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RichardsonLucyTV.java
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Wed, Jul 17, 10:03
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R2075 deconvolution
RichardsonLucyTV.java
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/*
* DeconvolutionLab2
*
* Conditions of use: You are free to use this software for research or
* educational purposes. In addition, we expect you to include adequate
* citations and acknowledgments whenever you present or publish results that
* are based on it.
*
* Reference: DeconvolutionLab2: An Open-Source Software for Deconvolution
* Microscopy D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz,
* R. Guiet, C. Vonesch, M Unser, Methods of Elsevier, 2017.
*/
/*
* Copyright 2010-2017 Biomedical Imaging Group at the EPFL.
*
* This file is part of DeconvolutionLab2 (DL2).
*
* DL2 is free software: you can redistribute it and/or modify it under the
* terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any later
* version.
*
* DL2 is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with
* DL2. If not, see <http://www.gnu.org/licenses/>.
*/
package
deconvolution.algorithm
;
import
java.util.concurrent.Callable
;
import
signal.ComplexSignal
;
import
signal.Operations
;
import
signal.RealSignal
;
public
class
RichardsonLucyTV
extends
AbstractAlgorithm
implements
Callable
<
RealSignal
>
{
private
double
lambda
=
0.1
;
public
RichardsonLucyTV
(
int
iter
,
double
lambda
)
{
super
();
controller
.
setIterationMax
(
iter
);
this
.
lambda
=
lambda
;
}
// x(k+1) = x(k) *. Hconj * ( y /. H x(k))
@Override
public
RealSignal
call
()
{
ComplexSignal
H
=
fft
.
transform
(
h
);
ComplexSignal
U
=
new
ComplexSignal
(
y
.
nx
,
y
.
ny
,
y
.
nz
);
RealSignal
x
=
y
.
duplicate
();
RealSignal
gx
=
y
.
duplicate
();
RealSignal
gy
=
y
.
duplicate
();
RealSignal
gz
=
y
.
duplicate
();
RealSignal
ggx
=
y
.
duplicate
();
RealSignal
ggy
=
y
.
duplicate
();
RealSignal
ggz
=
y
.
duplicate
();
RealSignal
u
=
gx
;
// resued memory
RealSignal
p
=
gy
;
// resued memory
RealSignal
tv
=
gz
;
// resued memory
while
(!
controller
.
ends
(
x
))
{
gradientX
(
x
,
gx
);
gradientY
(
x
,
gy
);
gradientZ
(
x
,
gz
);
normalize
(
gx
,
gy
,
gz
);
gradientX
(
gx
,
ggx
);
gradientY
(
gy
,
ggy
);
gradientZ
(
gz
,
ggz
);
compute
((
float
)
lambda
,
ggx
,
ggy
,
ggz
,
tv
);
fft
.
transform
(
x
,
U
);
U
.
times
(
H
);
fft
.
inverse
(
U
,
u
);
Operations
.
divide
(
y
,
u
,
p
);
fft
.
transform
(
p
,
U
);
U
.
timesConjugate
(
H
);
fft
.
inverse
(
U
,
u
);
x
.
times
(
u
);
x
.
times
(
tv
);
}
return
x
;
}
private
void
compute
(
float
lambda
,
RealSignal
gx
,
RealSignal
gy
,
RealSignal
gz
,
RealSignal
tv
)
{
int
nxy
=
gx
.
nx
*
gy
.
ny
;
for
(
int
k
=
0
;
k
<
gx
.
nz
;
k
++)
for
(
int
i
=
0
;
i
<
nxy
;
i
++)
{
double
dx
=
gx
.
data
[
k
][
i
];
double
dy
=
gy
.
data
[
k
][
i
];
double
dz
=
gz
.
data
[
k
][
i
];
tv
.
data
[
k
][
i
]
=
(
float
)(
1.0
/
(
(
dx
+
dy
+
dz
)
*
lambda
+
1.0
));
}
//Log.info("Norm TV "+ Math.sqrt(norm));
}
public
void
gradientX
(
RealSignal
signal
,
RealSignal
output
)
{
int
nx
=
signal
.
nx
;
int
ny
=
signal
.
ny
;
int
nz
=
signal
.
