CMakeLists.txt

@@ -8,7 +8,7 @@ project (plastimatch)
 ## The version here should be equal to the "most recent release"
 set (PLM_VERSION_MAJOR "1")
 set (PLM_VERSION_MINOR "7")
-set (PLM_VERSION_PATCH "3")
+set (PLM_VERSION_PATCH "4")
 
 ##-----------------------------------------------------------------------------
 ##  Set up CMake defaults
@@ -556,47 +556,6 @@ if (ITK_FOUND)
   include (HandleVXL)
 endif ()
 
-##-----------------------------------------------------------------------------
-##  GDCM
-##-----------------------------------------------------------------------------
-if (NOT DCMTK_FOUND AND ITK_FOUND)
-  # The default case is that ITK_USE_SYSTEM_GDCM was used,
-  # the gdcm use file was already loaded from UseITK.cmake, and therefore
-  # GDCM_VERSION is already known.  If this is not the case, we look
-  # in the ITK build dir for the header file which contains the version.
-  if (NOT GDCM_VERSION)
-    unset (GDCM_CONFIGURE_H CACHE)
-    find_file (GDCM_CONFIGURE_H gdcmConfigure.h PATHS ${ITK_INCLUDE_DIRS})
-    if (GDCM_CONFIGURE_H)
-      file (STRINGS "${GDCM_CONFIGURE_H}"
-	GDCM_VERSION
-	REGEX "^#define GDCM_VERSION *\"([^\"]*)\"")
-      string (REGEX REPLACE "[^\"]*\"([^\"]*)\".*" "\\1"
-	GDCM_VERSION "${GDCM_VERSION}")
-    endif ()
-    # When GDCM config file does not configure correctly, the value of
-    # the version might be "@GDCM_VERSION@".
-    if ("${GDCM_VERSION}" STREQUAL "\@GDCM_VERSION@")
-      set (GDCM_VERSION "2.0")
-    endif ()
-    set (GDCM_FOUND 1)
-  endif ()
-
-  if (GDCM_VERSION)
-    message (STATUS "GDCM version ${GDCM_VERSION} found")
-  else ()
-    message (FATAL_ERROR "Found ITK, but didn't find GDCM")
-  endif ()
-
-  if (GDCM_VERSION VERSION_LESS "2.0")
-    set (GDCM_VERSION_1 1)
-  else ()
-    set (GDCM_VERSION_2 1)
-  endif ()
-else ()
-  # No itk?  Use dcmtk instead
-endif ()
-
 ##-----------------------------------------------------------------------------
 ##  QT
 ##-----------------------------------------------------------------------------
@@ -690,7 +649,19 @@ add_subdirectory (src)
 if (ITK_FOUND)
   set (DLL_PATTERNS "ITKCommon*.dll" "ITKIO*.dll" "ITKOptimizers*.dll" "ITKStatistics*.dll" "ITKTransform*.dll")
   foreach (p ${DLL_PATTERNS})
-    file (GLOB DLLFILES "${ITK_DIR}/bin/release/${p}")
+    # .../bin/release/*.dll for build tree, .../bin/*.dll for install tree
+    file (GLOB DLLFILES "${ITK_DLL_DIR}/${p}")
+    if (DLLFILES)
+      install (FILES ${DLLFILES} DESTINATION bin)
+    endif ()
+  endforeach ()
+endif ()
+
+if (DCMTK_FOUND)
+  set (DLL_PATTERNS "oflog.dll" "ofstd.dll" "dcmdata.dll")
+  foreach (p ${DLL_PATTERNS})
+    # .../bin/release/*.dll for build tree, .../bin/*.dll for install tree
+    file (GLOB DLLFILES "${DCMTK_DIR}/bin/release/${p}")
     if (DLLFILES)
       install (FILES ${DLLFILES} DESTINATION bin)
     endif ()
@@ -783,23 +754,15 @@ if (WIN32 AND NOT CYGWIN AND NOT MINGW)
   set (PLM_PLASTIMATCH_TESTING_PATH
     ${PLM_BINARY_DIR}/Testing/Release)
   set (PLM_FFTW_PATH ${FFTW_DIR})
-  # At some point in time (presumably around ITK 4.1), ITK stopped
-  # creating the variable ITK_LIBRARY_DIRS.  Therefore, we have to
-  # use another method to find the ITK directory needed to run tests.
-  if (NOT ITK_FOUND)
-    set (PLM_ITK_LIBRARY_PATH_HACK
-      -DITK_LIBRARY_PATH=${PLM_BINARY_DIR}/ITK-build/bin/Release)
-  elseif (${ITK_VERSION} VERSION_LESS "4.1")
-    set (PLM_ITK_LIBRARY_PATH_HACK
-      -DITK_LIBRARY_PATH=${ITK_LIBRARY_DIRS}/Release)
+
+  if (NOT "${ITK_DLL_DIR}" STREQUAL "")
+    set (PLM_ITK_LIBRARY_PATH_HACK -DITK_LIBRARY_PATH=${ITK_DLL_DIR})
   else ()
-    string (REGEX REPLACE "/[^/]*$" "" ITK_LIBRARY_DIRS_41
-      "${ITK_CONFIG_TARGETS_FILE}")
-    set (PLM_ITK_LIBRARY_PATH_HACK
-      -DITK_LIBRARY_PATH=${ITK_LIBRARY_DIRS_41}/bin/Release)
+    set (PLM_ITK_LIBRARY_PATH_HACK "")
   endif ()
   set (PLM_PLASTIMATCH_PATH_HACK
      -DPLM_PLASTIMATCH_PATH=${PLM_PLASTIMATCH_PATH})
+  set (PLM_DCMTK_PATH_HACK -DPLM_DCMTK_PATH=${DCMTK_DIR}/bin/Release)
   set (PLM_FFTW_PATH_HACK
      -DPLM_FFTW_PATH=${PLM_FFTW_PATH})
 else ()
@@ -808,6 +771,7 @@ else ()
   set (PLM_FFTW_PATH "${FFTW_DIR}")
   set (PLM_ITK_LIBRARY_PATH_HACK "")
   set (PLM_PLASTIMATCH_PATH_HACK "")
+  set (PLM_DCMTK_PATH_HACK "")
   set (PLM_FFTW_PATH_HACK "")
 endif ()
 
