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MPIBP-Hummer
BioEM
Commits
8639adb7
Commit
8639adb7
authored
Apr 20, 2014
by
David Rohr
Browse files
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Browse Files
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Plain Diff
fix file endings
parent
4a123b50
Changes
4
Expand all
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Inline
Side-by-side
Showing
4 changed files
with
469 additions
and
469 deletions
+469
-469
bioem.cpp
bioem.cpp
+30
-30
include/map.h
include/map.h
+7
-7
map.cpp
map.cpp
+312
-312
param.cpp
param.cpp
+120
-120
No files found.
bioem.cpp
View file @
8639adb7
...
@@ -57,8 +57,8 @@ int bioem::configure(int ac, char* av[])
...
@@ -57,8 +57,8 @@ int bioem::configure(int ac, char* av[])
param
.
writeAngles
=
false
;
param
.
writeAngles
=
false
;
param
.
dumpMap
=
false
;
param
.
dumpMap
=
false
;
param
.
loadMap
=
false
;
param
.
loadMap
=
false
;
RefMap
.
readMRC
=
false
;
RefMap
.
readMRC
=
false
;
RefMap
.
readMultMRC
=
false
;
RefMap
.
readMultMRC
=
false
;
// *************************************************************************************
// *************************************************************************************
cout
<<
" ++++++++++++ FROM COMMAND LINE +++++++++++
\n\n
"
;
cout
<<
" ++++++++++++ FROM COMMAND LINE +++++++++++
\n\n
"
;
...
@@ -68,17 +68,17 @@ int bioem::configure(int ac, char* av[])
...
@@ -68,17 +68,17 @@ int bioem::configure(int ac, char* av[])
try
{
try
{
po
::
options_description
desc
(
"Command line inputs"
);
po
::
options_description
desc
(
"Command line inputs"
);
desc
.
add_options
()
desc
.
add_options
()
(
"Inputfile"
,
po
::
value
<
std
::
string
>
(),
"(Mandatory) Name of input parameter file"
)
(
"Inputfile"
,
po
::
value
<
std
::
string
>
(),
"(Mandatory) Name of input parameter file"
)
(
"Modelfile"
,
po
::
value
<
std
::
string
>
()
,
"(Mandatory) Name of model file"
)
(
"Modelfile"
,
po
::
value
<
std
::
string
>
()
,
"(Mandatory) Name of model file"
)
(
"Particlesfile"
,
po
::
value
<
std
::
string
>
(),
"(Mandatory) Name of paricles file"
)
(
"Particlesfile"
,
po
::
value
<
std
::
string
>
(),
"(Mandatory) Name of paricles file"
)
(
"ReadPDB"
,
"(Optional) If reading model file in PDB format"
)
(
"ReadPDB"
,
"(Optional) If reading model file in PDB format"
)
(
"ReadMRC"
,
"(Optional) If reading particle file in MRC format"
)
(
"ReadMRC"
,
"(Optional) If reading particle file in MRC format"
)
(
"ReadMultipleMRC"
,
"(Optional) If reading Multiple MRCs"
)
(
"ReadMultipleMRC"
,
"(Optional) If reading Multiple MRCs"
)
(
"DumpMaps"
,
"(Optional) Dump maps after they were red from maps file"
)
(
"DumpMaps"
,
"(Optional) Dump maps after they were red from maps file"
)
(
"LoadMapDump"
,
"(Optional) Read Maps from dump instead of maps file"
)
(
"LoadMapDump"
,
"(Optional) Read Maps from dump instead of maps file"
)
(
"help"
,
"(Optional) Produce help message"
)
(
"help"
,
"(Optional) Produce help message"
)
;
;
po
::
positional_options_description
p
;
po
::
positional_options_description
p
;
...
@@ -86,8 +86,8 @@ int bioem::configure(int ac, char* av[])
...
