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Fixed sign in compositeArea calc (polygons with holes now calc OK) #25

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Fixed sign in compositeArea calc (polygons with holes now calc OK) #25

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0b89569
Fixed sign in compositeArea calc (polygons with holes now calc OK)
tomadams1982 Mar 7, 2023
4806f26
Fix 'outdated function syntax' error
tomadams1982 Apr 5, 2023
84955ca
Added SB's findRuns.m
tomadams1982 Apr 5, 2023
9c284ae
Removed dependence on Mapping toolbox
tomadams1982 Apr 5, 2023
1503a48
Corrected feedWastePercentage=1
tomadams1982 Apr 5, 2023
0a63f87
Added runCommand option to run.execute
tomadams1982 Apr 18, 2023
8162bbf
Allowed option for plot extent calculation
tomadams-ssf Jun 27, 2023
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16 changes: 12 additions & 4 deletions lib/+Depomod/+Layout/Site.m
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Original file line number Diff line number Diff line change
Expand Up @@ -125,14 +125,22 @@
end
end

[x, y] = polybool('union', cageStruct(1).x, cageStruct(1).y, cageStruct(1).x, cageStruct(1).y);
%[x, y] = polybool('union', cageStruct(1).x, cageStruct(1).y, cageStruct(1).x, cageStruct(1).y);
A = polyshape(cageStruct(1).x,cageStruct(1).y,'Simplify',false);
[x,y] = boundary(A);


for ss = 2:length(cages)
x1 = x;
y1 = y;
x2 = cageStruct(ss).x;
y2 = cageStruct(ss).y;
[x, y] = polybool('union', x1, y1, x2, y2);
%[x, y] = polybool('union', x1, y1, x2, y2);
B = polyshape(x1,y1,'Simplify',false);
C = polyshape(x2,y2,'Simplify',false);
D = union(B,C);
[x,y] = boundary(D);

end
if plotPerimeter
figure;
Expand Down Expand Up @@ -171,9 +179,9 @@
a = polyarea(x(1:(idx(1)-1)), y(1:(idx(1)-1)));
for pidx = 1:numel(idx)
if pidx == numel(idx)
a = a + polyarea(x((idx(pidx)+1):end), y((idx(pidx)+1):end));
a = a - polyarea(x((idx(pidx)+1):end), y((idx(pidx)+1):end));
else
a = a + polyarea(x((idx(pidx)+1):(idx(pidx+1)-1)), y((idx(pidx)+1):(idx(pidx+1)-1)));
a = a - polyarea(x((idx(pidx)+1):(idx(pidx+1)-1)), y((idx(pidx)+1):(idx(pidx+1)-1)));
end
end
else
Expand Down
31 changes: 24 additions & 7 deletions lib/+Depomod/+Run/Base.m
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Expand Up @@ -232,11 +232,26 @@
% Here we generate x,y vectors covering extent of domain with size matching
% sur.Z value. This seems to fix things.
% Andy used double for loop to populate E,N. But can do it by manipulating meshgrid.
dom=R.project.bathymetry.Domain.spatial;
minX=str2double(dom.minX);
minY=str2double(dom.minY);
maxX=str2double(dom.maxX);
maxY=str2double(dom.maxY);
try
dom=R.project.bathymetry.Domain.spatial;
minX=str2double(dom.minX);
minY=str2double(dom.minY);
maxX=str2double(dom.maxX);
maxY=str2double(dom.maxY);
catch
% dom=R.project.bathymetry.Domain.spatial;
try
minX=str2double(min(R.project.bathymetry.NodeX));
minY=str2double(min(R.project.bathymetry.NodeY));
maxX=str2double(max(R.project.bathymetry.NodeX));
maxY=str2double(max(R.project.bathymetry.NodeY));
catch
print('Cannot define model extent')
end
end
set(gca,'Xlim',[minX,maxX])
set(gca,'Ylim',[minY,maxY])

Nx=length(sur.X)+1;
Ny=length(sur.Y)+1;
X=linspace(minX,maxX,Nx);
Expand Down Expand Up @@ -298,9 +313,9 @@

if ~isempty(legendContours)
if str2num(mv(1:4)) < 2017
leg = legend(legendContours,legendlabels);
leg = legend(legendContours,legendlabels,'color','w');
else
[~,leg] = legend(legendContours,legendlabels, 'AutoUpdate', 'off');
[~,leg] = legend(legendContours,legendlabels, 'AutoUpdate', 'off','color','w');
end