@@ -825,6 +789,7 @@ macro (PLM_ADD_TEST PLM_TEST_NAME PLM_TEST_COMMAND PARMS)
     -DPLM_TEST_NAME=${PLM_TEST_NAME}
     ${PLM_ITK_LIBRARY_PATH_HACK}
     ${PLM_PLASTIMATCH_PATH_HACK}
+    ${PLM_DCMTK_PATH_HACK}
     ${PLM_FFTW_PATH_HACK}
     -DPLM_TEST_COMMAND=${PLM_TEST_COMMAND}
     -DPLM_TESTING_SOURCE_DIR=${PLM_TESTING_SOURCE_DIR}

Testing/CTestCustom.cmake.in

@@ -5,8 +5,6 @@ set (FFTW_FOUND @FFTW_FOUND@)
 set (ITK_VERSION "@ITK_VERSION@")
 set (OPENCL_FOUND @OPENCL_FOUND@)
 set (PLM_DCM_USE_DCMTK "@PLM_DCM_USE_DCMTK@")
-set (PLM_DCM_USE_GDCM1 "@PLM_DCM_USE_GDCM1@")
-set (PLM_DCM_USE_GDCM2 "@PLM_DCM_USE_GDCM2@")
 set (PLM_PLASTIMATCH_PATH "@PLM_PLASTIMATCH_PATH@")
 set (PLM_PLASTIMATCH_PATH_HACK "@PLM_PLASTIMATCH_PATH_HACK@")
 set (PLM_REDUCED_TESTS @PLM_REDUCED_TESTS@)
@@ -305,57 +303,14 @@ if (NOT PLM_DCM_USE_DCMTK)
     )
 endif ()
 
