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| author | CoprDistGit <infra@openeuler.org> | 2023-05-10 08:20:02 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-10 08:20:02 +0000 |
| commit | 92ffe6948c9a5dc161ce51fdc5b7bb0a72e35379 (patch) | |
| tree | 8e7e94b1d17f462f7341f84b7f6ef4043226741b | |
| parent | 02004d6aea796a82cb892f3505d0d029951968bb (diff) | |
automatic import of python-cerebralcortex-kernel
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-cerebralcortex-kernel.spec | 668 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 670 insertions, 0 deletions
@@ -0,0 +1 @@ +/cerebralcortex-kernel-3.3.16.tar.gz diff --git a/python-cerebralcortex-kernel.spec b/python-cerebralcortex-kernel.spec new file mode 100644 index 0000000..debbd92 --- /dev/null +++ b/python-cerebralcortex-kernel.spec @@ -0,0 +1,668 @@ +%global _empty_manifest_terminate_build 0 +Name: python-cerebralcortex-kernel +Version: 3.3.16 +Release: 1 +Summary: Backend data analytics platform for MD2K software +License: BSD2 +URL: https://github.com/MD2Korg/CerebralCortex-Kernel/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/d2/72/8fa1db2c4c77656891d481a43b665dafa4099e758b4158269f83ecb507d3/cerebralcortex-kernel-3.3.16.tar.gz +BuildArch: noarch + +Requires: python3-wheel +Requires: python3-pytz +Requires: python3-PyYAML +Requires: python3-SQLAlchemy-Utils +Requires: python3-influxdb +Requires: python3-pyarrow +Requires: python3-hdfs3 +Requires: python3-pyspark +Requires: python3-msgpack +Requires: python3-PyJWT +Requires: python3-pandas +Requires: python3-plotly +Requires: python3-datascience +Requires: python3-matplotlib +Requires: python3-cufflinks +Requires: python3-sqlalchemy +Requires: python3-pennprov +Requires: python3-shapely +Requires: python3-numpy +Requires: python3-geopy +Requires: python3-py-ecg-detectors +Requires: python3-scikit-learn +Requires: python3-scipy + +%description +# CerebralCortex Kernel +Cerebral Cortex is the big data cloud companion of mCerebrum designed to support population-scale +data analysis, visualization, model development, and intervention design for mobile sensor data. + +You can find more information about MD2K software on our +[software website](https://md2k.org/software) or the MD2K organization on our +[MD2K website](https://md2k.org/). + +CerebralCortex Kernel is part of our +[CerebralCortex cloud platform](https://github.com/MD2Korg/CerebralCortex). +CerebralCortex-Kernel is capable of parallelizing tasks and scale a job to n-number of cores/machines. CerebralCortex Kernel offers some builtin features as follows: + +## Installation +### Dependencies +CerebralCortex Kernel requires `java 8` to run. Java 8 prior to version 8u92 support is deprecated as of CerebralCortex-Kernel 3.3.0. +- check java version - `java -version` +- set ``JAVA_HOME`` to `java 8` +- OR start python shell with ``JAVA_HOME=/path/to/java/Home python3`` + + +### Install using pip +CerebralCortex-Kernel requires minimum [Python3.6](https://www.python.org/downloads/release/python-360/). To install CerebralCortex-Kernel as an API: + +`pip3 install cerebralcortex-kernel` + +- Note: please use appropriate pip (e.g., pip, pip3, pip3.6 etc.) installed on your machine + +### Install from source code +- Clone repo - +` git clone https://github.com/MD2Korg/CerebralCortex-Kernel.git` +- `cd CerebralCortex-Kernel` +- `python3 setup.py install` + +## Usage + + from cerebralcortex.kernel import Kernel + CC = Kernel(cc_configs="default") + + # to view default configs + print(CC.config) + + # default data storage path is + # /user/home/folder/cc_data + + +By default Kernel will load default configs. Please have a look at all available [configurations](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/conf) for CerebralCortex-Kernel. +You may also load config files as: + +`CC = Kernel(configs_dir_path="dir/path/to/configs/", new_study=True)` + +### How to use builtin algorithms +Using builtin algorithms are as easy as loading data, passing it to algorithm and get the results. +Below is an example on how to compute CGM Glucose Variability Metrics. + +- [Download Glucose Data](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/test_suite/sample_data/cgm_glucose_variability_metrics/sample.csv). The device