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Fix versioning
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@edeno
edeno committed Jan 27, 2024
1 parent af463e4 commit e566e3e
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Showing 2 changed files with 185 additions and 94 deletions.
193 changes: 142 additions & 51 deletions notebooks/10_Spike_SortingV0.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@
"dj.config.load(\"dj_local_conf.json\") # load config for database connection info\n",
"\n",
"import spyglass.common as sgc\n",
"import spyglass.spikesorting as sgs\n",
"import spyglass.spikesorting.v0 as sgs\n",
"\n",
"# ignore datajoint+jupyter async warnings\n",
"import warnings\n",
Expand All @@ -109,19 +109,120 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 2,
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"text/html": [
"\n",
" \n",
" <style type=\"text/css\">\n",
" .Table{\n",
" border-collapse:collapse;\n",
" }\n",
" .Table th{\n",
" background: #A0A0A0; color: #ffffff; padding:4px; border:#f0e0e0 1px solid;\n",
" font-weight: normal; font-family: monospace; font-size: 100%;\n",
" }\n",
" .Table td{\n",
" padding:4px; border:#f0e0e0 1px solid; font-size:100%;\n",
" }\n",
" .Table tr:nth-child(odd){\n",
" background: #ffffff;\n",
" color: #000000;\n",
" }\n",
" .Table tr:nth-child(even){\n",
" background: #f3f1ff;\n",
" color: #000000;\n",
" }\n",
" /* Tooltip container */\n",
" .djtooltip {\n",
" }\n",
" /* Tooltip text */\n",
" .djtooltip .djtooltiptext {\n",
" visibility: hidden;\n",
" width: 120px;\n",
" background-color: black;\n",
" color: #fff;\n",
" text-align: center;\n",
" padding: 5px 0;\n",
" border-radius: 6px;\n",
" /* Position the tooltip text - see examples below! */\n",
" position: absolute;\n",
" z-index: 1;\n",
" }\n",
" #primary {\n",
" font-weight: bold;\n",
" color: black;\n",
" }\n",
" #nonprimary {\n",
" font-weight: normal;\n",
" color: white;\n",
" }\n",
"\n",
" /* Show the tooltip text when you mouse over the tooltip container */\n",
" .djtooltip:hover .djtooltiptext {\n",
" visibility: visible;\n",
" }\n",
" </style>\n",
" \n",
" <b>Information about lab member in the context of Frank lab network</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\">lab_member_name</p>\n",
" <span class=\"djtooltiptext\"></span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"nonprimary\">google_user_name</p>\n",
" <span class=\"djtooltiptext\">For permission to curate</span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"nonprimary\">datajoint_user_name</p>\n",
" <span class=\"djtooltiptext\">For permission to delete</span>\n",
" </div></th><th><div class=\"djtooltip\">\n",
" <p id=\"nonprimary\">admin</p>\n",
" <span class=\"djtooltiptext\">Ignore permission checks</span>\n",
" </div> </th> </tr> </thead>\n",
" <tbody> <tr> <td>Firstname Lastname</td>\n",
"<td>[email protected]</td>\n",
"<td>user</td>\n",
"<td>0</td> </tr> </tbody>\n",
" </table>\n",
" \n",
" <p>Total: 1</p></div>\n",
" "
],
"text/plain": [
"*lab_member_na google_user_na datajoint_user admin \n",
"+------------+ +------------+ +------------+ +-------+\n",
"Firstname Last example@gmail. user 0 \n",
" (Total: 1)"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"name, email, dj_user = \"Firstname Lastname\", \"[email protected]\", \"user\"\n",
"# Full name, Google email address, DataJoint username, admin\n",
