Installation

This tutorial demonstrates how to install Pysodb on a method which use for pseudo-spatiotemporal analysis.

Using spaceflow as an example, install Pysodb in its installation environment.

Reference tutorials presents can be found at https://github.com/hongleir/SpaceFlow and https://github.com/TencentAILabHealthcare/pysodb.

Installing softwares and tools

1. The first step is to install Visual Studio Code, Conda, Jupyter notebook, and CUDA in advance.

Reference tutorials presents how to install Visual Studio Code, Conda, Jupyter notebook and CUDA, respectively. And they can be found at https://code.visualstudio.com/Docs/setup/setup-overview, https://code.visualstudio.com/docs/python/environments#_activating-an-environment-in-the-terminal, https://code.visualstudio.com/docs/datascience/data-science-tutorial and https://developer.nvidia.com/cuda-downloads.

2. Launch Visual Studio Code and open a terminal window.

Henceforth, various packages or modules will be installed via the command line

Installation SpaceFlow

3. Create a conda environment

conda create -n <environment_name> python=3.8

4. Activate a conda environment

Run the following command on the terminal to activate the conda environment:

conda activate <environment_name>

5. Install torch with CUDA

eg. pip install torch==1.13.0+cu117 -f https://download.pytorch.org/whl/cu117/torch_stable.html

pip install torch==<torch_version>+<cuda_version> -f https://download.pytorch.org/whl/<cuda_version>/torch_stable.html

6. Install torch_scatter, torch_sparse and torch_cluster

Install a Torch_scatter, Torch_sparse and torch_cluster according to the version of pytorch and CUDA, system. Select the package and copy a run command to run on your terminal. https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html

eg. pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-1.13.0+cu117.html

7. Install SpaceFlow package

pip install SpaceFlow

8. Install palettable package

pip install palettable

Installation Pysodb

Keep the conda environment active

9. Select the installation path and open it

cd <path>

10. Clone Pysodb code

git clone https://github.com/TencentAILabHealthcare/pysodb.git

If cloning the code fails through git, please download it at https://github.com/TencentAILabHealthcare/pysodb, upload it to the folder created above, and extract it.

11. Open the Pysodb directory

cd pysodb

12. Install a Pysodb package from source code

python setup.py install

If “error: urllib3 2.0.0a3 is installed but urllib3<1.27,>=1.21.1 is required by {‘requests’}” appears, users can execute the following commands,respectively.

pip install 'urllib3>=1.21.1,<1.27'
python setup.py install

print('finish！')

finish！