XRMC: new device radionuclide

Makefile.am

@@ -7,4 +7,4 @@ SUBDIRS = src doc examples nsis
 
 EXTRA_DIST = test libxrmc.pc.in xrmc.spec.in
 #DISTCHECK_CONFIGURE_FLAGS = --disable-openmp --disable-xmi-msim
-DISTCHECK_CONFIGURE_FLAGS = CXX=g++-mp-4.8 CC=gcc-mp-4.8
+DISTCHECK_CONFIGURE_FLAGS = CXX=g++-mp-4.7 CC=gcc-mp-4.7

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([xrmc],[6.4.5],[golosio@uniss.it])
+AC_INIT([xrmc],[6.5.0],[golosio@uniss.it])
 AC_PREREQ([2.60])
 AC_CONFIG_SRCDIR([src/main/xrmc_main.cpp])
 AC_CONFIG_AUX_DIR([build-aux])
@@ -72,14 +72,14 @@ PKG_PROG_PKG_CONFIG
 
 
 #search for xraylib and other modules
-PKG_CHECK_MODULES([xraylib],libxrl >= 3.0.0)
+PKG_CHECK_MODULES([xraylib],libxrl >= 3.1.0)
 
 
 #determine if the xmi-msim should be built
 AC_ARG_ENABLE([xmi-msim], AS_HELP_STRING([--disable-xmi-msim],[build without XMI-MSIM support]), [enable_xmi_msim=$enableval], [enable_xmi_msim=check])
 
 if test x$enable_xmi_msim != "xno" ; then 
-	PKG_CHECK_MODULES(xmi_msim, libxmimsim >= 3.1, [XMIMSIM_FOUND=yes], [XMIMSIM_FOUND=no])
+	PKG_CHECK_MODULES(xmi_msim, libxmimsim > 3.1, [XMIMSIM_FOUND=yes], [XMIMSIM_FOUND=no])
 	PKG_CHECK_MODULES(gmodule, gmodule-2.0, [GMODULE_FOUND=yes],[GMODULE_FOUND=no])
 
 	if test "x$XMIMSIM_FOUND" = xyes && test "x$GMODULE_FOUND" = xyes ; then
@@ -116,6 +116,7 @@ AC_CONFIG_FILES([	Makefile
 			src/randmt/Makefile
 			src/fft/Makefile
 			src/xmi-msim/Makefile
+			src/radionuclide/Makefile
 			doc/Makefile
 			examples/Makefile
 			examples/cylind_shell/Makefile
@@ -130,6 +131,7 @@ AC_CONFIG_FILES([	Makefile
 			examples/anisotropicsource/Makefile
 			examples/beamsource/Makefile
 			examples/phasecontrast/Makefile
+			examples/radionuclide/Makefile
 			libxrmc.pc
 			xrmc.spec
 			nsis/Makefile

doc/Makefile.am

@@ -1,3 +1,3 @@
 xrmc_docdir = $(datadir)/doc/xrmc
 
-dist_xrmc_doc_DATA = xrmc_6.4.4_man.pdf
+dist_xrmc_doc_DATA = xrmc_6.4.5_man.pdf

examples/Makefile.am

@@ -9,4 +9,5 @@ SUBDIRS = cylind_shell \
 	  xmi-msim2 \
 	  anisotropicsource \
 	  beamsource \
-	  phasecontrast
+	  phasecontrast \
+	  radionuclide

examples/radionuclide/Makefile.am

@@ -0,0 +1,24 @@
+xrmc_exampledir = $(datadir)/examples/xrmc/radionuclide
+
+dist_xrmc_example_DATA = composition.dat detector.dat geom3d.dat input.dat quadric.dat sample.dat source.dat radionuclide.dat
+
+if ENABLE_XMIMSIM
+check_SCRIPTS = xrmc.sh
+TESTS_ENVIRONMENT = XRMC_XMIMSIM_MODULE="${top_builddir}/src/xmi-msim/.libs"
+TESTS = $(check_SCRIPTS)
+endif
+
+xrmc.sh:
+if !ABS_SRC_BUILD_EQUAL
+	cp ${srcdir}/*dat .
+endif
+	echo "${top_builddir}/src/main/xrmc input.dat" > xrmc.sh
+	chmod a+x xrmc.sh
+
+clean-local:
+	rm -f xrmc.sh
+	rm -f output.dat
+	rm -f unconvoluted.dat
+if !ABS_SRC_BUILD_EQUAL
+	rm -f $(dist_xrmc_example_DATA)
+endif