"name, email, dj_user, admin = (\n",
" \"Firstname Lastname\",\n",
" \"[email protected]\",\n",
" \"user\",\n",
" 0,\n",
")\n",
"sgc.LabMember.insert_from_name(name)\n",
"sgc.LabMember.LabMemberInfo.insert1(\n",
" [name, email, dj_user], skip_duplicates=True\n",
")\n",
"sgc.LabTeam.LabTeamMember.insert1(\n",
" {\"team_name\": \"My Team\", \"lab_member_name\": name},\n",
" [\n",
" name,\n",
" email,\n",
" dj_user,\n",
" admin,\n",
" ],\n",
" skip_duplicates=True,\n",
")"
")\n",
"sgc.LabMember.LabMemberInfo()"
]
},
{
Expand All @@ -137,17 +238,9 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"You made it in!\n"
]
}
],
"outputs": [],
"source": [
"my_team_members = (\n",
" (sgc.LabTeam.LabTeamMember & {\"team_name\": \"My Team\"})\n",
Expand Down Expand Up @@ -206,8 +299,6 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/home/cb/wrk/spyglass/src/spyglass/data_import/insert_sessions.py:41: UserWarning: Cannot insert data from minirec20230622.nwb: minirec20230622_.nwbis already in Nwbfile table.\n",
" warnings.warn(\n"
]
}
],
Expand Down Expand Up @@ -265,7 +356,7 @@
}
],
"source": [
"sgs.v0.SortGroup().set_group_by_shank(nwb_file_name)"
"sgs.SortGroup().set_group_by_shank(nwb_file_name)"
]
},
{
Expand Down Expand Up @@ -423,7 +514,7 @@
}
],
"source": [
"sgs.v0.SortGroup.SortGroupElectrode & {\"nwb_file_name\": nwb_file_name}"
"sgs.SortGroup.SortGroupElectrode & {\"nwb_file_name\": nwb_file_name}"
]
},
{
Expand Down Expand Up @@ -625,7 +716,7 @@
"metadata": {},
"outputs": [],
"source": [
"sgs.v0.SortInterval.insert1(\n",
"sgs.SortInterval.insert1(\n",
" {\n",
" \"nwb_file_name\": nwb_file_name,\n",
" \"sort_interval_name\": sort_interval_name,\n",
Expand Down Expand Up @@ -658,7 +749,7 @@
"source": [
"print_interval_duration(\n",
" (\n",
" sgs.v0.SortInterval\n",
" sgs.SortInterval\n",
" & {\n",
" \"nwb_file_name\": nwb_file_name,\n",
" \"sort_interval_name\": sort_interval_name,\n",
Expand Down Expand Up @@ -772,7 +863,7 @@
}
],
"source": [
"sgs.v0.SpikeSortingPreprocessingParameters()"
"sgs.SpikeSortingPreprocessingParameters()"
]
},
{
Expand All @@ -796,9 +887,9 @@
}
],
"source": [
"sgs.v0.SpikeSortingPreprocessingParameters().insert_default()\n",
"sgs.SpikeSortingPreprocessingParameters().insert_default()\n",
"preproc_params = (\n",
" sgs.v0.SpikeSortingPreprocessingParameters()\n",
" sgs.SpikeSortingPreprocessingParameters()\n",
" & {\"preproc_params_name\": \"default\"}\n",
").fetch1(\"preproc_params\")\n",
"print(preproc_params)"
Expand All @@ -819,7 +910,7 @@
"outputs": [],
"source": [
"preproc_params[\"frequency_min\"] = 600\n",
"sgs.v0.SpikeSortingPreprocessingParameters().insert1(\n",
"sgs.SpikeSortingPreprocessingParameters().insert1(\n",
" {\n",
" \"preproc_params_name\": \"default_hippocampus\",\n",
" \"preproc_params\": preproc_params,\n",
Expand Down Expand Up @@ -991,8 +1082,8 @@
}
],
"source": [
"sgs.v0.SpikeSortingRecordingSelection.insert1(ssr_key, skip_duplicates=True)\n",
"sgs.v0.SpikeSortingRecordingSelection() & ssr_key"
"sgs.SpikeSortingRecordingSelection.insert1(ssr_key, skip_duplicates=True)\n",
"sgs.SpikeSortingRecordingSelection() & ssr_key"
]
},
{
Expand All @@ -1013,7 +1104,7 @@
},
{
"cell_type": "code",
"execution_count": 38,
"execution_count": null,
"metadata": {},
"outputs": [
{
Expand All @@ -1039,8 +1130,8 @@
}
],
"source": [
"ssr_pk = (sgs.v0.SpikeSortingRecordingSelection & ssr_key).proj()\n",