@@ -86,8 +86,8 @@ int bioem::configure(int ac, char* av[])
p
.
add
(
"Modelfile"
,
-
1
);
p
.
add
(
"Modelfile"
,
-
1
);
p
.
add
(
"Particlesfile"
,
-
1
);
p
.
add
(
"Particlesfile"
,
-
1
);
p
.
add
(
"ReadPDB"
,
-
1
);
p
.
add
(
"ReadPDB"
,
-
1
);
p
.
add
(
"ReadMRC"
,
-
1
);
p
.
add
(
"ReadMRC"
,
-
1
);
p
.
add
(
"ReadMultipleMRC"
,
-
1
);
p
.
add
(
"ReadMultipleMRC"
,
-
1
);
p
.
add
(
"DumpMaps"
,
-
1
);
p
.
add
(
"DumpMaps"
,
-
1
);
p
.
add
(
"LoadMapDump"
,
-
1
);
p
.
add
(
"LoadMapDump"
,
-
1
);
...
@@ -125,17 +125,17 @@ int bioem::configure(int ac, char* av[])
...
@@ -125,17 +125,17 @@ int bioem::configure(int ac, char* av[])
Model
.
readPDB
=
true
;
Model
.
readPDB
=
true
;
}
}
if
(
vm
.
count
(
"ReadMRC"
))
if
(
vm
.
count
(
"ReadMRC"
))
{
{
cout
<<
"Reading particle file in MRC format.
\n
"
;
cout
<<
"Reading particle file in MRC format.
\n
"
;
RefMap
.
readMRC
=
true
;
RefMap
.
readMRC
=
true
;
}
}
if
(
vm
.
count
(
"ReadMultipleMRC"
))
if
(
vm
.
count
(
"ReadMultipleMRC"
))
{
{
cout
<<
"Reading Multiple MRCs.
\n
"
;
cout
<<
"Reading Multiple MRCs.
\n
"
;
RefMap
.
readMultMRC
=
true
;
RefMap
.
readMultMRC
=
true
;
}
}
if
(
vm
.
count
(
"DumpMaps"
))
if
(
vm
.
count
(
"DumpMaps"
))
{
{
...
@@ -379,8 +379,8 @@ int bioem::run()
...
@@ -379,8 +379,8 @@ int bioem::run()
int
bioem
::
compareRefMaps
(
int
iOrient
,
int
iConv
,
const
myfloat_t
*
conv_map
,
mycomplex_t
*
localmultFFT
,
myfloat_t
sumC
,
myfloat_t
sumsquareC
,
const
int
startMap
)
int
bioem
::
compareRefMaps
(
int
iOrient
,
int
iConv
,
const
myfloat_t
*
conv_map
,
mycomplex_t
*
localmultFFT
,
myfloat_t
sumC
,
myfloat_t
sumsquareC
,
const
int
startMap
)
{
{
//***************************************************************************************
//***************************************************************************************
//***** BioEM routine for comparing reference maps to convoluted maps *****
//***** BioEM routine for comparing reference maps to convoluted maps *****
if
(
FFTAlgo
)
if
(
FFTAlgo
)
{
{
//With FFT Algorithm
//With FFT Algorithm
...
@@ -405,8 +405,8 @@ int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, myc
...
@@ -405,8 +405,8 @@ int bioem::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map, myc
inline
void
bioem
::
calculateCCFFT
(
int
iRefMap
,
int
iOrient
,
int
iConv
,
myfloat_t
sumC
,
myfloat_t
sumsquareC
,
mycomplex_t
*
localConvFFT
,
mycomplex_t
*
localCCT
,
myfloat_t
*
lCC
)
inline
void
bioem
::
calculateCCFFT
(
int
iRefMap
,
int
iOrient
,
int
iConv
,
myfloat_t
sumC
,
myfloat_t
sumsquareC
,
mycomplex_t
*
localConvFFT
,
mycomplex_t
*
localCCT
,
myfloat_t
*
lCC
)
{
{
//***************************************************************************************
//***************************************************************************************
//***** Calculating cross correlation in FFTALGOrithm *****
//***** Calculating cross correlation in FFTALGOrithm *****
const
mycomplex_t
*
RefMapFFT
=
&
RefMap
.
RefMapsFFT
[
iRefMap
*
param
.
FFTMapSize
];
const
mycomplex_t
*
RefMapFFT
=
&
RefMap
.