examples/radionuclide/composition.dat

@@ -0,0 +1,30 @@
+; Composition file
+;
+Newdevice composition                     ; Device type
+Composition                     ; Device name
+
+Phase Air			; Air
+NElem 3				; Number of atomic species for this phase
+7  76.000000			; Atomic number, weight percent of 1st element
+8  23.000000			; 	 ....
+18  1.000000
+Rho 0.0012048			; mass density of the phase (g/cm3) 
+
+Phase Sample ; Multilayer
+NElem 3				; Number of atomic species for this phase
+26   70.0			; Atomic number, weight percent of 1st element
+24   18.0			; 	 ....
+28   12.0
+Rho 6.0				; mass density of the phase (g/cm3) 
+
+Phase Crystal ; 
+NElem 1
+14 100.0
+Rho 2.33
+
+Phase Window
+NElem 1
+4 100.0
+Rho 1.85
+
+End

examples/radionuclide/detector.dat

@@ -0,0 +1,38 @@
+; Detector array parameter file
+;
+Newdevice detectorconvolute ; Device type
+Detector                   ; Device name
+SourceName Sample               ; Source input device name
+NPixels 1 1			; Pixel number (NX x NY)
+PixelSize 0.79788452 0.79788452 ; Pixel Size (cm) 0.5 cm2 active detector area
+Shape 1	       			; Pixel shape (0 rectangular, 1 elliptical)
+;dOmegaLim 1e-2			; Cut on dOmega (default = 2*PI)
+X  -2  0  0			; detector center coordinates x, y, z
+				; Detector orientation :
+uk  1  0  0			; z direction (normal to the screen)
+ui   0 -1  0			; x direction
+ExpTime 1      	   			; Exposure time (sec)
+PhotonNum 2000			; Multiplicity of simulated events per pixel
+RandomPixelFlag 1		; Enable random point on pixels (0/1)
+PoissonFlag 0			; Enable poisson statistic on pix. counts (0/1)
+RoundFlag 0 			; Round pixel counts to integer (0/1)
+HeaderFlag 1                    ; Use header in output file (0/1)
+PixelType 2	   		; Pixel content type:
+	  			; 0: fluence, 1: energy fluence,
+				; 2: fluence(E), 3: energy fluence(E)
+Emin 0				; Emin
+Emax 40				; Emax
+NBins 2000			; Nbins
+SaturateEmin 0			; Saturate energies lower than Emin (0/1)
+SaturateEmax 0			; Saturate energies greater than Emax (0/1)
+;Rotate 0 0 0 1 0 0 -20		; rotation around axis x, u, angle theta
+;Rotate 0 0 0 0 0 1 -30		; rotation around axis x, u, angle theta
+
+;XMI-MSIM extras
+CompositionName Composition
+CrystalPhase Crystal
+WindowPhase Window
+CrystalThickness 0.035
+;PulseWidth 2E-09
+
+End

examples/radionuclide/geom3d.dat

@@ -0,0 +1,22 @@
+; 3D object geometric description file
+;
+Newdevice geom3d                          ; Device type
+Geom3D                          ; Device name
+QArrName QuadricArray		; Quadric array input device name
+CompName Composition            ; Composition input device name
+
+
+; 1st parallelepiped
+Object Par1
+Polymethyl\ Methacralate\ (Lucite,\ Perspex) Air ; Phase in, phase out
+6				; Number of quadrics
+P1 P2 P3 P4 P5 P6		; Quadric names
+
+; 2nd parallelepiped
+Object Par2
+Air Vacuum ; Phase in, phase out
+6				; Number of quadrics
+P7 P8 P9 P10 P11 P12		; Quadric names
+
+
+End

examples/radionuclide/input.dat

@@ -0,0 +1,25 @@
+; X-ray Monte Carlo (xrmc) input file
+; Files used by the simulation
+;
+
+Load source.dat		; Source position, orientation
+
+Load radionuclide.dat		; Energy Spectrum file
+
+Load sample.dat			; Sample file
+
+Load quadric.dat		; quadric file
+
+Load geom3d.dat			; qvolume file
+
+Load composition.dat		; composition file
+
+Load detector.dat		; Detector position, orientation, size
+
+Run Detector		; Run device
+
+Save Detector Image unconvoluted.dat ; save unconvoluted image
+
+Save Detector ConvolutedImage output.dat	; save convoluted image
+
+End

