Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
CryptStatistics.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
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10This file is part of Chaste.
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12Redistribution and use in source and binary forms, with or without
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15 this list of conditions and the following disclaimer.
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23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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34*/
35#include "CryptStatistics.hpp"
36#include "RandomNumberGenerator.hpp"
37
42bool CellsHeightComparison(const std::pair<CellPtr, double> lhs, const std::pair<CellPtr, double> rhs)
43{
44 return lhs.second < rhs.second;
45}
46
51
52std::vector<CellPtr> CryptStatistics::GetCryptSection(double yTop, double xBottom, double xTop, bool periodic)
53{
54 double crypt_width = mrCrypt.rGetMesh().GetWidth(0);
55
56 // Fill in the default values - in a sequential manner
57 if (xBottom == DBL_MAX)
58 {
59 xBottom = RandomNumberGenerator::Instance()->ranf()*crypt_width;
60 }
61
62 if (xTop == DBL_MAX)
63 {
64 xTop = RandomNumberGenerator::Instance()->ranf()*crypt_width;
65 }
66
67 assert(yTop>0.0);
68 std::list<std::pair<CellPtr, double> > cells_list; // the second entry is the y value (needed for sorting)
69
70 if (fabs(xTop-xBottom)<0.5*crypt_width)
71 {
72 // The periodic version isn't needed, ignore even if periodic was set to true
73 periodic = false;
74 }
75
76 // Loop over cells and add to the store if they are within a cell's radius of the specified line
78 cell_iter != mrCrypt.End();
79 ++cell_iter)
80 {
81 if (periodic)
82 {
83 if (CellIsInSectionPeriodic(xBottom, xTop, yTop, mrCrypt.GetLocationOfCellCentre(*cell_iter)))
84 {
85 // Set up a pair, equal to (cell,y_val) and insert
86 std::pair<CellPtr, double> pair(*cell_iter, mrCrypt.GetLocationOfCellCentre(*cell_iter)[1]);
87 cells_list.push_back(pair);
88 }
89 }
90 else
91 {
92 if (CellIsInSection(xBottom, xTop, yTop, mrCrypt.GetLocationOfCellCentre(*cell_iter)))
93 {
94 // Set up a pair, equal to (cell,y_val) and insert
95 std::pair<CellPtr, double> pair(*cell_iter, mrCrypt.GetLocationOfCellCentre(*cell_iter)[1]);
96 cells_list.push_back(pair);
97 }
98 }
99 }
100
101 // Sort the list
102 cells_list.sort(CellsHeightComparison);
103
104 // Copy to a vector
105 std::vector<CellPtr> ordered_cells;
106 for (std::list<std::pair<CellPtr, double> >::iterator iter = cells_list.begin();
107 iter!=cells_list.end();
108 ++iter)
109 {
110 ordered_cells.push_back(iter->first);
111 }
112
113 return ordered_cells;
114}
115
116std::vector<CellPtr> CryptStatistics::GetCryptSectionPeriodic(double yTop, double xBottom, double xTop)
117{
118 return GetCryptSection(yTop, xBottom, xTop, true);
119}
120bool CryptStatistics::CellIsInSection(double xBottom, double xTop, double yTop, const c_vector<double,2>& rCellPosition, double widthOfSection)
121{
122 c_vector<double,2> intercept;
123
124 if (xBottom == xTop)
125 {
126 intercept[0] = xTop;
127 intercept[1] = rCellPosition[1];
128 }
129 else
130 {
131 double m = (yTop)/(xTop-xBottom); // gradient of line
132
133 intercept[0] = (m*m*xBottom + rCellPosition[0] + m*rCellPosition[1])/(1+m*m);
134 intercept[1] = m*(intercept[0] - xBottom);
135 }
136
137 c_vector<double,2> vec_from_A_to_B = mrCrypt.rGetMesh().GetVectorFromAtoB(intercept, rCellPosition);
138 double dist = norm_2(vec_from_A_to_B);
139
140 return (dist <= widthOfSection);
141}
142
143bool CryptStatistics::CellIsInSectionPeriodic(double xBottom, double xTop, double yTop, const c_vector<double,2>& rCellPosition, double widthOfSection)
144{
145 bool is_in_section = false;
146
147 c_vector<double,2> intercept;
148 double crypt_width = mrCrypt.rGetMesh().GetWidth(0u);
149
150 double m; // gradient of line
151 double offset;
152
153 if (xBottom < xTop)
154 {
155 offset = -crypt_width;
156 }
157 else
158 {
159 offset = crypt_width;
160 }
161
162 m = (yTop)/(xTop-xBottom+offset); // gradient of line
163
164 // 1st line
165 intercept[0] = (m*m*xBottom + rCellPosition[0] + m*rCellPosition[1])/(1+m*m);
166 intercept[1] = m*(intercept[0] - xBottom);
167
168 c_vector<double,2> vec_from_A_to_B = mrCrypt.rGetMesh().GetVectorFromAtoB(intercept, rCellPosition);
169 double dist = norm_2(vec_from_A_to_B);
170
171 if (dist < widthOfSection)
172 {
173 is_in_section = true;
174 }
175
176 // 2nd line
177 intercept[0] = (m*m*(xBottom-offset) + rCellPosition[0] + m*rCellPosition[1])/(1+m*m);
178 intercept[1] = m*(intercept[0] - (xBottom-offset));
179
180 vec_from_A_to_B = mrCrypt.rGetMesh().GetVectorFromAtoB(intercept, rCellPosition);
181 dist = norm_2(vec_from_A_to_B);
182
183 if (dist < widthOfSection)
184 {
185 is_in_section = true;
186 }
187
188 return is_in_section;
189}
c_vector< double, SPACE_DIM > GetLocationOfCellCentre(CellPtr pCell)
MeshBasedCellPopulation< 2 > & mrCrypt
bool CellIsInSectionPeriodic(double xBottom, double xTop, double yTop, const c_vector< double, 2 > &rCellPosition, double widthOfSection=1.0)
std::vector< CellPtr > GetCryptSectionPeriodic(double yTop, double xBottom=DBL_MAX, double xTop=DBL_MAX)
std::vector< CellPtr > GetCryptSection(double yTop, double xBottom=DBL_MAX, double xTop=DBL_MAX, bool periodic=false)
bool CellIsInSection(double xBottom, double xTop, double yTop, const c_vector< double, 2 > &rCellPosition, double widthOfSection=0.5)
CryptStatistics(MeshBasedCellPopulation< 2 > &rCrypt)
MutableMesh< ELEMENT_DIM, SPACE_DIM > & rGetMesh()
static RandomNumberGenerator * Instance()