-## If we only have GDCM 2, don't run these tests
-if (PLM_DCM_USE_GDCM2)
-  set (CTEST_CUSTOM_TESTS_IGNORE
-    ${CTEST_CUSTOM_TESTS_IGNORE}
-    "plm-convert-dicom-donut-a" 
-    "plm-convert-dicom-donut-a-stats" 
-    "plm-convert-dicom-donut-a-check" 
-    "plm-convert-dicom-donut-b" 
-    "plm-convert-dicom-donut-b-stats" 
-    "plm-convert-dicom-donut-b-check" 
-    "plm-convert-dicom-a"
-    "plm-convert-dicom-a-stats" 
-    "plm-convert-dicom-a-check" 
-    "plm-convert-dicom-b"
-    "plm-convert-dicom-b-stats"
-    "plm-convert-dicom-b-check"
-    "plm-convert-dicom-c" 
-    "plm-convert-dicom-c-stats" 
-    "plm-convert-dicom-c-check" 
-    "plm-convert-dicom-f" 
-    "plm-convert-cxt"
-    "plm-convert-cxt-stats"
-    "plm-convert-cxt-check"
-    )
-endif ()
-
-## Dose calculation not yet supported on debian
+## These tests are failing
 if (PLM_CONFIG_DEBIAN_BUILD)
   set (CTEST_CUSTOM_TESTS_IGNORE
     ${CTEST_CUSTOM_TESTS_IGNORE}
-    "proton-dose-1"
-    "proton-dose-1-stats"
-    "proton-dose-1-check"
-    "proton-dose-2"
-    "proton-dose-2-stats"
-    "proton-dose-2-check"
-    "proton-dose-3"
-    "proton-dose-3-stats"
-    "proton-dose-3-check"
-    "proton-dose-5a"
-    "proton-dose-5a-stats"
-    "proton-dose-5a-check"
-    "proton-dose-5d"
-    "proton-dose-5d-stats"
-    "proton-dose-5d-check"
-    "proton-dose-5g"
-    "proton-dose-5g-stats"
-    "proton-dose-5g-check"
-    "proton-dose-6a"
-    "proton-dose-6a-stats"
-    "proton-dose-6a-check"
+    "proton-dose-7a"
+    "proton-dose-8d"
+    "proton-dose-8d-stats"
+    "proton-dose-8d-check"
     )
 endif ()
 

Testing/Data/plm-bsp-rect.txt

 [GLOBAL]
 fixed=@PLM_BUILD_TESTING_DIR@/rect-2.mha
 moving=@PLM_BUILD_TESTING_DIR@/rect-3.mha
-vf_out=@PLM_BUILD_TESTING_DIR@/plm-bsp-rect-vf.mha
+vf_out=@PLM_BUILD_TESTING_DIR@/plm-bsp-rect-vf.nrrd
 xform_out=@PLM_BUILD_TESTING_DIR@/plm-bsp-rect-xf.txt
 img_out=@PLM_BUILD_TESTING_DIR@/plm-bsp-rect-img.mha
 

Testing/Data/proton-dose-4.txt

-[PLAN]
-patient = @PLM_BUILD_TESTING_DIR@/rect-18.mha
-dose_out = @PLM_BUILD_TESTING_DIR@/proton-dose4.mha
-
-[BEAM]
-flavor = h
-homo_approx = n
-depth_dose_z_max = 400
-
-source = 0 -2200 0
-isocenter = 0 0 0
-
-aperture_origin = -37.5 -37.5
-aperture_offset = 1500
-aperture_spacing = 7.5 7.5
-aperture_resolution = 10 10
-range_compensator_file_in = @PLM_BUILD_TESTING_DIR@/rgc-1.mha
-source_size = 0
-
-[PEAK]
-energy=100.0000
-spread=1.000000
-weight=1

