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OpenWalnut
OpenWalnut Core
Commits
2ca0e93b
Commit
2ca0e93b
authored
Nov 22, 2009
by
Alexander Wiebel
Browse files
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Plain Diff
[ADD
#119
] transferred and adapted the smoothing implementation from the
fiberNavigator
parent
34f0defa
Changes
4
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Inline
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Showing
4 changed files
with
327 additions
and
3 deletions
+327
-3
src/dataHandler/WValueSet.hpp
src/dataHandler/WValueSet.hpp
+8
-0
src/dataHandler/WValueSetBase.h
src/dataHandler/WValueSetBase.h
+8
-0
src/modules/distanceMap/WMDistanceMap.cpp
src/modules/distanceMap/WMDistanceMap.cpp
+303
-2
src/modules/distanceMap/WMDistanceMap.h
src/modules/distanceMap/WMDistanceMap.h
+8
-1
No files found.
src/dataHandler/WValueSet.hpp
View file @
2ca0e93b
...
...
@@ -102,6 +102,14 @@ public:
return
&
m_data
[
0
];
}
/**
* Sometimes we need raw access to the data vector.
*/
const
std
::
vector
<
T
>*
rawDataVectorPointer
()
const
{
return
&
m_data
;
}
protected:
...
...
src/dataHandler/WValueSetBase.h
View file @
2ca0e93b
...
...
@@ -64,6 +64,14 @@ public:
return
m_dimension
;
}
/**
* \return Order of the values in this ValueSet
*/
virtual
size_t
order
()
{
return
m_dimension
;
}
/**
* \return Dimension of the values in this ValueSet
*/
...
...
src/modules/distanceMap/WMDistanceMap.cpp
View file @
2ca0e93b
...
...
@@ -23,6 +23,8 @@
//---------------------------------------------------------------------------
#include <string>
#include <algorithm>
#include <vector>
#include "WMDistanceMap.h"
...
...
@@ -53,8 +55,8 @@ const std::string WMDistanceMap::getName() const
const
std
::
string
WMDistanceMap
::
getDescription
()
const
{
return
"This description has to be improved when the module is completed."
" By now lets say the following: Computes a smoothed version of the dataset"
" and a distance map on it. Finally it renders this distance map using MarchinCubes"
;
" By now lets say the following: Computes a smoothed version of the dataset"
" and a distance map on it. Finally it renders this distance map using MarchinCubes"
;
}
...
...
@@ -96,3 +98,302 @@ void WMDistanceMap::properties()
{
// ( m_properties->addDouble( "isoValue", 80 ) )->connect( boost::bind( &WMMarchingCubes::slotPropertyChanged, this, _1 ) );
}
boost
::
shared_ptr
<
WDataSetSingle
>
WMDistanceMap
::
createOffset
(
boost
::
shared_ptr
<
WDataSetSingle
>
dataSet
)
{
std
::
vector
<
float
>
floatDataset
;
// TODO(wiebel): we should be able to do all this without the value vector.
boost
::
shared_ptr
<
WValueSet
<
float
>
>
valueSet
=
boost
::
shared_dynamic_cast
<
WValueSet
<
float
>
>
(
(
*
dataSet
).
getValueSet
()
);
assert
(
valueSet
);
boost
::
shared_ptr
<
WGridRegular3D
>
grid
=
boost
::
shared_dynamic_cast
<
WGridRegular3D
>
(
(
*
dataSet
).
getValueSet
()
);
assert
(
grid
);
const
std
::
vector
<
float
>*
source
=
valueSet
->
rawDataVectorPointer
();
int
b
,
r
,
c
,
bb
,
rr
,
r0
,
b0
,
c0
;
int
i
,
istart
,
iend
;
int
nbands
,
nrows
,
ncols
,
npixels
;
int
d
,
d1
,
d2
,
cc1
,
cc2
;
float
u
,
dmin
,
dmax
;
bool
*
srcpix
;
double
g
,
*
array
;
// nbands = m_frame;
// nrows = m_rows;
// ncols = m_columns;
nbands
=
grid
->
getNbCoordsZ
();
nrows
=
grid
->
getNbCoordsY
();
ncols
=
grid
->
getNbCoordsX
();
npixels
=
std
::
max
(
nbands
,
nrows
);
array
=
new
double
[
npixels
];
npixels
=
nbands
*
nrows
*
ncols
;
floatDataset
.