used to collect glucose was the [Dexcom G6 Continuous Glucose Monitor](https://www.dexcom.com/g6-cgm-system) +- Install Cerebral Cortex Kernel `pip install cerebralcortex-kernel` +- Open terminal and start python3 shell + +### Python Code + # import packages + from cerebralcortex.kernel import Kernel + from cerebralcortex.algorithms.glucose.glucose_variability_metrics import glucose_var + + # Create Kernel object + CC = Kernel(cc_configs="default", new_study=True) + + # Read sample CSV data + ds = CC.read_csv("/path/of/the/downloaded/file/sample.csv", stream_name="cgm_glucose_variability_metrics", header=True) + + # view sample data + ds.show(2) + + # Apply glucose_variability_metrics algorithm on the data + results = glucose_var(ds) + + # view results + results.show(2) + + # save computed data + CC.save_stream(results) + +Please have a look at [jupyter notebook](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/datastream_operation.ipynb) for basic operation that could be perform on DataStream object. + +### Algorithms to Analyze Sensor Data +External CerebralCortex-Kernel offers following builtin algorithms to analyze sensor data. + +- ECG sensor data quality +- ECG RR Interval Computation +- Heart Rate Variability Feature Computation +- CGM Glucose Variability Metrics +- [GPS Data Clustering](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/cc_algorithms.ipynb) +- Sensor Data Interpolation +- Statistical Features Computation +- [List of all available algorithms](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/algorithms) + +### Markers with ML Models +- [Stress Detection using ECG data](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/markers/ecg_stress) +- [mContain Social Crowding](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/markers/mcontain) +- Brushing Detection using Accelerometer and Gyro Data (TODO) + +### Visualization +- [Basic Plots for Timeseries Data](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/plotting_demo.ipynb) +- [Plot GPS Clusters on Map](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/cc_algorithms.ipynb) +- [Stress Visualization](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/plotting_demo.ipynb) + +### Import and Document Data +- [Import CSV Data in CerebralCortex-Kernel Format](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/import_and_analyse_data.ipynb) +- [Document imported Data using MetaData Module](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/import_and_analyse_data.ipynb) + +### External CerebralCortex-Kernel Supported Platforms +- mProv +- mFlow + + +## Examples +- [Jupyter Notebooks](https://github.com/MD2Korg/CerebralCortex/tree/master/jupyter_demo) + +## Documentation + +- [Source code documentation](https://cerebralcortex-kernel.readthedocs.io/en/latest/) + +## Deploy on Cloud +CerebralCortex-Kernel is a part of CerebralCortex cloud platform. To test the complete cloud platform, please visit [CerebralCortex](https://github.com/MD2Korg/CerebralCortex). + + +## FAQ +**1 - Do I need whole CerebralCortex cloud platform to use CerebralCortex-Kernal?** + +No! If you want to use CerebralCortex-Kernel independently. + + +**2 - How can I change NoSQL backend storage layer?** + +CerebralCortex-Kernel follows component based structure. This makes it easier to add/remove features. +* Add a new class in [Data manager-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/). +* New class must have read/write methods. Here is a sample [skeleton class](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/storage_blueprint.py) with mandatory methods required in the new class. +* Create an object of new class in [Data-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/data.py) with appropriate parameters. +* Add appropriate configurations in [cerebralcortex.yml](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml) in (NoSQL Storage)[https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml#L8] section. + +**3 - How can I replace MySQL with another SQL storage system?