nz
;
for
(
int
k
=
0
;
k
<
nz
;
k
++)
for
(
int
j
=
0
;
j
<
ny
;
j
++)
for
(
int
i
=
0
;
i
<
nx
-
1
;
i
++)
{
int
index
=
i
+
signal
.
nx
*
j
;
output
.
data
[
k
][
index
]
=
signal
.
data
[
k
][
index
]
-
signal
.
data
[
k
][
index
+
1
];
}
}
public
void
gradientY
(
RealSignal
signal
,
RealSignal
output
)
{
int
nx
=
signal
.
nx
;
int
ny
=
signal
.
ny
;
int
nz
=
signal
.
nz
;
for
(
int
k
=
0
;
k
<
nz
;
k
++)
for
(
int
j
=
0
;
j
<
ny
-
1
;
j
++)
for
(
int
i
=
0
;
i
<
nx
;
i
++)
{
int
index
=
i
+
signal
.
nx
*
j
;
output
.
data
[
k
][
index
]
=
signal
.
data
[
k
][
index
]
-
signal
.
data
[
k
][
index
+
nx
];
}
}
public
void
gradientZ
(
RealSignal
signal
,
RealSignal
output
)
{
int
nx
=
signal
.
nx
;
int
ny
=
signal
.
ny
;
int
nz
=
signal
.
nz
;
for
(
int
k
=
0
;
k
<
nz
-
1
;
k
++)
for
(
int
j
=
0
;
j
<
ny
;
j
++)
for
(
int
i
=
0
;
i
<
nx
;
i
++)
{
int
index
=
i
+
signal
.
nx
*
j
;
output
.
data
[
k
][
index
]
=
signal
.
data
[
k
][
index
]
-
signal
.
data
[
k
+
1
][
index
];
}
}
public
void
normalize
(
RealSignal
x
,
RealSignal
y
,
RealSignal
z
)
{
int
nx
=
x
.
nx
;
int
ny
=
y
.
ny
;
int
nz
=
z
.
nz
;
float
e
=
(
float
)
RealSignal
.
epsilon
;
for
(
int
k
=
0
;
k
<
nz
;
k
++)
for
(
int
i
=
0
;
i
<
nx
*
ny
;
i
++)
{
double
norm
=
Math
.
sqrt
(
x
.
data
[
k
][
i
]
*
x
.
data
[
k
][
i
]
+
y
.
data
[
k
][
i
]
*
y
.
data
[
k
][
i
]
+
z
.
data
[
k
][
i
]
*
z
.
data
[
k
][
i
]);
if
(
norm
<
e
)
{
x
.
data
[
k
][
i
]
=
e
;
y
.
data
[
k
][
i
]
=
e
;
z
.
data
[
k
][
i
]
=
e
;
}
else
{
x
.
data
[
k
][
i
]
/=
norm
;
y
.
data
[
k
][
i
]
/=
norm
;
z
.
data
[
k
][
i
]
/=
norm
;
}
}
}
@Override
public
String
getName
()
{
return
"Richardson-Lucy TV"
;
}
@Override
public
String
getShortname
()
{
return
"RLTV"
;
}
@Override
public
boolean
isRegularized
()
{
return
true
;
}
@Override
public
boolean
isStepControllable
()
{
return
true
;
}
@Override
public
boolean
isIterative
()
{
return
true
;
}
@Override
public
boolean
isWaveletsBased
()
{
return
false
;
}
@Override
public
void
setParameters
(
double
[]
params
)
{
if
(
params
==
null
)
return
;
if
(
params
.
length
>
0
)
controller
.
setIterationMax
((
int
)
Math
.
round
(
params
[
0
]));
if
(
params
.
length
>
1
)
lambda
=
(
float
)
params
[
1
];
}
@Override
public
double
[]
getDefaultParameters
()
{
return
new
double
[]
{
10
,
0.1
};
}
@Override
public
double
[]
getParameters
()
{
return
new
double
[]
{
controller
.
getIterationMax
(),
lambda
};
}
@Override
public
double
getRegularizationFactor
()
{
return
lambda
;
}
@Override
public
double
getStepFactor
()
{
return
0.0
;
}
}
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