"sgs.v0.SpikeSortingRecording.populate([ssr_pk])"
"ssr_pk = (sgs.SpikeSortingRecordingSelection & ssr_key).proj()\n",
"sgs.SpikeSortingRecording.populate([ssr_pk])"
]
},
{
Expand Down Expand Up @@ -1160,7 +1251,7 @@
}
],
"source": [
"sgs.v0.SpikeSortingRecording() & ssr_key"
"sgs.SpikeSortingRecording() & ssr_key"
]
},
{
Expand All @@ -1183,8 +1274,8 @@
"metadata": {},
"outputs": [],
"source": [
"sgs.v0.ArtifactDetectionParameters().insert_default()\n",
"artifact_key = (sgs.v0.SpikeSortingRecording() & ssr_key).fetch1(\"KEY\")\n",
"sgs.ArtifactDetectionParameters().insert_default()\n",
"artifact_key = (sgs.SpikeSortingRecording() & ssr_key).fetch1(\"KEY\")\n",
"artifact_key[\"artifact_params_name\"] = \"none\""
]
},
Expand Down Expand Up @@ -1307,8 +1398,8 @@
}
],
"source": [
"sgs.v0.ArtifactDetectionSelection().insert1(artifact_key)\n",
"sgs.v0.ArtifactDetectionSelection() & artifact_key"
"sgs.ArtifactDetectionSelection().insert1(artifact_key)\n",
"sgs.ArtifactDetectionSelection() & artifact_key"
]
},
{
Expand All @@ -1333,7 +1424,7 @@
}
],
"source": [
"sgs.v0.ArtifactDetection.populate(artifact_key)"
"sgs.ArtifactDetection.populate(artifact_key)"
]
},
{
Expand Down Expand Up @@ -1461,7 +1552,7 @@
}
],
"source": [
"sgs.v0.ArtifactRemovedIntervalList() & artifact_key"
"sgs.ArtifactRemovedIntervalList() & artifact_key"
]
},
{
Expand Down Expand Up @@ -1494,12 +1585,12 @@
}
],
"source": [
"sgs.v0.SpikeSorterParameters().insert_default()\n",
"sgs.SpikeSorterParameters().insert_default()\n",
"\n",
"# Let's look at the default params\n",
"sorter_name = \"mountainsort4\"\n",
"ms4_default_params = (\n",
" sgs.v0.SpikeSorterParameters\n",
" sgs.SpikeSorterParameters\n",
" & {\"sorter\": sorter_name, \"sorter_params_name\": \"default\"}\n",
").fetch1()\n",
"print(ms4_default_params)"
Expand Down Expand Up @@ -1599,7 +1690,7 @@
],
"source": [
"sorter_params_name = \"hippocampus_tutorial\"\n",
"sgs.v0.SpikeSorterParameters.insert1(\n",
"sgs.SpikeSorterParameters.insert1(\n",
" {\n",
" \"sorter\": sorter_name,\n",
" \"sorter_params_name\": sorter_params_name,\n",
Expand All @@ -1608,7 +1699,7 @@
" skip_duplicates=True,\n",
")\n",
"(\n",
" sgs.v0.SpikeSorterParameters\n",
" sgs.SpikeSorterParameters\n",
" & {\"sorter\": sorter_name, \"sorter_params_name\": sorter_params_name}\n",
").fetch1()"
]
Expand Down Expand Up @@ -1652,8 +1743,8 @@
],
"source": [
"ss_key = dict(\n",
" **(sgs.v0.ArtifactDetection & ssr_key).fetch1(\"KEY\"),\n",
" **(sgs.v0.ArtifactRemovedIntervalList() & ssr_key).fetch1(\"KEY\"),\n",
" **(sgs.ArtifactDetection & ssr_key).fetch1(\"KEY\"),\n",
" **(sgs.ArtifactRemovedIntervalList() & ssr_key).fetch1(\"KEY\"),\n",
" sorter=sorter_name,\n",
" sorter_params_name=sorter_params_name,\n",
")\n",
Expand Down Expand Up @@ -1779,8 +1870,8 @@
}
],
"source": [
"sgs.v0.SpikeSortingSelection.insert1(ss_key, skip_duplicates=True)\n",
"(sgs.v0.SpikeSortingSelection & ss_key)"
"sgs.SpikeSortingSelection.insert1(ss_key, skip_duplicates=True)\n",
"(sgs.SpikeSortingSelection & ss_key)"
]
},
{
Expand Down Expand Up @@ -2267,7 +2358,7 @@
],
"source": [
"# [(sgs.SpikeSortingSelection & ss_key).proj()]\n",
"sgs.v0.SpikeSorting.populate()"
"sgs.SpikeSorting.populate()"
]
},
{
Expand Down Expand Up @@ -2399,7 +2490,7 @@
}
],
"source": [
"sgs.v0.SpikeSorting() & ss_key"
"sgs.SpikeSorting() & ss_key"
]
},
{
Expand Down
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