RefMapsFFT
[
iRefMap
*
param
.
FFTMapSize
];
for
(
int
i
=
0
;
i
<
param
.
param_device
.
NumberPixels
*
param
.
param_device
.
NumberFFTPixels1D
;
i
++
)
for
(
int
i
=
0
;
i
<
param
.
param_device
.
NumberPixels
*
param
.
param_device
.
NumberFFTPixels1D
;
i
++
)
...
...
include/map.h
View file @
8639adb7
...
@@ -34,16 +34,16 @@ public:
...
@@ -34,16 +34,16 @@ public:
int
precalculate
(
bioem_param
&
param
,
bioem
&
bio
);
int
precalculate
(
bioem_param
&
param
,
bioem
&
bio
);
int
PreCalculateMapsFFT
(
bioem_param
&
param
);
int
PreCalculateMapsFFT
(
bioem_param
&
param
);
int
read_int
(
int
*
currlong
,
FILE
*
fin
,
int
swap
);
int
read_int
(
int
*
currlong
,
FILE
*
fin
,
int
swap
);
int
read_float
(
float
*
currfloat
,
FILE
*
fin
,
int
swap
);
int
read_float
(
float
*
currfloat
,
FILE
*
fin
,
int
swap
);
int
read_float_empty
(
FILE
*
fin
);
int
read_float_empty
(
FILE
*
fin
);
int
read_char_float
(
float
*
currfloat
,
FILE
*
fin
)
;
int
read_char_float
(
float
*
currfloat
,
FILE
*
fin
)
;
int
test_mrc
(
const
char
*
vol_file
,
int
swap
);
int
test_mrc
(
const
char
*
vol_file
,
int
swap
);
int
read_MRC
(
const
char
*
filename
,
bioem_param
&
param
);
int
read_MRC
(
const
char
*
filename
,
bioem_param
&
param
);
mycomplex_t
*
RefMapsFFT
;
mycomplex_t
*
RefMapsFFT
;
bool
readMRC
,
readMultMRC
;
bool
readMRC
,
readMultMRC
;
int
ntotRefMap
;
int
ntotRefMap
;
int
numPixels
;
int
numPixels
;
...
...
map.cpp
View file @
8639adb7
This diff is collapsed.
Click to expand it.
param.cpp
View file @
8639adb7
...
@@ -42,22 +42,22 @@ int bioem_param::readParameters()
...
@@ -42,22 +42,22 @@ int bioem_param::readParameters()
// ***************************** Reading Input Parameters ******************************
// ***************************** Reading Input Parameters ******************************
// **************************************************************************************
// **************************************************************************************
// Control for Parameters
// Control for Parameters
bool
yesPixSi
=
false
;
bool
yesPixSi
=
false
;
bool
yesNumPix
=
false
;
bool
yesNumPix
=
false
;
bool
yesGPal
=
false
;
bool
yesGPal
=
false
;
bool
yesGPbe
=
false
;
bool
yesGPbe
=
false
;
bool
yesGPEnv
=
false
;
bool
yesGPEnv
=
false
;
bool
yesGPamp
=
false
;
bool
yesGPamp
=
false
;
bool
yesGPpha
=
false
;
bool
yesGPpha
=
false
;
bool
yesSTEnv
=
false
;
bool
yesSTEnv
=
false
;
bool
yesSTamp
=
false
;
bool
yesSTamp
=
false
;
bool
yesSTpha
=
false
;
bool
yesSTpha
=
false
;
bool
yesGSPamp
=
false
;
bool
yesGSPamp
=
false
;
bool
yesGSPEnv
=
false
;
bool
yesGSPEnv
=
false
;
bool
yesGSPpha
=
false
;
bool
yesGSPpha
=
false
;
bool
yesMDC
=
false
;
bool
yesMDC
=
false
;
bool
yesGCen
=
false
;
bool
yesGCen
=
false
;
ifstream
input
(
fileinput
);
ifstream
input
(
fileinput
);
if
(
!
input
.
good
())
if
(
!
input
.
good
())
...
@@ -87,116 +87,116 @@ int bioem_param::readParameters()
...