examples/radionuclide/quadric.dat

@@ -0,0 +1,43 @@
+; Quadric array file
+;
+Newdevice quadricarray        ; Device type
+QuadricArray        ; Device name
+
+Plane P1
+0 0 0 -1 -1 0
+
+Plane P2
+2 2 0 1 1 0
+
+Plane P3
+2 -2 0 1 -1 0
+
+Plane P4
+-2 2 0 -1 1 0
+
+Plane P5
+0 0 2 0 0 1
+
+Plane P6
+0 0 -2 0 0 -1
+
+Plane P7
+-5 -5 0 -1 -1 0
+
+Plane P8
+5 5 0 1 1 0
+
+Plane P9
+5 -5 0 1 -1 0
+
+Plane P10
+-5 5 0 -1 1 0
+
+Plane P11
+0 0 5 0 0 1
+
+Plane P12
+0 0 -5 0 0 -1
+
+
+End

examples/radionuclide/radionuclide.dat

@@ -0,0 +1,13 @@
+; Radionuclide file
+;
+Newdevice radionuclide
+Radionuclide
+LoopFlag 0              ; 0: extract random energies on the whole spectrum
+                        ; 1: loop on all lines and sampling points
+LinePhotonNum 1		; Multiplicity of events for each line in the spectrum
+Unit mCi
+Activity 100
+RadioNuclideSource 55Fe
+
+
+End

examples/radionuclide/run.pro

@@ -0,0 +1,9 @@
+a=xrmc_read_angio_image2('output.dat')
+help,a
+;b=read_spe('stainlesssteel_4.spe')
+my_plot = plot(dindgen(2000)/50.0, total(a.data[1:4, * , 0 , 0],1) > 1,'r',/ylog)
+;my_plot = plot(dindgen(2000)/40.0, b.data > 1,'b',/ylog,/overplot)
+
+
+
+END

examples/radionuclide/run.sh

@@ -0,0 +1,3 @@
+xrmc input.dat
+#xmimsim --enable-pile-up -v --spe-file=stainlesssteel stainlesssteel.xmsi
+xmimsim -v --spe-file=stainlesssteel stainlesssteel.xmsi

examples/radionuclide/sample.dat

@@ -0,0 +1,18 @@
+; Sample parameters file
+;
+;
+Newdevice sample      ; Device type
+Sample      ; Device name
+SourceName Source               ; Source input device name
+Geom3DName Geom3D               ; Geom3d input device name
+CompName Composition		; Composition input device name
+WeightedStepLength 0		; Weighted step length (0/1)
+FluorFlag 1                     ; Activate Fluorescence (0/1)
+ScattOrderNum 4			; Maximum scattering order
+0	      			; Multiplicity of simulated events for order 0
+500				; Multiplicity of simulated events for order 1
+500				; Multiplicity of simulated events for order 2
+500				; Multiplicity of simulated events for order 3
+500
+
+End

examples/radionuclide/source.dat

@@ -0,0 +1,13 @@
+; Source position/orientation file
+;
+Newdevice source                          ; Device type
+Source                          ; Device name
+SpectrumName Radionuclide ; Spectrum input device name
+X 0   -100   0                        ; source x, y, z
+; Source orientation :
+uk 0 1 0                                ; z direction (main source direction)
+ui -1  0 0                              ; x direction
+Divergence 2.5e-6       2.5e-6                  ; beam divergency (sigma x, y)
+Size 0 0 0
+
+End

nsis/xrmc-win32.nsi.in

@@ -26,8 +26,8 @@
 !define XRAYLIB_VERSION "3.0.0"
 !define XRAYLIB_VERSION_MIN "3.0.0"
 
-!define XMI_MSIM_VERSION "3.1"
-!define XMI_MSIM_VERSION_MIN "3.1"
+!define XMI_MSIM_VERSION "4.0"
+!define XMI_MSIM_VERSION_MIN "4.0"
 
 
 

nsis/xrmc-win64.nsi.in

@@ -26,8 +26,8 @@
 !define XRAYLIB_VERSION "3.0.0"
 !define XRAYLIB_VERSION_MIN "3.0.0"
 
-!define XMI_MSIM_VERSION "3.1"
-!define XMI_MSIM_VERSION_MIN "3.1"
+!define XMI_MSIM_VERSION "4.0"
+!define XMI_MSIM_VERSION_MIN "4.0"
 
