More cnmf stuff

examples/cnmf.ipynb

@@ -2,34 +2,20 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "c0e29f1f-a33b-45ab-877a-29291bb5fd01",
    "metadata": {
     "tags": []
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "2023-06-11 07:34:01.073007: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.\n",
-      "2023-06-11 07:34:01.095009: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.\n",
-      "2023-06-11 07:34:01.095386: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.\n",
-      "To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.\n",
-      "2023-06-11 07:34:01.605728: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n",
-      "/home/kushal/repos/mesmerize-viz/mesmerize_viz/_mcorr.py:336: UserWarning: registration of accessor <class 'mesmerize_viz._mcorr.MCorrExtensionsViz'> under name 'mcorr' for type <class 'pandas.core.series.Series'> is overriding a preexisting attribute with the same name.\n",
-      "  @pd.api.extensions.register_series_accessor(\"mcorr\")\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from mesmerize_core import *\n",
     "from mesmerize_viz import *"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "326b9f89-7bcd-4b76-be74-9d1d84b96ca2",
    "metadata": {
     "tags": []
@@ -45,120 +31,75 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "id": "e95b0266-5056-48d0-9410-df0d6fdb151e",
+   "execution_count": null,
+   "id": "c5ba8e2e-e1ec-447c-8cdb-4e6b35680e11",
    "metadata": {
     "tags": []
    },
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/kushal/venvs/mescore/lib/python3.11/site-packages/ipydatagrid/datagrid.py:445: UserWarning: Index name of 'index' is not round-trippable.\n",
-      "  schema = pd.io.json.build_table_schema(dataframe)\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "cb892b243f1e4ff1b8d3bea0fe890e9c",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "RFBOutputContext()"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "8836f855be97406d8f2246bd5a1e932f",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "RFBOutputContext()"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Decode mmap filename /home/kushal/caiman_data/mesmerize-batch/b3503ab5-6376-4cd4-8c33-7f80735fca82/b3503ab5-6376-4cd4-8c33-7f80735fca82-Sue_2x_3000_40_-46_els__d1_170_d2_170_d3_1_order_F_frames_3000.mmap\n",
-      "Decode mmap filename /home/kushal/caiman_data/mesmerize-batch/b3503ab5-6376-4cd4-8c33-7f80735fca82/b3503ab5-6376-4cd4-8c33-7f80735fca82-Sue_2x_3000_40_-46_els__d1_170_d2_170_d3_1_order_F_frames_3000.mmap\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/kushal/repos/fastplotlib/fastplotlib/graphics/features/_base.py:34: UserWarning: converting float64 array to float32\n",
-      "  warn(f\"converting {array.dtype} array to float32\")\n",
-      "/home/kushal/repos/fastplotlib/fastplotlib/graphics/features/_base.py:123: UserWarning: Event handler <bound method GridPlotWrapper.set_frame_index of <mesmerize_viz._cnmf.GridPlotWrapper object at 0x7f10e7ca0190>> is already registered.\n",
-      "  warn(f\"Event handler {handler} is already registered.\")\n",
-      "/home/kushal/repos/fastplotlib/fastplotlib/graphics/features/_base.py:123: UserWarning: Event handler <bound method Interaction._event_handler of 'contours': LineCollection @ 0x7f10d8284590\n",
-      "Collection of <155> Graphics> is already registered.\n",
-      "  warn(f\"Event handler {handler} is already registered.\")\n",
-      "/home/kushal/repos/fastplotlib/fastplotlib/graphics/features/_base.py:123: UserWarning: Event handler <bound method Interaction._event_handler of 'contours': LineCollection @ 0x7f10c444c590\n",
-      "Collection of <155> Graphics> is already registered.\n",
-      "  warn(f\"Event handler {handler} is already registered.\")\n",
-      "/home/kushal/repos/fastplotlib/fastplotlib/graphics/features/_base.py:123: UserWarning: Event handler <bound method Interaction._event_handler of 'contours': LineCollection @ 0x7f10c41bc590\n",
-      "Collection of <155> Graphics> is already registered.\n",
-      "  warn(f\"Event handler {handler} is already registered.\")\n",
-      "/home/kushal/repos/fastplotlib/fastplotlib/graphics/features/_base.py:123: UserWarning: Event handler <bound method Interaction._event_handler of 'contours': LineCollection @ 0x7f10a453c590\n",
-      "Collection of <155> Graphics> is already registered.\n",
-      "  warn(f\"Event handler {handler} is already registered.\")\n",
-      "/home/kushal/repos/mesmerize-viz/mesmerize_viz/_cnmf.py:854: FutureWarning: You are trying to use the following experimental feature, this may change in the future without warning:\n",
-      "CaimanDataFrameExtensions.get_params_diffs\n",
-      "This feature is new and the might improve in the future\n",
-      "\n",
-      "  param_diffs = self._dataframe.caiman.get_params_diffs(\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "container_widget = df.cnmf.viz(start_index=1)"
+    "# optional\n",
+    "# %gui qt"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "id": "96636ad0-cde7-437d-a1ce-609287f6d005",
+   "execution_count": null,
+   "id": "914fb902-1476-4ba8-9b8e-85c338211fba",
    "metadata": {
     "tags": []
    },
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "19a4952086494afa9089e11a1bf2eace",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "VBox(children=(HBox(children=(DataGrid(auto_fit_params={'area': 'all', 'padding': 30, 'numCols': None}, base_r…"
-      ]
-     },
-     "execution_count": 4,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
+   "source": [
+    "viz = df.cnmf.viz(temporal_kwargs={\"add_residuals\": True})"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c0427b7d-b14b-4cfe-91af-d555c92e5557",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "viz.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "510b2710-744a-4e26-a485-e494d22fbd81",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "viz.cnmf_obj.estimates.idx_components"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "517e9e01-0f45-49b0-b1b7-ff0a9b3a03bb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "viz.cnmf_obj.estimates.idx_components_bad"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "78c3bcf5-7147-44cc-a9af-c8c0969b9940",
+   "metadata": {},
+   "outputs": [],
    "source": [
-    "container_widget.show()"
+    "df.iloc[1].cnmf.get_output().estimates.idx_components, df.iloc[1].cnmf.get_output().estimates.idx_components_bad"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2e0f395a-17c3-45ae-9fe6-adef0dd4ac44",
+   "id": "c32a7f90-6121-4e2e-8cd3-399cf0d5acd4",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -180,7 +121,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.3"
+   "version": "3.11.2"
   }
  },
  "nbformat": 4,