@@ -87,116 +87,116 @@ int bioem_param::readParameters()
{
{
token
=
strtok
(
NULL
,
" "
);
token
=
strtok
(
NULL
,
" "
);
pixelSize
=
atof
(
token
);
pixelSize
=
atof
(
token
);
if
(
pixelSize
<
0
)
{
cout
<<
"*** Error: Negative pixelSize "
;
exit
(
1
);}
if
(
pixelSize
<
0
)
{
cout
<<
"*** Error: Negative pixelSize "
;
exit
(
1
);}
cout
<<
"Pixel Sixe "
<<
pixelSize
<<
"
\n
"
;
cout
<<
"Pixel Sixe "
<<
pixelSize
<<
"
\n
"
;
yesPixSi
=
true
;
yesPixSi
=
true
;
}
}
else
if
(
strcmp
(
token
,
"NUMBER_PIXELS"
)
==
0
)
else
if
(
strcmp
(
token
,
"NUMBER_PIXELS"
)
==
0
)
{
{
token
=
strtok
(
NULL
,
" "
);
token
=
strtok
(
NULL
,
" "
);
param_device
.
NumberPixels
=
int
(
atoi
(
token
));
param_device
.
NumberPixels
=
int
(
atoi
(
token
));
if
(
param_device
.
NumberPixels
<
0
)
{
cout
<<
"*** Error: Negative Number of Pixels "
;
exit
(
1
);}
if
(
param_device
.
NumberPixels
<
0
)
{
cout
<<
"*** Error: Negative Number of Pixels "
;
exit
(
1
);}
cout
<<
"Number of Pixels "
<<
param_device
.
NumberPixels
<<
"
\n
"
;
cout
<<
"Number of Pixels "
<<
param_device
.
NumberPixels
<<
"
\n
"
;
yesNumPix
=
true
;
yesNumPix
=
true
;
}
}
else
if
(
strcmp
(
token
,
"GRIDPOINTS_ALPHA"
)
==
0
)
else
if
(
strcmp
(
token
,
"GRIDPOINTS_ALPHA"
)
==
0
)
{
{
token
=
strtok
(
NULL
,
" "
);
token
=
strtok
(
NULL
,
" "
);
angleGridPointsAlpha
=
int
(
atoi
(
token
));
angleGridPointsAlpha
=
int
(
atoi
(
token
));
if
(
angleGridPointsAlpha
<
0
)
{
cout
<<
"*** Error: Negative GRIDPOINTS_ALPHA "
;
exit
(
1
);}
if
(
angleGridPointsAlpha
<
0
)
{
cout
<<
"*** Error: Negative GRIDPOINTS_ALPHA "
;
exit
(
1
);}
cout
<<
"Grid points alpha "
<<
angleGridPointsAlpha
<<
"
\n
"
;
cout
<<
"Grid points alpha "
<<
angleGridPointsAlpha
<<
"
\n
"
;
yesGPal
=
true
;
yesGPal
=
true
;
}
}
else
if
(
strcmp
(
token
,
"GRIDPOINTS_BETA"
)
==
0
)
else
if
(
strcmp
(
token
,
"GRIDPOINTS_BETA"
)
==
0
)
{
{
token
=
strtok
(
NULL
,
" "
);
token
=
strtok
(
NULL
,
" "
);
angleGridPointsBeta
=
int
(
atoi
(
token
));
angleGridPointsBeta
=
int
(
atoi
(
token
));
if
(
angleGridPointsBeta
<
0
)
{
cout
<<
"*** Error: Negative GRIDPOINTS_BETA "
;
exit
(
1
);}
if
(
angleGridPointsBeta
<
0
)
{
cout
<<
"*** Error: Negative GRIDPOINTS_BETA "
;
exit
(
1
);}
cout
<<
"Grid points beta "
<<
angleGridPointsBeta
<<
"
\n
"
;
cout
<<
"Grid points beta "
<<
angleGridPointsBeta
<<
"
\n
"
;
yesGPbe
=
true
;
yesGPbe
=
true
;
}
}
else
if
(
strcmp
(
token
,
"GRIDPOINTS_ENVELOPE"
)
==
0
)
else
if
(
strcmp
(
token
,
"GRIDPOINTS_ENVELOPE"
)
==
0
)
{
{
token
=
strtok
(
NULL
,
" "
);
token
=
strtok
(
NULL
,
" "
);
