demo script cleanup

Author: Julie-Fabre

py_bombcell/demos/BC_demo_open_ephys.ipynb

@@ -252,6 +252,44 @@
     "pprint(param)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "##### Optionally, customize parameters (more on this later, below)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# you might to change:\n",
+    "\n",
+    "# 1. classification thresholds like: \n",
+    "# param[\"maxRPVviolations\"] = 0.1\n",
+    "\n",
+    "\n",
+    "#  2. or which quality metrics are computed (by default these are not): \n",
+    "param[\"computeDistanceMetrics\"] = 0\n",
+    "param[\"computeDrift\"] = 0\n",
+    "param[\"splitGoodAndMua_NonSomatic\"] = 0\n",
+    "\n",
+    "\n",
+    "#  3. how quality metricsa are calculated:\n",
+    "# a. how refractory period window is defined\n",
+    "param[\"tauR_valuesMin\"]= 0.5 / 1000  # minumum refractory period time (s), usually 0.002 s\n",
+    "param[\"tauR_valuesMax\"]= 5 / 1000  # maximum refractory period time (s)\n",
+    "param[\"tauR_valuesStep\"]= 0.5 / 1000  # if tauR_valuesMin and tauR_valuesMax are different, bombcell \n",
+    "# will calculate refractory period violations from param[\"tauR_valuesMin\"] to param[\"tauR_valuesMax\"] param[\"tauR_valuesStep\"] \n",
+    "# bins and determine the option window for each unit before calculating the violations. \n",
+    "        # tauR_valuesStep\n",
+    "#  b. or whether the recording is split into time chunks to detemrine \"good\" time chunks: \n",
+    "# param[\"computeTimeChunks\"] = 0\n",
+    "# full list in the wiki or in the bc.get_default_parameters function"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 9,
@@ -393,7 +431,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -801,7 +839,7 @@
     "# quality metric values\n",
     "quality_metrics_table = pd.DataFrame(quality_metrics)\n",
     "quality_metrics_table.insert(0, 'Bombcell_unit_type', unit_type_string)\n",
-    "quality_metrics_table"
+    "quality_metrics_table    "
    ]
   },
   {

py_bombcell/demos/BC_demo_spikeGLX.ipynb

@@ -252,6 +252,44 @@
     "pprint(param)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "##### Optionally, customize parameters (more on this later, below)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# you might to change:\n",
+    "\n",
+    "# 1. classification thresholds like: \n",
+    "# param[\"maxRPVviolations\"] = 0.1\n",
+    "\n",
+    "\n",
+    "#  2. or which quality metrics are computed (by default these are not): \n",
+    "param[\"computeDistanceMetrics\"] = 0\n",
+    "param[\"computeDrift\"] = 0\n",
+    "param[\"splitGoodAndMua_NonSomatic\"] = 0\n",
+    "\n",
+    "\n",
+    "#  3. how quality metricsa are calculated:\n",
+    "# a. how refractory period window is defined\n",
+    "param[\"tauR_valuesMin\"]= 0.5 / 1000  # minumum refractory period time (s), usually 0.002 s\n",
+    "param[\"tauR_valuesMax\"]= 5 / 1000  # maximum refractory period time (s)\n",
+    "param[\"tauR_valuesStep\"]= 0.5 / 1000  # if tauR_valuesMin and tauR_valuesMax are different, bombcell \n",
+    "# will calculate refractory period violations from param[\"tauR_valuesMin\"] to param[\"tauR_valuesMax\"] param[\"tauR_valuesStep\"] \n",
+    "# bins and determine the option window for each unit before calculating the violations. \n",
+    "        # tauR_valuesStep\n",
+    "#  b. or whether the recording is split into time chunks to detemrine \"good\" time chunks: \n",
+    "# param[\"computeTimeChunks\"] = 0\n",
+    "# full list in the wiki or in the bc.get_default_parameters function"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 9,

py_bombcell/demos/BC_demo_toy_data.ipynb

@@ -155,7 +155,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -252,6 +252,44 @@
     "pprint(param)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "##### Optionally, customize parameters (more on this later, below)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# you might to change:\n",
+    "\n",
+    "# 1. classification thresholds like: \n",
+    "# param[\"maxRPVviolations\"] = 0.1\n",
+    "\n",
+    "\n",
+    "#  2. or which quality metrics are computed (by default these are not): \n",
+    "param[\"computeDistanceMetrics\"] = 0\n",
+    "param[\"computeDrift\"] = 0\n",
+    "param[\"splitGoodAndMua_NonSomatic\"] = 0\n",
+    "\n",
+    "\n",
+    "#  3. how quality metricsa are calculated:\n",
+    "# a. how refractory period window is defined\n",
+    "param[\"tauR_valuesMin\"]= 0.5 / 1000  # minumum refractory period time (s), usually 0.002 s\n",
+    "param[\"tauR_valuesMax\"]= 5 / 1000  # maximum refractory period time (s)\n",
+    "param[\"tauR_valuesStep\"]= 0.5 / 1000  # if tauR_valuesMin and tauR_valuesMax are different, bombcell \n",
+    "# will calculate refractory period violations from param[\"tauR_valuesMin\"] to param[\"tauR_valuesMax\"] param[\"tauR_valuesStep\"] \n",
+    "# bins and determine the option window for each unit before calculating the violations. \n",
+    "        # tauR_valuesStep\n",
+    "#  b. or whether the recording is split into time chunks to detemrine \"good\" time chunks: \n",
+    "# param[\"computeTimeChunks\"] = 0\n",
+    "# full list in the wiki or in the bc.get_default_parameters function"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 5,

py_bombcell/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "bombcell"
-version = "0.69"
+version = "0.70"
 description = "Python port of bombcell. Automated quality control, curation and neuron classification of spike-sorted electrophysiology data."
 readme = "README.md"
 license = {text = "GPL-3.0"}