From 5d88bff07d15eaf35e5a9ec886bced3740e358df Mon Sep 17 00:00:00 2001
From: mpalmsten <meg.palmsten@nrlssc.navy.mil>
Date: Tue, 4 Apr 2017 22:29:14 -0500
Subject: [PATCH] script that went with cBathy practicum at CIRN Boot Camp #1

---
 cBathyDemoWithPlots/cBathyDemoWithPlots.m | 116 ++++++++++++++++++++++
 1 file changed, 116 insertions(+)
 create mode 100644 cBathyDemoWithPlots/cBathyDemoWithPlots.m

diff --git a/cBathyDemoWithPlots/cBathyDemoWithPlots.m b/cBathyDemoWithPlots/cBathyDemoWithPlots.m
new file mode 100644
index 0000000..eb5f14b
--- /dev/null
+++ b/cBathyDemoWithPlots/cBathyDemoWithPlots.m
@@ -0,0 +1,116 @@
+% This script is designed to demonstrate the cBathy Toolbox in production
+% mode and in debug mode. It also demonstrates some of the plotting
+% functions to investigate cBathy results. It was developed as a
+% demonstration for CIRN Boot Camp #1, 3/2017. It is designed to be stepped
+% through line by line while reading the comments.
+
+clear
+
+% find the path to the cBathy Toolbox
+cBathyToolboxPath = what('cbathy-Toolbox');
+
+% cd to the cBathy Toolbox directory to run demo
+cd(cBathyToolboxPath.path)
+
+% look at the contents of the toolbox
+help cbathy-Toolbox
+
+%% set to production mode and process
+% First open the "settings" file argus02a.m in the editor and look at inputs
+edit argus02a
+
+% run the cBathyDemo
+democBathy
+
+% look at cBathy result compared to survey plotted in figure 1
+
+% look at the output variable names in the command window
+whos 
+
+% plot the different components for each frequency of cBathy output
+figure
+examineSingleBathyResult(bathy)
+
+% plot the fCombined cBathy result (left panel) and the fCombined error
+% (right panel) of figure 2
+figure(2)
+plotBathyCollect(bathy)
+
+%% run again in debug mode
+% set to debug mode by changing value of params.debug.production = 0
+% in argus02a.m 
+edit argus02a
+
+% pre-open figures and set colormap to jet to view that phase maps more
+% clearly
+figure(10)
+colormap jet
+
+figure(11)
+colormap jet
+
+% run cBathy again in debug mode
+democBathy
+
+% In the debug mode, cBathy will ask at the command line if you want to 
+% look at a subset of the cBathy domain. You only want to look at a few 
+% pixels in the middle of the cBathy domain for debugging. Copy and paste
+% these values for the range of pixels to look at: 
+%[250 275 25 700 725 25]
+
+% follow instructions in command window
+
+% get rid of all of those plots
+close all
+
+% plot the cBathy matrix in time to look like a low resolution movie (you 
+% should see waves)
+figure
+map = showcBathyTimeSeriesMovieNotCIL(stackName,[80 10 500 500 25 700]);
+
+%% run the Kalman filter demo
+% should step through Kalman filtered results with 2 second pause between
+% results
+figure(1)
+demoKalmanFiltering
+
+% open a prior and current bathy. 
+pb = load([cBathyToolboxPath.path,'\102210cBathysSmoothed\1287759600.Fri.Oct.22_15_00_00.GMT.2010.argus02a.cx.cBathy.mat']);
+priorBathy = pb.bathy;
+load([cBathyToolboxPath.path,'\102210cBathysSmoothed\1287763200.Fri.Oct.22_16_00_00.GMT.2010.argus02a.cx.cBathy.mat'])
+
+% compare the prior Kalman filtered bathymetry, the updated bathy, and the
+% updated Kalman filtered bathymetry
+plotBathyKalmanStep(bathy, priorBathy)
+
+% In the plot, the upper left panel is the prior
+% Kalman filtered bathymetry, the lower left panel is the prior Kalman
+% filtered error, the upper middle plot is the updated bathymetry from cBathy
+% phase 2, the lower middle panel is the updated error from phase 2, the
+% right upper panel is the phase 3 Kalman filtered bathymetry, and the
+% phase 3 error
+
+%
+%   Copyright (C) 2017  Coastal Imaging Research Network
+%                       and Oregon State 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 the Free Software Foundation, version 3 of the 
+%    License.
+
+%    This program is distributed in the hope that it will be useful,
+%    but WITHOUT ANY WARRANTY; without even the implied warranty of
+%    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%    GNU General Public License for more details.
+
+%    You should have received a copy of the GNU General Public License
+%    along with this program.  If not, see
+%                                <http://www.gnu.org/licenses/>.
+
+% CIRN: https://coastal-imaging-research-network.github.io/
+% CIL:  http://cil-www.coas.oregonstate.edu
+%
+%key cBathy
+%
+