** + +* Add a new class in [Data manager-SQL](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/core/data_manager/sql). +* New class must implement all of the methods available in [stream_handler.py](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/sql/stream_handler.py) class. +* Create an object of new class in [Data-SQL](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/sql/data.py) with appropriate parameters. +* Add appropriate configurations in [cerebralcortex.yml](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml) in [Relational Storage](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml) section. + +**4 - Where are all the backend storage related classes/methods?** + +In [Data manager-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/). You can add/change any backend storage. + + +## Contributing +Please read our [Contributing Guidelines](https://md2k.org/contributing/contributing-guidelines.html) for details on the process for submitting pull requests to us. + +We use the [Python PEP 8 Style Guide](https://www.python.org/dev/peps/pep-0008/). + +Our [Code of Conduct](https://md2k.org/contributing/code-of-conduct.html) is the [Contributor Covenant](https://www.contributor-covenant.org/). + +Bug reports can be submitted through [JIRA](https://md2korg.atlassian.net/secure/Dashboard.jspa). + +Our discussion forum can be found [here](https://discuss.md2k.org/). + +## Versioning + +We use [Semantic Versioning](https://semver.org/) for versioning the software which is based on the following guidelines. + +MAJOR.MINOR.PATCH (example: 3.0.12) + + 1. MAJOR version when incompatible API changes are made, + 2. MINOR version when functionality is added in a backwards-compatible manner, and + 3. PATCH version when backwards-compatible bug fixes are introduced. + +For the versions available, see [this repository's tags](https://github.com/MD2Korg/CerebralCortex/tags). + +## Contributors + +Link to the [list of contributors](https://github.com/MD2Korg/CerebralCortex-Kernel/graphs/contributors) who participated in this project. + +## License + +This project is licensed under the BSD 2-Clause - see the [license](https://md2k.org/software-under-the-hood/software-uth-license) file for details. + +## Acknowledgments + +* [National Institutes of Health](https://www.nih.gov/) - [Big Data to Knowledge Initiative](https://datascience.nih.gov/bd2k) + * Grants: R01MD010362, 1UG1DA04030901, 1U54EB020404, 1R01CA190329, 1R01DE02524, R00MD010468, 3UH2DA041713, 10555SC +* [National Science Foundation](https://www.nsf.gov/) + * Grants: 1640813, 1722646 +* [Intelligence Advanced Research Projects Activity](https://www.iarpa.gov/) + * Contract: 2017-17042800006 + + + +%package -n python3-cerebralcortex-kernel +Summary: Backend data analytics platform for MD2K software +Provides: python-cerebralcortex-kernel +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-cerebralcortex-kernel +# CerebralCortex Kernel +Cerebral Cortex is the big data cloud companion of mCerebrum designed to support population-scale +data analysis, visualization, model development, and intervention design for mobile sensor data. + +You can find more information about MD2K software on our +[software website](https://md2k.org/software) or the MD2K organization on our +[MD2K website](https://md2k.org/). + +CerebralCortex Kernel is part of our +[CerebralCortex cloud platform](https://github.com/MD2Korg/CerebralCortex). +CerebralCortex-Kernel is capable of parallelizing tasks and scale a job to n-number of cores/machines. CerebralCortex Kernel offers some builtin features as follows: + +## Installation +### Dependencies +CerebralCortex Kernel requires `java 8` to run. Java 8 prior to version 8u92 support is deprecated as of CerebralCortex-Kernel 3.3.0. +- check java version - `java -version` +- set ``JAVA_HOME`` to `java 8` +- OR start python shell with ``JAVA_HOME=/path/to/java/Home python3`` + + +### Install using pip +CerebralCortex-Kernel requires minimum [Python3.6](https://www.python.org/downloads/release/python-360/). To install CerebralCortex-Kernel as an API: + +`pip3 install cerebralcortex-kernel` + +- Note: please use appropriate pip (e.g., pip, pip3, pip3.6 etc.) installed on your machine + +### Install from source code +- Clone repo - +` git clone https://github.com/MD2Korg/CerebralCortex-Kernel.git` +- `cd CerebralCortex-Kernel` +- `python3 setup.py install` + +## Usage + + from cerebralcortex.kernel import Kernel + CC = Kernel(cc_configs="default") + + # to