Testing/Data/proton-dose-4a.txt

+[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 = a
+homo_approx = n
+beam_line = passive
+
+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

Testing/Data/proton-dose-4d.txt

+[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
+beam_line = passive
+
+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

Testing/Data/proton-dose-5d.txt

@@ -16,3 +16,5 @@ aperture_spacing = 3.75 3.75
 aperture_resolution = 41 41
 aperture_smearing = 5
 source_size = 0
+
+particle_number_out = @PLM_BUILD_TESTING_DIR@/@PLM_TEST_NAME@-pn.txt

Testing/Data/proton-dose-8d.txt

+[PLAN]
+patient = @PLM_BUILD_TESTING_DIR@/rect-17.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
+
+particle_number_in = @PLM_BUILD_TESTING_DIR@/proton-dose-5d-pn.txt

cmake/CheckDCMTK.cmake

+##---------------------------------------------------------------------------
+## See COPYRIGHT.TXT and LICENSE.TXT for copyright and license information
+##---------------------------------------------------------------------------
+
+include (CheckCXXSourceCompiles)
+
+file (READ "${PLM_SOURCE_DIR}/cmake/check_dcmtk_ec_invalidvalue.cxx"
+  CHECK_DCMTK_EC_INVALIDVALUE_SOURCE)
+push_vars (CMAKE_REQUIRED_INCLUDES CMAKE_REQUIRED_LIBRARIES)
+set (CMAKE_REQUIRED_INCLUDES ${DCMTK_INCLUDE_DIRS})
+set (CMAKE_REQUIRED_LIBRARIES ${DCMTK_LIBRARIES})
+check_cxx_source_compiles ("${CHECK_DCMTK_EC_INVALIDVALUE_SOURCE}"
+  DCMTK_HAS_EC_INVALIDVALUE)
+pop_vars (CMAKE_REQUIRED_INCLUDES CMAKE_REQUIRED_LIBRARIES)

cmake/FindDCMTK_wrap.cmake

@@ -23,3 +23,8 @@ endif ()
 # The DCMTK 3.6.2 DCMTKConfig.cmake seems to be broken on windows
 string (REPLACE "DCMTK_INCLUDE_DIRS-NOTFOUND;" "" DCMTK_INCLUDE_DIRS
   "${DCMTK_INCLUDE_DIRS}")
+
+# Additional test for compatibility across DCMTK versions
+if (DCMTK_FOUND)
+  include (CheckDCMTK)
+endif ()

cmake/HandleITK.cmake

@@ -44,3 +44,36 @@ else ()
     "Fatal Error. ITK version should be either 3.X or 4.X")
 endif ()
 message (STATUS "ITK_VERSION = ${ITK_VERSION} found")
+
+
+# Find ITK DLL directory.  This is used on Windows for both regression testing and packaging.
+if (NOT ITK_FOUND)
+  set (ITK_BASE "${PLM_BINARY_DIR}/ITK-build")
+elseif (${ITK_VERSION} VERSION_LESS "4.1")
+  set (ITK_BASE "${ITK_LIBRARY_DIRS}")
+else ()
+  # At some point in time (presumably around ITK 4.1), ITK stopped
+  # creating the variable ITK_LIBRARY_DIRS.  Therefore, we infer from the 
+  # configuration filename.
+  # Remove filename
+  string (REGEX REPLACE "/[^/]*$" "" ITK_LIBRARY_DIRS_41
+    "${ITK_CONFIG_TARGETS_FILE}")
+  # If configuring against installation directory, walk up to base directory
+  string (REGEX REPLACE "/lib/cmake/ITK-.*]*$" "" ITK_LIBRARY_DIRS_41
+    "${ITK_LIBRARY_DIRS_41}")
+  set (ITK_BASE "${ITK_LIBRARY_DIRS_41}")
+endif ()
+
+message (STATUS "ITK_BASE = ${ITK_BASE}")
+if (NOT WIN32)
+  set (ITK_DLL_DIR "")
+elseif (IS_DIRECTORY "${ITK_BASE}/bin/Release")
+  set (ITK_DLL_DIR "${ITK_BASE}/bin/Release")
+elseif (IS_DIRECTORY "${ITK_BASE}/Release")
+  set (ITK_DLL_DIR "${ITK_BASE}/Release")
+elseif (IS_DIRECTORY "${ITK_BASE}/bin")
+  set (ITK_DLL_DIR "${ITK_BASE}/bin")
+else ()
+  set (ITK_DLL_DIR "")
+endif ()
+