resize
(
npixels
);
for
(
int
i
=
0
;
i
<
npixels
;
++
i
)
{
floatDataset
[
i
]
=
0.0
;
}
bool
*
bitmask
=
new
bool
[
npixels
];
for
(
int
i
=
0
;
i
<
npixels
;
++
i
)
{
if
(
source
->
at
(
i
)
<
0.01
)
bitmask
[
i
]
=
true
;
else
bitmask
[
i
]
=
false
;
}
dmax
=
999999999.0
;
// first pass
for
(
b
=
0
;
b
<
nbands
;
++
b
)
{
for
(
r
=
0
;
r
<
nrows
;
++
r
)
{
for
(
c
=
0
;
c
<
ncols
;
++
c
)
{
//if (VPixel(src,b,r,c,VBit) == 1)
if
(
bitmask
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
)
{
floatDataset
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
=
0
;
continue
;
}
srcpix
=
bitmask
+
b
*
nrows
*
ncols
+
r
*
ncols
+
c
;
cc1
=
c
;
while
(
cc1
<
ncols
&&
*
srcpix
++
==
0
)
cc1
++
;
d1
=
(
cc1
>=
ncols
?
ncols
:
(
cc1
-
c
)
);
srcpix
=
bitmask
+
b
*
nrows
*
ncols
+
r
*
ncols
+
c
;
cc2
=
c
;
while
(
cc2
>=
0
&&
*
srcpix
--
==
0
)
cc2
--
;
d2
=
(
cc2
<=
0
?
ncols
:
(
c
-
cc2
)
);
if
(
d1
<=
d2
)
{
d
=
d1
;
c0
=
cc1
;
}
else
{
d
=
d2
;
c0
=
cc2
;
}
floatDataset
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
=
static_cast
<
float
>
(
d
*
d
);
}
}
}
// second pass
for
(
b
=
0
;
b
<
nbands
;
b
++
)
{
for
(
c
=
0
;
c
<
ncols
;
c
++
)
{
for
(
r
=
0
;
r
<
nrows
;
r
++
)
array
[
r
]
=
static_cast
<
double
>
(
floatDataset
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
);
for
(
r
=
0
;
r
<
nrows
;
r
++
)
{
if
(
bitmask
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
==
1
)
continue
;
dmin
=
dmax
;
r0
=
r
;
g
=
sqrt
(
array
[
r
]
);
istart
=
r
-
static_cast
<
int
>
(
g
);
if
(
istart
<
0
)
istart
=
0
;
iend
=
r
+
static_cast
<
int
>
(
g
+
1
);
if
(
iend
>=
nrows
)
iend
=
nrows
;
for
(
rr
=
istart
;
rr
<
iend
;
rr
++
)
{
u
=
array
[
rr
]
+
(
r
-
rr
)
*
(
r
-
rr
);
if
(
u
<
dmin
)
{
dmin
=
u
;
r0
=
rr
;
}
}
floatDataset
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
=
dmin
;
}
}
}
// third pass
for
(
r
=
0
;
r
<
nrows
;
r
++
)
{
for
(
c
=
0
;
c
<
ncols
;
c
++
)
{
for
(
b
=
0
;
b
<
nbands
;
b
++
)
array
[
b
]
=
static_cast
<
double
>
(
floatDataset
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
);
for
(
b
=
0
;
b
<
nbands
;
b
++
)
{
if
(
bitmask
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
==
1
)
continue
;
dmin
=
dmax
;
b0
=
b
;
g
=
sqrt
(
array
[
b
]
);
istart
=
b
-
static_cast
<
int
>
(
g
-
1
);
if
(
istart
<
0
)
istart
=
0
;
iend
=
b
+
static_cast
<
int
>
(
g
+
1
);
if
(
iend
>=
nbands
)
iend
=
nbands
;
for
(
bb
=
istart
;
bb
<
iend
;
bb
++
)
{
u
=
array
[
bb
]
+
(
b
-
bb
)
*
(
b
-
bb
);
if
(
u
<
dmin
)
{
dmin
=
u
;
b0
=
bb
;
}
}
floatDataset
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
=
dmin
;
}
}
}
delete
[]
array
;
float
max
=
0
;
for
(
i
=
0
;
i
<
npixels
;
++
i
)
{
floatDataset
[
i
]
=
sqrt
(
static_cast
<
double
>
(
floatDataset
[
i
]
)
);
if
(
floatDataset
[
i
]
>
max
)
max
=
floatDataset
[
i
];
}
for
(
i
=
0
;
i
<
npixels
;
++
i
)
{
floatDataset
[
i
]
=
floatDataset
[
i
]
/
max
;
}
// filter with gauss
// create the filter kernel
double
sigma
=
4
;
int
dim
=
static_cast
<
int
>
(
(
3.0
*
sigma
+
1
)
);
int
n
=
2
*
dim
+
1
;
double
step
=
1
;
float
*
kernel
=
new
float
[
n
];