 
 

src/Makefile.am

@@ -15,7 +15,8 @@ SUBDIRS = \
 	xrmc_math \
 	beamsource \
 	phasecontrast \
-	fft
+	fft \
+	radionuclide
 
 SUBLIBS = \
 	arrayNd/libarrayNd.la \
@@ -33,7 +34,8 @@ SUBLIBS = \
 	xrmc_math/libxrmcmath.la \
 	beamsource/libbeamsource.la \
 	phasecontrast/libphcdetector.la \
-	fft/libfft.la
+	fft/libfft.la \
+	radionuclide/libradionuclide.la
 lib_LTLIBRARIES = libxrmc.la
 libxrmc_la_SOURCES = 
 libxrmc_la_LIBADD = $(SUBLIBS) @xraylib_LIBS@ -lm

src/device/Makefile.am

@@ -4,7 +4,7 @@ xrmcinclude_HEADERS = xrmc_device.h
 noinst_LTLIBRARIES = libdevice.la
 
 libdevice_la_SOURCES = device.cpp loadnewdevice.cpp xrmc_device.h
-libdevice_la_CPPFLAGS = -I${srcdir}/../main -I${srcdir}/../xrmc_math -I${srcdir}/../exception -I${srcdir}/../gettoken -I${srcdir}/../sample -I${srcdir}/../composition -I${srcdir}/../geom3d -I${srcdir}/../detector -I${srcdir}/../spectrum -I${srcdir}/../source -I${srcdir}/../randmt -I${srcdir}/../photon  -I${srcdir}/../arrayNd -I${srcdir}/../beamsource -I${srcdir}/../phasecontrast
+libdevice_la_CPPFLAGS = -I${srcdir}/../main -I${srcdir}/../xrmc_math -I${srcdir}/../exception -I${srcdir}/../gettoken -I${srcdir}/../sample -I${srcdir}/../composition -I${srcdir}/../geom3d -I${srcdir}/../detector -I${srcdir}/../spectrum -I${srcdir}/../source -I${srcdir}/../randmt -I${srcdir}/../photon  -I${srcdir}/../arrayNd -I${srcdir}/../beamsource -I${srcdir}/../phasecontrast -I${srcdir}/../radionuclide
 if ENABLE_XMIMSIM
 libdevice_la_CPPFLAGS += -I${srcdir}/../xmi-msim @xmi_msim_CFLAGS@ @gmodule_CFLAGS@ -DXRMC_XMIMSIM_LIB=\"$(libdir)/xrmc\"
 endif

src/device/loadnewdevice.cpp

@@ -35,6 +35,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "xrmc_geom3d.h"
 #include "xrmc_sample.h"
 #include "xrmc_detector.h"
+#include "xrmc_radionuclide.h"
 #include "beamsource.h"
 #include "beamscreen.h"
 #include "anisotropicsource.h"
@@ -110,6 +111,9 @@ int xrmc_device::LoadNewDevice(istream &dev_fs,  xrmc_device*& dev_pt)
     throw xrmc_exception(string("Device type ") + dev_type + " not supported.\nRecompile XRMC with the XMI-MSIM plug-in\n");
 #endif
   }
+  else if (dev_type=="radionuclide") {
+    dev_pt = new radionuclide(dev_name);
+  }
   else // unknown device type
     throw xrmc_exception(string("Device type ") + dev_type + " not known.\n");
 

src/radionuclide/Makefile.am

@@ -0,0 +1,8 @@
+xrmcincludedir = ${includedir}/xrmc
+xrmcinclude_HEADERS = xrmc_radionuclide.h
+
+noinst_LTLIBRARIES = libradionuclide.la
+
+libradionuclide_la_SOURCES = loadradionuclide.cpp radionuclide.cpp xrmc_radionuclide.h
+libradionuclide_la_CPPFLAGS = -I${srcdir}/../xrmc_math -I${srcdir}/../xrmc_algo -I${srcdir}/../arrayNd -I${srcdir}/../device -I${srcdir}/../source -I${srcdir}/../photon -I${srcdir}/../spectrum -I${srcdir}/../exception -I${srcdir}/../main -I${srcdir}/../gettoken @xraylib_CFLAGS@ -I${srcdir}/../sample -I${srcdir}/../composition -I${srcdir}/../geom3d -I${srcdir}/../randmt -I${srcdir}/../phasecontrast
+