PatchInLegend = findobj(leg, 'type', 'patch');
Expand Down Expand Up @@ -405,6 +420,8 @@
end
end

set(gca,'Xlim',[min(R.project.bathymetry.NodeX),max(R.project.bathymetry.NodeX)])
set(gca,'Ylim',[min(R.project.bathymetry.NodeY),max(R.project.bathymetry.NodeY)])
set(gca,'layer','top');

end
Expand Down
10 changes: 5 additions & 5 deletions lib/+Depomod/Project.m
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@@ -1,11 +1,11 @@
classdef (Abstract) Project < dynamicprops

properties
name@char;
path@char;
solidsRuns@Depomod.Run.Collection;
EmBZRuns@Depomod.Run.Collection;
TFBZRuns@Depomod.Run.Collection;
name char;
path char;
solidsRuns Depomod.Run.Collection;
EmBZRuns Depomod.Run.Collection;
TFBZRuns Depomod.Run.Collection;
end

methods (Static = true)
Expand Down
36 changes: 20 additions & 16 deletions lib/+NewDepomod/+Run/Base.m
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Expand Up @@ -124,16 +124,16 @@
end

properties
modelFile@NewDepomod.PropertiesFile;
physicalPropertiesFile@NewDepomod.PropertiesFile;
configurationFile@NewDepomod.PropertiesFile;
runtimeFile@NewDepomod.PropertiesFile;
inputsFile@NewDepomod.InputsPropertiesFile;
iterationInputsFile@NewDepomod.InputsPropertiesFile;
exportedTimeSeriesFile@NewDepomod.TimeSeriesFile;
consolidatedTimeSeriesFile@NewDepomod.TimeSeriesFile;
solidsSur@Depomod.Sur.Solids;
carbonSur@Depomod.Sur.Solids;
modelFile NewDepomod.PropertiesFile;
physicalPropertiesFile NewDepomod.PropertiesFile;
configurationFile NewDepomod.PropertiesFile;
runtimeFile NewDepomod.PropertiesFile;
inputsFile NewDepomod.InputsPropertiesFile;
iterationInputsFile NewDepomod.InputsPropertiesFile;
exportedTimeSeriesFile NewDepomod.TimeSeriesFile;
consolidatedTimeSeriesFile NewDepomod.TimeSeriesFile;
solidsSur Depomod.Sur.Solids;
carbonSur Depomod.Sur.Solids;
label; % generalisation of run number
iterationRunNumber = [];
modelFileName = '';
Expand Down Expand Up @@ -672,6 +672,7 @@ function setOutputTimes(R, varargin)

jv = NewDepomod.Java;

runCommand = '"C:\Program Files\depomodruntimecontainer\bin\depomodruntimecontainer"'
commandStringOnly = 0;
singleRunOnly = 1;
showConsoleOutput = 1;
Expand All @@ -680,20 +681,23 @@ function setOutputTimes(R, varargin)

for i = 1:2:length(varargin)
switch varargin{i}
case 'commandStringOnly'
commandStringOnly = varargin{i+1};
case 'runCommand'
runCommand = varargin{i+1}
case 'commandStringOnly'
commandStringOnly = varargin{i+1};
case 'singleRunOnly'
singleRunOnly = varargin{i+1};
singleRunOnly = varargin{i+1};
case 'showConsoleOutput'
showConsoleOutput = varargin{i+1};
showConsoleOutput = varargin{i+1};
case 'noSplash'
noSplash = varargin{i+1};
noSplash = varargin{i+1};
case 'runInBackground'
runInBackground = varargin{i+1};
runInBackground = varargin{i+1};
end
end

cmd = jv.run(...
'runCommand', runCommand, ...
'singleRunOnly', singleRunOnly, ...
'commandStringOnly', commandStringOnly, ...
'modelRunTimeFile', R.runtimePath, ...
Expand Down
29 changes: 22 additions & 7 deletions lib/+NewDepomod/BathymetryMikeMesh.m
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Expand Up @@ -154,12 +154,17 @@ function fromFile(BMM, filePath)

function h = plot(BMM, varargin)
mesh = 0;

% TPA 08/05/2023
numCElems = 0;

if ~isempty(varargin)
for i = 1:2:size(varargin,2) % only bother with odd arguments, i.e. the labels
switch varargin{i}
case 'mesh'
mesh = varargin{i + 1};
case 'mesh'
mesh = varargin{i + 1};
% TPA 08/05/2023
case 'contour'
numCElems = varargin{i + 1};
end
end
end
Expand All @@ -171,8 +176,13 @@ function fromFile(BMM, filePath)

minDepth = max(BMM.NodeZ);
maxDepth = min(BMM.NodeZ);
numCElems = ceil(minDepth) - floor(maxDepth);

