Georg Willer
commited on
Commit
·
708c7e0
1
Parent(s):
75eac09
Remove unused code
Browse files- 01_Model_Deployment_Research.ipynb +199 -99
- src/ecg_2_hrv_pipeline.py +1 -12
- usage_instructions.ipynb +298 -10
01_Model_Deployment_Research.ipynb
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"pipe = pipeline(\"rpeaks-feature-extraction\", model = \"willergeorg/hubii-dummy\", trust_remote_code=True)"
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"\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[2]\u001b[39m\u001b[32m, line 2\u001b[39m\n\u001b[32m 1\u001b[39m file_path = \u001b[33m\"\u001b[39m\u001b[33m./Data/hr_rr_Elias-Rec_1703_162053.csv\u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m2\u001b[39m result = \u001b[43mpipe\u001b[49m(inputs=file_path, windowing_method=\u001b[33m\"\u001b[39m\u001b[33mrolling\u001b[39m\u001b[33m\"\u001b[39m, window_size=\u001b[33m\"\u001b[39m\u001b[33m60s\u001b[39m\u001b[33m\"\u001b[39m, frequency=\u001b[32m10\u001b[39m)\n\u001b[32m 3\u001b[39m result.head()\n",
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"c:\\Users\\georg\\Desktop\\HIWI\\ECG2HRV\\.venv\\Lib\\site-packages\\huggingface_hub\\file_download.py:140: UserWarning: `huggingface_hub` cache-system uses symlinks by default to efficiently store duplicated files but your machine does not support them in C:\\Users\\georg\\.cache\\huggingface\\hub\\models--willergeorg--rpeaks-to-hrv-pipeline. Caching files will still work but in a degraded version that might require more space on your disk. This warning can be disabled by setting the `HF_HUB_DISABLE_SYMLINKS_WARNING` environment variable. For more details, see https://huggingface.co/docs/huggingface_hub/how-to-cache#limitations.\n",
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+
"To support symlinks on Windows, you either need to activate Developer Mode or to run Python as an administrator. In order to activate developer mode, see this article: https://docs.microsoft.com/en-us/windows/apps/get-started/enable-your-device-for-development\n",
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},
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| 11912 |
"outputs": [
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| 11913 |
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"name": "stderr",
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| 11916 |
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"text": [
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| 11917 |
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"c:\\Users\\georg\\Desktop\\HIWI\\ECG2HRV\\src\\rpeaks2hrv.py:24: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation.\n",
|
| 11918 |
+
" hrv_values = pd.concat([hrv_values, hrv_time], ignore_index=True)\n"
|
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| 11919 |
]
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},
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"data": {
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"text/html": [
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"<div>\n",
|
| 11925 |
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"<style scoped>\n",
|
| 11926 |
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|
| 11927 |
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| 11928 |
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" }\n",
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"\n",
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| 11939 |
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" <thead>\n",
|
| 11940 |
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" <tr style=\"text-align: right;\">\n",
|
| 11941 |
+
" <th></th>\n",
|
| 11942 |
+
" <th>window_start</th>\n",
|
| 11943 |
+
" <th>window_end</th>\n",
|
| 11944 |
+
" <th>HRV_MeanNN</th>\n",
|
| 11945 |
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" <th>HRV_SDNN</th>\n",
|
| 11946 |
+
" <th>HRV_SDANN1</th>\n",
|
| 11947 |
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" <th>HRV_SDNNI1</th>\n",
|
| 11948 |
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" <th>HRV_SDANN2</th>\n",
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| 11949 |
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" <th>HRV_SDNNI2</th>\n",
|
| 11950 |
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" <th>HRV_SDANN5</th>\n",
|
