uniovi-simur-wearablepermed-ml 1.1.0__py3-none-any.whl

uniovi_simur_wearablepermed_ml-1.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: uniovi-simur-wearablepermed-ml
+Version: 1.1.0
+Summary: Uniovi Simur WearablePerMed Machine Learning.
+Home-page: https://github.com/Simur-project/uniovi-simur-wearablepermed-ml.git
+Author: Miguel Salinas Gancedo
+Author-email: masalinas.gancedo@gmail.com
+License: MIT
+Project-URL: Documentation, https://pyscaffold.org/
+Platform: any
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+License-File: LICENSE.txt
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+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+Dynamic: license-file
+
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+
+[![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
+
+# Description
+
+> Uniovi Simur WearablePerMed Machine Learning.
+
+*********************************************************************
+* Pasos para lanzar el entrenamiento de un modelo de clasificación: *
+*********************************************************************
+
+1. Abrir el archivo "train_automatizado.py".
+
+2. Entre las líneas 27 y 37, descomentar el modelo de clasificación que se desea entrenar. Comentamos
+   el resto de modelos. Para una misma clase de modelo tenemos 3 posibilidades, en función de si
+   empleamos datos de muslo, muñeca o muslo+muñeca durante el entrenamiento.
+
+3. Ejecutar el archivo "train_automatizado.py". Este código ya empleará el resto de dependencias auxiliares:
+   Datareader, modelGenerator, etc.
+
+Como resultado se guardará el modelo entrenado en formato ".h5" (para las CNNs) o ".pkl" (para RandomForest y XGBoost).
+Estos modelos pueden cargarse para estudiar resultados en la fase de test mediante el fichero "scriptResults_v2.ipynb".
+
+Fragmento del pipeline:
+
+**********************************           **********************************
+* Stack de datos/características *  -------> *    Modelos de clasificación    *
+**********************************           **********************************
+
+
+-------------------------------------------------------
+- Repositorio Machine Learning (desarrollosPMP_SiMuR) -
+-------------------------------------------------------
+
+Árbol de directorios:
+
+/Raíz (desarrollosPMP_SiMuR)
+|
+…
+|
+|-- modelGenerator.py
+|-- train_automatizado.py (PROGRAMA PRINCIPAL)
+|-- Models
+|	|
+|	|-- SiMuRModel.py  (Implementación de las clases, junto con sus métodos, asociada a cada modelo)
+|	|-- *.h5, *.pkl    (Se generan tras entrenar cada modelo)
+|	|-- __init__.py
+|
+|-- scriptResults_v2.ipynb (Resultados en la etapa de test para los modelos entrenados)
+|-- train_hyperparameter_searching_v2.py (Búsqueda de hiperparámetros óptimos de cada modelo, empleando
+					  el algoritmo ASHA).
+
+
+*******************************************
+*       Contenido de SiMuRModel.py        *
+*******************************************
+
+1 clase para cada modelo de clasificación:
+	class SiMuRModel_ESANN        (Red Neuronal Convolucional, CNN)
+	class SiMuRModel_CAPTURE24    (CNN de arquitectura más compleja)
+	class SiMuRModel_RandomForest (Balanced Random Forest)
+	class SiMuRModel_XGBoost <---- Tengo que actualizarlo en GitHub, lo tengo local en mi PC.
+
+Cada modelo para datos de:
+	* thigh (muslo).
+	* wrist (muñeca).
+	* thigh + wrist (muslo + muñeca).
+
+En "train_automatizado.py" se crea un objeto de cada clase y se lanza el entrenamiento del modelo
+de clasificación.
+
+<!-- pyscaffold-notes -->
+
+## Scaffold your project from scratch
+
+- **STEP01**: Install PyScaffold and pyscaffoldext-markdown extension
+
+     - You can install PyScaffold and extensions globally in your systems but ins recomendes use a virtual environment:
+
+          Craate a temp folder and use a virtual environment to install PyScaffold tool and scaffold your project. Later will copy the results under the final git folder and remove the last temporal one:
+
+          ```
+          $ mkdir temp
+          $ cd temp
+          $ python3 -m venv .venv
+          $ source .venv/bin/activate
+          $ pip install pyscaffold
+          $ pip install pyscaffoldext-markdown
+          $ putup --markdown uniovi-simur-wearablepermed-ml -p wearablepermed_ml \
+               -d "Uniovi Simur WearablePerMed ML." \
+               -u https://github.com/Simur-project/uniovi-simur-wearablepermed-ml.git
+          $ deactivate               
+          ```
+
+     - Also you can install **pyscaffold** and **pyscaffoldext-markdown** packages in your system and avoid the error from Python 3.11+: ```"error-externally-managed-environment" this environemnt is externally managed``` you can execute this command to force instalation:
+
+          ```
+          $ pip3 install pyscaffold --break-system-packages
+          $ pip3 install pyscaffoldext-markdown --break-system-packages
+          $ putup --markdown uniovi-simur-wearablepermed-ml -p wearablepermed_ml \
+               -d "Uniovi Simur WearablePerMed ML." \
+               -u https://github.com/Simur-project/uniovi-simur-wearablepermed-ml.git
+          ```
+
+          or permanent configure pip3 with this command to avoid the previous errors from 3.11+
+
+          ```
+          $ python3 -m pip config set global.break-system-packages true
