Merge branch 'main' of github.com:Chaste/OpenVT

Matlab /PlotTest2aMonolayerGrowth.m

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+
+clear; close all;
+
+load ../../../testoutput_2/Test02aMonolayerGrowth/results_from_time_0/tissuewidth.dat
+
+plot(tissuewidth(:,1),tissuewidth(:,4), 'k')
+
+xlabel("Time(h)")
+ylabel("Tissue Width (\mu m)")
+
+SaveAsPngEpsAndFig(-1,['Figs/ChasteMonolayerGrowth'], 12, 7/5, 12);
+

Matlab /SaveAsPngEpsAndFig.m

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+% Save a figure as a .png .eps and .fig and adjust font sizes according to the
+% expected graph size in the .pdf file
+% filename          file name WITHOUT EXTENSION
+% h                 list of plot handles in the current figure whose marker size or
+%                   line width should be modified. If h is -1, then all
+%                   markers/lines in the figure have their sizes changed
+% pdfwidth          graph width in the pdf file
+% widthheightratio  16/9, 4/3, Pi whatever you prefer
+% pdflabelsize      desired label font size in the pdf file. Axis tick
+%                   labels and legends have a fontsize of 0.8xpdflabelsize 
+%
+%
+% Warnings: 
+% 1 - the current figure should be the one we want to export (i.e. function acts on 'gcf')
+% 2 - at the end of the function axis object is in manual mode. Type 'axis
+% auto' to put them in 'auto mode'. Units of the gcf are also modified to
+% "centimeters"
+% 3 - the first 5 parameters defined just after the function declaration
+% could be parameters. Sensibly modifying their value should not cause the
+% function to fail. Reasonable ranges are indicated between brackets.
+% 4 - generated pdf and eps do not look exactly the same. Nothing I can't
+% do about that.
+% 5 - Not tested for 3D plots. It might work though.
+%
+% Edited by Ozzy on 11/08/2011
+
+function SaveAsPngEpsandFig(h,filename, pdfwidth, widthheightratio,pdflabelsize)
+
+
+linewidth = 0.8;                              % line width in ? (between 1 and 3)
+markersize = 1;                             % size of markers in pt (1-20)
+labeloveraxislabelratio = 0.8;              % ratio between label font size and axis label font size (between 0 and 1)
+gridwidth = 0.5;                              % line width of the grid (between 1 and 3)
+resolution = 300;                           % resolution in dpi (between 150 and 600)
+
+
+set(gcf, 'Units','centimeters')             % Change units of the gcf to centimeters
+dimensions = [pdfwidth (pdfwidth/widthheightratio)]         % Work out new dimensions
+labelsize = pdflabelsize;                       
+axeslabelsize =floor(labeloveraxislabelratio*labelsize);    % Work out axis label font size
+
+hold on;
+axis manual                                  % to prevent scale change when resizing
+
+set(gca,'fontsize',axeslabelsize);           % set font size of the axes tick labels
+set(gca,'linewidth',gridwidth);              % set line width of axis and grid (not plots)
+set(gcf,'position', [0,0, dimensions]);      % set display size
+set(gcf,'PaperPositionMode','auto');         % Prevent redimensioning by the print function
+set(get(gca,'XLabel'),'fontsize',labelsize); % set font size for xlabel
+set(get(gca,'YLabel'),'fontsize',labelsize); % set font size for ylabel
+set(get(gca,'ZLabel'),'fontsize',labelsize); % set font size for zlabel
+set(get(gca,'Title'),'fontsize',labelsize);  % set font size for title
+
+if (h == -1)                                 % if plot handles that need line width change is -1
+    h = get(gca,'Children');                 % do it for all
+end
+
+for i=1:length(h)
+    set(h(i), 'linewidth' , linewidth);      % set line width
+    %set(h(i), 'MarkerSize' , markersize);    % set marker size
+end
+
+resolution_str = ['-r' num2str(resolution)];
+
+%Rescale so dont cut off xLabel
+set(gca,'OuterPosition',[0.01 0.01 0.99 0.99])
+
+print('-depsc2',resolution_str, filename);   % export .eps (In fact, eps does not really care about the resolution)
+print('-dpng',resolution_str, filename);     % export .png
+
+savefig(filename); %save the fig for backup
+
+
+
+
+
+
+

