1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
|
#include <rumba/baseManifold.h>
#include <rumba/exception.h>
#include "normalize.h"
#include "stats.h"
namespace
{
void get_shift_and_scale
( const RUMBA::StatFunctor& f, int type, double& shift, double& scale);
}
namespace RUMBA
{
const int MEAN_NORMALIZE = 1;
const int Z_NORMALIZE = 2;
const int RANGE_NORMALIZE = 4;
}
namespace
{
void get_shift_and_scale
( const RUMBA::StatFunctor& f, int type, double& shift, double& scale)
{
if ( type == RUMBA::RANGE_NORMALIZE )
{
scale = f.max() - f.min();
shift = f.min();
}
else if ( type == RUMBA::Z_NORMALIZE )
{
shift = f.mean();
scale = f.sd();
}
else if ( type == RUMBA::MEAN_NORMALIZE )
{
shift = f.mean();
scale = 1;
}
else
{
throw RUMBA::Exception ("Invalid normalize type in get_shift_and_scale()");
}
}
}
void RUMBA::global_normalize(RUMBA::BaseManifold* pM, int type)
{
RUMBA::BaseManifold& M = *pM;
RUMBA::StatFunctor f(pM);
double shift=0,scale=1;
get_shift_and_scale(f,type,shift,scale);
if (scale != 0 )
{
for ( int i = 0; i < M.size(); ++i )
M[i] = ((double)M[i] - shift) / scale;
}
else
{
for ( int i = 0; i < M.size(); ++i )
M[i] = 0;
}
}
void RUMBA::volume_normalize(RUMBA::BaseManifold* pM, int type)
{
RUMBA::BaseManifold& M = *pM;
double shift =0, scale=1;
intPoint ext = M.extent();
ext.t()=1;
for ( int i = 0; i < M.timepoints(); ++i )
{
RUMBA::StatFunctor f(pM, intPoint(0,0,0,i), ext);
get_shift_and_scale(f,type,shift,scale);
if (scale != 0 )
{
for ( int j = 0; j < M.pixels(); ++j )
M[i*M.pixels()+j] = ( (double)M[i*M.pixels()+j] - shift)/scale;
}
else
{
for ( int j = 0; j < M.pixels(); ++j )
M[i*M.pixels()+j] = 0;
}
}
}
void RUMBA::pixel_normalize(RUMBA::BaseManifold* pM, int type)
{
RUMBA::BaseManifold& M = *pM;
double shift =0, scale=1;
int x,y,z;
for ( int i = 0; i < M.pixels(); ++i )
{
x = i % M.width();
y = (i / M.width()) % M.height();
z = (i / (M.width()*M.height()) ) % M.depth();
RUMBA::StatFunctor
f(pM, intPoint(x,y,z,0), intPoint(1,1,1,M.timepoints()));
get_shift_and_scale(f,type,shift,scale);
if (scale != 0 )
{
for ( int j = 0; j < M.timepoints(); ++j )
M[i+j*M.pixels()] = ((double)M[i+j*M.pixels()] - shift )/scale;
}
else
{
for ( int j = 0; j < M.timepoints(); ++j )
M[i+j*M.pixels()] = 0;
}
}
}
|
