revise others
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@CBroz1
CBroz1 committed Sep 28, 2023
1 parent 742f5cb commit d12e4d4
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40 changes: 21 additions & 19 deletions docs/mkdocs.yml
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Expand Up @@ -47,28 +47,30 @@ nav:
- Home: index.md
- Installation: installation.md
- Miscellaneous:
- FigURL: misc/figurl_views.md
- Session Groups: misc/session_groups.md
- Insert Data: misc/insert_data.md
- Merge Tables: misc/merge_tables.md
- FigURL: misc/figurl_views.md
- Session Groups: misc/session_groups.md
- Insert Data: misc/insert_data.md
- Merge Tables: misc/merge_tables.md
- Tutorials:
- General:
- Setup: notebooks/00_Setup.ipynb
- Insert Data: notebooks/01_Insert_Data.ipynb
- Spike Sorting: notebooks/02_Spike_Sorting.ipynb
- Curation: notebooks/03_Curation.ipynb
- LFP: notebooks/03_lfp.ipynb
- Position:
- Information: notebooks/4_position_info.ipynb
- Pipeline: notebooks/04_Trodes_position.ipynb
- From Scratch: notebooks/05_DLC_from_scratch.ipynb
- From Pre-Trained: notebooks/06_DLC_from_dir.ipynb
- Linearization Pipeline: notebooks/07_linearization.ipynb
- Mark Indicators: notebooks/08_Extract_Mark_indicators.ipynb
- GPU: notebooks/09_Decoding_with_GPUs_on_the_GPU_cluster.ipynb
- 1D Clusterless Decoding: notebooks/10_1D_Clusterless_Decoding.ipynb
- 2D Clusterless Decoding: notebooks/11_2D_Clusterless_Decoding.ipynb
- Ripple Detection: notebooks/12_Ripple_Detection.ipynb
- Spyglass Kachery Setup: notebooks/Spyglass_kachery_setup.ipynb
- Data Sync: notebooks/02_Data_Sync.ipynb
- Ephys:
- Spike Sorting: notebooks/10_Spike_Sorting.ipynb
- Curation: notebooks/11_Curation.ipynb
- LFP: notebooks/12_LFP.ipynb
- Theta: notebooks/14_Theta.ipynb
- Position:
- Position Trodes: notebooks/20_Position_Trodes.ipynb
- Position DLC 1: notebooks/21_Position_DLC_1.ipynb
- Position DLC 2: notebooks/22_Position_DLC_2.ipynb
- Linearization: notebooks/24_Linearization.ipynb
- Combined:
- Ripple Detection: notebooks/30_Ripple_Detection.ipynb
- Extract Mark Indicators: notebooks/31_Extract_Mark_Indicators.ipynb
- Decoding with GPUs: notebooks/32_Decoding_with_GPUs.ipynb
- Decoding Clusterless: notebooks/33_Decoding_Clusterless.ipynb
- API Reference: api/ # defer to gen-files + literate-nav
- How to Contribute: contribute.md
- Change Log: CHANGELOG.md
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117 changes: 79 additions & 38 deletions notebooks/00_Setup.ipynb
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Expand Up @@ -231,19 +231,54 @@
"source": [
"### Loading the config\n",
"\n",
"We can check that the paths are correctly set up by loading the config.\n"
"We can check that the paths are correctly set up by loading the config from \n",
"the main Spyglass directory.\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"id": "912ac84b",
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"text/plain": [
"{'debug_mode': True,\n",
" 'prepopulate': True,\n",
" 'SPYGLASS_BASE_DIR': '/stelmo/nwb',\n",
" 'SPYGLASS_RAW_DIR': '/stelmo/nwb/raw',\n",
" 'SPYGLASS_ANALYSIS_DIR': '/stelmo/nwb/analysis',\n",
" 'SPYGLASS_RECORDING_DIR': '/stelmo/nwb/recording',\n",
" 'SPYGLASS_SORTING_DIR': '/stelmo/nwb/spikesorting',\n",
" 'SPYGLASS_WAVEFORMS_DIR': '/stelmo/nwb/waveforms',\n",
" 'SPYGLASS_TEMP_DIR': '/stelmo/nwb/tmp',\n",
" 'SPYGLASS_VIDEO_DIR': '/stelmo/nwb/video',\n",
" 'KACHERY_CLOUD_DIR': '/stelmo/nwb/kachery_storage',\n",
" 'KACHERY_STORAGE_DIR': '/stelmo/nwb/kachery_storage',\n",
" 'KACHERY_TEMP_DIR': '/stelmo/nwb/tmp',\n",
" 'KACHERY_ZONE': 'franklab.default',\n",
" 'FIGURL_CHANNEL': 'franklab2',\n",
" 'DJ_SUPPORT_FILEPATH_MANAGEMENT': 'TRUE',\n",
