Last commit before updated oneData

(empty)
landoskape · Jun 22, 2023 · 70b7004 · 70b7004
1 parent b360faa
commit 70b7004
Showing 1 changed file with 79 additions and 12 deletions.
diff --git a/testingPipelineFunctions.ipynb b/testingPipelineFunctions.ipynb
@@ -56,27 +56,96 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 54,
+   "execution_count": 4,
+   "id": "266df662-bc89-4dc4-ad54-58669e96b403",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "mouseName = 'ATL020'\n",
+    "dateString = '2023-05-04'\n",
+    "session = '702'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "3232a21b-e0f7-43c3-99a2-d2b4b67d3530",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "In session: CR_Hippocannula6/2022-09-05/701, vrFile['rigInfo'] does not exist. Assuming default settings for B2!\n",
+      "In session CR_Hippocannula6/2022-09-05/701, the one file behave.timestamps.npy doesn't exist. Here is a list of saved oneData files:\n",
+      "lick.timelinesample\n",
+      "reward.timelinesample\n",
+      "timeline.rotaryposition\n",
+      "timeline.timestamps\n",
+      "trial.starttimes\n"
+     ]
+    },
+    {
+     "ename": "ValueError",
+     "evalue": "oneData requested is not available",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mValueError\u001b[0m                                Traceback (most recent call last)",
+      "Cell \u001b[1;32mIn[8], line 10\u001b[0m\n\u001b[0;32m      8\u001b[0m vrReg\u001b[38;5;241m.\u001b[39mprocessTimeline()\n\u001b[0;32m      9\u001b[0m \u001b[38;5;66;03m# vrReg.processBehavior()\u001b[39;00m\n\u001b[1;32m---> 10\u001b[0m \u001b[43mvrReg\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprocessImaging\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m     11\u001b[0m vrReg\u001b[38;5;241m.\u001b[39mprocessFacecam()\n",
+      "File \u001b[1;32m~\\Documents\\GitHub\\vrAnalysis\\vrExperiment.py:500\u001b[0m, in \u001b[0;36mvrExperimentRegistration.processImaging\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m    497\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mregisterValue(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msamplingDeviationMaximumPercentError\u001b[39m\u001b[38;5;124m'\u001b[39m,np\u001b[38;5;241m.\u001b[39mexp(np\u001b[38;5;241m.\u001b[39mmax(np\u001b[38;5;241m.\u001b[39mabs(np\u001b[38;5;241m.\u001b[39mlog(np\u001b[38;5;241m.\u001b[39mdiff(frame2time)\u001b[38;5;241m/\u001b[39mnp\u001b[38;5;241m.\u001b[39mmedian(np\u001b[38;5;241m.\u001b[39mdiff(frame2time)))))))\n\u001b[0;32m    499\u001b[0m \u001b[38;5;66;03m# compute translation mapping from behave frames to imaging frames\u001b[39;00m\n\u001b[1;32m--> 500\u001b[0m idxBehaveToFrame,distBehaveToFrame \u001b[38;5;241m=\u001b[39m bf\u001b[38;5;241m.\u001b[39mnearestpoint(\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mloadone\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mbehave.timestamps\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m, frame2time)\n\u001b[0;32m    502\u001b[0m \u001b[38;5;66;03m# recompute deconvolution if requested\u001b[39;00m\n\u001b[0;32m    503\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mopts[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124moasis\u001b[39m\u001b[38;5;124m'\u001b[39m]:\n",
+      "File \u001b[1;32m~\\Documents\\GitHub\\vrAnalysis\\vrExperiment.py:97\u001b[0m, in \u001b[0;36mvrExperiment.loadone\u001b[1;34m(self, force, *names)\u001b[0m\n\u001b[0;32m     95\u001b[0m     \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mIn session \u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msessionPrint()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, the one file \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mfileName\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m doesn\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mt exist. Here is a list of saved oneData files:\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m     96\u001b[0m     \u001b[38;5;28;01mfor\u001b[39;00m oneFile \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprintSavedOne(): \u001b[38;5;28mprint\u001b[39m(oneFile)\n\u001b[1;32m---> 97\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124moneData requested is not available\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m     98\u001b[0m oneVar \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mload(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39monePath() \u001b[38;5;241m/\u001b[39m fileName)\n\u001b[0;32m     99\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mloadBuffer[fileName] \u001b[38;5;241m=\u001b[39m oneVar\n",
+      "\u001b[1;31mValueError\u001b[0m: oneData requested is not available"
+     ]
+    }
+   ],
+   "source": [
+    "mouseName = 'CR_Hippocannula6'\n",
+    "dateString = '2022-09-05'\n",
+    "session = '701'\n",
+    "\n",
+    "# Test vrRegistration for CR_Hippocannula6\n",