numberGridPointsEnvelop
=
int
(
atoi
(
token
));
numberGridPointsEnvelop
=
int
(
atoi
(
token
));
if
(
numberGridPointsDisplaceCenter
<
0
)
{
cout
<<
"*** Error: Negative GRIDPOINTS_ENVELOPE "
;
exit
(
1
);}
if
(
numberGridPointsDisplaceCenter
<
0
)
{
cout
<<
"*** Error: Negative GRIDPOINTS_ENVELOPE "
;
exit
(
1
);}
cout
<<
"Grid points envelope "
<<
numberGridPointsEnvelop
<<
"
\n
"
;
cout
<<
"Grid points envelope "
<<
numberGridPointsEnvelop
<<
"
\n
"
;
yesGPEnv
=
true
;
yesGPEnv
=
true
;
}
}
else
if
(
strcmp
(
token
,
"START_ENVELOPE"
)
==
0
)
else
if
(
strcmp
(
token
,
"START_ENVELOPE"
)
==
0
)
{
{
token
=
strtok
(
NULL
,
" "
);
token
=
strtok
(
NULL
,
" "
);
startGridEnvelop
=
atof
(
token
);
startGridEnvelop
=
atof
(
token
);
if
(
startGridEnvelop
<
0
)
{
cout
<<
"*** Error: Negative START_ENVELOPE "
;
exit
(
1
);}
if
(
startGridEnvelop
<
0
)
{
cout
<<
"*** Error: Negative START_ENVELOPE "
;
exit
(
1
);}
cout
<<
"Start Envelope "
<<
startGridEnvelop
<<
"
\n
"
;
cout
<<
"Start Envelope "
<<
startGridEnvelop
<<
"
\n
"
;
yesSTEnv
=
true
;
yesSTEnv
=
true
;
}
}
else
if
(
strcmp
(
token
,
"GRIDSPACE_ENVELOPE"
)
==
0
)
else
if
(
strcmp
(
token
,
"GRIDSPACE_ENVELOPE"
)
==
0
)
{
{
token
=
strtok
(
NULL
,
" "
);
token
=
strtok
(
NULL
,
" "
);
gridEnvelop
=
atof
(
token
);
gridEnvelop
=
atof
(
token
);
if
(
gridEnvelop
<
0
)
{
cout
<<
"*** Error: Negative GRIDSPACE_ENVELOPE "
;
exit
(
1
);}
if
(
gridEnvelop
<
0
)
{
cout
<<
"*** Error: Negative GRIDSPACE_ENVELOPE "
;
exit
(
1
);}
cout
<<
"Grid spacing Envelope "
<<
gridEnvelop
<<
"
\n
"
;
cout
<<
"Grid spacing Envelope "
<<
gridEnvelop
<<
"
\n
"
;
yesGSPEnv
=
true
;
yesGSPEnv
=
true
;
}
else
if
(
strcmp
(
token
,
"GRIDPOINTS_PSF_PHASE"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
numberGridPointsCTF_phase
=
int
(
atoi
(
token
));
cout
<<
"Grid points PSF "
<<
numberGridPointsCTF_phase
<<
"
\n
"
;
yesGPpha
=
true
;
}
else
if
(
strcmp
(
token
,
"START_PSF_PHASE"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
startGridCTF_phase
=
atof
(
token
);
cout
<<
"Start PSF "
<<
startGridCTF_phase
<<
"
\n
"
;
yesSTpha
=
true
;
}
else
if
(
strcmp
(
token
,
"GRIDSPACE_PSF_PHASE"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
gridCTF_phase
=
atof
(
token
);
cout
<<
"Grid Space PSF "
<<
gridCTF_phase
<<
"
\n
"
;
yesGSPpha
=
true
;
}
else
if
(
strcmp
(
token
,
"GRIDPOINTS_PSF_AMP"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
numberGridPointsCTF_amp
=
int
(
atoi
(
token
));
cout
<<
"Grid points PSF "
<<
numberGridPointsCTF_amp
<<
"
\n
"
;
yesGPamp
=
true
;
}
else
if
(
strcmp
(
token
