sci_compute_env

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sci_compute_env

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A Stock Scientific Computing / Deep Learning Environment for Analysis of Remote Sensing Data

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// repository documentation

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## A Stock Scientific Computing / Deep Learning Environment for Analysis of  Remote Sensing Data

#### This was initially intended to serve as a framework for object detection and semantic segmentation in satellite or drone imagery, but should serve as a general reproducible environment for analysis of remote sensing data as well as machine learning.

### Set up your environment

1. Install Docker Desktop on Windows/Mac (https://www.docker.com/products/docker-desktop) or Ubuntu which I recommend above Mac/PC (https://docs.docker.com/install/linux/docker-ce/ubuntu/).
2. Install Git
3. Clone this repository (or the one you're using)
```
git clone https://github.com/patrickcgray/uas_obj_detection.git
```
4. Move into that directory
```
cd sci_compute_env
```

5. Create a Docker Image and Container based on the Dockerfile in the repo. The `-p` makes that port on the Docker container visible on the host machine and the `-v` does a same for a specifc volume, so basically you're passing those through from the VM to your host. If you're building a deep learning environment change `Dockerfile` to `DockerfileGPU` or just use your own Dockerfile that you've written.
```
docker build -t <img_name> Dockerfile
docker run --name <cont_name> -it -p 8888:8888 -p 6006:6006 -v ~/:/host <img_name>
```
Your Docker image is now built and you instantiated a container from that image that is now running. Exit that container (which also stops it).
```
exit
```
Now the container is stopped, restart it and attach it to the terminal.
```
docker start <cont_name>
docker attach <cont_name>
```
Now your terminal is in the container, start jupyter:
```
jupyter notebook --allow-root --ip 0.0.0.0 /host
```

5. Navigate to the URL shown in the terminal after starting jupyter and test if everything works. Start a new jupyter notebook or open an existing one and run some simple python commands such as:

```
1+1
>>> 2
```
```
import numpy
```

### If you're using this as a general scientific computing environment you're all set!

### If you're using this for ML/DL continue on to the data processing, analysis, and machine learning steps.

6. Do you have training data and labels? If yes skip 7, if no you'll likely spend a while doing 7.

7. Tile data and manually create labels in VIA http://www.robots.ox.ac.uk/~vgg/software/via/. There may be better tools depending on your use case. Arc is potentially viable for manual labels, but can be inaccurate without a very rigorous workflow and most CNNs will require tiles because of memory constraints anyway.
  
Make sure you generate training, validation, and testing splits of your dataset.

8. Build your deep learning model, or if you're using a pre-built CNN simply make sure it is loaded and functions correctly. This step of course may take a while for a custom model but is not as challenging as it may seem unless you're planning to do research more in the DL field itself.
  
8. Ensure labels are in the correct format for model.

9. Train the model.

10. Tweak hyperparameters on the model.

Repeat 9 and 10 until happy.

12. Now run the model on your whole dataset and finally get the products that are motivating this whole analysis.

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