view default configs + print(CC.config) + + # default data storage path is + # /user/home/folder/cc_data + + +By default Kernel will load default configs. Please have a look at all available [configurations](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/conf) for CerebralCortex-Kernel. +You may also load config files as: + +`CC = Kernel(configs_dir_path="dir/path/to/configs/", new_study=True)` + +### How to use builtin algorithms +Using builtin algorithms are as easy as loading data, passing it to algorithm and get the results. +Below is an example on how to compute CGM Glucose Variability Metrics. + +- [Download Glucose Data](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/test_suite/sample_data/cgm_glucose_variability_metrics/sample.csv). The device used to collect glucose was the [Dexcom G6 Continuous Glucose Monitor](https://www.dexcom.com/g6-cgm-system) +- Install Cerebral Cortex Kernel `pip install cerebralcortex-kernel` +- Open terminal and start python3 shell + +### Python Code + # import packages + from cerebralcortex.kernel import Kernel + from cerebralcortex.algorithms.glucose.glucose_variability_metrics import glucose_var + + # Create Kernel object + CC = Kernel(cc_configs="default", new_study=True) + + # Read sample CSV data + ds = CC.read_csv("/path/of/the/downloaded/file/sample.csv", stream_name="cgm_glucose_variability_metrics", header=True) + + # view sample data + ds.show(2) + + # Apply glucose_variability_metrics algorithm on the data + results = glucose_var(ds) + + # view results + results.show(2) + + # save computed data + CC.save_stream(results) + +Please have a look at [jupyter notebook](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/datastream_operation.ipynb) for basic operation that could be perform on DataStream object. + +### Algorithms to Analyze Sensor Data +External CerebralCortex-Kernel offers following builtin algorithms to analyze sensor data. + +- ECG sensor data quality +- ECG RR Interval Computation +- Heart Rate Variability Feature Computation +- CGM Glucose Variability Metrics +- [GPS Data Clustering](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/cc_algorithms.ipynb) +- Sensor Data Interpolation +- Statistical Features Computation +- [List of all available algorithms](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/algorithms) + +### Markers with ML Models +- [Stress Detection using ECG data](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/markers/ecg_stress) +- [mContain Social Crowding](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/markers/mcontain) +- Brushing Detection using Accelerometer and Gyro Data (TODO) + +### Visualization +- [Basic Plots for Timeseries Data](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/plotting_demo.ipynb) +- [Plot GPS Clusters on Map](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/cc_algorithms.ipynb) +- [Stress Visualization](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/plotting_demo.ipynb) + +### Import and Document Data +- [Import CSV Data in CerebralCortex-Kernel Format](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/import_and_analyse_data.ipynb) +- [Document imported Data using MetaData Module](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/import_and_analyse_data.ipynb) + +### External CerebralCortex-Kernel Supported Platforms +- mProv +- mFlow + + +## Examples +- [Jupyter Notebooks](https://github.com/MD2Korg/CerebralCortex/tree/master/jupyter_demo) + +## Documentation + +- [Source code documentation](https://cerebralcortex-kernel.readthedocs.io/en/latest/) + +## Deploy on Cloud +CerebralCortex-Kernel is a part of CerebralCortex cloud platform. To test the complete cloud platform, please visit [CerebralCortex](https://github.com/MD2Korg/CerebralCortex). + + +## FAQ +**1 - Do I need whole CerebralCortex cloud platform to use CerebralCortex-Kernal?** + +No! If you want to use CerebralCortex-Kernel independently. + + +**2 - How can I change NoSQL backend storage layer?