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Predictions #12

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merged 7 commits into from
Mar 26, 2024
Merged

Predictions #12

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c635e1d
Set up for loading data and classifier
Erikpostt Mar 5, 2024
8893da6
Merge branch 'main' of github.com:biomarkersParkinson/dbpd-toolbox in…
Erikpostt Mar 14, 2024
620c98d
Add classifier and classification thresholds
Erikpostt Mar 14, 2024
ad46258
Fix issue with channels/units not equal
Erikpostt Mar 14, 2024
cd57aa2
Create example of predicting gait
Erikpostt Mar 14, 2024
7c2f176
Store files for tests
Erikpostt Mar 14, 2024
7794a67
Finalize arm swing predictions
Erikpostt Mar 14, 2024
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72 changes: 37 additions & 35 deletions docs/notebooks/gait/1.preprocess_imu.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -16,18 +16,9 @@
},
{
"cell_type": "code",
"execution_count": 22,
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The autoreload extension is already loaded. To reload it, use:\n",
" %reload_ext autoreload\n"
]
}
],
"outputs": [],
"source": [
"# Automatically reload modules\n",
"%load_ext autoreload\n",
Expand All @@ -50,7 +41,7 @@
},
{
"cell_type": "code",
"execution_count": 23,
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -91,7 +82,7 @@
},
{
"cell_type": "code",
"execution_count": 24,
"execution_count": 8,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -126,40 +117,40 @@
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>31013</th>\n",
" <th>22885</th>\n",
" <td>10.0</td>\n",
" <td>322</td>\n",
" <td>973</td>\n",
" <td>-1681</td>\n",
" <td>51</td>\n",
" <td>-18</td>\n",
" <td>2</td>\n",
" <td>304</td>\n",
" <td>1569</td>\n",
" <td>-1124</td>\n",
" <td>42</td>\n",
" <td>-19</td>\n",
" <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>43503</th>\n",
" <th>46205</th>\n",
" <td>10.0</td>\n",
" <td>1291</td>\n",
" <td>604</td>\n",
" <td>-1394</td>\n",
" <td>168</td>\n",
" <td>80</td>\n",
" <td>-12</td>\n",
" <td>1341</td>\n",
" <td>1097</td>\n",
" <td>-714</td>\n",
" <td>635</td>\n",
" <td>60</td>\n",
" <td>90</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" time acceleration_x acceleration_y acceleration_z rotation_x \\\n",
"31013 10.0 322 973 -1681 51 \n",
"43503 10.0 1291 604 -1394 168 \n",
"22885 10.0 304 1569 -1124 42 \n",
"46205 10.0 1341 1097 -714 635 \n",
"\n",
" rotation_y rotation_z \n",
"31013 -18 2 \n",
"43503 80 -12 "
"22885 -19 3 \n",
"46205 60 90 "
]
},
"execution_count": 24,
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -182,7 +173,7 @@
},
{
"cell_type": "code",
"execution_count": 25,
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -205,8 +196,19 @@
" values_unscaled=np.array(df[list(d_channels_units.keys())]),\n",
" scale_factors=metadata_samples.scale_factors)\n",
"\n",
"# correct for sensor orientation - this subject has watch on right-hand side\n",
"side_watch = 'left'\n",
"df[DataColumns.ACCELERATION_Z] *= -1\n",
"if side_watch == 'right':\n",
" df[DataColumns.ACCELERATION_X] *= -1\n",
"\n",
"for col in [x for x in d_channels_units.keys() if 'acceleration' in x]:\n",
" for result, side_pass in zip(['filt', 'grav'], ['lp', 'hp']):\n",
"\n",
" # change to correct units [g]\n",
" if acceleration_units == 'm/s^2':\n",
" df[col] /= 9.81\n",
"\n",
" for result, side_pass in zip(['filt', 'grav'], ['hp', 'lp']):\n",
" df[f'{result}_{col}'] = dbpd.imu_preprocessing.butterworth_filter(\n",
" config=ppp,\n",
" single_sensor_col=np.array(df[col]),\n",
Expand All @@ -228,7 +230,7 @@
},
{
"cell_type": "code",
"execution_count": 26,
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
Expand Down
104 changes: 70 additions & 34 deletions docs/notebooks/gait/2.extract_features_gait.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 52,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -51,7 +51,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 53,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -94,10 +94,46 @@
"l_data_point_level_cols = l_acceleration_cols + l_gravity_cols\n",
"\n",
"# store data\n",
"l_channels = ([f'{x}_{y}' for x in l_gravity_cols for y in ['mean', 'std']] + \n",
" [f'{x}_{y}' for x in l_acceleration_cols for y in ['power_below_gait', 'power_gait', 'power_tremor', 'power_above_tremor']] + \n",
" ['std_norm_acc']\n",
")"
"d_channels_values = {\n",
" 'grav_acceleration_x_mean': 'g',\n",
" 'grav_acceleration_y_mean': 'g',\n",
" 'grav_acceleration_z_mean': 'g',\n",
" 'grav_acceleration_x_std': 'g',\n",