+    "vrReg = vre.vrExperimentRegistration(mouseName, dateString, session, oasis=False, imaging=True)\n",
+    "\n",
+    "vrReg.processTimeline()\n",
+    "# vrReg.processBehavior()\n",
+    "vrReg.processImaging()\n",
+    "vrReg.processFacecam()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
    "id": "b546e957-03cd-48ca-98e8-70c1db297f51",
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "In session: ATL020/2023-05-04/702, vrFile['rigInfo'] does not exist. Assuming default settings for B2!\n",
-      "Self.value['numTrials'] set by trialInfo.trialIdx>0, but this might not be right. There might be smarter ways to determine which trials are 'good' trials...\n",
-      "frameSamples had 2 more than suite2p output. This happens sometimes. I don't like it. I think it's because scanimage sends a TTL before starting the frame\n",
-      "Facecam preprocessing has not been coded yet!\n",
-      "C:\\Users\\andrew\\Documents\\localData\\ATL020\\2023-05-04\\702\n"
+      "In session: CR_Hippocannula6/2022-09-05/701, vrFile['rigInfo'] does not exist. Assuming default settings for B2!\n"
+     ]
+    },
+    {
+     "ename": "KeyError",
+     "evalue": "'expInfo'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
+      "Cell \u001b[1;32mIn[7], line 3\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[38;5;66;03m# vrExperiment registration and preprocessing \u001b[39;00m\n\u001b[0;32m      2\u001b[0m vrReg \u001b[38;5;241m=\u001b[39m vre\u001b[38;5;241m.\u001b[39mvrExperimentRegistration(mouseName, dateString, session, oasis\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, imaging\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[1;32m----> 3\u001b[0m \u001b[43mvrReg\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdoPreprocessing\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m      4\u001b[0m vrReg\u001b[38;5;241m.\u001b[39msaveParams()\n\u001b[0;32m      5\u001b[0m \u001b[38;5;28mprint\u001b[39m(vrReg\u001b[38;5;241m.\u001b[39msessionPath())\n",
+      "File \u001b[1;32m~\\Documents\\GitHub\\vrAnalysis\\vrExperiment.py:271\u001b[0m, in \u001b[0;36mvrExperimentRegistration.doPreprocessing\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m    269\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdoPreprocessing\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[0;32m    270\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprocessTimeline()\n\u001b[1;32m--> 271\u001b[0m     \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mprocessBehavior\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m    272\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprocessImaging()\n\u001b[0;32m    273\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mprocessFacecam()\n",
+      "File \u001b[1;32m~\\Documents\\GitHub\\vrAnalysis\\vrExperiment.py:348\u001b[0m, in \u001b[0;36mvrExperimentRegistration.processBehavior\u001b[1;34m(self)\u001b[0m\n\u001b[0;32m    345\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mprocessBehavior\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[0;32m    346\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mopts[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mvrBehaviorVersion\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m!=\u001b[39m \u001b[38;5;241m1\u001b[39m: \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mHave not coded alternative vrBehavior outputs... \u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m--> 348\u001b[0m     expInfo \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mvrFile\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mexpInfo\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[0;32m    349\u001b[0m     trialInfo \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mvrFile[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mtrialInfo\u001b[39m\u001b[38;5;124m'\u001b[39m]\n\u001b[0;32m    350\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mregisterValue(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mnumTrials\u001b[39m\u001b[38;5;124m'\u001b[39m,np\u001b[38;5;241m.\u001b[39msum(trialInfo\u001b[38;5;241m.\u001b[39mtrialIdx\u001b[38;5;241m>\u001b[39m\u001b[38;5;241m0\u001b[39m))\n",
+      "\u001b[1;31mKeyError\u001b[0m: 'expInfo'"
      ]
     }
    ],
    "source": [
     "# vrExperiment registration and preprocessing \n",
-    "mouseName = 'ATL020'\n",
-    "dateString = '2023-05-04'\n",
-    "session = '702'\n",
     "vrReg = vre.vrExperimentRegistration(mouseName, dateString, session, oasis=False, imaging=True)\n",
     "vrReg.doPreprocessing()\n",
     "vrReg.saveParams()\n",
@@ -93,9 +162,7 @@
    },
    "outputs": [],
    "source": [
-    "mouseName = 'ATL020'\n",
-    "dateString = '2023-05-04'\n",
-    "session = '702'\n",
+    "# Load registered vrExperiment\n",
     "vrexp = vre.vrExperiment(mouseName, dateString, session)"
    ]
   },