| 11951 |
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" <th>HRV_SDNNI5</th>\n",
|
| 11952 |
+
" <th>...</th>\n",
|
| 11953 |
+
" <th>HRV_IQRNN</th>\n",
|
| 11954 |
+
" <th>HRV_SDRMSSD</th>\n",
|
| 11955 |
+
" <th>HRV_Prc20NN</th>\n",
|
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+
" <th>HRV_Prc80NN</th>\n",
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" <th>HRV_pNN50</th>\n",
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" <th>HRV_pNN20</th>\n",
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" <th>HRV_MinNN</th>\n",
|
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" <th>HRV_MaxNN</th>\n",
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" <th>HRV_HTI</th>\n",
|
| 11962 |
+
" <th>HRV_TINN</th>\n",
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| 11963 |
+
" </tr>\n",
|
| 11964 |
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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| 11967 |
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" <th>0</th>\n",
|
| 11968 |
+
" <td>2025-03-17 17:32:40.430678701</td>\n",
|
| 11969 |
+
" <td>2025-03-17 17:33:39.436569259</td>\n",
|
| 11970 |
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" <td>826.449008</td>\n",
|
| 11971 |
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" <td>199.477249</td>\n",
|
| 11972 |
+
" <td>NaN</td>\n",
|
| 11973 |
+
" <td>NaN</td>\n",
|
| 11974 |
+
" <td>NaN</td>\n",
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+
" <td>NaN</td>\n",
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| 11976 |
+
" <td>NaN</td>\n",
|
| 11977 |
+
" <td>NaN</td>\n",
|
| 11978 |
+
" <td>...</td>\n",
|
| 11979 |
+
" <td>156.738281</td>\n",
|
| 11980 |
+
" <td>7.174916</td>\n",
|
| 11981 |
+
" <td>693.945312</td>\n",
|
| 11982 |
+
" <td>927.929688</td>\n",
|
| 11983 |
+
" <td>0.0</td>\n",
|
| 11984 |
+
" <td>33.333333</td>\n",
|
| 11985 |
+
" <td>273.4375</td>\n",
|
| 11986 |
+
" <td>1605.46875</td>\n",
|
| 11987 |
+
" <td>14.8</td>\n",
|
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+
" <td>554.6875</td>\n",
|
| 11989 |
+
" </tr>\n",
|
| 11990 |
+
" </tbody>\n",
|
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+
"</table>\n",
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"<p>1 rows × 27 columns</p>\n",
|
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+
"</div>"
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+
],
|
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+
"text/plain": [
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" window_start window_end HRV_MeanNN \\\n",
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| 11997 |
+
"0 2025-03-17 17:32:40.430678701 2025-03-17 17:33:39.436569259 826.449008 \n",
|
| 11998 |
+
"\n",
|
| 11999 |
+
" HRV_SDNN HRV_SDANN1 HRV_SDNNI1 HRV_SDANN2 HRV_SDNNI2 HRV_SDANN5 \\\n",
|
| 12000 |
+
"0 199.477249 NaN NaN NaN NaN NaN \n",
|
| 12001 |
+
"\n",
|
| 12002 |
+
" HRV_SDNNI5 ... HRV_IQRNN HRV_SDRMSSD HRV_Prc20NN HRV_Prc80NN \\\n",
|
| 12003 |
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"0 NaN ... 156.738281 7.174916 693.945312 927.929688 \n",
|
| 12004 |
+
"\n",
|
| 12005 |
+
" HRV_pNN50 HRV_pNN20 HRV_MinNN HRV_MaxNN HRV_HTI HRV_TINN \n",
|
| 12006 |
+
"0 0.0 33.333333 273.4375 1605.46875 14.8 554.6875 \n",
|
| 12007 |
+
"\n",
|
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+
"[1 rows x 27 columns]"
|
| 12009 |
+
]
|
| 12010 |
+
},
|
| 12011 |
+
"execution_count": 4,
|
| 12012 |
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"metadata": {},
|
| 12013 |
+
"output_type": "execute_result"
|
| 12014 |
}
|
| 12015 |
],
|
| 12016 |
"source": [
|
| 12017 |
"file_path = \"./Data/hr_rr_Elias-Rec_1703_162053.csv\"\n",
|
| 12018 |
+
"result = pipe(inputs=file_path, windowing_method=\"last_interval\", window_size=\"60s\", frequency=10)\n",
|
| 12019 |
"result.head()"
|
| 12020 |
]
|
| 12021 |
},
|
| 12022 |
{
|
| 12023 |
"cell_type": "code",
|
| 12024 |
+
"execution_count": 5,
|
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|
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|
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+
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+
"name": "stderr",
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"output_type": "stream",
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"text": [
|
| 12045 |
+