** + +CerebralCortex-Kernel follows component based structure. This makes it easier to add/remove features. +* Add a new class in [Data manager-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/). +* New class must have read/write methods. Here is a sample [skeleton class](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/storage_blueprint.py) with mandatory methods required in the new class. +* Create an object of new class in [Data-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/data.py) with appropriate parameters. +* Add appropriate configurations in [cerebralcortex.yml](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml) in (NoSQL Storage)[https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml#L8] section. + +**3 - How can I replace MySQL with another SQL storage system?** + +* Add a new class in [Data manager-SQL](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/core/data_manager/sql). +* New class must implement all of the methods available in [stream_handler.py](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/sql/stream_handler.py) class. +* Create an object of new class in [Data-SQL](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/sql/data.py) with appropriate parameters. +* Add appropriate configurations in [cerebralcortex.yml](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml) in [Relational Storage](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml) section. + +**4 - Where are all the backend storage related classes/methods?** + +In [Data manager-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/). You can add/change any backend storage. + + +## Contributing +Please read our [Contributing Guidelines](https://md2k.org/contributing/contributing-guidelines.html) for details on the process for submitting pull requests to us. + +We use the [Python PEP 8 Style Guide](https://www.python.org/dev/peps/pep-0008/). + +Our [Code of Conduct](https://md2k.org/contributing/code-of-conduct.html) is the [Contributor Covenant](https://www.contributor-covenant.org/). + +Bug reports can be submitted through [JIRA](https://md2korg.atlassian.net/secure/Dashboard.jspa). + +Our discussion forum can be found [here](https://discuss.md2k.org/). + +## Versioning + +We use [Semantic Versioning](https://semver.org/) for versioning the software which is based on the following guidelines. + +MAJOR.MINOR.PATCH (example: 3.0.12) + + 1. MAJOR version when incompatible API changes are made, + 2. MINOR version when functionality is added in a backwards-compatible manner, and + 3. PATCH version when backwards-compatible bug fixes are introduced. + +For the versions available, see [this repository's tags](https://github.com/MD2Korg/CerebralCortex/tags). + +## Contributors + +Link to the [list of contributors](https://github.com/MD2Korg/CerebralCortex-Kernel/graphs/contributors) who participated in this project. + +## License + +This project is licensed under the BSD 2-Clause - see the [license](https://md2k.org/software-under-the-hood/software-uth-license) file for details. + +## Acknowledgments + +* [National Institutes of Health](https://www.nih.gov/) - [Big Data to Knowledge Initiative](https://datascience.nih.gov/bd2k) + * Grants: R01MD010362, 1UG1DA04030901, 1U54EB020404, 1R01CA190329, 1R01DE02524, R00MD010468, 3UH2DA041713, 10555SC +* [National Science Foundation](https://www.nsf.gov/) + * Grants: 1640813, 1722646 +* [Intelligence Advanced Research Projects Activity](https://www.iarpa.gov/) + * Contract: 2017-17042800006 + + + +%package help +Summary: Development documents and examples for cerebralcortex-kernel +Provides: python3-cerebralcortex-kernel-doc +%description help +# CerebralCortex Kernel +Cerebral Cortex is the big data cloud companion of mCerebrum designed to support population-scale +data analysis, visualization, model development, and intervention design for mobile sensor data. + +You can find more information about MD2K software on our +[software website](https://md2k.org/software) or the MD2K organization on our +[MD2K website](https://md2k.org/). + +CerebralCortex Kernel is part of our +[CerebralCortex cloud platform](https://github.com/MD2Korg/CerebralCortex). +CerebralCortex-Kernel is capable of parallelizing tasks and scale a job to n-number of cores/machines. CerebralCortex Kernel offers some builtin features as follows: + +## Installation +### Dependencies +CerebralCortex Kernel requires `java 8` to run. Java 8 prior to version 8u92 support is deprecated as of CerebralCortex-Kernel 3.3.0. +- check java version - `java -version` +- set ``JAVA_HOME`` to `java 8` +- OR start python shell with ``JAVA_HOME=/path/to/java/Home python3`` + + +### Install using pip +CerebralCortex-Kernel requires minimum [Python3.6](https://www.python.org/downloads/release/python-360/). To install CerebralCortex-Kernel as an API: + +`pip3 install cerebralcortex-kernel` + +- Note: please use appropriate pip (e.g., pip, pip3, pip3.6 etc.) installed on your machine + +### Install from source code +- Clone repo - +` git clone https://github.com/MD2Korg/CerebralCortex-Kernel.git` +- `cd CerebralCortex-Kernel` +- `python3 setup.py install` + +## Usage + + from cerebralcortex.kernel import Kernel + CC = Kernel(cc_configs="default") + + # to view default configs + print(CC.config) + + # default data storage path is + # /user/home/folder/cc_data + + +By default Kernel will load default configs. Please have a look at all available [configurations](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/conf) for CerebralCortex-Kernel. +You may also load config files as: + +`CC = Kernel(configs_dir_path="dir/path/to/configs/", new_study=True)` + +### How to use builtin algorithms +Using builtin algorithms are as easy as loading data, passing it to algorithm and get the results. +Below is an example on how to compute CGM Glucose Variability Metrics. + +- [Download Glucose Data](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/test_suite/sample_data/cgm_glucose_variability_metrics/sample.csv). The device used to collect glucose was the [Dexcom G6 Continuous Glucose Monitor](https://www.dexcom.com/g6-cgm-system) +- Install Cerebral Cortex Kernel `pip install cerebralcortex-kernel` +- Open terminal and start python3 shell + +### Python Code + # import packages + from cerebralcortex.kernel import Kernel + from cerebralcortex.algorithms.glucose.glucose_variability_metrics import glucose_var + + # Create Kernel object + CC = Kernel(cc_configs="default", new_study=True) + + # Read sample CSV data + ds = CC.read_csv("/path/of/the/downloaded/file/sample.csv", stream_name="cgm_glucose_variability_metrics", header=True) + + # view sample data + ds.show(2) + + # Apply glucose_variability_metrics algorithm on the data + results = glucose_var(ds) + + # view results + results.show(2) + + # save computed data + CC.save_stream(results) + +Please have a look at [jupyter notebook](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/datastream_operation.ipynb) for basic operation that could be perform on DataStream object. + +### Algorithms to Analyze Sensor Data +External CerebralCortex-Kernel offers following builtin algorithms to analyze sensor data. + +- ECG sensor data quality +- ECG RR Interval Computation +- Heart Rate Variability Feature Computation +- CGM Glucose Variability Metrics +- [GPS Data Clustering](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/cc_algorithms.ipynb) +- Sensor Data Interpolation +- Statistical Features Computation +- [List of all available algorithms](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/algorithms) + +### Markers with ML Models +- [Stress Detection using ECG data](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/markers/ecg_stress) +- [mContain Social Crowding](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/markers/mcontain) +- Brushing Detection using Accelerometer and Gyro Data (TODO) + +### Visualization +- [Basic Plots for Timeseries Data](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/plotting_demo.ipynb) +- [Plot GPS Clusters on Map](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/cc_algorithms.ipynb) +- [Stress Visualization](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/plotting_demo.ipynb) + +### Import and Document Data +- [Import CSV Data in CerebralCortex-Kernel Format](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/import_and_analyse_data.ipynb) +- [Document imported Data using MetaData Module](https://github.com/MD2Korg/CerebralCortex/blob/master/jupyter_demo/import_and_analyse_data.ipynb) + +### External CerebralCortex-Kernel Supported Platforms +- mProv +- mFlow + + +## Examples +- [Jupyter Notebooks](https://github.com/MD2Korg/CerebralCortex/tree/master/jupyter_demo) + +## Documentation + +- [Source code documentation](https://cerebralcortex-kernel.readthedocs.io/en/latest/) + +## Deploy on Cloud +CerebralCortex-Kernel is a part of CerebralCortex cloud platform. To test the complete cloud platform, please visit [CerebralCortex](https://github.com/MD2Korg/CerebralCortex). + + +## FAQ +**1 - Do I need whole CerebralCortex cloud platform to use CerebralCortex-Kernal?