# Myofibrometry

Welcome to the myofibrometry project. Follow all the detailed steps described in `README.md` in sequence. After you follow all steps you will have one sample dataset called SAS3 in the `data/` sub-folder and streamline generation scripts in the `visualization/heart_vis` sub-folder and plots and images in the `results/` folder. The source matlab code for generating these results is in the `matlab/` folder and requires `Matlab` to run. After running the matlab scripts, the `data/` folder will contain `.mat` files which can be used as inputs for visualizing streamlines using the blender scripts in the `visualization/heart_vis` sub-folder. Detailed instructions on running the blender scripts will be in the README.md file in the `visualization/heart_vis` sub_folder.

Carry out the following sequence of steps to reproduce the results:
## [1] Clone This Repository
To clone this repository first  `git clone` this repository  and install all submodules of the repository. 
```bash
$ git clone https://gitfront.io/r/myoarch/fZmkh5iHEJae/myofibrometry.git
$ cd myofibrometry
$ bash install.sh
```
## [2] Download Dataset
To download the image dataset run the data download script inside the main folder.
```bash
$ cd myofibrometry
$ chmod +x download.sh
$ ./download.sh
```
If the download finishes successfully, you should see a sub folder `SAS3` inside the `data` folder containing two tif files, `wga.tif` and `denoised.tif`.
The download time will depend on your internet connection.

## [3] Generate Field Files
This and the following step should be run using Matlab.
The code requires atleast matlab-2021. However, you manage with version `2019` if you skip saving the final generated plots. 

After launching Matlab enter the `matlab` folder and run the `startup` script.
This script sets up the proper paths required to run the subsequent scripts. 
```matlab
>> startup
```

Field files can be generated by running the  `generateOrientationFields` Matlab script.
```matlab
>> generateOrientationFields
```
For this script to run successfully your machine should have least around 128 GB RAM.
This script may take a while to run, so it is best run it overnight.
Once successfully run your `SAS3` sub folder should contain two new `mat` files.
Specifically, it should now contain two files named `field2d.mat` and `field_sigma_4.mat`.

## [4] Generate Helix Angle plots
To reproduce helix angle plots for different sectors run the `generateSectorPlots` script
```matlab
>> generateSectorPlots
```
The script should run within a few minutes and save the generated figures inside the `results` folder.

Enjoy looking at the plots!