update statistics

actions/calculate-statistics/data/10_calculate_spatial_statistics.html

@@ -13173,7 +13173,7 @@ div#notebook {
 
 
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-<pre>14:03:52 [I] klustakwik KlustaKwik2 version 0.2.6
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-<div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
+<div class="prompt input_prompt">In&nbsp;[7]:</div>
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 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">data_loader</span> <span class="o">=</span> <span class="n">dp</span><span class="o">.</span><span class="n">Data</span><span class="p">(</span>
@@ -13378,7 +13378,7 @@ div#notebook {
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-<div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
+<div class="prompt input_prompt">In&nbsp;[8]:</div>
 <div class="inner_cell">
     <div class="input_area">
 <div class=" highlight hl-ipython3"><pre><span></span><span class="n">first_row</span> <span class="o">=</span> <span class="n">units</span><span class="p">[</span><span class="n">units</span><span class="p">[</span><span class="s1">&#39;action&#39;</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;1849-060319-3&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
@@ -13473,6 +13473,8 @@ div#notebook {
 
     <span class="n">information_rate</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">information_rate</span><span class="p">(</span><span class="n">smooth_high_rate_map</span><span class="p">,</span> <span class="n">prob_dist</span><span class="p">)</span>
     
+    <span class="n">information_spec</span> <span class="o">=</span> <span class="n">stats</span><span class="o">.</span><span class="n">information_specificity</span><span class="p">(</span><span class="n">smooth_high_rate_map</span><span class="p">,</span> <span class="n">prob_dist</span><span class="p">)</span>
+
     <span class="n">single_spikes</span><span class="p">,</span> <span class="n">bursts</span><span class="p">,</span> <span class="n">bursty_spikes</span> <span class="o">=</span> <span class="n">spikes</span><span class="o">.</span><span class="n">find_bursts</span><span class="p">(</span><span class="n">spike_times</span><span class="p">,</span> <span class="n">threshold</span><span class="o">=</span><span class="mf">0.01</span><span class="p">)</span>
     <span class="n">burst_event_ratio</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">bursts</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">single_spikes</span><span class="p">)</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">bursts</span><span class="p">))</span>
     <span class="n">bursty_spike_ratio</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">bursty_spikes</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">bursty_spikes</span><span class="p">)</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">single_spikes</span><span class="p">))</span>
@@ -13500,6 +13502,7 @@ div#notebook {
         <span class="s1">&#39;gridness&#39;</span><span class="p">:</span> <span class="n">gridness</span><span class="p">,</span>
         <span class="s1">&#39;border_score&#39;</span><span class="p">:</span> <span class="n">border_score</span><span class="p">,</span>
         <span class="s1">&#39;information_rate&#39;</span><span class="p">:</span> <span class="n">information_rate</span><span class="p">,</span>
+        <span class="s1">&#39;information_specificity&#39;</span><span class="p">:</span> <span class="n">information_spec</span><span class="p">,</span>
         <span class="s1">&#39;head_mean_ang&#39;</span><span class="p">:</span> <span class="n">head_mean_ang</span><span class="p">,</span>
         <span class="s1">&#39;head_mean_vec_len&#39;</span><span class="p">:</span> <span class="n">head_mean_vec_len</span><span class="p">,</span>
         <span class="s1">&#39;spacing&#39;</span><span class="p">:</span> <span class="n">spacing</span><span class="p">,</span>
@@ -13552,6 +13555,7 @@ bursty_spike_ratio         0.676486
 gridness                   -0.459487
 border_score                0.078474
 information_rate            0.965845
+information_specificity     0.309723
 head_mean_ang               5.788704
 head_mean_vec_len           0.043321
 spacing                     0.624971
@@ -13593,13 +13597,13 @@ dtype: float64</pre>
 
  
  