% TPA 08/05/2023: Encase in "if" to allow effective plotting of a contour by
% supplying number of levels as 'bathyContour' argument to main
% plot function
if numCElems == 0 || numCElems == 1
numCElems = ceil(minDepth) - floor(maxDepth);
end

cmap = colormap(flipud(bone(numCElems)));

bathyColour = zeros(numel(BMM.NodeZ),3);
Expand All @@ -189,8 +199,8 @@ function fromFile(BMM, filePath)
end

end
bathyHandle=trisurf(tri,x,y,z,'FaceVertexCData',bathyColour,'FaceColor', 'interp','EdgeColor','none','FaceAlpha',0.7);

bathyHandle=trisurf(tri,x,y,z,'FaceVertexCData',bathyColour,'FaceColor', 'interp','EdgeColor','none','FaceAlpha',1);
hold on;
view(2);

Expand Down Expand Up @@ -221,6 +231,11 @@ function fromFile(BMM, filePath)
xtickformat('%8.f');
ytickformat('%8.f');
end

% TPA 08/05/2023: Note that the above attempt to colour the land green does
% nothing for an irregular mesh. The line below works, at the
% expense of putting extra green around the water boundary too
set(gca,'Color',[0 0.3 0])
end

function boolMatrix = shallowSeabedIndexes(B, depth)
Expand Down
3 changes: 2 additions & 1 deletion lib/+NewDepomod/InputsPropertiesFile.m
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Expand Up @@ -34,7 +34,8 @@ function setBiomass(IPF, biomass, varargin) % tonnes
IPF.FeedInputs.stockingDensity = num2str(biomass * 1000.0 / IPF.run.cages.cageVolume);

feedWaterPercentage = 9;
feedWastePercentage = 3;
%feedWastePercentage = 3;
feedWastePercentage = 1;
feedAbsorbedPercentage = 85;
feedCarbonPercentage = 49;
faecesCarbonPercentage = 30;
Expand Down
11 changes: 9 additions & 2 deletions lib/+NewDepomod/Java.m
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Expand Up @@ -3,9 +3,12 @@
properties (Constant = true)
versionName = 'newDEPOMOD'
versionNo = 2;
runCommand = '"C:\Program Files\depomodruntimecontainer\bin\depomodruntimecontainer"';
% runCommand = '"C:\Program Files\depomodruntimecontainer\bin\depomodruntimecontainer"';
exportCommand = 'newDEPOMOD\scripts\RunExporter.bat';
end
properties
runCommand = '"C:\Program Files\depomodruntimecontainer\bin\depomodruntimecontainer"';
end

methods (Static = true)
function [newProject, oldProject] = export(run, newProjectPath, varargin)
Expand Down Expand Up @@ -101,13 +104,15 @@
end

function command = run(J, varargin)
command = J.runCommandStringWithOptions(varargin{:});

commandStringOnly = 0;
runInBackground = 1;
verbose = 1;

for i = 1:2:length(varargin) % only bother with odd arguments, i.e. the labels
switch varargin{i}
case 'runCommand'
J.runCommand = varargin{i+1};
case 'commandStringOnly'
commandStringOnly = varargin{i+1};
case 'runInBackground'
Expand All @@ -116,6 +121,8 @@
verbose = varargin{i+1};
end
end

command = J.runCommandStringWithOptions(varargin{:});

if ~commandStringOnly
if verbose
Expand Down
6 changes: 3 additions & 3 deletions lib/+NewDepomod/Project.m
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Expand Up @@ -73,9 +73,9 @@
end

properties
location@NewDepomod.PropertiesFile;
bathymetry% @NewDepomod.BathymetryFile
flowmetry@NewDepomod.FlowmetryFile
location NewDepomod.PropertiesFile;
bathymetry% NewDepomod.BathymetryFile
flowmetry NewDepomod.FlowmetryFile
end

methods
Expand Down
20 changes: 20 additions & 0 deletions lib/findRuns.m
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@@ -0,0 +1,20 @@
function Runs=findRuns(project)

Runs=table;
for i=1:length(project.solidsRuns.labels)
Runs.runType(i)={'NONE'};
Runs.Number(i)=project.solidsRuns.numbers(i);
Runs.Label(i)=project.solidsRuns.labels(i);
end
for j=1:length(project.EmBZRuns.labels)
Runs.runType(i+j)={'EmBZ'};
Runs.Number(i+j)=project.EmBZRuns.numbers(j);
Runs.Label(i+j)=project.EmBZRuns.labels(j);
end
for k=1:length(project.TFBZRuns.labels)
Runs.runType(i+j+k)={'TFBZ'};
Runs.Number(i+j+k)=project.TFBZRuns.numbers(k);
Runs.Label(i+j+k)=project.TFBZRuns.labels(k);
end
Runs=sortrows(Runs);
end