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‎python/pipeline_demo.ipynb‎

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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"colab": {
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"base_uri": "https://localhost:8080/"
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},
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"id": "XcNTecnGRfXb",
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"outputId": "542e47fb-b21d-4be1-c963-451de28dcc00"
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Collecting git+https://github.com/ieeg-portal/ieegpy.git\n",
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" Cloning https://github.com/ieeg-portal/ieegpy.git to /tmp/pip-req-build-jts8gjmw\n",
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" Running command git clone --filter=blob:none --quiet https://github.com/ieeg-portal/ieegpy.git /tmp/pip-req-build-jts8gjmw\n",
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" Resolved https://github.com/ieeg-portal/ieegpy.git to commit 080bfa42a8503380ef164b5e7b116613f75073bb\n",
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" Preparing metadata (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
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"Collecting deprecation (from ieeg==1.6)\n",
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" Downloading deprecation-2.1.0-py2.py3-none-any.whl (11 kB)\n",
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"Requirement already satisfied: requests in /usr/local/lib/python3.10/dist-packages (from ieeg==1.6) (2.31.0)\n",
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"Collecting pennprov==2.2.4 (from ieeg==1.6)\n",
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" Downloading pennprov-2.2.4-py2.py3-none-any.whl (98 kB)\n",
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"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m98.0/98.0 kB\u001b[0m \u001b[31m2.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
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"\u001b[?25hRequirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from pennprov==2.2.4->ieeg==1.6) (2023.7.22)\n",
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"Requirement already satisfied: packaging in /usr/local/lib/python3.10/dist-packages (from deprecation->ieeg==1.6) (23.2)\n",
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"Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas->ieeg==1.6) (2023.3.post1)\n",
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"Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests->ieeg==1.6) (3.3.1)\n",
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"Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests->ieeg==1.6) (3.4)\n",
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"Building wheels for collected packages: ieeg\n",
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" Building wheel for ieeg (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
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" Created wheel for ieeg: filename=ieeg-1.6-py3-none-any.whl size=27498 sha256=7d186788202c2e96639f7170a6e63275159a6f34ce47a517b94c5dcccf1aa3d0\n",
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" Stored in directory: /tmp/pip-ephem-wheel-cache-10p9_yqj/wheels/c0/2a/4d/452574b1c3c63e86df54de09161463c0509e9eeffc1aad898e\n",
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"Successfully built ieeg\n",
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"Installing collected packages: deprecation, pennprov, ieeg\n",
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"Successfully installed deprecation-2.1.0 ieeg-1.6 pennprov-2.2.4\n",
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"Collecting git+https://github.com/haoershi/CNT_research_tools.git#subdirectory=python\n",
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" Cloning https://github.com/haoershi/CNT_research_tools.git to /tmp/pip-req-build-p036f__u\n",
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" Running command git clone --filter=blob:none --quiet https://github.com/haoershi/CNT_research_tools.git /tmp/pip-req-build-p036f__u\n",
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" Resolved https://github.com/haoershi/CNT_research_tools.git to commit 628c573b6ffa2bb575867bd1919e98f44a8f242d\n",
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" Preparing metadata (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
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"Requirement already satisfied: pennprov==2.2.4 in /usr/local/lib/python3.10/dist-packages (from CNTtools==0.1) (2.2.4)\n",
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"Collecting pyqt5-sip==12.9.0 (from CNTtools==0.1)\n",
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" Downloading PyQt5_sip-12.9.0-cp310-cp310-manylinux1_x86_64.whl (351 kB)\n",
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"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m351.8/351.8 kB\u001b[0m \u001b[31m6.5 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
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"\u001b[?25hRequirement already satisfied: install==1.3.5 in /usr/local/lib/python3.10/dist-packages (from CNTtools==0.1) (1.3.5)\n",
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"Requirement already satisfied: pytest in /usr/local/lib/python3.10/dist-packages (from CNTtools==0.1) (7.4.3)\n",
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"Collecting beartype (from CNTtools==0.1)\n",
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" Downloading beartype-0.16.4-py3-none-any.whl (819 kB)\n",
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"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m819.1/819.1 kB\u001b[0m \u001b[31m39.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
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"\u001b[?25hCollecting pytest-html (from CNTtools==0.1)\n",
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" Downloading pytest_html-4.0.2-py3-none-any.whl (23 kB)\n",
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"Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from pennprov==2.2.4->CNTtools==0.1) (2023.7.22)\n",
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"Collecting pytest-metadata>=2.0.0 (from pytest-html->CNTtools==0.1)\n",
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" Downloading pytest_metadata-3.0.0-py3-none-any.whl (10 kB)\n",
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"Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/dist-packages (from jinja2>=3.0.0->pytest-html->CNTtools==0.1) (2.1.3)\n",
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"Building wheels for collected packages: CNTtools\n",
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" Building wheel for CNTtools (setup.py) ... \u001b[?25l\u001b[?25hdone\n",
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" Created wheel for CNTtools: filename=CNTtools-0.1-py3-none-any.whl size=371274 sha256=b40dafcf85fa8ce0be146d9de84a8f8f3938fcdcc30058810a92d83418ae4387\n",
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" Stored in directory: /tmp/pip-ephem-wheel-cache-16gi9pnk/wheels/f3/c3/a0/692561f283907da48ee8fe0fc32452fa451913ff46e92a7719\n",
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"Successfully built CNTtools\n",
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"Installing collected packages: pyqt5-sip, beartype, pytest-metadata, pytest-html, CNTtools\n",
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"Successfully installed CNTtools-0.1 beartype-0.16.4 pyqt5-sip-12.9.0 pytest-html-4.0.2 pytest-metadata-3.0.0\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"# set search path\n",
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"import os,sys\n",
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"!pip install git+https://github.com/ieeg-portal/ieegpy.git # Install ieegpy toolbox directly from github\n",
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"from ieeg.auth import Session\n",
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"\n",
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"!pip install git+https://github.com/haoershi/CNT_research_tools.git#subdirectory=python\n",
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"!pip install git+https://github.com/penn-cnt/CNT_Preprocessing_Toolkit.git#subdirectory=python\n",
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"from CNTtools import iEEGPreprocess\n",
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"from CNTtools import settings\n",
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"\n",
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"metadata": {
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"cellView": "form",
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"id": "Z-EuFZbW3Ds2"
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"outputs": [],
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"outputs": [
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"-- -- IEEG password file saved -- --\n",
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"\n",
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"-- -- IEEG user config file saved -- --\n",
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"\n",
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"Login as : qaq233tvt\n"
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]
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}
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],
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"source": [
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"#@title Login Configuration\n",
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"#@markdown Set up iEEG.org login info for obtaining data\n",
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"colab": {
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"['datasets', 'meta', 'num_data', 'user', 'user_data_dir']\n",
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"Methods of class iEEGPreprocess:\n",
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"['download_data', 'list_data', 'load_data', 'login', 'login_config', 'save']\n"
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"['download_data', 'list_data', 'load_data', 'login', 'login_config', 'remove_data', 'save']\n"
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" document.querySelector('#df-ee1f4dec-4459-49d3-9fa4-d2a89bd3bda5 button.colab-df-convert');\n",
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" buttonEl.style.display =\n",
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" google.colab.kernel.accessAllowed ? 'block' : 'none';\n",
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"\n",
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" async function convertToInteractive(key) {\n",
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" const docLinkHtml = 'Like what you see? Visit the ' +\n",
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" '<a target=\"_blank\" href=https://colab.research.google.com/notebooks/data_table.ipynb>data table notebook</a>'\n",
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" element.innerHTML = '';\n",
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