Commit 151a1827 authored by Gregory C. Sharp's avatar Gregory C. Sharp

Change DOS EOL to Unix

parent 60223bcf
This diff is collapsed.
[PLAN]
patient = @PLM_BUILD_TESTING_DIR@/rect-17.mha
target = @PLM_BUILD_TESTING_DIR@/ptv-1.mha
dose_out = @PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@.mha
[BEAM]
flavor = f
homo_approx = n
source = 0 -2000 0
isocenter = 0 0 0
aperture_offset = 1500
aperture_origin = -75 -75
aperture_spacing = 3.75 3.75
aperture_resolution = 41 41
aperture_smearing = 5
source_size = 0
[PEAK]
energy=100.00000
spread=1.000000
weight=1.0
[PLAN]
patient = @PLM_BUILD_TESTING_DIR@/rect-17.mha
target = @PLM_BUILD_TESTING_DIR@/ptv-1.mha
dose_out = @PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@.mha
[BEAM]
flavor = f
homo_approx = n
source = 0 -2000 0
isocenter = 0 0 0
aperture_offset = 1500
aperture_origin = -75 -75
aperture_spacing = 3.75 3.75
aperture_resolution = 41 41
aperture_smearing = 5
source_size = 0
[PEAK]
energy=100.00000
spread=1.000000
weight=1.0
[PLAN]
patient = @PLM_BUILD_TESTING_DIR@/rect-17.mha
target = @PLM_BUILD_TESTING_DIR@/ptv-1.mha
dose_out = @PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@.mha
[BEAM]
flavor = d
homo_approx = n
source = 0 -2000 0
isocenter = 0 0 0
aperture_offset = 1500
aperture_origin = -75 -75
aperture_spacing = 3.75 3.75
aperture_resolution = 41 41
aperture_smearing = 5
source_size = 0
[PLAN]
patient = @PLM_BUILD_TESTING_DIR@/rect-17.mha
target = @PLM_BUILD_TESTING_DIR@/ptv-1.mha
dose_out = @PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@.mha
[BEAM]
flavor = d
homo_approx = n
source = 0 -2000 0
isocenter = 0 0 0
aperture_offset = 1500
aperture_origin = -75 -75
aperture_spacing = 3.75 3.75
aperture_resolution = 41 41
aperture_smearing = 5
source_size = 0
[PLAN]
patient = @PLM_BUILD_TESTING_DIR@/rect-17.mha
dose_out = @PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@.mha
dose_prescription = 70
[BEAM]
flavor = a
homo_approx = n
source = 0 -2000 0
isocenter = 0 0 0
aperture_origin = -20 -20
aperture_offset = 1500
aperture_spacing = 1 1
aperture_resolution = 41 41
source_size = 0
spot = -5,0,120,6.0,1.5
[PLAN]
patient = @PLM_BUILD_TESTING_DIR@/rect-17.mha
dose_out = @PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@.mha
dose_prescription = 70
[BEAM]
flavor = a
homo_approx = n
source = 0 -2000 0
isocenter = 0 0 0
aperture_origin = -20 -20
aperture_offset = 1500
aperture_spacing = 1 1
aperture_resolution = 41 41
source_size = 0
spot = -5,0,120,6.0,1.5
[GLOBAL]
fixed=@PLM_BUILD_TESTING_DIR@/gauss-1.mha
moving=@PLM_BUILD_TESTING_DIR@/gauss-2.mha
[STAGE]
xform=bspline
optim=lbfgsb
impl=plastimatch
threading=single
alg_flavor=c
max_its=5
convergence_tol=3
grad_tol=0.1
grid_spac=30 30 30
res=2 2 2
[GLOBAL]
fixed=@PLM_BUILD_TESTING_DIR@/gauss-1.mha
moving=@PLM_BUILD_TESTING_DIR@/gauss-2.mha
[STAGE]
xform=bspline
optim=lbfgsb
impl=plastimatch
threading=single
alg_flavor=c
max_its=5
convergence_tol=3
grad_tol=0.1
grid_spac=30 30 30
res=2 2 2
[INPUT SETTINGS]
ct=@PLM_BUILD_TESTING_DIR@/lung-1.mha