"c:\\Users\\georg\\Desktop\\HIWI\\ECG2HRV\\.venv\\Lib\\site-packages\\huggingface_hub\\file_download.py:140: UserWarning: `huggingface_hub` cache-system uses symlinks by default to efficiently store duplicated files but your machine does not support them in C:\\Users\\georg\\.cache\\huggingface\\hub\\models--willergeorg--rpeaks-to-hrv-pipeline. Caching files will still work but in a degraded version that might require more space on your disk. This warning can be disabled by setting the `HF_HUB_DISABLE_SYMLINKS_WARNING` environment variable. For more details, see https://huggingface.co/docs/huggingface_hub/how-to-cache#limitations.\n",
|
| 12046 |
+
"To support symlinks on Windows, you either need to activate Developer Mode or to run Python as an administrator. In order to activate developer mode, see this article: https://docs.microsoft.com/en-us/windows/apps/get-started/enable-your-device-for-development\n",
|
| 12047 |
+
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|
| 12048 |
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+
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|
| 12050 |
+
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"data": {
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|
| 12053 |
+
"CommitInfo(commit_url='https://huggingface.co/willergeorg/rpeaks-to-hrv-pipeline/commit/70436e8045dae6e105e52f1cdb6a7bfece698a6d', commit_message='Upload RPeak2HRVPipeline', commit_description='', oid='70436e8045dae6e105e52f1cdb6a7bfece698a6d', pr_url=None, repo_url=RepoUrl('https://huggingface.co/willergeorg/rpeaks-to-hrv-pipeline', endpoint='https://huggingface.co', repo_type='model', repo_id='willergeorg/rpeaks-to-hrv-pipeline'), pr_revision=None, pr_num=None)"
|
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+
"version": "3.11.6"
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"nbformat": 4,
|
src/ecg_2_hrv_pipeline.py
CHANGED
|
@@ -23,15 +23,4 @@ class Ecg2HrvPipeline(Pipeline):
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| 23 |
return model_inputs
|
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def postprocess(self, model_outputs):
|
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|
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""" def __init__(self, model):
|
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|
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|
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-
def __init__(self, frequency = 100, baseline = None, normalization_method = None, **):
|
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self.ecg2HrvExtractor = ECG2HRV()
|
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-
self.frequency = 100
|
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-
self.baseline = baseline
|
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-
self.normalization_method = normalization_method
|
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super.__init__(model) """
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return model_inputs
|
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def postprocess(self, model_outputs):
|
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+
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CHANGED
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"source": [
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"\n",
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-
"rpeak2hrv_pipeline = pipeline(model = \"
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" <th></th>\n",
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" <th>HRV_MeanNN</th>\n",
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" <th>HRV_SDNN</th>\n",
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" <th>HRV_SDANN1</th>\n",
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" <th>HRV_LFn</th>\n",
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" <th>HRV_HFn</th>\n",
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" <th>HRV_LnHF</th>\n",
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|
| 211 |
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" <td>1006.894005</td>\n",
|
| 212 |
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|
| 213 |
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" <td>72.830794</td>\n",
|
| 214 |
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|
| 215 |
