diff --git a/notebooks/10_Spike_SortingV0.ipynb b/notebooks/10_Spike_SortingV0.ipynb
index 5174c136b..4c9e50ff6 100644
--- a/notebooks/10_Spike_SortingV0.ipynb
+++ b/notebooks/10_Spike_SortingV0.ipynb
@@ -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",
@@ -109,19 +109,120 @@
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": 2,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ " \n",
+ " \n",
+ " \n",
+ " Information about lab member in the context of Frank lab network\n",
+ "
\n",
+ "
\n",
+ " | | | |
\n",
+ " Firstname Lastname | \n",
+ "example@gmail.com | \n",
+ "user | \n",
+ "0 |
\n",
+ "
\n",
+ " \n",
+ "
Total: 1
\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\", \"example@gmail.com\", \"user\"\n",
+ "# Full name, Google email address, DataJoint username, admin\n",
+ "name, email, dj_user, admin = (\n",
+ " \"Firstname Lastname\",\n",
+ " \"example@gmail.com\",\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()"
]
},
{
@@ -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",
@@ -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"
]
}
],
@@ -265,7 +356,7 @@
}
],
"source": [
- "sgs.v0.SortGroup().set_group_by_shank(nwb_file_name)"
+ "sgs.SortGroup().set_group_by_shank(nwb_file_name)"
]
},
{
@@ -423,7 +514,7 @@
}
],
"source": [
- "sgs.v0.SortGroup.SortGroupElectrode & {\"nwb_file_name\": nwb_file_name}"
+ "sgs.SortGroup.SortGroupElectrode & {\"nwb_file_name\": nwb_file_name}"
]
},
{
@@ -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",
@@ -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",
@@ -772,7 +863,7 @@
}
],
"source": [
- "sgs.v0.SpikeSortingPreprocessingParameters()"
+ "sgs.SpikeSortingPreprocessingParameters()"
]
},
{
@@ -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)"
@@ -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",
@@ -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"
]
},
{
@@ -1013,7 +1104,7 @@
},
{
"cell_type": "code",
- "execution_count": 38,
+ "execution_count": null,
"metadata": {},
"outputs": [
{
@@ -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])"
]
},
{
@@ -1160,7 +1251,7 @@
}
],
"source": [
- "sgs.v0.SpikeSortingRecording() & ssr_key"
+ "sgs.SpikeSortingRecording() & ssr_key"
]
},
{
@@ -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\""
]
},
@@ -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"
]
},
{
@@ -1333,7 +1424,7 @@
}
],
"source": [
- "sgs.v0.ArtifactDetection.populate(artifact_key)"
+ "sgs.ArtifactDetection.populate(artifact_key)"
]
},
{
@@ -1461,7 +1552,7 @@
}
],
"source": [
- "sgs.v0.ArtifactRemovedIntervalList() & artifact_key"
+ "sgs.ArtifactRemovedIntervalList() & artifact_key"
]
},
{
@@ -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)"
@@ -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",
@@ -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()"
]
@@ -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",
@@ -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)"
]
},
{
@@ -2267,7 +2358,7 @@
],
"source": [
"# [(sgs.SpikeSortingSelection & ss_key).proj()]\n",
- "sgs.v0.SpikeSorting.populate()"
+ "sgs.SpikeSorting.populate()"
]
},
{
@@ -2399,7 +2490,7 @@
}
],
"source": [
- "sgs.v0.SpikeSorting() & ss_key"
+ "sgs.SpikeSorting() & ss_key"
]
},
{
diff --git a/notebooks/10_Spike_SortingV1.ipynb b/notebooks/10_Spike_SortingV1.ipynb
index 451f0cd06..0c00fc498 100644
--- a/notebooks/10_Spike_SortingV1.ipynb
+++ b/notebooks/10_Spike_SortingV1.ipynb
@@ -47,7 +47,7 @@
"outputs": [],
"source": [
"import spyglass.common as sgc\n",
- "import spyglass.spikesorting as sgs\n",
+ "import spyglass.spikesorting.v1 as sgs\n",
"import spyglass.data_import as sgi"