proj_wed=@PLM_BUILD_TESTING_DIR@/wed-a-proj-wed.rpl
target=@PLM_BUILD_TESTING_DIR@/lung-1-prefix/Tumor.mha
skin=@PLM_BUILD_TESTING_DIR@/lung-1-prefix/Body.mha
[OUTPUT SETTINGS]
proj_ct=@PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@-proj-ct.rpl
wed_ct=@PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@-wed-ct.mha
[BEAM]
pos=-2270.5 0 0
isocenter=0 0 0
res=1
[APERTURE]
offset=1700
center=49.5 49.5
resolution=100 100
[INPUT SETTINGS]
ct=@PLM_BUILD_TESTING_DIR@/lung-1.mha
proj_wed=@PLM_BUILD_TESTING_DIR@/wed-a-proj-wed.rpl
target=@PLM_BUILD_TESTING_DIR@/lung-1-prefix/Tumor.mha
skin=@PLM_BUILD_TESTING_DIR@/lung-1-prefix/Body.mha
[OUTPUT SETTINGS]
proj_ct=@PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@-proj-ct.rpl
wed_ct=@PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@-wed-ct.mha
[BEAM]
pos=-2270.5 0 0
isocenter=0 0 0
res=1
[APERTURE]
offset=1700
center=49.5 49.5
resolution=100 100
[INPUT SETTINGS]
ct=@PLM_BUILD_TESTING_DIR@/lung-1.mha
proj_wed=@PLM_BUILD_TESTING_DIR@/wed-a-proj-wed.mha
target=@PLM_BUILD_TESTING_DIR@/lung-1-prefix/Tumor.mha
skin=@PLM_BUILD_TESTING_DIR@/lung-1-prefix/Body.mha
[OUTPUT SETTINGS]
dew_ct=@PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@-dew-ct.mha
[BEAM]
pos=-2270.5 0 0
isocenter=0 0 0
res=1
[APERTURE]
offset=1700
center=49.5 49.5
resolution=100 100
[INPUT SETTINGS]
ct=@PLM_BUILD_TESTING_DIR@/lung-1.mha
proj_wed=@PLM_BUILD_TESTING_DIR@/wed-a-proj-wed.mha
target=@PLM_BUILD_TESTING_DIR@/lung-1-prefix/Tumor.mha
skin=@PLM_BUILD_TESTING_DIR@/lung-1-prefix/Body.mha
[OUTPUT SETTINGS]
dew_ct=@PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@-dew-ct.mha
[BEAM]
pos=-2270.5 0 0
isocenter=0 0 0
res=1
[APERTURE]
offset=1700
center=49.5 49.5
resolution=100 100
## This script compares a value in a text file against lower and
## upper thresholds
message (STATUS "INFILE is ${INFILE}")
message (STATUS "REGEX is ${REGEX}")
message (STATUS "LOWER_THRESH is ${LOWER_THRESH}")
message (STATUS "UPPER_THRESH is ${UPPER_THRESH}")
file (STRINGS ${INFILE} TEST_OUTPUT REGEX "${REGEX}")
message (STATUS "PARSED VALUE=|${TEST_OUTPUT}|")
string (REGEX MATCH "${REGEX}" TEST_OUTPUT ${TEST_OUTPUT})
set (TEST_OUTPUT ${CMAKE_MATCH_1})
message (STATUS "PARSED_VALUE=|${TEST_OUTPUT}|")
string (LENGTH "${CMAKE_MATCH_1}" MATCH_LENGTH)
if (MATCH_LENGTH GREATER 0
AND NOT CMAKE_MATCH_1 LESS ${LOWER_THRESH}
AND NOT CMAKE_MATCH_1 GREATER ${UPPER_THRESH})
message ("Not an error")
else ()
message (SEND_ERROR "An error")
endif ()
## This script compares a value in a text file against lower and
## upper thresholds
message (STATUS "INFILE is ${INFILE}")
message (STATUS "REGEX is ${REGEX}")
message (STATUS "LOWER_THRESH is ${LOWER_THRESH}")
message (STATUS "UPPER_THRESH is ${UPPER_THRESH}")
file (STRINGS ${INFILE} TEST_OUTPUT REGEX "${REGEX}")
message (STATUS "PARSED VALUE=|${TEST_OUTPUT}|")
string (REGEX MATCH "${REGEX}" TEST_OUTPUT ${TEST_OUTPUT})
set (TEST_OUTPUT ${CMAKE_MATCH_1})
message (STATUS "PARSED_VALUE=|${TEST_OUTPUT}|")
string (LENGTH "${CMAKE_MATCH_1}" MATCH_LENGTH)
if (MATCH_LENGTH GREATER 0