,
"START_PSF_AMP"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
startGridCTF_amp
=
atof
(
token
);
cout
<<
"Start PSF "
<<
startGridCTF_amp
<<
"
\n
"
;
yesSTamp
=
true
;
}
else
if
(
strcmp
(
token
,
"GRIDSPACE_PSF_AMP"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
gridCTF_amp
=
atof
(
token
);
cout
<<
"Grid Space PSF "
<<
gridCTF_amp
<<
"
\n
"
;
yesGSPamp
=
true
;
}
}
else
if
(
strcmp
(
token
,
"GRIDPOINTS_PSF_PHASE"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
numberGridPointsCTF_phase
=
int
(
atoi
(
token
));
cout
<<
"Grid points PSF "
<<
numberGridPointsCTF_phase
<<
"
\n
"
;
yesGPpha
=
true
;
}
else
if
(
strcmp
(
token
,
"START_PSF_PHASE"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
startGridCTF_phase
=
atof
(
token
);
cout
<<
"Start PSF "
<<
startGridCTF_phase
<<
"
\n
"
;
yesSTpha
=
true
;
}
else
if
(
strcmp
(
token
,
"GRIDSPACE_PSF_PHASE"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
gridCTF_phase
=
atof
(
token
);
cout
<<
"Grid Space PSF "
<<
gridCTF_phase
<<
"
\n
"
;
yesGSPpha
=
true
;
}
else
if
(
strcmp
(
token
,
"GRIDPOINTS_PSF_AMP"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
numberGridPointsCTF_amp
=
int
(
atoi
(
token
));
cout
<<
"Grid points PSF "
<<
numberGridPointsCTF_amp
<<
"
\n
"
;
yesGPamp
=
true
;
}
else
if
(
strcmp
(
token
,
"START_PSF_AMP"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
startGridCTF_amp
=
atof
(
token
);
cout
<<
"Start PSF "
<<
startGridCTF_amp
<<
"
\n
"
;
yesSTamp
=
true
;
}
else
if
(
strcmp
(
token
,
"GRIDSPACE_PSF_AMP"
)
==
0
)
{
token
=
strtok
(
NULL
,
" "
);
gridCTF_amp
=
atof
(
token
);
cout
<<
"Grid Space PSF "
<<
gridCTF_amp
<<
"
\n
"
;
yesGSPamp
=
true
;
}
else
if
(
strcmp
(
token
,
"MAX_D_CENTER"
)
==
0
)
else
if
(
strcmp
(
token
,
"MAX_D_CENTER"
)
==
0
)
{
{
token
=
strtok
(
NULL
,
" "
);
token
=
strtok
(
NULL
,
" "
);
param_device
.
maxDisplaceCenter
=
int
(
atoi
(
token
));
param_device
.
maxDisplaceCenter
=
int
(
atoi
(
token
));
if
(
param_device
.
maxDisplaceCenter
<
0
)
{
cout
<<
"*** Error: Negative MAX_D_CENTER "
;
exit
(
1
);}
if
(
param_device
.
maxDisplaceCenter
<
0
)
{
cout
<<
"*** Error: Negative MAX_D_CENTER "
;
exit
(
1
);}
cout
<<
"Maximum displacement Center "
<<
param_device
.
maxDisplaceCenter
<<
"
\n
"
;
cout
<<
"Maximum displacement Center "
<<
param_device
.
maxDisplaceCenter
<<
"
\n
"
;
yesMDC
=
true
;
yesMDC
=
true
;
}
}
else
if
(
strcmp
(
token
,
"PIXEL_GRID_CENTER"
)
==
0
)
else
if
(
strcmp
(
token
,
"PIXEL_GRID_CENTER"
)
==
0
)
{
{
token
=
strtok
(
NULL
,
" "
);
token
=
strtok
(
NULL
,
" "
);
param_device
.