-<div id="2b4825d6-9766-4260-96f8-a8462ab148ed"></div>
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@@ -13629,7 +13633,6 @@ var element = $('#2b4825d6-9766-4260-96f8-a8462ab148ed');
   ret = ret.dtype.type(ret / rcount)
 /home/mikkel/.virtualenvs/expipe/lib/python3.6/site-packages/quantities/quantity.py:624: RuntimeWarning: Mean of empty slice.
   ret = self.magnitude.mean(axis, dtype, None if out is None else out.magnitude)
-/home/mikkel/.virtualenvs/expipe/lib/python3.6/site-packages/ipykernel_launcher.py:82: RuntimeWarning: invalid value encountered in long_scalars
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@@ -13711,6 +13714,28 @@ var element = $('#2b4825d6-9766-4260-96f8-a8462ab148ed');
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+</div>
+<div class="cell border-box-sizing code_cell rendered">
+<div class="input">
+<div class="prompt input_prompt">In&nbsp;[&nbsp;]:</div>
+<div class="inner_cell">
+    <div class="input_area">
+<div class=" highlight hl-ipython3"><pre><span></span><span class="n">statistics_action</span><span class="o">.</span><span class="n">modules</span><span class="p">[</span><span class="s1">&#39;parameters&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+    <span class="s1">&#39;max_speed&#39;</span><span class="p">:</span> <span class="n">max_speed</span><span class="p">,</span>
+    <span class="s1">&#39;min_speed&#39;</span><span class="p">:</span> <span class="n">min_speed</span><span class="p">,</span>
+    <span class="s1">&#39;position_sampling_rate&#39;</span><span class="p">:</span> <span class="n">position_sampling_rate</span><span class="p">,</span>
+    <span class="s1">&#39;position_low_pass_frequency&#39;</span><span class="p">:</span> <span class="n">position_low_pass_frequency</span><span class="p">,</span>
+    <span class="s1">&#39;box_size&#39;</span><span class="p">:</span> <span class="n">box_size</span><span class="p">,</span>
+    <span class="s1">&#39;bin_size&#39;</span><span class="p">:</span> <span class="n">bin_size</span><span class="p">,</span>
+    <span class="s1">&#39;smoothing_low&#39;</span><span class="p">:</span> <span class="n">smoothing_low</span><span class="p">,</span>
+    <span class="s1">&#39;smoothing_high&#39;</span><span class="p">:</span> <span class="n">smoothing_high</span>
+<span class="p">}</span>
+</pre></div>
+
+    </div>
+</div>
+</div>
+
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actions/calculate-statistics/data/10_calculate_spatial_statistics.ipynb

@@ -19,7 +19,7 @@
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      "output_type": "stream",
      "text": [
-      "14:03:52 [I] klustakwik KlustaKwik2 version 0.2.6\n"
+      "14:18:41 [I] klustakwik KlustaKwik2 version 0.2.6\n"
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@@ -175,7 +175,7 @@
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@@ -202,7 +202,7 @@
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+   "execution_count": 7,
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@@ -215,7 +215,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -255,6 +255,7 @@
        "gridness                   -0.459487\n",
        "border_score                0.078474\n",
        "information_rate            0.965845\n",
+       "information_specificity     0.309723\n",
        "head_mean_ang               5.788704\n",
        "head_mean_vec_len           0.043321\n",
        "spacing                     0.624971\n",
@@ -346,6 +347,8 @@
     "\n",
     "    information_rate = stats.information_rate(smooth_high_rate_map, prob_dist)\n",
     "    \n",
+    "    information_spec = stats.information_specificity(smooth_high_rate_map, prob_dist)\n",
+    "\n",
     "    single_spikes, bursts, bursty_spikes = spikes.find_bursts(spike_times, threshold=0.01)\n",
     "    burst_event_ratio = np.sum(bursts) / (np.sum(single_spikes) + np.sum(bursts))\n",
     "    bursty_spike_ratio = np.sum(bursty_spikes) / (np.sum(bursty_spikes) + np.sum(single_spikes))\n",
@@ -373,6 +376,7 @@
     "        'gridness': gridness,\n",
     "        'border_score': border_score,\n",
     "        'information_rate': information_rate,\n",
+    "        'information_specificity': information_spec,\n",
     "        'head_mean_ang': head_mean_ang,\n",
     "        'head_mean_vec_len': head_mean_vec_len,\n",
     "        'spacing': spacing,\n",
@@ -393,7 +397,7 @@
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@@ -425,8 +429,7 @@
       "/home/mikkel/.virtualenvs/expipe/lib/python3.6/site-packages/numpy/core/_methods.py:132: RuntimeWarning: invalid value encountered in double_scalars\n",
       "  ret = ret.dtype.type(ret / rcount)\n",
       "/home/mikkel/.virtualenvs/expipe/lib/python3.6/site-packages/quantities/quantity.py:624: RuntimeWarning: Mean of empty slice.\n",
-      "  ret = self.magnitude.mean(axis, dtype, None if out is None else out.magnitude)\n",
+      "  ret = self.magnitude.mean(axis, dtype, None if out is None else out.magnitude)\n"
-      "/home/mikkel/.virtualenvs/expipe/lib/python3.6/site-packages/ipykernel_launcher.py:82: RuntimeWarning: invalid value encountered in long_scalars\n"
      ]
     }
    ],
@@ -490,6 +493,24 @@
     "copy_tree(output_path, str(statistics_action.data_path()))"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "statistics_action.modules['parameters'] = {\n",
+    "    'max_speed': max_speed,\n",
+    "    'min_speed': min_speed,\n",
+    "    'position_sampling_rate': position_sampling_rate,\n",
+    "    'position_low_pass_frequency': position_low_pass_frequency,\n",
+    "    'box_size': box_size,\n",
+    "    'bin_size': bin_size,\n",
+    "    'smoothing_low': smoothing_low,\n",
+    "    'smoothing_high': smoothing_high\n",
+    "}"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,