Project structure and readme updates

.gitignore

@@ -56,3 +56,6 @@ docs/_build/
 
 # PyBuilder
 target/
+
+# other
+.idea/

README.md

@@ -1 +1,26 @@
-sweep_recon
+# sweep-recon
+
+---
+## Introduction
+Reconstruction code for respiration resolved SWEEP acquisitions. The code presented here is a builds upon the reconstructiion pipeline described in the paper below. If you find this code useful please acknowledge this paper (in press).
+
+>Jackson LH, Price AN, Hutter J et al. Respiration resolved imaging with continuous stable state 2D acquisition using linear frequency SWEEP. Magn Reson Med. 2019;00:1–15.
+
+An outline of the reconstruction pipeline is given in the figure below. For more details please refer to the paper given above.
+
+![](./data/figures/Figure_1_pipeline.png)
+
+## Example
+```
+Usage:
+     sweeprecon -i path_to_nii <optional args>
+     
+     Optional arguments:
+     --thickness <float>       :: thickness of acquisition slices in mm (default 4mm)
+     --nstates <int>           :: number of respiration states to receonstruct to (defualt 4)
+     --recon_thickness <float> :: thickness of reconstructed slices in mm (default isotropic)
+     --redo                    :: flag to redo processing from scratch
+     --resort_only             :: flag to stop processing after resort step
+     --crop <float>            :: factor to crop from either side of image for bodyarea mask (default 0.2)
+```
+

__main__.py

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+import sys
+
+from sweeprecon.applications.app_sweep_recon import main
+
+if __name__ == "__main__":
+    print('running __main__')
+    sys.exit(main())

sweeprecon/applications/app_sweep_recon.py

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+
+
+def main():
+    return