src/Test02aMonolayerGrowth/FixedDurationCellCycleModel.cpp

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+/*
+
+Copyright (c) 2005-2022, University of Oxford.
+All rights reserved.
+
+University of Oxford means the Chancellor, Masters and Scholars of the
+University of Oxford, having an administrative office at Wellington
+Square, Oxford OX1 2JD, UK.
+
+This file is part of Chaste.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of the University of Oxford nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+*/
+
+#include "AbstractSimplePhaseBasedCellCycleModel.hpp"
+#include "DifferentiatedCellProliferativeType.hpp"
+
+#include "FixedDurationCellCycleModel.hpp"
+
+template<class Archive>
+void FixedDurationCellCycleModel::serialize(Archive & archive, const unsigned int version)
+{
+    // Archive cell-cycle model using serialization code from AbstractSimplePhaseBasedCellCycleModel
+    archive & boost::serialization::base_object<AbstractSimplePhaseBasedCellCycleModel>(*this);
+}
+
+FixedDurationCellCycleModel::FixedDurationCellCycleModel()
+    : AbstractSimplePhaseBasedCellCycleModel()
+{
+  SetPhaseDurations();
+}
+
+void FixedDurationCellCycleModel::SetPhaseDurations()
+{
+    SetStemCellG1Duration(7.0);
+    SetTransitCellG1Duration(7.0);
+    SetSDuration(6.0);
+    SetG2Duration(3.0);
+    SetMDuration(2.0);
+    SetMinimumGapDuration(3.0);
+}
+
+void FixedDurationCellCycleModel::SetG1Duration()
+{
+    assert(mpCell != NULL);  // Make sure cell exists
+
+    mG1Duration = 7.0;
+}
+
+AbstractCellCycleModel* FixedDurationCellCycleModel::CreateCellCycleModel()
+{
+    // Create a new cell-cycle model
+    FixedDurationCellCycleModel* pCellCycleModel = new FixedDurationCellCycleModel();
+    return pCellCycleModel;
+}
+
+void FixedDurationCellCycleModel::UpdateCellCyclePhase()
+{
+    double timeSinceBirth = GetAge();
+    assert(timeSinceBirth >= 0);
+
+    if (mpCell->GetCellProliferativeType()->IsType<DifferentiatedCellProliferativeType>())
+    {
+        mCurrentCellCyclePhase = G_ZERO_PHASE;
+    }
+    else if (timeSinceBirth < GetG1Duration())
+    {
+        mCurrentCellCyclePhase = G_ONE_PHASE;
+    }
+    else if (timeSinceBirth <  GetG1Duration() + GetSDuration())
+    {
+        mCurrentCellCyclePhase = S_PHASE;
+    }
+    else if (timeSinceBirth < GetG1Duration() + GetSDuration() + GetG2Duration())
+    {
+        mCurrentCellCyclePhase = G_TWO_PHASE;
+    }
+    else if (timeSinceBirth < GetG1Duration() + GetSDuration() + GetG2Duration() + GetMDuration())
+    {
+        mCurrentCellCyclePhase = M_PHASE;
+    }
+}
+
+#include "SerializationExportWrapperForCpp.hpp"
+CHASTE_CLASS_EXPORT(FixedDurationCellCycleModel)

src/Test02aMonolayerGrowth/FixedDurationCellCycleModel.hpp

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+/*
+
+Copyright (c) 2005-2022, University of Oxford.
+All rights reserved.
+
+University of Oxford means the Chancellor, Masters and Scholars of the
+University of Oxford, having an administrative office at Wellington
+Square, Oxford OX1 2JD, UK.
+
+This file is part of Chaste.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of the University of Oxford nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+*/
+
+#ifndef FIXEDDURATIONCELLCYCLEMODEL_HPP_
+#define FIXEDDURATIONCELLCYCLEMODEL_HPP_
+
+#include "AbstractSimplePhaseBasedCellCycleModel.hpp"
+
+// "Simple" cell-cycle model: phase durations are set when the model is created.
+class FixedDurationCellCycleModel : public AbstractSimplePhaseBasedCellCycleModel
+{
+private:
+    // For archiving (saving or loading) the cell-cycle model object in a cell-based simulation. 
+    friend class boost::serialization::access;
+    template<class Archive>
+    void serialize(Archive & archive, const unsigned int version);
+
+    void SetPhaseDurations();
+    void SetG1Duration() override;
+
+public:
+    FixedDurationCellCycleModel();
+
+    // Override builder method for new copies of the cell-cycle model.
+    AbstractCellCycleModel* CreateCellCycleModel() override;
+
+    // Override to start phase from G1
+    void UpdateCellCyclePhase() override;
+};
+
+// Provides a unique identifier for the custom cell-cycle model.
+// Needed for archiving and for writing out parameters file.
+// Simulations will throw errors if missing.
+#include "SerializationExportWrapper.hpp"
+CHASTE_CLASS_EXPORT(FixedDurationCellCycleModel)
+
+#endif // FIXEDDURATIONCELLCYCLEMODEL_HPP_