double
sum
=
0
;
double
x
=
-
static_cast
<
float
>
(
dim
);
double
uu
;
for
(
int
i
=
0
;
i
<
n
;
++
i
)
{
uu
=
xxgauss
(
x
,
sigma
);
sum
+=
uu
;
kernel
[
i
]
=
uu
;
x
+=
step
;
}
/* normalize */
for
(
int
i
=
0
;
i
<
n
;
++
i
)
{
uu
=
kernel
[
i
];
uu
/=
sum
;
kernel
[
i
]
=
uu
;
}
d
=
n
/
2
;
float
*
float_pp
;
std
::
vector
<
float
>
tmp
(
npixels
);
int
c1
,
cc
;
for
(
int
i
=
0
;
i
<
npixels
;
++
i
)
{
tmp
[
i
]
=
0.0
;
}
for
(
b
=
0
;
b
<
nbands
;
++
b
)
{
for
(
r
=
0
;
r
<
nrows
;
++
r
)
{
for
(
c
=
d
;
c
<
ncols
-
d
;
++
c
)
{
float_pp
=
kernel
;
sum
=
0
;
c0
=
c
-
d
;
c1
=
c
+
d
;
for
(
cc
=
c0
;
cc
<=
c1
;
cc
++
)
{
x
=
floatDataset
[
b
*
nrows
*
ncols
+
r
*
ncols
+
cc
];
sum
+=
x
*
(
*
float_pp
++
);
}
tmp
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
=
sum
;
}
}
}
int
r1
;
for
(
b
=
0
;
b
<
nbands
;
++
b
)
{
for
(
r
=
d
;
r
<
nrows
-
d
;
++
r
)
{
for
(
c
=
0
;
c
<
ncols
;
++
c
)
{
float_pp
=
kernel
;
sum
=
0
;
r0
=
r
-
d
;
r1
=
r
+
d
;
for
(
rr
=
r0
;
rr
<=
r1
;
rr
++
)
{
x
=
tmp
[
b
*
nrows
*
ncols
+
rr
*
ncols
+
c
];
sum
+=
x
*
(
*
float_pp
++
);
}
floatDataset
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
=
sum
;
}
}
}
int
b1
;
for
(
b
=
d
;
b
<
nbands
-
d
;
++
b
)
{
for
(
r
=
0
;
r
<
nrows
;
++
r
)
{
for
(
c
=
0
;
c
<
ncols
;
++
c
)
{
float_pp
=
kernel
;
sum
=
0
;
b0
=
b
-
d
;
b1
=
b
+
d
;
for
(
bb
=
b0
;
bb
<=
b1
;
bb
++
)
{
x
=
floatDataset
[
bb
*
nrows
*
ncols
+
r
*
ncols
+
c
];
sum
+=
x
*
(
*
float_pp
++
);
}
tmp
[
b
*
nrows
*
ncols
+
r
*
ncols
+
c
]
=
sum
;
}
}
}
delete
[]
bitmask
;
delete
[]
kernel
;
floatDataset
=
tmp
;
boost
::
shared_ptr
<
WValueSet
<
float
>
>
vset
;
vset
=
boost
::
shared_ptr
<
WValueSet
<
float
>
>
(
new
WValueSet
<
float
>
(
valueSet
->
order
(),
valueSet
->
dimension
(),
floatDataset
,
W_DT_FLOAT
)
);
boost
::
shared_ptr
<
WDataSetSingle
>
newDataSet
;
newDataSet
=
boost
::
shared_ptr
<
WDataSetSingle
>
(
new
WDataSetSingle
(
vset
,
grid
)
);
return
newDataSet
;
}
double
WMDistanceMap
::
xxgauss
(
double
x
,
double
sigma
)
{
double
y
,
z
,
a
=
2.506628273
;
z
=
x
/
sigma
;
y
=
exp
(
(
double
)
-
z
*
z
*
0.5
)
/
(
sigma
*
a
);
return
y
;
}
src/modules/distanceMap/WMDistanceMap.h
View file @
2ca0e93b
...
...
@@ -66,7 +66,7 @@ public:
/**
* Due to the prototype design pattern used to build modules, this method returns a new instance of this method. NOTE: it
* should never be initialized or modified in some other way. A simple new instance is required.
*
*
* \return the prototype used to create every module in OpenWalnut.
*/
virtual
boost
::
shared_ptr
<
WModule
>
factory
()
const
;
...
...
@@ -89,6 +89,13 @@ protected:
private:
boost
::
shared_ptr
<
WModuleInputData
<
boost
::
shared_ptr
<
WDataSet
>
>
>
m_input
;
//!< Input connector required by this module.
/**
* Function to create a distance map from Anatomy data set.
* Take from FiberNavigator.
*/
boost
::
shared_ptr
<
WDataSetSingle
>
createOffset
(
boost
::
shared_ptr
<
WDataSetSingle
>
dataSet
);
double
xxgauss
(
double
x
,
double
sigma
);
};
#endif // WMDISTANCEMAP_H
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