AND NOT CMAKE_MATCH_1 LESS ${LOWER_THRESH}
AND NOT CMAKE_MATCH_1 GREATER ${UPPER_THRESH})
message ("Not an error")
else ()
message (SEND_ERROR "An error")
endif ()
## This script finds a regex in a file and compares the first match
## with an input string
message (STATUS "INFILE is ${INFILE}")
message (STATUS "REGEX is ${REGEX}")
message (STATUS "MATCH_STRING is ${MATCH_STRING}")
file (STRINGS ${INFILE} test_output REGEX "${REGEX}")
message (STATUS "PARSED VALUE=|${test_output}|")
string (REGEX MATCH "${REGEX}" test_output ${test_output})
set (test_output ${CMAKE_MATCH_1})
message (STATUS "PARSED_VALUE=|${test_output}|")
string (LENGTH "${test_output}" match_length)
message (STATUS "LENGTH=${match_length}")
message (STATUS "|${test_output}|${MATCH_STRING}|")
if ("${match_length}" GREATER 0
AND "${test_output}" STREQUAL "${MATCH_STRING}")
message("Not an error")
else ()
message (SEND_ERROR "An error")
endif ()
## This script finds a regex in a file and compares the first match
## with an input string
message (STATUS "INFILE is ${INFILE}")
message (STATUS "REGEX is ${REGEX}")
message (STATUS "MATCH_STRING is ${MATCH_STRING}")
file (STRINGS ${INFILE} test_output REGEX "${REGEX}")
message (STATUS "PARSED VALUE=|${test_output}|")
string (REGEX MATCH "${REGEX}" test_output ${test_output})
set (test_output ${CMAKE_MATCH_1})
message (STATUS "PARSED_VALUE=|${test_output}|")
string (LENGTH "${test_output}" match_length)
message (STATUS "LENGTH=${match_length}")
message (STATUS "|${test_output}|${MATCH_STRING}|")
if ("${match_length}" GREATER 0
AND "${test_output}" STREQUAL "${MATCH_STRING}")
message("Not an error")
else ()
message (SEND_ERROR "An error")
endif ()
## This script runs the speed tests
execute_process (
COMMAND "${PLM_PLASTIMATCH_PATH}/plastimatch"
# OUTPUT_FILE ${PLM_BUILD_TESTING_DIR}/hello.txt
OUTPUT_VARIABLE STDOUT
ERROR_VARIABLE STDOUT
)
message (STATUS "${PLM_PLASTIMATCH_PATH}/plastimatch")
message (STATUS "${STDOUT}")
file (WRITE "${PLM_BUILD_TESTING_DIR}/hello.txt"
"${PLM_PLASTIMATCH_PATH}/plastimatch\n")
file (APPEND "${PLM_BUILD_TESTING_DIR}/hello.txt"
"STDOUT = ${STDOUT}\n")
file (APPEND "${PLM_BUILD_TESTING_DIR}/hello.txt"
"STDERR = ${STDERR}\n")
## This script runs the speed tests
execute_process (
COMMAND "${PLM_PLASTIMATCH_PATH}/plastimatch"
# OUTPUT_FILE ${PLM_BUILD_TESTING_DIR}/hello.txt
OUTPUT_VARIABLE STDOUT
ERROR_VARIABLE STDOUT
)
message (STATUS "${PLM_PLASTIMATCH_PATH}/plastimatch")
message (STATUS "${STDOUT}")
file (WRITE "${PLM_BUILD_TESTING_DIR}/hello.txt"
"${PLM_PLASTIMATCH_PATH}/plastimatch\n")
file (APPEND "${PLM_BUILD_TESTING_DIR}/hello.txt"
"STDOUT = ${STDOUT}\n")
file (APPEND "${PLM_BUILD_TESTING_DIR}/hello.txt"
"STDERR = ${STDERR}\n")
Man pages
=========
.. toctree::
:maxdepth: 2
drr
fdk
landmarks
plastimatch
Man pages
=========
.. toctree::
:maxdepth: 2
drr
fdk
landmarks
plastimatch
landmark_warp
=============
Synopsis
--------
``landmark_warp [options]``
Description
-----------
The landmark_warp executable performs registration by matching
fiducials on reference and test images.
The list of possible options can be seen by typing::
landmark_warp --help
The command line usage is given as follows::
Usage: landmark_warp [options]
Options:
-a, --algorithm <arg> RBF warping algorithm {tps,gauss,
wendland}
-d, --default-value <arg> Value to set for pixels with unknown
value
--dim <arg> Size of output image
in voxels "x [y z]"
-F, --fixed <arg> Fixed image (match output size to this
image)
-f, --fixed-landmarks <arg> Input fixed landmarks
-h, --help Display this help message
-I, --input-image <arg> Input image to warp
-v, --input-vf <arg> Input vector field (applied prior to
landmark warping)
-m, --moving-landmarks <arg>
Output moving landmarks
-N, --numclusters <arg> Number of clusters of landmarks
--origin <arg> Location of first image voxel
in mm "x y z"
-O, --output-image <arg> Output warped image
-L, --output-landmarks <arg>
Output warped landmarks
-V, --output-vf <arg> Output vector field
-r, --radius <arg> Radius of radial basis function
(in mm)
--spacing <arg> Voxel spacing in mm "x [y z]"
-Y, --stiffness <arg> Young modulus (default = 0.0)
Options "-a", "-r", "-Y", "-d" are set by default to::
-a=gauss Gaussian RBFs with infinite support
-r=50.0 Gaussian width 50 mm
-Y=0.0 No regularization of vector field
-d=-1000 Air
You may want to choose different algorithm::
-a=tps Thin-plate splines (for global registration)
-a=wendland Wendland RBFs with compact support (for
local registration)
In the case of Wendland RBFs "-r" option sets the radius of support.
Regularization of vector field is available for "gauss" and "wendland" algorithms. To regularize the output vector field increase "-Y" to '0.1' and up with increment '0.1'.
landmark_warp
=============
Synopsis
--------
``landmark_warp [options]``
Description
-----------
The landmark_warp executable performs registration by matching
fiducials on reference and test images.
The list of possible options can be seen by typing::
landmark_warp --help
The command line usage is given as follows::
Usage: landmark_warp [options]
Options:
-a, --algorithm <arg> RBF warping algorithm {tps,gauss,
wendland}
-d, --default-value <arg> Value to set for pixels with unknown
value
--dim <arg> Size of output image
in voxels "x [y z]"
-F, --fixed <arg> Fixed image (match output size to this
image)
-f, --fixed-landmarks <arg> Input fixed landmarks
-h, --help Display this help message
-I, --input-image <arg> Input image to warp
-v, --input-vf <arg> Input vector field (applied prior to
landmark warping)
-m, --moving-landmarks <arg>
Output moving landmarks
-N, --numclusters <arg> Number of clusters of landmarks
--origin <arg> Location of first image voxel
in mm "x y z"
-O, --output-image <arg> Output warped image
-L, --output-landmarks <arg>
Output warped landmarks
-V, --output-vf <arg> Output vector field
-r, --radius <arg> Radius of radial basis function
(in mm)
--spacing <arg> Voxel spacing in mm "x [y z]"
-Y, --stiffness <arg> Young modulus (default = 0.0)
Options "-a", "-r", "-Y", "-d" are set by default to::
-a=gauss Gaussian RBFs with infinite support
-r=50.0 Gaussian width 50 mm
-Y=0.0 No regularization of vector field
-d=-1000 Air
You may want to choose different algorithm::
-a=tps Thin-plate splines (for global registration)
-a=wendland Wendland RBFs with compact support (for
local registration)
In the case of Wendland RBFs "-r" option sets the radius of support.
Regularization of vector field is available for "gauss" and "wendland" algorithms. To regularize the output vector field increase "-Y" to '0.1' and up with increment '0.1'.
User guide
==========
.. toctree::
:maxdepth: 1
getting_started
windows_installation
image_registration_guidebook
registration_command_file_reference
registration_tutorial
mabs_guidebook
mabs_commands
segmentation_command_file_reference
fdk_tutorial_i
fdk_tutorial_ii
dose_calculation_command_file_reference
3d_slicer_integration
User guide
==========
.. toctree::
:maxdepth: 1
getting_started
windows_installation
image_registration_guidebook
registration_command_file_reference
registration_tutorial
mabs_guidebook
mabs_commands
segmentation_command_file_reference
fdk_tutorial_i
fdk_tutorial_ii
dose_calculation_command_file_reference
3d_slicer_integration
/* -----------------------------------------------------------------------
See COPYRIGHT.TXT and LICENSE.TXT for copyright and license information
----------------------------------------------------------------------- */
#include "plmdose_config.h"
#include <list>
#include "rt_spot_map.h"
class Rt_spot_map_private {
public:
std::list<Rt_spot> spot_list;
};
Rt_spot_map::Rt_spot_map ()
{
d_ptr = new Rt_spot_map_private;
}
Rt_spot_map::~Rt_spot_map ()
{
delete d_ptr;
}
void
Rt_spot_map::add_spot (
float xpos,
float ypos,
float energy,
float sigma,
float weight)
{
d_ptr->spot_list.push_back (
Rt_spot (xpos, ypos, energy, sigma, weight));
}
size_t
Rt_spot_map::num_spots () const
{
return d_ptr->spot_list.size ();
}
const std::list<Rt_spot>&
Rt_spot_map::get_spot_list () const
{
return d_ptr->spot_list;
}
void
Rt_spot_map::load_spot_map (const std::string& fn)
{
}
void
Rt_spot_map::save_spot_map (const std::string& fn) const
{
}
/* -----------------------------------------------------------------------
See COPYRIGHT.TXT and LICENSE.TXT for copyright and license information
----------------------------------------------------------------------- */
#include "plmdose_config.h"
#include <list>
#include "rt_spot_map.h"
class Rt_spot_map_private {
public:
std::list<Rt_spot> spot_list;
};
Rt_spot_map::Rt_spot_map ()
{
d_ptr = new Rt_spot_map_private;
}
Rt_spot_map::~Rt_spot_map ()
{
delete d_ptr;
}
void
Rt_spot_map::add_spot (
float xpos,
float ypos,
float energy,
float sigma,
float weight)
{
d_ptr->spot_list.push_back (
Rt_spot (xpos, ypos, energy, sigma, weight));
}
size_t
Rt_spot_map::num_spots () const
{
return d_ptr->spot_list.size ();
}
const std::list<Rt_spot>&
Rt_spot_map::get_spot_list () const
{
return d_ptr->spot_list;
}
void
Rt_spot_map::load_spot_map (const std::string& fn)
{
}
void
Rt_spot_map::save_spot_map (const std::string& fn) const
{
}
/* -----------------------------------------------------------------------
See COPYRIGHT.TXT and LICENSE.TXT for copyright and license information
----------------------------------------------------------------------- */
#ifndef _rt_spot_map_h_
#define _rt_spot_map_h_
#include "plmdose_config.h"
#include "smart_pointer.h"
class Rt_spot_map_private;
class PLMDOSE_API Rt_spot {
public:
Rt_spot (
float xpos, float ypos, float energy, float sigma, float weight)
: xpos(xpos), ypos(ypos), energy(energy), sigma(sigma), weight(weight)
{}
public:
float xpos;
float ypos;
float energy;
float sigma;
float weight;
};
class PLMDOSE_API Rt_spot_map {
public:
SMART_POINTER_SUPPORT (Rt_spot_map);
Rt_spot_map_private *d_ptr;
public:
Rt_spot_map ();
~Rt_spot_map ();
public:
void add_spot (
float xpos, float ypos, float energy, float sigma, float weight);
size_t num_spots () const;
const std::list<Rt_spot>& get_spot_list () const;
void load_spot_map (const std::string& fn);
void save_spot_map (const std::string& fn) const;
};
#endif
/* -----------------------------------------------------------------------
See COPYRIGHT.TXT and LICENSE.TXT for copyright and license information
----------------------------------------------------------------------- */
#ifndef _rt_spot_map_h_
#define _rt_spot_map_h_
#include "plmdose_config.h"
#include "smart_pointer.h"
class Rt_spot_map_private;
class PLMDOSE_API Rt_spot {
public:
Rt_spot (
float xpos, float ypos, float energy, float sigma, float weight)
: xpos(xpos), ypos(ypos), energy(energy), sigma(sigma), weight(weight)
{}
public:
float xpos;
float ypos;
float energy;
float sigma;
float weight;
};
class PLMDOSE_API Rt_spot_map {
public:
SMART_POINTER_SUPPORT (Rt_spot_map);