]
},
@@ -115,7 +115,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.SortGroup.set_group_by_shank(nwb_file_name=nwb_file_name2)"
+ "sgs.SortGroup.set_group_by_shank(nwb_file_name=nwb_file_name2)"
]
},
{
@@ -149,7 +149,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.SpikeSortingRecordingSelection.insert_selection(key)"
+ "sgs.SpikeSortingRecordingSelection.insert_selection(key)"
]
},
{
@@ -159,7 +159,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.SpikeSortingRecordingSelection()"
+ "sgs.SpikeSortingRecordingSelection()"
]
},
{
@@ -177,7 +177,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.SpikeSortingRecording.populate()"
+ "sgs.SpikeSortingRecording.populate()"
]
},
{
@@ -187,7 +187,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.SpikeSortingRecording()"
+ "sgs.SpikeSortingRecording()"
]
},
{
@@ -198,7 +198,7 @@
"outputs": [],
"source": [
"key = (\n",
- " sgs.v1.SpikeSortingRecordingSelection & {\"nwb_file_name\": nwb_file_name2}\n",
+ " sgs.SpikeSortingRecordingSelection & {\"nwb_file_name\": nwb_file_name2}\n",
").fetch1()"
]
},
@@ -217,7 +217,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.ArtifactDetectionSelection.insert_selection(\n",
+ "sgs.ArtifactDetectionSelection.insert_selection(\n",
" {\"recording_id\": key[\"recording_id\"], \"artifact_param_name\": \"default\"}\n",
")"
]
@@ -237,7 +237,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.ArtifactDetection.populate()"
+ "sgs.ArtifactDetection.populate()"
]
},
{
@@ -247,7 +247,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.ArtifactDetection()"
+ "sgs.ArtifactDetection()"
]
},
{
@@ -286,7 +286,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.SpikeSortingSelection()"
+ "sgs.SpikeSortingSelection()"
]
},
{
@@ -296,7 +296,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.SpikeSortingSelection.insert_selection(key)"
+ "sgs.SpikeSortingSelection.insert_selection(key)"
]
},
{
@@ -306,7 +306,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.SpikeSortingSelection()"
+ "sgs.SpikeSortingSelection()"
]
},
{
@@ -324,7 +324,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.SpikeSorting.populate()"
+ "sgs.SpikeSorting.populate()"
]
},
{
@@ -334,7 +334,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.SpikeSorting()"
+ "sgs.SpikeSorting()"
]
},
{
@@ -352,7 +352,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.CurationV1.insert_curation(\n",
+ "sgs.CurationV1.insert_curation(\n",
" sorting_id=(\n",
" sgs.SpikeSortingSelection & {\"recording_id\": key[\"recording_id\"]}\n",
" ).fetch1(\"sorting_id\"),\n",
@@ -367,7 +367,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.CurationV1()"
+ "sgs.CurationV1()"
]
},
{
@@ -387,7 +387,7 @@
"source": [
"key = {\n",
" \"sorting_id\": (\n",
- " sgs.v1.SpikeSortingSelection & {\"recording_id\": key[\"recording_id\"]}\n",
+ " sgs.SpikeSortingSelection & {\"recording_id\": key[\"recording_id\"]}\n",
" ).fetch1(\"sorting_id\"),\n",
" \"curation_id\": 0,\n",
" \"waveform_param_name\": \"default_not_whitened\",\n",
@@ -403,7 +403,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.MetricCurationSelection.insert_selection(key)"
+ "sgs.MetricCurationSelection.insert_selection(key)"
]
},
{
@@ -413,7 +413,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.MetricCurationSelection()"
+ "sgs.MetricCurationSelection()"
]
},
{
@@ -423,7 +423,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.MetricCuration.populate()"
+ "sgs.MetricCuration.populate()"
]
},
{
@@ -433,7 +433,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.MetricCuration()"
+ "sgs.MetricCuration()"
]
},
{
@@ -453,7 +453,7 @@
"source": [
"key = {\n",
" \"metric_curation_id\": (\n",
