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Added more instructions for setup to readme.
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shakes76 committed Aug 13, 2018
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Expand Up @@ -29,11 +29,30 @@ The main scripts for generating the results of the [publication](https://doi.org
* projects/simulation - To run simulations of the reconstruction algorithms see test_finite_slices_osem_plot.py and test_finite_slices_ossirt_plot.py. Then run the test_compute_metrikz.py to generate the relevant metrics and figures.

## Setup/Dependencies
### WinPython Method
The ChaoS library is dependent on the usual Numpy, Scipy, Matplotlib and scikit-image libraries. You may need pyFFTW installed as well.
The best way to set this up in Windows is using the [WinPython scientific distribution](https://sourceforge.net/projects/winpython/files/WinPython_2.7/2.7.13.1/) for Python 2.7.13.
WinPython sets up a Python distribution with minimal libraries, but in a compact stand-alone directory without the need to install.
In the interest of reproducibility, I have uploaded my WinPython distribution. Simply download, extract, launch Spyder from the distribution, open the script you wish to run and run it.

### Anaconda Method
Give this a go in a conda environment. By default, mine had Qt5 installed, so it breaks lines which explicitly selects Qt4Agg. I suggest just removing that line.
The environment I used is attached in Releases section, created with:
```
$ conda env export > environment.yml
```

To reproduce it if you want, install miniconda then do
```
$ conda env create -f environment.yml
```

After that,
```
python -m test_finite_farey_fractal.py
```
etc.

## Known Issues
* Python 3.5 has issues running the SSIM metric.

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