+          ```
+
+- **STEP02**: creare your repo under SIMUR Organization with the name **uniovi-simur-wearablepermed-ml** and clone the previous scaffoled project
+
+     ```
+     $ cd git
+     $ git clone https://github.com/Simur-project/uniovi-simur-wearablepermed-ml.git
+     ```
+
+- **STEP03**: copy PyScaffold project to your git folder without .venv folder
+
+- **STEP04**: install tox project manager used by PyScaffold. Install project dependencies
+     ```
+     $ python3 -m venv .venv
+     $ source .venv/bin/activate
+     $ pip install tox
+     $ pip install pandas
+     $ pip install matplotlib
+     $ pip install openpyxl
+     $ tox list
+     ```
+
+     Installation your python pipeline packages in your virtual environment in development mode:
+
+     ```
+     $ pip freeze > requirements.txt
+     ```
+## Start develop your project
+- **STEP01**: Clone your project
+     ```
+     $ git clone https://github.com/Simur-project/uniovi-simur-wearablepermed-ml.git
+     ```
+
+- **STEP01**: Build and Debug your project
+     ```
+     $ tox list
+     default environments:
+     default   -> Invoke pytest to run automated tests
+
+     additional environments:
+     build     -> Build the package in isolation according to PEP517, see https://github.com/pypa/build
+     clean     -> Remove old distribution files and temporary build artifacts (./build and ./dist)
+     docs      -> Invoke sphinx-build to build the docs
+     doctests  -> Invoke sphinx-build to run doctests
+     linkcheck -> Check for broken links in the documentation
+     publish   -> Publish the package you have been developing to a package index server. By default, it uses testpypi. If you really want to publish your package to be publicly accessible in PyPI, use the `-- --repository pypi` option
+     ```
+
+     ```
+     $ tox -e clean
+     $ tox -e build
+     $ tox -e docs
+     ```
+
+- **STEP02 Build service**
+     ```
+     $ docker build -t uniovi-simur-wearablepermed-ml:1.0.0 .
+     ```
+
+- **STEP03: Tag service**
+     ```
+     $ docker tag uniovi-simur-wearablepermed-ml:1.0.0 ofertoio/uniovi-simur-wearablepermed-ml:1.0.0
+     ```
+
+- **STEP04: Publish service**
+     ```
+     $ docker logout
+     $ docker login
+     $ docker push ofertoio/uniovi-simur-wearablepermed-ml:1.0.0
+     ```
+
+## Using GPU
+Follow these steps to use GPU from your python script:
+
+- **STEP01: Install NVIDIA Drivers**
+     Install NVIDIA Drivers for your card, in our case: NVIDIA GeForce RTX 4060 Ti card
+
+- **STEP02: Install CUDA Toolkit**
+     ```
+     $ sudo apt-get install -y nvidia-cuda-toolkit
+     ```
+
+     Get CUDA version installed:
+
+     ```
+     $ nvcc --version
+     nvcc: NVIDIA (R) Cuda compiler driver
+     Copyright (c) 2005-2023 NVIDIA Corporation
+     Built on Fri_Jan__6_16:45:21_PST_2023
+     Cuda compilation tools, release 12.0, V12.0.140
+     Build cuda_12.0.r12.0/compiler.32267302_0
+     ```
+
+- **STEP03: Install cuDNN**
+
+     Install cuDNN for DeepLearning from python compatible with your CUDA version:
+
+     ```
+	wget https://developer.download.nvidia.com/compute/cudnn/9.10.2/local_installers/cudnn-local-repo-ubuntu2404-9.10.2_1.0-1_amd64.deb
+	sudo dpkg -i cudnn-local-repo-ubuntu2404-9.10.2_1.0-1_amd64.deb
+	sudo cp /var/cudnn-local-repo-ubuntu2404-9.10.2/cudnn-*-keyring.gpg /usr/share/keyrings/
+	sudo apt-get update
+	sudo apt-get -y install cudnn
+     ```
+
+	Install CUDA 12 from aptitude, perform the above configuration but install the CUDA 12 specific package:
+
+     ```
+	sudo apt-get -y install cudnn-cuda-12
+     ```
+
+     Check cuDNN installed:
+     ```
+     $ dpkg -l | grep libcudnn
+     ii  libcudnn9-cuda-12                             9.10.2.21-1                              amd64        cuDNN runtime libraries for CUDA 12.9
+     ii  libcudnn9-dev-cuda-12                         9.10.2.21-1                              amd64        cuDNN development libraries for CUDA 12.9
+     ii  libcudnn9-headers-cuda-12                     9.10.2.21-1                              amd64        cuDNN header files for CUDA 12.9
+     ii  libcudnn9-static-cuda-12                      9.10.2.21-1                              amd64        cuDNN static libraries for CUDA 12.9
+     ```
+
+- **STEP04: Configure CUDA environment**
+     Create a file called **cuda_env.sh** with these env variables configurations:
+
+     ```
+     export CUDA_HOME=/usr/lib/nvidia-cuda-toolkit
+     export PATH=$CUDA_HOME/bin:$PATH
+     export LD_LIBRARY_PATH=$CUDA_HOME/compute-sanitizer:$LD_LIBRARY_PATH
+     export XLA_FLAGS=--xla_gpu_cuda_data_dir=/usr/lib/cuda
+     ```
+
+     make executable the **cuda_env.sh** file:
+
+     ```
+     $ chmod +x cuda_env.sh 
+     ```
+
+     Move the file to profile.d folder, to have these env variables globally, for any user server sessions     
+     ```
+     $ sudo mv cuda_env.sh /etc/profile.d/
+     ```
+     
+- **STEP05: Relogin a session**
+     You must logout and login again using your accout to have access to CUDA env variables. Check it:
+
+     ```
+     echo $CUDA_HOME
+     echo $PATH
+     echo $LD_LIBRARY_PATH
+     echo $XLA_FLAGS
+     ```
+
+## Note
+
+This project has been set up using PyScaffold 4.6. For details and usage
+information on PyScaffold see https://pyscaffold.org/.