- " sgs.v1.MetricCurationSelection & {\"sorting_id\": key[\"sorting_id\"]}\n",
+ " sgs.MetricCurationSelection & {\"sorting_id\": key[\"sorting_id\"]}\n",
" ).fetch1(\"metric_curation_id\")\n",
"}"
]
@@ -465,7 +465,7 @@
"metadata": {},
"outputs": [],
"source": [
- "labels = sgs.v1.MetricCuration.get_labels(key)"
+ "labels = sgs.MetricCuration.get_labels(key)"
]
},
{
@@ -475,7 +475,7 @@
"metadata": {},
"outputs": [],
"source": [
- "merge_groups = sgs.v1.MetricCuration.get_merge_groups(key)"
+ "merge_groups = sgs.MetricCuration.get_merge_groups(key)"
]
},
{
@@ -485,7 +485,7 @@
"metadata": {},
"outputs": [],
"source": [
- "metrics = sgs.v1.MetricCuration.get_metrics(key)"
+ "metrics = sgs.MetricCuration.get_metrics(key)"
]
},
{
@@ -495,9 +495,9 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.CurationV1.insert_curation(\n",
+ "sgs.CurationV1.insert_curation(\n",
" sorting_id=(\n",
- " sgs.v1.MetricCurationSelection\n",
+ " sgs.MetricCurationSelection\n",
" & {\"metric_curation_id\": key[\"metric_curation_id\"]}\n",
" ).fetch1(\"sorting_id\"),\n",
" parent_curation_id=0,\n",
@@ -515,7 +515,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.CurationV1()"
+ "sgs.CurationV1()"
]
},
{
@@ -533,7 +533,7 @@
"metadata": {},
"outputs": [],
"source": [
- "curation_uri = sgs.v1.FigURLCurationSelection.generate_curation_uri(\n",
+ "curation_uri = sgs.FigURLCurationSelection.generate_curation_uri(\n",
" {\n",
" \"sorting_id\": (\n",
" sgs.MetricCurationSelection\n",
@@ -553,7 +553,7 @@
"source": [
"key = {\n",
" \"sorting_id\": (\n",
- " sgs.v1.MetricCurationSelection\n",
+ " sgs.MetricCurationSelection\n",
" & {\"metric_curation_id\": key[\"metric_curation_id\"]}\n",
" ).fetch1(\"sorting_id\"),\n",
" \"curation_id\": 1,\n",
@@ -569,7 +569,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.FigURLCurationSelection()"
+ "sgs.FigURLCurationSelection()"
]
},
{
@@ -579,7 +579,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.FigURLCurationSelection.insert_selection(key)"
+ "sgs.FigURLCurationSelection.insert_selection(key)"
]
},
{
@@ -589,7 +589,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.FigURLCurationSelection()"
+ "sgs.FigURLCurationSelection()"
]
},
{
@@ -599,7 +599,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.FigURLCuration.populate()"
+ "sgs.FigURLCuration.populate()"
]
},
{
@@ -609,7 +609,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.FigURLCuration()"
+ "sgs.FigURLCuration()"
]
},
{
@@ -646,7 +646,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.FigURLCurationSelection.insert_selection(key)"
+ "sgs.FigURLCurationSelection.insert_selection(key)"
]
},
{
@@ -656,7 +656,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.FigURLCuration.populate()"
+ "sgs.FigURLCuration.populate()"
]
},
{
@@ -666,7 +666,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.FigURLCuration()"
+ "sgs.FigURLCuration()"
]
},
{
@@ -684,7 +684,7 @@
"metadata": {},
"outputs": [],
"source": [
- "labels = sgs.v1.FigURLCuration.get_labels(gh_curation_uri)"
+ "labels = sgs.FigURLCuration.get_labels(gh_curation_uri)"
]
},
{
@@ -694,7 +694,7 @@
"metadata": {},
"outputs": [],
"source": [
- "merge_groups = sgs.v1.FigURLCuration.get_merge_groups(gh_curation_uri)"
+ "merge_groups = sgs.FigURLCuration.get_merge_groups(gh_curation_uri)"
]
},
{
@@ -704,7 +704,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.CurationV1.insert_curation(\n",
+ "sgs.CurationV1.insert_curation(\n",
" sorting_id=key[\"sorting_id\"],\n",
" parent_curation_id=1,\n",
" labels=labels,\n",
@@ -721,7 +721,7 @@
"metadata": {},
"outputs": [],
"source": [
- "sgs.v1.CurationV1()"
+ "sgs.CurationV1()"
]
},
{