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|
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|
| 217 |
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|
| 218 |
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|
| 219 |
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|
| 220 |
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|
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|
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|
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" <td>-2.649243</td>\n",
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|
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|
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|
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],
|
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"text/plain": [
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" HRV_MeanNN HRV_SDNN HRV_SDANN1 HRV_SDNNI1 HRV_SDANN2 HRV_SDNNI2 \\\n",
|
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"0 1006.894005 159.530641 72.830794 137.277955 56.912177 143.4821 \n",
|
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"\n",
|
| 242 |
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" HRV_SDANN5 HRV_SDNNI5 HRV_RMSSD HRV_SDSD ... HRV_ULF HRV_VLF \\\n",
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"0 45.675812 152.633402 107.280546 102.397785 ... 0.000497 0.010289 \n",
|
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"\n",
|
| 245 |
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" HRV_LF HRV_HF HRV_VHF HRV_TP HRV_LFHF HRV_LFn HRV_HFn \\\n",
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+
"0 0.024415 0.070705 0.026376 0.132282 0.345306 0.184566 0.5345 \n",
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"\n",
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" HRV_LnHF \n",
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"0 -2.649243 \n",
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"\n",
|
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"[1 rows x 35 columns]"
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]
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},
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"execution_count": 9,
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"metadata": {},
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|
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}
|
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],
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"source": [
|
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"file_path = \"./Data/hr_rr_Elias-Rec_1703_162053.csv\"\n",
|
| 261 |
+
"result = rpeak2hrv_pipeline(inputs=file_path, feature_domains=['time', 'freq'], sampling_rate=1000)\n",
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"result.head()"
|
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|
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"c:\\Users\\georg\\Desktop\\HIWI\\ECG2HRV\\.venv\\Lib\\site-packages\\neurokit2\\hrv\\hrv_nonlinear.py:268: NeuroKitWarning: Missing interbeat intervals have been detected. Note that missing intervals can distort some HRV features, in particular nonlinear indices.\n",
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" warn(\n",
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"c:\\Users\\georg\\Desktop\\HIWI\\ECG2HRV\\.venv\\Lib\\site-packages\\neurokit2\\hrv\\hrv_nonlinear.py:529: NeuroKitWarning: DFA_alpha2 related indices will not be calculated. The maximum duration of the windows provided for the long-term correlation is smaller than the minimum duration of windows. Refer to the `scale` argument in `nk.fractal_dfa()` for more information.\n",
|
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" warn(\n",
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" hrv_values = pd.concat([hrv_values, hrv_time], ignore_index=True)\n"
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" <th></th>\n",
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| 356 |
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" <th>window_start</th>\n",
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| 357 |
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" <th>window_end</th>\n",
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| 358 |
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" <th>HRV_MeanNN</th>\n",