" 'grav_acceleration_y_std': 'g',\n",
" 'grav_acceleration_z_std': 'g',\n",
" 'acceleration_x_power_below_gait': 'X',\n",
" 'acceleration_y_power_below_gait': 'X',\n",
" 'acceleration_z_power_below_gait': 'X',\n",
" 'acceleration_x_power_gait': 'X',\n",
" 'acceleration_y_power_gait': 'X',\n",
" 'acceleration_z_power_gait': 'X',\n",
" 'acceleration_x_power_tremor': 'X',\n",
" 'acceleration_y_power_tremor': 'X',\n",
" 'acceleration_z_power_tremor': 'X',\n",
" 'acceleration_x_power_above_tremor': 'X',\n",
" 'acceleration_y_power_above_tremor': 'X',\n",
" 'acceleration_z_power_above_tremor': 'X',\n",
" 'acceleration_x_dominant_frequency': 'Hz',\n",
" 'acceleration_y_dominant_frequency': 'Hz',\n",
" 'acceleration_z_dominant_frequency': 'Hz',\n",
" 'std_norm_acc': 'X',\n",
" 'cc_1_acc': 'X',\n",
" 'cc_2_acc': 'X',\n",
" 'cc_3_acc': 'X',\n",
" 'cc_4_acc': 'X',\n",
" 'cc_5_acc': 'X',\n",
" 'cc_6_acc': 'X',\n",
" 'cc_7_acc': 'X',\n",
" 'cc_8_acc': 'X',\n",
" 'cc_9_acc': 'X',\n",
" 'cc_10_acc': 'X',\n",
" 'cc_11_acc': 'X',\n",
" 'cc_12_acc': 'X',\n",
" 'cc_13_acc': 'X',\n",
" 'cc_14_acc': 'X',\n",
" 'cc_15_acc': 'X',\n",
" 'cc_16_acc': 'X'\n",
"}"
]
},
{
Expand All @@ -116,7 +152,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 54,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -153,38 +189,38 @@
" <tr>\n",
" <th>0</th>\n",
" <td>0.00</td>\n",
" <td>-4.159470e-08</td>\n",
" <td>-5.271109</td>\n",
" <td>4.336545e-08</td>\n",
" <td>5.495509</td>\n",
" <td>-2.067087e-08</td>\n",
" <td>-2.619526</td>\n",
" <td>-0.537320</td>\n",
" <td>-4.240030e-09</td>\n",
" <td>0.560195</td>\n",
" <td>4.420535e-09</td>\n",
" <td>0.267026</td>\n",
" <td>2.107122e-09</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>0.01</td>\n",
" <td>-3.711922e-07</td>\n",
" <td>-4.870643</td>\n",
" <td>3.918652e-07</td>\n",
" <td>5.695250</td>\n",
" <td>-1.835777e-07</td>\n",
" <td>-2.307776</td>\n",
" <td>-0.496498</td>\n",
" <td>-3.783814e-08</td>\n",
" <td>0.580556</td>\n",
" <td>3.994549e-08</td>\n",
" <td>0.235247</td>\n",
" <td>1.871333e-08</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" time acceleration_x grav_acceleration_x acceleration_y \\\n",
"0 0.00 -4.159470e-08 -5.271109 4.336545e-08 \n",
"1 0.01 -3.711922e-07 -4.870643 3.918652e-07 \n",
"0 0.00 -0.537320 -4.240030e-09 0.560195 \n",
"1 0.01 -0.496498 -3.783814e-08 0.580556 \n",
"\n",
" grav_acceleration_y acceleration_z grav_acceleration_z \n",
"0 5.495509 -2.067087e-08 -2.619526 \n",
"1 5.695250 -1.835777e-07 -2.307776 "
"0 4.420535e-09 0.267026 2.107122e-09 \n",
"1 3.994549e-08 0.235247 1.871333e-08 "
]
},
"execution_count": 11,
"execution_count": 54,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -208,7 +244,7 @@
},
{
"cell_type": "code",
"execution_count": 34,
"execution_count": 55,
"metadata": {},
"outputs": [
{
Expand All @@ -233,7 +269,7 @@
},
{
"cell_type": "code",
"execution_count": 35,
"execution_count": 56,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -248,7 +284,7 @@
},
{
"cell_type": "code",
"execution_count": 36,
"execution_count": 57,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -261,7 +297,7 @@
},
{
"cell_type": "code",
"execution_count": 37,
"execution_count": 58,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -297,7 +333,7 @@
},
{
"cell_type": "code",
"execution_count": 38,
"execution_count": 59,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -323,7 +359,7 @@
},
{
"cell_type": "code",
"execution_count": 39,
"execution_count": 60,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -341,7 +377,7 @@
},
{
"cell_type": "code",
"execution_count": 88,
"execution_count": 61,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -357,8 +393,8 @@
"metadata_time.__setattr__('file_name', 'gait_time.bin')\n",
"metadata_time.__setattr__('file_dir_path', output_path)\n",
"\n",
"metadata_samples.__setattr__('channels', [x for x in df_windowed.columns if x != 'time'])\n",
"metadata_samples.__setattr__('units', np.concatenate([np.repeat('m/s^2', 7), np.repeat([np.repeat('X', 4).tolist() + ['Hz']], 3), np.repeat('X', 16)]).tolist())\n",
"metadata_samples.__setattr__('channels', list(d_channels_values.keys()))\n",
"metadata_samples.__setattr__('units', list(d_channels_values.values()))\n",
"\n",
"metadata_time.__setattr__('channels', ['time'])\n",
"metadata_time.__setattr__('units', ['s'])\n",
Expand All @@ -367,7 +403,7 @@
},
{
"cell_type": "code",
"execution_count": 89,
"execution_count": 62,
"metadata": {},
"outputs": [],
"source": [
Expand Down
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