cmake/RUN_CTEST.cmake

@@ -3,7 +3,7 @@
 ## Apparently this is how to make the CMake script return status
 ##   http://www.cmake.org/Wiki/CMake/C_Plugins_for_Loadable_Commands
 
-set (ENV{PATH} "$ENV{PATH};${ITK_LIBRARY_PATH};${PLM_PLASTIMATCH_PATH};${PLM_FFTW_PATH}")
+set (ENV{PATH} "$ENV{PATH};${ITK_LIBRARY_PATH};${PLM_PLASTIMATCH_PATH};${PLM_DCMTK_PATH};${PLM_FFTW_PATH}")
 
 message ("PLM_TEST_COMMAND is ${PLM_TEST_COMMAND}")
 message ("PARMS is ${PARMS}")

cmake/check_dcmtk_ec_invalidvalue.cxx

+#include "dcmtk/dcmdata/dcerror.h"
+
+int 
+main (void)
+{
+    OFCondition o = EC_InvalidValue;
+    return 0;
+}

doc/NOTES.TXT

+******************************************************************************
+DRR, WED, BSTV = beam specific target volume
+
+DRR pro
+-------
+Drr uses command line options
+
+DRR con
+-------
+Drr does not use IEC
+Wed maintains an actual wed volume
+Drr does not have programmable LUT
+
+
+******************************************************************************
+Dose calc notes #4
+
+Deep dive (priority 1, n/a, no test)
+------------------------------------
+Plan_calc::compute_beam_dose
+ Beam_calc::prepare_for_calc
+ for each energy
+   compute_dose_{a,b,d}
+
+Beam_calc::prepare_for_calc
+ Beam_calc::compute_beam_data_from_target
+  Beam_calc::compute_beam_modifiers_passive_scattering_b
+   Beam_calc::compute_beam_modifiers
+    Beam_calc::compute_target_wepl_min_max
+    Beam_calc::apply_smearing_to_target
+   Rt_mebs::set_prescription_depths
+    Rt_mebs::update_energies_from_prescription
+   Rpl_volume::apply_beam_modifiers
+   Beam_calc::compute_beam_data_from_prescription
+    Rt_mebs::optimize_sobp
+    Beam_calc::compute_beam_data_from_manual_peaks
+     Rt_mebs::generate_part_num_from_weight
+     // compute_beam_modifiers not re-run
+
+Deep dive (priority 5, passive target, test 4d)
+-----------------------------------------------
+Plan_calc::compute_beam_dose
+ Beam_calc::prepare_for_calc
+ for each energy
+   compute_dose_{a,b,d}
+
+Beam_calc::prepare_for_calc
+ Beam_calc::compute_beam_data_from_target
+  Beam_calc::compute_beam_modifiers_passive_scattering_b
+   Beam_calc::compute_beam_modifiers
+    Beam_calc::compute_target_wepl_min_max
+    Beam_calc::apply_smearing_to_target
+   Rt_mebs::set_prescription_depths
+    Rt_mebs::update_energies_from_prescription
+   Rpl_volume::apply_beam_modifiers
+   Beam_calc::compute_beam_data_from_prescription
+    Rt_mebs::optimize_sobp
+    Beam_calc::compute_beam_data_from_manual_peaks
+     Rt_mebs::generate_part_num_from_weight
+     // compute_beam_modifiers not re-run
+
+******************************************************************************
+Dose calc notes #3
+
+Command file
+------------
+Overrides for any beam model parameter
+
+Beam model
+----------
+Allowed energies (min/max/res or list)
+Depth dose for each energy (analytic parameters or files)
+Field size
+Beamlet spacing
+Beamline type
+Allowed spot positions
+Spot sigma
+Source distance
+Aperture distance
+Flavor/homo approx/ray step
+
+
+******************************************************************************
+Dose calc notes #2
+
+(A1) Aperture
+(A2) Range compensator