** + +No! If you want to use CerebralCortex-Kernel independently. + + +**2 - How can I change NoSQL backend storage layer?** + +CerebralCortex-Kernel follows component based structure. This makes it easier to add/remove features. +* Add a new class in [Data manager-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/). +* New class must have read/write methods. Here is a sample [skeleton class](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/storage_blueprint.py) with mandatory methods required in the new class. +* Create an object of new class in [Data-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/data.py) with appropriate parameters. +* Add appropriate configurations in [cerebralcortex.yml](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml) in (NoSQL Storage)[https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml#L8] section. + +**3 - How can I replace MySQL with another SQL storage system?** + +* Add a new class in [Data manager-SQL](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/core/data_manager/sql). +* New class must implement all of the methods available in [stream_handler.py](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/sql/stream_handler.py) class. +* Create an object of new class in [Data-SQL](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/sql/data.py) with appropriate parameters. +* Add appropriate configurations in [cerebralcortex.yml](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml) in [Relational Storage](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml) section. + +**4 - Where are all the backend storage related classes/methods?** + +In [Data manager-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/). You can add/change any backend storage. + + +## Contributing +Please read our [Contributing Guidelines](https://md2k.org/contributing/contributing-guidelines.html) for details on the process for submitting pull requests to us. + +We use the [Python PEP 8 Style Guide](https://www.python.org/dev/peps/pep-0008/). + +Our [Code of Conduct](https://md2k.org/contributing/code-of-conduct.html) is the [Contributor Covenant](https://www.contributor-covenant.org/). + +Bug reports can be submitted through [JIRA](https://md2korg.atlassian.net/secure/Dashboard.jspa). + +Our discussion forum can be found [here](https://discuss.md2k.org/). + +## Versioning + +We use [Semantic Versioning](https://semver.org/) for versioning the software which is based on the following guidelines. + +MAJOR.MINOR.PATCH (example: 3.0.12) + + 1. MAJOR version when incompatible API changes are made, + 2. MINOR version when functionality is added in a backwards-compatible manner, and + 3. PATCH version when backwards-compatible bug fixes are introduced. + +For the versions available, see [this repository's tags](https://github.com/MD2Korg/CerebralCortex/tags). + +## Contributors + +Link to the [list of contributors](https://github.com/MD2Korg/CerebralCortex-Kernel/graphs/contributors) who participated in this project. + +## License + +This project is licensed under the BSD 2-Clause - see the [license](https://md2k.org/software-under-the-hood/software-uth-license) file for details. + +## Acknowledgments + +* [National Institutes of Health](https://www.nih.gov/) - [Big Data to Knowledge Initiative](https://datascience.nih.gov/bd2k) + * Grants: R01MD010362, 1UG1DA04030901, 1U54EB020404, 1R01CA190329, 1R01DE02524, R00MD010468, 3UH2DA041713, 10555SC +* [National Science Foundation](https://www.nsf.gov/) + * Grants: 1640813, 1722646 +* [Intelligence Advanced Research Projects Activity](https://www.iarpa.gov/) + * Contract: 2017-17042800006 + + + +%prep +%autosetup -n cerebralcortex-kernel-3.3.16 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-cerebralcortex-kernel -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 3.3.16-1 +- Package Spec generated @@ -0,0 +1 @@ +d145de0f9fbe2208cff26f17da1aaa5f cerebralcortex-kernel-3.3.16.tar.gz |