" 'KACHERY_CLOUD_EPHEMERAL': 'TRUE'}"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from spyglass.settings import load_config\n",
"import os\n",
"import datajoint as dj\n",
"\n",
"load_config()"
"if os.path.basename(os.getcwd()) == \"notebooks\":\n",
" os.chdir(\"..\")\n",
"dj.config.load(\"dj_local_conf.json\")\n",
"\n",
"from spyglass.settings import config\n",
"\n",
"config"
]
},
{
Expand All @@ -260,10 +295,32 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 2,
"id": "afb63913-4e6b-4049-ae1d-55ab1ac8d42c",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"[2023-09-28 08:07:06,176][INFO]: Connecting root@localhost:3307\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"[2023-09-28 08:07:06,254][INFO]: Connected root@localhost:3307\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Populate: Populating table DataAcquisitionDeviceSystem with data {'data_acquisition_device_system': 'SpikeGadgets'} using insert1.\n",
"Populate: Populating table DataAcquisitionDeviceAmplifier with data {'data_acquisition_device_amplifier': 'Intan'} using insert1.\n"
]
},
{
"data": {
"text/html": [
Expand Down Expand Up @@ -319,38 +376,14 @@
" }\n",
" </style>\n",
" \n",
" <b></b>\n",
" <b>Table for holding the NWB files.</b>\n",
" <div style=\"max-height:1000px;max-width:1500px;overflow:auto;\">\n",
" <table border=\"1\" class=\"Table\">\n",
" <thead> <tr style=\"text-align: right;\"> <th> <div class=\"djtooltip\">\n",
" <p id=\"primary\">nwb_file_name</p>\n",
" <span class=\"djtooltiptext\"></span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"primary\">sort_group_id</p>\n",
" <span class=\"djtooltiptext\"></span>\n",
" <span class=\"djtooltiptext\">name of the NWB file</span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"primary\">sort_interval_name</p>\n",
" <span class=\"djtooltiptext\"></span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"primary\">filter_parameter_set_name</p>\n",
" <span class=\"djtooltiptext\"></span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"primary\">sorter_name</p>\n",
" <span class=\"djtooltiptext\"></span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"primary\">spikesorter_parameter_set_name</p>\n",
" <span class=\"djtooltiptext\"></span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"nonprimary\">sorting_id</p>\n",
" <span class=\"djtooltiptext\"></span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"nonprimary\">analysis_file_name</p>\n",
" <span class=\"djtooltiptext\"></span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"nonprimary\">time_of_sort</p>\n",
" <span class=\"djtooltiptext\">in Unix time, to the nearest second</span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"nonprimary\">units_object_id</p>\n",
" <p id=\"nonprimary\">nwb_file_abs_path</p>\n",
" <span class=\"djtooltiptext\"></span>\n",
" </div> </th> </tr> </thead>\n",
" <tbody> <tr> </tr> </tbody>\n",
Expand All @@ -360,21 +393,29 @@
" "
],
"text/plain": [
"*nwb_file_name *sort_group_id *sort_interval *filter_parame *sorter_name *spikesorter_p sorting_id analysis_file_ time_of_sort units_object_i\n",
"+------------+ +------------+ +------------+ +------------+ +------------+ +------------+ +------------+ +------------+ +------------+ +------------+\n",
"*nwb_file_name nwb_file_a\n",
"+------------+ +--------+\n",
"\n",
" (Total: 0)"
]
},
"execution_count": 3,
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from spyglass.common import SpikeSortingBackUp\n",
"from spyglass.common import Nwbfile\n",
"\n",
"SpikeSortingBackUp()"
"Nwbfile()"
]
},
{
"cell_type": "markdown",
"id": "13fd64af",
"metadata": {},
"source": [
"# Up Next"
]
},
{
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