Update Field Synthesis code for publication in Nature Methods:

1. Document python code in README.txt
2. Update abstract in README.txt
3. Fix python code to run on Windows
4. Allow later half of FieldSynthesisTheorem.m to run if more than 3 arguments are output

FieldSynthesis/FieldSynthesisTheorem.m

@@ -172,7 +172,7 @@
 
 % disp('Press any key');
 % pause;
-return;
+if(nargout > 3)
 
 %% Explanation of the profile of individual line scans
 % T represents a selected column in the spectral field selected by the scan
@@ -260,3 +260,5 @@
 % end;
 
 end
+
+end

README.md

@@ -6,7 +6,7 @@ We introduce Field Synthesis, a theorem and method that can be used to synthesiz
 ## Manuscript
 
 
-Bo-Jui Chang<sup>1</sup>, Mark Kittisopikul<sup>2,4</sup>, Kevin M. Dean<sup>1,3</sup>, Phillipe Roudot<sup>1,3</sup>, Erik Welf<sup>1,3</sup> and Reto Fiolka<sup>1,3</sup>.
+Bo-Jui Chang<sup>1,*</sup>, Mark Kittisopikul<sup>2,4,*</sup>, Kevin M. Dean<sup>1,3</sup>, Phillipe Roudot<sup>1,3</sup>, Erik Welf<sup>1,3</sup> and Reto Fiolka<sup>1,3</sup>.
 "Universal Light-Sheet Generation with Field Synthesis."
 
 ### Affiliations
@@ -15,6 +15,8 @@ Bo-Jui Chang<sup>1</sup>, Mark Kittisopikul<sup>2,4</sup>, Kevin M. Dean<sup>1,3
 3. Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
 4. Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
 
+*These authors contributed equally to this work
+
 ### BioRxiv Preprint
 [https://www.biorxiv.org/content/early/2018/09/26/427468](https://www.biorxiv.org/content/early/2018/09/26/427468)
 
@@ -27,10 +29,19 @@ A more [general Field Synthesis Theorem proof for the an arbitrary, non-ideal li
 
 ## System Requirements
 
+To retrieve code:
+* Git 2.18.0 or above
+
+For MATLAB code:
 * [MATLAB (2017a or above), Mathworks, Natick, MA](https://www.mathworks.com/support/sysreq.html)
 	* Image Processing Toolbox
 	* Follow MATLAB link above for operating system requirements
-* Git 2.18.0 or above
+
+For Python code:
+* Python 3.6.2 or above
+    * NumPy
+    * SciPy
+    * Matplotlib
 
 ## Installation and Demo
 
@@ -40,7 +51,7 @@ git clone https://github.com/AdvancedImagingUTSW/FieldSynthesis.git
 
 See below documentation for demonstration. Typical run time: 10 minutes
 
-## Code
+## MATLAB Code
 
 ### FieldSynthesisTheorem.m
 
@@ -204,13 +215,90 @@ FieldSynthesisVersusLattice.m
  Lab of Robert D. Goldman  
  Northwestern University
 
+
+### Python code - fieldSynthesis.py
+
+ #### USAGE
+
+From a shell:
+```shell
+ python fieldSynthesis.py
+```
+
+From inside IPython:
+```python
+ from fieldSynthesis.py import *
+ demoFieldSynthesis()
+```
+
+![Top row (left to right): F(x,z) beam illumination pattern in front focal plane, L(x)\delta(z) line scan profile in front focal plane, square modulus of line scan profile in front focal plane, \hat{L}(k_x) line scan profile in back focal plane; Bottom row (left to right): Scanned light-sheet, Convolved light-sheet, Convolved light-sheet using Fourier Transform, Field Synthesis light-sheet](images/fieldSynthesisPy.png)
+
+ #### createAnnulus
+```python
+def createAnnulus(n=256, r=32, w=4):
+    ''' createAnnulus - create a ring-like structure
+    INPUT
+    n - size of square array or vector
+    r - radius of the ring
+    w - width of the ring
+    OUTPUT
+    an array n x n
+    '''
+```
+
+ #### doConventionalScan
+```python
+    '''Simulate Conventional digital scanning / dithering
+        INPUT
+        F_sqmod - Square modulus of F at the front focal plane
+        L_sqmod - Square modulus of L at the front focal plane
+        OUTPUT
+        scanned - Scanned (dithered) intensity of Fsqmod by Lsqmod
+    '''
+```
+
+ #### doConventionalScanHat
+```python
+def doConventionalScanHat(F_hat,L_hat):
+    '''Simulate Conventional digital scanning / dithering from frequency space representations
+       INPUT
+       F_hat - Mask at back focal plane
+       L_hat - Line scan profile in frequency space at the back focal plane
+       OUTPUT
+       scanned - Scanned (dithered) intensity of Fsqmod by Lsqmod at front focal plane
+    '''
+```
+
+#### doFieldSynthesisLineScan
+```python
+def doFieldSynthesisLineScan(F_hat,L_hat):
+    '''Simulate Field Synthesis Method
+        INPUT
+        F_hat - Frequency space representation of illumination pattern, mask at back focal plane
+        L_hat - Line scan profile in frequency space at the back focal plane
+        OUTPUT
+        fieldSynthesis - Field synthesis construction by doing a line scan in the back focal plane
+    '''
+```
+
+#### demoFieldSynthesis
+```python
+def demoFieldSynthesis():
+    '''Demonstrate Field Synthesis Method with Plots
+        INPUT
+         None
+        OUTPUT
+         None
+    '''
+```
+
 ## License
 
     See LICENSE.txt
 
     Field Synthesis Demonstration - MATLAB code to demonstrate field synthesis light sheet microscopy
-    Copyright (C) 2018 Reto Fioka, University of Texas Southwestern Medical Center
-    Copyright (C) 2018 Mark Kittisopikul, Northwestern University
+    Copyright (C) 2019 Reto Fioka, University of Texas Southwestern Medical Center
+    Copyright (C) 2019 Mark Kittisopikul, Northwestern University
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by

python/fieldSynthesis.py

@@ -100,8 +100,14 @@ def doFieldSynthesisLineScan(F_hat,L_hat):
 
     return fieldSynthesis
 
-def main():
-    plt.rc('text', usetex=True)
+def demoFieldSynthesis():
+    '''Demonstrate Field Synthesis Method with Plots
+        INPUT
+         None
+        OUTPUT
+         None
+    '''
+    # plt.rc('text', usetex=True)
     fig, ax = plt.subplots(2,4,sharey=True,sharex=True,figsize=(16,9))
 
     # Create F, the illumination pattern
@@ -158,15 +164,16 @@ def main():
     convolvedft = np.real(convolvedft)
 
     ax[1,2].imshow(convolvedft, cmap='plasma')
-    ax[1,2].set_title(r'Convolved FT: $ \mathcal{F}^{-1} \{ \mathcal{F}\{|F|^2\} \mathcal{F}\{|L\delta(z)|^2\} \} $')
+    ax[1,2].set_title(r'Convolved FT: $ \mathcal{F}^{-1} \{ \mathcal{F}\{|F|^2\} \mathcal{F}\{|L(x)\delta(z)|^2\} \} $')
 
     # Do the Field Synthesis method of performing a line scan at the back focal plane
     fieldSynthesis = doFieldSynthesisLineScan(F_hat,L_hat)
 
     ax[1,3].imshow(fieldSynthesis, cmap='plasma')
     ax[1,3].set_title('Field Synthesis: $ \sum_a |\mathcal{F}^{-1}\{ \hat{F}(k_x,k_z)\hat{L}(k_x-a) \}|^2 $')
 
-    plt.show(block=True)
+    plt.ion()
+    plt.show()
 
 if __name__ == "__main__":
-    main()
+    demoFieldSynthesis()