+(B1) Allowed energies (e.g. energy res)
+(B2) Energy min/max
+(B3) Energy weights (passive)
+(C) Target
+(D1) Spot map
+(D2) Beamlet map
+
+What combinations are acceptable?
+
+D alone
+D + A
+C alone
+C + A
+C + B
+B + A
+B alone
+
+To wit:
+
+A is a modifier, can be added to anything
+D defines B
+C may be used to compute A and/or B through optimization
+What about manually specified energy weights?
+
+A possible strategy
+
+1) Evaluate which items (A-E) need computed
+2) Optimize (A,B) from (C)
+3) Create MEBS structure
+4) Optimize (D) from (A,B,C)
+
+
+******************************************************************************
+Dose calc notes
+
+Rt_mebs
+  - add_peak()
+    - Create depth dose curve (ensuring all curves have same start/stop)
+    - Appends to depth_dose
+    - Appends to depth_dose_weight
+    - Appends to energies
+  - generate() seems to add together several pristine peaks, stored in
+    the depth_dose array, and put the results into e_lut and f_lut.
+    It is only used in the sobp_main() standalone.
+  - add_peak() is called from:
+    - Beam_calc::compute_default_beam()
+    - Rt_parms::append_peak() -- while interpreting [PEAK] sections
+    - Rt_mebs::optimize_sobp()
+    - Rt_mebs::load_beamlet_map()
+    - Rt_mebs::compute_particle_number_matrix_from_target_active()
+Rt_depth_dose
+  - lookup_energy() gets an interpolated value from the lut
+
+Overview of beam preparation tasks
+
+- Beam_calc::prepare_for_calc 
+  (1) Beam_calc::compute_beam_data_from_beamlet_map
+    - Rt_mebs::load_beamlet_map
+  (2) Beam_calc::compute_beam_data_from_spot_map
+    - Rt_mebs::set_from_spot_map
+  (3) Beam_calc::compute_beam_data_from_manual_peaks
+    - Beam_calc::compute_beam_modifiers_active_scanning
+  (4) Beam_calc::compute_beam_data_from_prescription
+    - Beam_calc::compute_beam_modifiers_active_scanning
+  (5) Beam_calc::compute_beam_data_from_target
+    (5a) Beam_calc::compute_beam_data_from_prescription
+    (5b) Beam_calc::compute_beam_modifiers_active_scanning
+           Beam_calc::compute_beam_modifiers_core
+         Rt_mebs::compute_particle_number_matrix_from_target_active
+  (6) Beam_calc::compute_default_beam
+
+
 ******************************************************************************
 B-spline mismatch
 

doc/STYLE_GUIDE_1.TXT

@@ -16,7 +16,7 @@ Conformance
 Plastimatch 1.X series must conform to the C++03 standard.
 
 Supported hosts:
-  Microsoft Windows 7 SP1           Visual Studio 2017
+  Microsoft Windows 7 SP1           Visual Studio 2015 (for CUDA 8)
   Ubuntu 12.04 LTS                  gcc 4.6.3
   Debian 8 "Jessie"                 gcc 4.9.2
   CentOS 6                          gcc 4.4.7
@@ -29,7 +29,7 @@ features available in the stock compilers provided on
 a fully-updated install of the supported platforms.
 
 Supported hosts:
-  Microsoft Windows 7 SP1           Visual Studio 2017
+  Microsoft Windows 7 SP1           Visual Studio 2015 (for CUDA 8)
   Ubuntu 14.04                      gcc 4.8.4; clang 3.4
   Debian 9 "Stretch"                gcc 6.3.0; clang 3.8.1
   CentOS 7                          gcc 4.8.5
@@ -52,9 +52,8 @@ clearly identified, so that no mistake in licensing occurs.
 
