Merge branch 'master' of https://github.com/LorenFrankLab/spyglass

CBroz1 · Jul 28, 2023 · 15d1369 · 15d1369
2 parents 5d66f25 + f4cc73d
commit 15d1369
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Showing 16 changed files with 2,981 additions and 1,586 deletions.
diff --git a/examples/db_alter.ipynb b/examples/db_alter.ipynb
diff --git a/notebooks/03_lfp.ipynb b/notebooks/03_lfp.ipynb
@@ -16,6 +16,24 @@
     "#### First, we select the NWB file, which corresponds to the dataset we want to extract LFP from"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import copy\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import os\n",
+    "import pandas as pd\n",
+    "from spyglass.common import Electrode, BrainRegion, FirFilterParameters, IntervalList, Raw, get_electrode_indices\n",
+    "from spyglass.lfp import LFPOutput\n",
+    "from spyglass.lfp.lfp_electrode import LFPElectrodeGroup\n",
+    "from spyglass.lfp.v1 import LFPV1, LFPSelection\n",
+    "from spyglass.lfp.analysis.v1.lfp_band import LFPBandV1, LFPBandSelection"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -33,8 +51,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import os\n",
-    "\n",
     "os.environ[\"SPYGLASS_BASE_DIR\"] = \"/stelmo/nwb\"\n",
     "os.environ[\"DJ_SUPPORT_FILEPATH_MANAGEMENT\"] = \"TRUE\""
    ]
@@ -324,8 +340,6 @@
     }
    ],
    "source": [
-    "from spyglass.common import FirFilterParameters\n",
-    "\n",
     "FirFilterParameters().create_standard_filters()\n",
     "FirFilterParameters()"
    ]
@@ -465,9 +479,6 @@
     }
    ],
    "source": [
-    "from spyglass.common import Electrode, BrainRegion\n",
-    "import pandas as pd\n",
-    "\n",
     "electrodes_df = (\n",
     "    pd.DataFrame(\n",
     "        (Electrode & {\"nwb_file_name\": nwb_file_name, \"probe_electrode\": 0})\n",
@@ -493,8 +504,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from spyglass.lfp.v1 import LFPElectrodeGroup\n",
-    "\n",
     "lfp_electrode_ids = electrodes_df.loc[\n",
     "    electrodes_df.region_name == \"ca1\"\n",
     "].electrode_id\n",
@@ -815,9 +824,6 @@
     }
    ],
    "source": [
-    "from spyglass.common import IntervalList\n",
-    "\n",
-    "\n",
     "pd.DataFrame(IntervalList & {\"nwb_file_name\": nwb_file_name})"
    ]
   },
@@ -827,9 +833,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
-    "\n",
-    "\n",
     "orig_interval_list_name = \"02_r1\"\n",
     "valid_times = (\n",
     "    IntervalList\n",
@@ -963,9 +966,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import copy\n",
-    "from spyglass.lfp.v1 import LFPSelection\n",
-    "\n",
     "filter_name = \"LFP 0-400 Hz\"\n",
     "filter_sampling_rate = 30_000\n",
     "\n",
@@ -1121,8 +1121,6 @@
    },
    "outputs": [],
    "source": [
-    "from spyglass.lfp.v1 import LFPV1\n",
-    "\n",
     "LFPV1().populate(lfp_s_key)"
    ]
   },
@@ -1238,8 +1236,6 @@
     }
    ],
    "source": [
-    "from spyglass.lfp import LFPOutput\n",
-    "\n",
     "LFPOutput.LFPV1() & lfp_s_key"
    ]
   },
@@ -1889,8 +1885,6 @@
     }
    ],
    "source": [
-    "from spyglass.common.common_filter import FirFilterParameters\n",
-    "\n",
     "lfp_sampling_rate = LFPOutput.merge_get_parent(lfp_key).fetch1(\n",
     "    \"lfp_sampling_rate\"\n",
     ")\n",
@@ -2024,8 +2018,6 @@
     }
    ],
    "source": [
-    "from spyglass.lfp_band.v1.lfp_band import LFPBandSelection\n",
-    "\n",
     "# assume that we've filtered these electrodes; change this if not\n",
     "lfp_band_electrode_ids = [28, 32]\n",
     "\n",
@@ -2366,8 +2358,6 @@
     }
    ],
    "source": [
-    "from spyglass.lfp_band.v1 import LFPBandV1\n",
-    "\n",
     "LFPBandV1().populate(LFPBandSelection() & lfp_band_key)\n",
     "LFPBandV1()"
    ]
@@ -2382,15 +2372,7 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 24,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import matplotlib.pyplot as plt"
-   ]
-  },
-  {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -2428,9 +2410,6 @@
     }
    ],
    "source": [
-    "from spyglass.common import Raw, get_electrode_indices\n",
-    "\n",
-    "\n",
     "orig_eseries = (Raw() & {\"nwb_file_name\": nwb_file_name}).fetch_nwb()[0][\"raw\"]\n",
     "orig_elect_indices = get_electrode_indices(orig_eseries, lfp_band_electrode_ids)\n",
     "orig_timestamps = np.asarray(orig_eseries.timestamps)"
@@ -2453,16 +2432,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from spyglass.lfp_band import LFPBandOutput\n",
-    "\n",
-    "lfp_band_eseries = LFPBandOutput.fetch_nwb(lfp_band_key)[0][\"lfp_band\"]\n",
+    "lfp_band_eseries = (LFPBandV1 & lfp_band_key).fetch_nwb()[0][\"lfp_band\"]\n",
     "lfp_band_elect_indices = get_electrode_indices(\n",
     "    lfp_band_eseries, lfp_band_electrode_ids\n",
     ")\n",
     "lfp_band_timestamps = np.asarray(lfp_band_eseries.timestamps)"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [