From a036d77901cf32b79544f44b83a73b884b88ded4 Mon Sep 17 00:00:00 2001
From: Andrew Leifer <leifer@fas.harvard.edu>
Date: Thu, 16 Sep 2010 11:18:41 -0400
Subject: [PATCH] Wrote new protocol generation for flp13 to hit the ventral
 nerve cord.

---
 ProtocolGeneration/flp13_protocol.m | 92 +++++++++++++++++++++++++++++
 1 file changed, 92 insertions(+)
 create mode 100644 ProtocolGeneration/flp13_protocol.m

diff --git a/ProtocolGeneration/flp13_protocol.m b/ProtocolGeneration/flp13_protocol.m
new file mode 100644
index 0000000..ed74319
--- /dev/null
+++ b/ProtocolGeneration/flp13_protocol.m
@@ -0,0 +1,92 @@
+%% Notes
+% Tip of HEAD is (0, 0). 
+% Tail is (99,0)
+%
+% 
+% Pictorially:
+%      (-10,0)  (0,0)  (10,0)
+%             Head
+%                ^ 
+%              /  \
+%             /    \
+%             |    |
+%             |    |
+%             |    |
+%             |    |
+%             |    |
+%             |    |
+%             |    |
+%             |    |
+%             |    |
+%             |    |
+%             |    |
+%             |    |
+%             \    /
+%              \  /
+%               \/
+%             Tail  
+%        (-10,99)  (0,99)  (10,99)
+%
+%
+%    y
+%    ^
+%    |     (axis)
+%    |
+%    ------------> x
+%
+% Note also, you can walk off the worm in y (but not in x).
+
+
+clear all; close all;
+
+
+% Header informatoin
+filename='flip13_ventral.yml';
+gridHeight=100;
+gridWidth=21; %must be odd
+%Note: No carriage return at the end of the description
+description= sprintf('Heuristic ventral illumination of DD motor neurons.');
+
+
+%Index notation
+X=1; Y=2;
+
+%Defualt Radii
+dRad(X)=5;
+dRad(Y)=37;
+
+%We have to convert from the slider bar manual illumination coordinate convention
+%To the protocol illumiantion convention.
+annoyingXOffset=-10;
+%Neuron centroid & radii
+VentralNerveCord(X)=3+annoyingXOffset;
+VentralNerveCord(Y)=57;
+
+%predefine protocol
+protocol=cell(0);
+
+% Protocol = [x1, y1, x2,y2, etc..]
+
+%VentralNerveCord
+protocol{end+1}=rect(VentralNerveCord(X)-dRad(X), VentralNerveCord(Y)-dRad(Y), VentralNerveCord(X)+dRad(X), VentralNerveCord(Y)+dRad(Y) );
+
+% %ALM
+% protocol{end+1}=rect(ALM(X)-dRad(X), ALM(Y)-dRad(Y), ALM(X)+dRad(X), ALM(Y)+dRad(Y) );
+% 
+% %PVM
+% protocol{end+1}=rect(PVM(X)-dRad(X), PVM(Y)-dRad(Y), PVM(X)+dRad(X), PVM(Y)+dRad(Y) );
+% 
+% %PLM
+% protocol{end+1}=rect(PLM(X)-dRad(X), PLM(Y)-dRad(Y), PLM(X)+dRad(X), PLM(Y)+dRad(Y) );
+% 
+
+
+writeProto(filename,description,gridWidth,gridHeight,protocol)
+
+figure;
+for n=1:length(protocol)
+plotProtocol(protocol{n},gridHeight,gridWidth)
+pause
+end
+
+