GridSpaceCenter
=
int
(
atoi
(
token
));
param_device
.
GridSpaceCenter
=
int
(
atoi
(
token
));
if
(
param_device
.
GridSpaceCenter
<
0
)
{
cout
<<
"*** Error: Negative PIXEL_GRID_CENTER "
;
exit
(
1
);}
if
(
param_device
.
GridSpaceCenter
<
0
)
{
cout
<<
"*** Error: Negative PIXEL_GRID_CENTER "
;
exit
(
1
);}
cout
<<
"Grid space displacement center "
<<
param_device
.
GridSpaceCenter
<<
"
\n
"
;
cout
<<
"Grid space displacement center "
<<
param_device
.
GridSpaceCenter
<<
"
\n
"
;
yesGCen
=
true
;
yesGCen
=
true
;
}
}
else
if
(
strcmp
(
token
,
"WRITE_PROB_ANGLES"
)
==
0
)
else
if
(
strcmp
(
token
,
"WRITE_PROB_ANGLES"
)
==
0
)
{
{
...
@@ -206,41 +206,41 @@ int bioem_param::readParameters()
...
@@ -206,41 +206,41 @@ int bioem_param::readParameters()
}
}
input
.
close
();
input
.
close
();
// Checks for ALL INPUT
// Checks for ALL INPUT
if
(
not
(
yesPixSi
)
){
cout
<<
"**** INPUT MISSING: Please provide PIXEL_SIZE
\n
"
;
exit
(
1
);};
if
(
not
(
yesPixSi
)
){
cout
<<
"**** INPUT MISSING: Please provide PIXEL_SIZE
\n
"
;
exit
(
1
);};
if
(
not
(
yesNumPix
)
){
cout
<<
"**** INPUT MISSING: Please provide NUMBER_PIXELS
\n
"
;
exit
(
1
);};
if
(
not
(
yesNumPix
)
){
cout
<<
"**** INPUT MISSING: Please provide NUMBER_PIXELS
\n
"
;
exit
(
1
);};
if
(
not
(
yesGPal
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDPOINTS_ALPHA
\n
"
;
exit
(
1
);};
if
(
not
(
yesGPal
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDPOINTS_ALPHA
\n
"
;
exit
(
1
);};
if
(
not
(
yesGPbe
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDPOINTS_BETA
\n
"
;
exit
(
1
);};
if
(
not
(
yesGPbe
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDPOINTS_BETA
\n
"
;
exit
(
1
);};
if
(
not
(
yesGPEnv
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDPOINTS_ENVELOPE
\n
"
;
exit
(
1
);};
if
(
not
(
yesGPEnv
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDPOINTS_ENVELOPE
\n
"
;
exit
(
1
);};
if
(
not
(
yesGPamp
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDPOINTS_PSF_AMP
\n
"
;
exit
(
1
);};
if
(
not
(
yesGPamp
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDPOINTS_PSF_AMP
\n
"
;
exit
(
1
);};
if
(
not
(
yesGPpha
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDPOINTS_PSF_PHASE
\n
"
;
exit
(
1
);};
if
(
not
(
yesGPpha
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDPOINTS_PSF_PHASE
\n
"
;
exit
(
1
);};
if
(
not
(
yesSTEnv
)
)
{
cout
<<
"**** INPUT MISSING: Please provide START_ENVELOPE
\n
"
;
exit
(
1
);};
if
(
not
(
yesSTEnv
)
)
{
cout
<<
"**** INPUT MISSING: Please provide START_ENVELOPE
\n
"
;
exit
(
1
);};
if
(
not
(
yesSTamp
)
)
{
cout
<<
"**** INPUT MISSING: Please provide START_PSF_AMP
\n
"
;
exit
(
1
);};
if
(
not
(
yesSTamp
)
)
{
cout
<<
"**** INPUT MISSING: Please provide START_PSF_AMP
\n
"
;
exit
(
1
);};
if
(
not
(
yesSTpha
)
)
{
cout
<<
"**** INPUT MISSING: Please provide START_PSF_PHASE
\n
"