 Indentation
 -----------
-Indentation should be 4 spaces.  Tabs are allowed, but you must set 
-your tab stop to 8 spaces.  Note that this is not the default 
-for Microsoft Visual Studio compilers, so you should adjust your setting.
+Indentation should be 4 spaces.  Tabs are not allowed.
+For Microsoft Visual Studio compilers, you should adjust your setting.
 
 Line breaking
 -------------
@@ -122,11 +121,10 @@ Declaritors and return values go on a separate line (GNU style):
     foo (int bar)
     {
 
-Use explicit "void" in the argument list if there are no arguments
-is optional:
+Explicit "void" in the argument list is discouraged::
 
     void
-    foo (void)
+    foo ()   // rather than foo (void)
     {
 
 Horizontal whitespace
@@ -144,6 +142,11 @@ When there are no arguments, you may omit the space:
 
     foo();
 
+When the return value is used with member reference, omitting space
+is preferred::
+
+    foo(bar,baz)->boo().fuz
+
 Pointers and references
 -----------------------
 As per linux kernel style, put the '*' adjacent to the data name or 

doc/man/drr.1

 .\" Man page generated from reStructuredText.
 .
-.TH "DRR" "1" "Jul 09, 2018" "Plastimatch 1.7.3" "Plastimatch"
+.TH "DRR" "1" "Jan 08, 2019" "Plastimatch 1.7.4" "Plastimatch"
 .SH NAME
 drr \- create a digitally reconstructed radiograph
 .

doc/man/fdk.1

 .\" Man page generated from reStructuredText.
 .
-.TH "FDK" "1" "Jul 09, 2018" "Plastimatch 1.7.3" "Plastimatch"
+.TH "FDK" "1" "Jan 08, 2019" "Plastimatch 1.7.4" "Plastimatch"
 .SH NAME
 fdk \- cone-beam reconstruction from projections using the FDK algorithm
 .

doc/man/landmark_warp.1

 .\" Man page generated from reStructuredText.
 .
-.TH "LANDMARK_WARP" "1" "Jul 09, 2018" "Plastimatch 1.7.3" "Plastimatch"
+.TH "LANDMARK_WARP" "1" "Jan 08, 2019" "Plastimatch 1.7.4" "Plastimatch"
 .SH NAME
 landmark_warp \- warp an image using point landmarks
 .

doc/man/plastimatch.1

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-.TH "PLASTIMATCH" "1" "Jul 09, 2018" "Plastimatch 1.7.3" "Plastimatch"
+.TH "PLASTIMATCH" "1" "Jan 08, 2019" "Plastimatch 1.7.4" "Plastimatch"
 .SH NAME
 plastimatch \- register, convert, warp, or manipulate images
 .
@@ -47,17 +47,17 @@ without any additional command line arguments:
 .nf
 .ft C
 $ plastimatch
-plastimatch version 1.7.3
+plastimatch version 1.7.4
 Usage: plastimatch command [options]
 Commands:
  add           adjust        average       bbox          boundary
  crop          compare       compose       convert       dice
- diff          dmap          dose          dvh           fill
- filter        gamma         header        jacobian      mabs
- mask          maximum       ml\-convert    multiply      probe
- register      resample      scale         segment       stats
- synth         synth\-vf      threshold     thumbnail     union
- vf\-invert     warp          xf\-convert
+ diff          dmap          dose          drr           dvh
+ fill          filter        gamma         header        jacobian
+ mabs          mask          maximum       ml\-convert    multiply
+ probe         register      resample      scale         segment
+ sift          stats         synth         synth\-vf      threshold
+ thumbnail     union         warp          xf\-convert    xf\-invert
 
 For detailed usage of a specific command, type:
   plastimatch command