Chaste Commit::ca8ccdedf819b6e02855bc0e8e6f50bdecbc5208
CryptStatistics.cpp
1/*
2
3Copyright (c) 2005-2024, University of Oxford.
4All rights reserved.
5
6University of Oxford means the Chancellor, Masters and Scholars of the
7University of Oxford, having an administrative office at Wellington
8Square, Oxford OX1 2JD, UK.
9
10This file is part of Chaste.
11
12Redistribution and use in source and binary forms, with or without
13modification, are permitted provided that the following conditions are met:
14 * Redistributions of source code must retain the above copyright notice,
15 this list of conditions and the following disclaimer.
16 * Redistributions in binary form must reproduce the above copyright notice,
17 this list of conditions and the following disclaimer in the documentation
18 and/or other materials provided with the distribution.
19 * Neither the name of the University of Oxford nor the names of its
20 contributors may be used to endorse or promote products derived from this
21 software without specific prior written permission.
22
23THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
24AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
25IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
26ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
27LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
28CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
29GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
30HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
31LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
32OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33
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()