;
exit
(
1
);};
if
(
not
(
yesSTpha
)
)
{
cout
<<
"**** INPUT MISSING: Please provide START_PSF_PHASE
\n
"
;
exit
(
1
);};
if
(
not
(
yesGSPamp
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDSPACE_PSF_AMP
\n
"
;
exit
(
1
);};
if
(
not
(
yesGSPamp
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDSPACE_PSF_AMP
\n
"
;
exit
(
1
);};
if
(
not
(
yesGSPEnv
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDSPACE_ENVELOPE
\n
"
;
exit
(
1
);};
if
(
not
(
yesGSPEnv
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDSPACE_ENVELOPE
\n
"
;
exit
(
1
);};
if
(
not
(
yesGSPpha
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDSPACE_PSF_PHASE
\n
"
;
exit
(
1
);};
if
(
not
(
yesGSPpha
)
)
{
cout
<<
"**** INPUT MISSING: Please provide GRIDSPACE_PSF_PHASE
\n
"
;
exit
(
1
);};
if
(
not
(
yesMDC
)
)
{
cout
<<
"**** INPUT MISSING: Please provide MAX_D_CENTER
\n
"
;
exit
(
1
);};
if
(
not
(
yesMDC
)
)
{
cout
<<
"**** INPUT MISSING: Please provide MAX_D_CENTER
\n
"
;
exit
(
1
);};
if
(
not
(
yesGCen
)
)
{
cout
<<
"**** INPUT MISSING: Please provide PIXEL_GRID_CENTER
\n
"
;
exit
(
1
);};
if
(
not
(
yesGCen
)
)
{
cout
<<
"**** INPUT MISSING: Please provide PIXEL_GRID_CENTER
\n
"
;
exit
(
1
);};
//More checks with input parameters
//More checks with input parameters
// Envelope should not have a standard deviation greater than Npix/2
// Envelope should not have a standard deviation greater than Npix/2
if
(
sqrt
(
1.
/
(
(
myfloat_t
)
numberGridPointsDisplaceCenter
*
gridEnvelop
+
startGridEnvelop
))
>
float
(
param_device
.
NumberPixels
)
/
2.0
)
{
if
(
sqrt
(
1.
/
(
(
myfloat_t
)
numberGridPointsDisplaceCenter
*
gridEnvelop
+
startGridEnvelop
))
>
float
(
param_device
.
NumberPixels
)
/
2.0
)
{
cout
<<
"MAX Standar deviation of envelope is larger than Allowed KERNEL Length "
;
cout
<<
"MAX Standar deviation of envelope is larger than Allowed KERNEL Length "
;
exit
(
1
);
exit
(
1
);
}
}
// Envelop param should be positive
// Envelop param should be positive
if
(
startGridCTF_amp
<
0
||
startGridCTF_amp
>
1
){
if
(
startGridCTF_amp
<
0
||
startGridCTF_amp
>
1
){
cout
<<
"PSF Amplitud should be between 0 and 1
\n
"
;
cout
<<
"PSF Amplitud should be between 0 and 1
\n
"
;
exit
(
1
);
exit
(
1
);
}
}
if
(
(
myfloat_t
)
numberGridPointsCTF_amp
*
gridCTF_amp
+
startGridCTF_amp
<
0
||
(
myfloat_t
)
numberGridPointsCTF_amp
*
gridCTF_amp
+
startGridCTF_amp
>
1
){
if
(
(
myfloat_t
)
numberGridPointsCTF_amp
*
gridCTF_amp
+
startGridCTF_amp
<
0
||
(
myfloat_t
)
numberGridPointsCTF_amp
*
gridCTF_amp
+
startGridCTF_amp
>
1
){
cout
<<
"PSF Amplitud should be between 0 and 1
\n
"
;
cout
<<
"PSF Amplitud should be between 0 and 1
\n
"
;
exit
(
1
);
exit
(
1
);
}
}
cout
<<
" +++++++++++++++++++++++++++++++++++++++++
\n
"
;
cout
<<
" +++++++++++++++++++++++++++++++++++++++++
\n
"
;
...
...
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