Added start prompt and shell script to open interface

The shell script to open the interface is itself being opened by a .Command file created on the desktop of the Mac used to develop SedSettle.

SettlingTubeInterface.m

@@ -1,3 +1,7 @@
+%% WELCOME TO THE SETTLING TUBE INTERFACE
+% SIMPLY SET THE FOLLOWING VARIABLES IN THE 'SETUP' SECTION:
+%    sample_short_name, dry_weight_input, minutes, sampling_interval, water_temp
+% ...and press 'Run' to begin the data collection
 %% CLEANUP
 clear; clc;
 %% SETUP
@@ -6,24 +10,16 @@
     string(datetime('now','Format','d-MMM-y_HH:mm')));
 dry_weight_input = 9.80; % g
 minutes = 10; % number of minutes to collect data (default is 10 minutes)
-sampling_interval = 0.2; % how often should the data be collected (seconds)?
-water_temp = 24; % degrees C
+sampling_interval = 0.1; % how often should the data be collected (seconds)?
+water_temp = 23; % degrees C
 settling_tube_length = 203.3; % cm
-use_synthetic_data = false; % set to true to use synthetic data for testing purposes
 time_collected = datetime;
 %% PACKAGE DATA AS STRUCTS
 SampleVars = struct('minutes',minutes,'sampling_interval',sampling_interval, ...
     'dry_weight_input',dry_weight_input);
 STvars = struct('water_temp',water_temp,'st_length',settling_tube_length);
-%% OPTIONALLY, USE SYNTHETIC DATA
-% NOTE: This code requires the MATLAB Fuzzy Logic Toolbox
-if use_synthetic_data == true
-    [data_grainSizeResults, mass_plot, dry_weight_input] = runSyntheticData(SampleVars, STvars);
-end
 %% TAKE MEASUREMENTS WITH THE MASS BALANCE
-if use_synthetic_data == false
-    [data_grainSizeResults, mass_plot, data_mass_timeseries, data_expected_kinematics] = runSettlingTube(SampleVars, STvars);
-end
+[data_grainSizeResults, mass_plot, data_mass_timeseries, data_expected_kinematics] = runSettlingTube(SampleVars, STvars);
 %% RUN THE STATISTICS
 grainStatistics(dry_weight_input, data_grainSizeResults)
 folkWardStats(data_grainSizeResults, phiPercentiles(data_grainSizeResults))
@@ -33,16 +29,14 @@
 phi_size_distribution = plotPhiDistribution(data_grainSizeResults);
 %% SAVE RESULTS
 % NOTE: This happens automatically if you are in the SedSettle directory
-if use_synthetic_data == false
-    pwd_parts = strsplit(pwd,'/');
-    if strcmp(pwd_parts(end), 'SedSettle') == 1
-        workspaceOut = fullfile('results',sample_long_name);
-    else % if not in the SedSettle directory, prompt to choose a save location
-        msgbox('Select a directory to save the SedSettle results in.')
-        selpath = uigetdir(pwd,'Select save location for SedSettle results');
-        workspaceOut = fullfile(selpath,sample_long_name);
-    end
-    warning('off','MATLAB:Figure:FigureSavedToMATFile')
-    save(strcat(workspaceOut,'.mat'))
+pwd_parts = strsplit(pwd,'/');
+if strcmp(pwd_parts(end), 'SedSettle') == 1
+    workspaceOut = fullfile('results',sample_long_name);
+else % if not in the SedSettle directory, prompt to choose a save location
+    msgbox('Select a directory to save the SedSettle results in.')
+    selpath = uigetdir(pwd,'Select save location for SedSettle results');
+    workspaceOut = fullfile(selpath,sample_long_name);
 end
+warning('off','MATLAB:Figure:FigureSavedToMATFile')
+save(strcat(workspaceOut,'.mat'))
 disp('Settling tube data collection COMPLETE')

functions/runSyntheticData.m

@@ -1,6 +1,9 @@
 function [new_mass_timeseries, figHandle, dry_weight_input] = runSyntheticData(SampleVars, STvars)
 % Use artificial data instead of data collected with the settling tube.
 %   Requires the Fuzzy Logic Toolbox.
+%
+%   To run from SettlingTubeInterface.m:
+%       [data_grainSizeResults, mass_plot, dry_weight_input] = runSyntheticData(SampleVars, STvars);
     minutes = SampleVars.minutes;
     sampling_interval = SampleVars.sampling_interval;
     x = (0:sampling_interval:((60*minutes)-sampling_interval)); % time in seconds

functions/startSounds.m

@@ -25,6 +25,12 @@ function startSounds(~, ~, firstbeeps, secondbeeps, time_between_beeps)
 t1.TimerFcn = @(~,thisEvent)sound(c_tone);
 t1.StopFcn = @(~,thisEvent)start(t2);
 
-start(t1)
+t0 = timer();
+t0.ExecutionMode = 'singleShot';
+t0.TimerFcn = @(~,thisEvent)waitfor(msgbox('Press OK to begin the Settling Tube data collection.'));
+t0.StopFcn = @(~,thisEvent)start(t1);
+
+start(t0)
+
 end
 

shell/SettlingTube.sh

@@ -0,0 +1,4 @@
+#/bin/bash
+matlabroot='/Applications/MATLAB_R2018a.app/bin/'
+cd $matlabroot
+./matlab -r "open('SettlingTubeInterface.m')" -sd '~/Documents/GitHub/SedSettle'