uniovi_simur_wearablepermed_ml-1.1.0.dist-info/RECORD

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uniovi_simur_wearablepermed_ml-1.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

uniovi_simur_wearablepermed_ml-1.1.0.dist-info/entry_points.txt

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+[console_scripts]
+tester = wearablepermed_ml.tester:run
+trainer = wearablepermed_ml.trainer:run

uniovi_simur_wearablepermed_ml-1.1.0.dist-info/licenses/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2025 Miguel Salinas Gancedo
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

uniovi_simur_wearablepermed_ml-1.1.0.dist-info/top_level.txt

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+wearablepermed_ml

wearablepermed_ml/__init__.py

@@ -0,0 +1,16 @@
+import sys
+
+if sys.version_info[:2] >= (3, 8):
+    # TODO: Import directly (no need for conditional) when `python_requires = >= 3.8`
+    from importlib.metadata import PackageNotFoundError, version  # pragma: no cover
+else:
+    from importlib_metadata import PackageNotFoundError, version  # pragma: no cover
+
+try:
+    # Change here if project is renamed and does not equal the package name
+    dist_name = "uniovi-simur-wearablepermed-ml"
+    __version__ = version(dist_name)
+except PackageNotFoundError:  # pragma: no cover
+    __version__ = "unknown"
+finally:
+    del version, PackageNotFoundError

wearablepermed_ml/basic_functions/address.py

@@ -0,0 +1,17 @@
+import os
+
+path_here = os.path.abspath('')
+dataset_dir = str(path_here)+'/Data/'
+results_grid_search = str(path_here)+'/Results/Params/'
+path_results_metrics = str(path_here)+'/Results/'
+
+
+def get_param_path(modelID):
+    return os.path.join(results_grid_search,modelID+'.csv')
+
+def get_model_path(modelID, args):
+    path_models = os.path.join(args.case_id_folder, args.case_id)
+    if modelID == 'SiMuRModel_RandomForest_data_tot' or modelID == 'SiMuRModel_RandomForest_data_thigh' or modelID == 'SiMuRModel_RandomForest_data_wrist':
+        return os.path.join(path_models,modelID+'.pkl')
+    else:
+        return os.path.join(path_models,modelID+'.weights.h5')