finished plotting adjacent frames

deisseroth-lab · Feb 15, 2021 · 32cc9d5 · 32cc9d5
1 parent 95e3050
commit 32cc9d5
Showing 1 changed file with 41 additions and 55 deletions.
diff --git a/notebooks/check_artefact_removal.ipynb b/notebooks/check_artefact_removal.ipynb
@@ -93,66 +93,52 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "['Index',\n",
-       " '__add__',\n",
-       " '__class__',\n",
-       " '__contains__',\n",
-       " '__delattr__',\n",
-       " '__dir__',\n",
-       " '__doc__',\n",
-       " '__eq__',\n",
-       " '__format__',\n",
-       " '__ge__',\n",
-       " '__getattribute__',\n",
-       " '__getitem__',\n",
-       " '__getnewargs__',\n",
-       " '__gt__',\n",
-       " '__hash__',\n",
-       " '__init__',\n",
-       " '__init_subclass__',\n",
-       " '__iter__',\n",
-       " '__le__',\n",
-       " '__len__',\n",
-       " '__lt__',\n",
-       " '__module__',\n",
-       " '__mul__',\n",
-       " '__ne__',\n",
-       " '__new__',\n",
-       " '__reduce__',\n",
-       " '__reduce_ex__',\n",
-       " '__repr__',\n",
-       " '__rmul__',\n",
-       " '__setattr__',\n",
-       " '__sizeof__',\n",
-       " '__slots__',\n",
-       " '__str__',\n",
-       " '__subclasshook__',\n",
-       " '_asdict',\n",
-       " '_fields',\n",
-       " '_fields_defaults',\n",
-       " '_make',\n",
-       " '_replace',\n",
-       " 'count',\n",
-       " 'frame',\n",
-       " 'index',\n",
-       " 'y_max',\n",
-       " 'y_min',\n",
-       " 'z_plane']"
-      ]
-     },
-     "execution_count": 21,
-     "metadata": {},
-     "output_type": "execute_result"
+     "ename": "NameError",
+     "evalue": "name 'artefact' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[1;32m<ipython-input-1-abc95ac08ef1>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[0mnsamples\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m5\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 2\u001b[1;33m \u001b[0msamples\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0martefact\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m:\u001b[0m\u001b[0mnsamples\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mreset_index\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      3\u001b[0m \u001b[0mncols\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;36m6\u001b[0m\u001b[1;33m;\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      4\u001b[0m _, axes = plt.subplots(nsamples, ncols, figsize=(5*ncols, 5*nsamples), \n\u001b[0;32m      5\u001b[0m                        \u001b[0msharex\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;32mTrue\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0msharey\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;32mTrue\u001b[0m\u001b[1;33m,\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
+      "\u001b[1;31mNameError\u001b[0m: name 'artefact' is not defined"
+     ]
     }
    ],
    "source": [
-    "dir(s)"
+    "nsamples = 5\n",
+    "samples = artefact[:nsamples].reset_index()\n",
+    "ncols = 6;\n",
+    "_, axes = plt.subplots(nsamples, ncols, figsize=(5*ncols, 5*nsamples), \n",
+    "                       sharex=True, sharey=True,\n",
+    "                       constrained_layout=True) \n",
+    "\n",
+    "for icol, ii in enumerate(range(-1,2)):\n",
+    "    axes[0][icol].set_title('Uncorrected: {}'.format(ii),fontsize=20)\n",
+    "    axes[0][icol+3].set_title('Corrected: {}'.format(ii),fontsize=20)\n",
+    "\n",
+    "\n",
+    "for row, s in enumerate(samples.itertuples()):\n",
+    "    axes[row][0].set_ylabel('Frame {} ,plane {}'.format(s.frame,s.z_plane), fontsize=20)\n",
+    "    for icol,ii in enumerate(range(-1,2)):\n",
+    "        axes[row][icol].imshow(uncorrected[s.frame+ii, s.z_plane],vmin=corrected[s.frame,s.z_plane].min(),vmax=corrected[s.frame,s.z_plane].max())\n",
+    "        axes[row][icol].axhline(s.y_min, c='r', lw=2)\n",
+    "        axes[row][icol].axhline(s.y_max, c='r', lw=2)\n",
+    "        axes[row][icol+3].imshow(corrected[s.frame+ii, s.z_plane],vmin=corrected[s.frame,s.z_plane].min(),vmax=corrected[s.frame,s.z_plane].max())\n",
+    "        axes[row][icol+3].axhline(s.y_min, c='r', lw=2)\n",
+    "        axes[row][icol+3].axhline(s.y_max, c='r', lw=2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plt.imshow(uncorrected[149,1])"
    ]
   }
  ],
@@ -172,7 +158,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.7.1"
   }
  },
  "nbformat": 4,