{"action":"created","comment":{"url":"https://api.github.com/repos/sagol-python-for-neuroscientists/hw5/pulls/comments/193382105","pull_request_review_id":126339055,"id":193382105,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDE5MzM4MjEwNQ==","diff_hunk":"@@ -6,32 +8,110 @@ class VisualStimData:\n     Data and methods for the visual stimulus ePhys experiment.\r\n     The data table itself is held in self.data, an `xarray` object.\r\n     Inputs:\r\n-        data: xr.DataArray or xr.Dataset\r\n-        ...\r\n+        data: xr.Dataset\r\n     Methods:\r\n-         ...\r\n+         plot_electrode(rep_number: int, id_number: int, elec_number: list):\r\n+             plots electrodes of single rat repetition\r\n+             rep_number - repetition number (1 to 4)\r\n+             id_number - rat id\r\n+             elec_number - electrode numbers, as list\r\n+         experimenter_bias()\r\n+             plots statistics for different experimenters\r\n     \"\"\"\r\n-    def __init__(self, data, ):\r\n-        pass\r\n+    def __init__(self, data):\r\n+        self.data = data\r\n \r\n-    def plot_electrode(self, rep_number: int, rat_id: int, elec_number: tuple=(0,)):\r\n+\r\n+    def plot_electrode(self, rep_number: int, id_number: int, elec_number: list):\r\n         \"\"\"\r\n         Plots the voltage of the electrodes in \"elec_number\" for the rat \"rat_id\" in the repetition\r\n         \"rep_number\". Shows a single figure with subplots.\r\n         \"\"\"\r\n-        pass\r\n+        fig = plt.figure()\r\n+        num_of_electrods = len(elec_number)\r\n+        xplots = np.ceil(np.sqrt(num_of_electrods))\r\n+        yplots = np.round(np.sqrt(num_of_electrods))\r\n+        ymin = self.data.measurements.data.min()\r\n+        ymax = self.data.measurements.data.max()\r\n+        subplot_counter = 0\r\n+        for i in elec_number:\r\n+            subplot_counter += 1\r\n+            ax = fig.add_subplot(xplots,yplots,subplot_counter)\r\n+            ax.plot(self.data.time.data,\r\n+                    self.data.measurements[dict(rat_id=id_number,\r\n+                                                repetition=rep_number,\r\n+                                                electrode=i)].data)\r\n+            ax.set_ylim([ymin,ymax])\r\n+            ax.set_xlim([0,2000])\r\n+            ax.yaxis.set_label_text('Voltage [mV]')\r\n+            ax.xaxis.set_label_text('Time [ms]')\r\n+            plt.tight_layout()\r\n+            ax.set_title('Electrode# '+str(i))\r\n+        \r\n+        fig.suptitle('Rat ID: ' + str(id_number) + ', repetition #' + str(rep_number))\r\n+        fig.tight_layout(rect=[0, 0.03, 1, 0.95])\r\n+            \r\n \r\n     def experimenter_bias(self):\r\n         \"\"\" Shows the statistics of the average recording across all experimenters \"\"\"\r\n-        pass\r\n+        experimenters = list(set(self.data.experimenter.data.tolist()))\r\n+        mean = np.ndarray(0)\r\n+        std = np.ndarray(0)\r\n+        median = np.ndarray(0)\r\n+        for e in experimenters:\r\n+            idx = [i for i, s in enumerate(list(self.data.experimenter.data)) if e==s]\r\n+            mean = np.append(mean,self.data.measurements.data[:,idx,:,:].mean())\r\n+            std = np.append(std,self.data.measurements.data[:,idx,:,:].std())\r\n+            median = np.append(median,np.median(self.data.measurements.data[:,idx,:,:]))\r\n+        \r\n+        fig,ax = plt.subplots(1)\r\n+        ax.set_ylim([0,-110])\r\n+        w = 0.35\r\n+        t = np.arange(len(experimenters))\r\n+        ax.bar(t,mean,w)\r\n+        ax.errorbar(t,mean,yerr=std,fmt='none',ecolor='black')\r\n+        ax.bar(t+w,median,w)\r\n+        ax.set_xticks(t+w/2)\r\n+        ax.set_xticklabels(experimenters)\r\n+        ax.legend(('Mean voltage','Voltage st. dev.','Median voltage'),loc='best')\r\n+        ax.yaxis.set_label_text('Voltage [mV]')\r\n+        ax.xaxis.set_label_text('Experimenter')\r\n+        ax.set_title('Experimenter statistics')\r\n+        \r\n+            \r\n+            \r\n+            \r\n \r\n \r\n-def mock_stim_data() -> VisualStimData:\r\n+def mock_stim_data(num_of_rats: int=5) -> VisualStimData:\r\n     \"\"\" Creates a new VisualStimData instance with mock data \"\"\"\r\n-    pass\r\n+    rat_id = np.linspace(1,num_of_rats,num_of_rats,dtype=int)\r\n+    experimenter_list = ['Jon','Robb','Sansa','Arya','Bran','Rickon']\r\n+    gender_list = ['F','M']\r\n+    np.random.normal(25,2,num_of_rats)\r\n+    experimenter = [experimenter_list[np.random.randint(0,len(experimenter_list))] \\\r\n+                          for i in range(num_of_rats)]\r\n+    gender = [gender_list[np.random.randint(0,len(gender_list))] \\\r\n+                          for i in range(num_of_rats)]\r\n+    temperature = np.random.normal(25,2,num_of_rats)\r\n+    humidity = np.random.random(num_of_rats)\r\n+    time=np.linspace(2000,0,10000,endpoint=False)[::-1]\r\n+    measurements = np.random.normal(-70,10,(num_of_rats,10000,4,10))\r\n+    stim_index = np.concatenate((np.tile(0,5000),np.tile(1,500),np.tile(2,4500)))\r\n+    repetition = np.linspace(1,4,4,dtype=int)\r\n+    electrode = np.linspace(1,10,10,dtype=int)\r","path":"visual_stim_data.py","position":111,"original_position":111,"commit_id":"813c84270a6dfd25e43f8c7be46a22353169613c","original_commit_id":"813c84270a6dfd25e43f8c7be46a22353169613c","user":{"login":"HagaiHargil","id":17546299,"node_id":"MDQ6VXNlcjE3NTQ2Mjk5","avatar_url":"https://avatars3.githubusercontent.com/u/17546299?v=4","gravatar_id":"","url":"https://api.github.com/users/HagaiHargil","html_url":"https://github.com/HagaiHargil","followers_url":"https://api.github.com/users/HagaiHargil/followers","following_url":"https://api.github.com/users/HagaiHargil/following{/other_user}","gists_url":"https://api.github.com/users/HagaiHargil/gists{/gist_id}","starred_url":"https://api.github.com/users/HagaiHargil/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/HagaiHargil/subscriptions","organizations_url":"https://api.github.com/users/HagaiHargil/orgs","repos_url":"https://api.github.com/users/HagaiHargil/repos","events_url":"https://api.github.com/users/HagaiHargil/events{/privacy}","received_events_url":"https://api.github.com/users/HagaiHargil/received_events","type":"User","site_admin":false},"body":"You 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