A MicroAnalysis Toolkit.
Project description
SMAK3.0
MicroAnalysis Toolkit v3
If you haven't recently used conda, it is a good idea to update your installation before beginning. conda update conda
Installation with Conda
- Create a new environment from Anaconda prompt/navigator. Choose 'y' when prompted.
conda create -n smakenv python==3.10
- Activate the new environment
conda activate smakenv
- Install package via pip
pip install smak
- Navigate to the folder within your anaconda environment where smak has been installed. This can be tricky to find.
- To start, type in
PATH
(windows) or$PATH
(mac). This will provide a list of Anaconda directories. Yours may look something like this: "C:\Users\yourUsername\AppData\Local\anaconda3\envs\smakenv" (windows) - Copy the first of the paths from the previous step and navigate to that folder on your computer in finder/file explorer. This is the folder for your smak specific virtual environment.
- From the virtual environment folder, navigate to "Lib\site-packages\smak" (windows) or "Lib\python 3.10\site-packages\smak"(mac)
- In this folder, you will see the code for smak, including "smak.py". Bookmark this folder, you will need to access it frequently.
- To start, type in
Optional: Segmentation and image registration
To use the full functionality of SMAK, you will need to follow a few additional steps. This is not necessary unless you plan to use segmentation and image registration.
- Download the files from the following links. They are quite large and may take a while to download.
- Move the files into the main smak folder. This is the folder you found and bookmarked in step 4 of "Installation with Conda".
- From Anacoda prompt, with your smakenv virtual environment active, run the following commands to install packages. Please follow this exact order of package installation.
pip install pycocotools
pip install git+https://github.com/facebookresearch/segment-anything.git
pip install pytorch
pip install torchvision
conda install lap -c conda-forge
pip install numpy==1.24
- To check this functionality, open SMAK and navigate to the Analyze/Segmentation. An expanded menu including "Initialize SAM" will be available to you.
Running SMAK
- Open Anaconda prompt/navigator.
- Activate the environment you use to run smak
conda activate smakenv
- Navigate to the folder within your anaconda environment where smak has been installed. This is the folder you found and bookmarked in step 4 of "Installation with Conda". Using quotes aroung the path may be helpful.
- Run smak
python smak.py
Improvements on this installation process and guide are underway! In the meantime, don't hesitate to reach out to Joy (joy.a.wood@dartmouth.edu) or Sam (samwebb@slac.stanford.edu) for assistance.
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