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| 359 |
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" <th>HRV_SDNN</th>\n",
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| 360 |
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" <th>HRV_SDANN1</th>\n",
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" <th>HRV_SDNNI1</th>\n",
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" <th>HRV_SDNNI5</th>\n",
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" <th>...</th>\n",
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" <th>HRV_SampEn</th>\n",
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" <th>HRV_ShanEn</th>\n",
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" <th>HRV_FuzzyEn</th>\n",
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" <th>HRV_MSEn</th>\n",
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" <th>HRV_CMSEn</th>\n",
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" <th>HRV_RCMSEn</th>\n",
|
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" <th>HRV_CD</th>\n",
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" <th>HRV_HFD</th>\n",
|
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" <th>HRV_KFD</th>\n",
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" <th>HRV_LZC</th>\n",
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" </tr>\n",
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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" <th>0</th>\n",
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| 382 |
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" <td>2025-03-17 16:20:54.760848</td>\n",
|
| 383 |
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" <td>2025-03-17 16:21:53.596623680</td>\n",
|
| 384 |
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" <td>1060.358416</td>\n",
|
| 385 |
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" <td>153.515505</td>\n",
|
| 386 |
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" <td>NaN</td>\n",
|
| 387 |
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" <td>NaN</td>\n",
|
| 388 |
+
" <td>NaN</td>\n",
|
| 389 |
+
" <td>NaN</td>\n",
|
| 390 |
+
" <td>NaN</td>\n",
|
| 391 |
+
" <td>NaN</td>\n",
|
| 392 |
+
" <td>...</td>\n",
|
| 393 |
+
" <td>1.265666</td>\n",
|
| 394 |
+
" <td>5.657451</td>\n",
|
| 395 |
+
" <td>1.330316</td>\n",
|
| 396 |
+
" <td>0.856145</td>\n",
|
| 397 |
+
" <td>0.9913</td>\n",
|
| 398 |
+
" <td>1.267671</td>\n",
|
| 399 |
+
" <td>1.82538</td>\n",
|
| 400 |
+
" <td>2.016523</td>\n",
|
| 401 |
+
" <td>2.937446</td>\n",
|
| 402 |
+
" <td>1.227977</td>\n",
|
| 403 |
+
" </tr>\n",
|
| 404 |
+
" </tbody>\n",
|
| 405 |
+
"</table>\n",
|
| 406 |
+
"<p>1 rows × 84 columns</p>\n",
|
| 407 |
+
"</div>"
|
| 408 |
+
],
|
| 409 |
+
"text/plain": [
|
| 410 |
+
" window_start window_end HRV_MeanNN \\\n",
|
| 411 |
+
"0 2025-03-17 16:20:54.760848 2025-03-17 16:21:53.596623680 1060.358416 \n",
|
| 412 |
+
"\n",
|
| 413 |
+
" HRV_SDNN HRV_SDANN1 HRV_SDNNI1 HRV_SDANN2 HRV_SDNNI2 HRV_SDANN5 \\\n",
|
| 414 |
+
"0 153.515505 NaN NaN NaN NaN NaN \n",
|
| 415 |
+
"\n",
|
| 416 |
+
" HRV_SDNNI5 ... HRV_SampEn HRV_ShanEn HRV_FuzzyEn HRV_MSEn HRV_CMSEn \\\n",
|
| 417 |
+
"0 NaN ... 1.265666 5.657451 1.330316 0.856145 0.9913 \n",
|
| 418 |
+
"\n",
|
| 419 |
+
" HRV_RCMSEn HRV_CD HRV_HFD HRV_KFD HRV_LZC \n",
|
| 420 |
+
"0 1.267671 1.82538 2.016523 2.937446 1.227977 \n",
|
| 421 |
+
"\n",
|
| 422 |
+
"[1 rows x 84 columns]"
|
| 423 |
+
]
|
| 424 |
+
},
|
| 425 |
+
"execution_count": 4,
|
| 426 |
+
"metadata": {},
|
| 427 |
+
"output_type": "execute_result"
|
| 428 |
+
}
|
| 429 |
+
],
|
| 430 |
"source": [
|
| 431 |
"file_path = \"./Data/hr_rr_Elias-Rec_1703_162053.csv\"\n",
|
| 432 |
+
"result = rpeak2hrv_pipeline(inputs=file_path, windowing_method=\"first_interval\", window_size=\"60s\", sampling_rate=1000)\n",
|
| 433 |
"result.head()"
|
| 434 |
]
|
| 435 |
},
|
|
|
|
| 478 |
"name": "python3"
|
| 479 |
},
|
| 480 |
"language_info": {
|
| 481 |
+
"codemirror_mode": {
|
| 482 |
+
"name": "ipython",
|
| 483 |
+
"version": 3
|
| 484 |
+
},
|
| 485 |
+
"file_extension": ".py",
|
| 486 |
+
"mimetype": "text/x-python",
|
| 487 |
"name": "python",
|
| 488 |
+
"nbconvert_exporter": "python",
|
| 489 |
+
"pygments_lexer": "ipython3",
|
| 490 |
+
"version": "3.11.6"
|
| 491 |
}
|
| 492 |
},
|
| 493 |
"nbformat": 4,
|