optics / ricalc

Commit 1b0b5c1d96632608c05635cff8079b688b2ae61e

Authored by dmayerich
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first commit

Showing 11 changed files with 3485 additions and 0 deletions   Show diff stats
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CMakeLists.txt 0 → 100644
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  1 +++ a/CMakeLists.txt
  1 +#Specify the version being used aswell as the language
  2 +cmake_minimum_required(VERSION 2.8)
  3 +#Name your project here
  4 +project(ricalc)
  5 +
  6 +#set the module directory
  7 +set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
  8 +
  9 +#find BOOST
  10 +set(Boost_USE_STATIC_LIBS ON)
  11 +set(Boost_USE_MULTITHREADED ON)
  12 +set(Boost_USE_STATIC_RUNTIME OFF)
  13 +find_package( Boost 1.54.0 COMPONENTS program_options )
  14 +
  15 +#set up CUDA
  16 +find_package(CUDA)
  17 +if(CUDA_FOUND)
  18 + link_libraries(${CUDA_cufft_LIBRARY})
  19 + add_definitions(-DCUDA_AVAILABLE)
  20 +endif(CUDA_FOUND)
  21 +
  22 +#set up the FFTW package (fast Fourier transform)
  23 +find_package(FFTW)
  24 +if(FFTW_FOUND)
  25 + include_directories(${FFTW_INCLUDE_DIR})
  26 + link_libraries(${FFTW_LIBRARY})
  27 + add_definitions(-DFFTW_AVAILABLE)
  28 +endif(FFTW_FOUND)
  29 +
  30 +#ask the user for the RTS location
  31 +set(RTS_ROOT_PATH $ENV{RTS_ROOT_PATH})
  32 +find_package(RTS REQUIRED)
  33 +
  34 +#set the include directories
  35 +include_directories(
  36 + ${CMAKE_CURRENT_BINARY_DIR}
  37 + ${RTS_INCLUDE_DIR}
  38 + ${Boost_INCLUDE_DIR}
  39 +)
  40 +
  41 +#enable warnings
  42 +if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
  43 + add_definitions(-Wall -lfftw3 -lm)
  44 +endif()
  45 +
  46 +#Assign source files to the appropriate variables
  47 +file(GLOB SRC_CPP "*.cpp")
  48 +file(GLOB SRC_H "*.h")
  49 +file(GLOB SRC_CU "*.cu")
  50 +
  51 +#copy example material files
  52 +configure_file(etaPolyethylene.txt ${CMAKE_CURRENT_BINARY_DIR}/etaPolyethylene.txt COPYONLY)
  53 +configure_file(etaTeflon.txt ${CMAKE_CURRENT_BINARY_DIR}/etaTeflon.txt COPYONLY)
  54 +configure_file(etaToluene.txt ${CMAKE_CURRENT_BINARY_DIR}/etaToluene.txt COPYONLY)
  55 +
  56 +
  57 +#create an executable
  58 +cuda_add_executable(ricalc ${SRC_CPP} ${SRC_H} ${SRC_CU})
  59 +
  60 +#set the link libraries
  61 +target_link_libraries(ricalc ${Boost_LIBRARIES})
  62 +
  63 +
  64 +
FindCUDASDK.cmake 0 → 100644
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  1 +++ a/FindCUDASDK.cmake
  1 +#
  2 +# The script defines the following variables:
  3 +#
  4 +##############################################################################
  5 +# Note: Removed everything related to CUDA_SDK_ROOT_DIR and only left this as
  6 +# a possible environment variable to set the SDK directory.
  7 +# Include file will be: CUDA_CUT_INCLUDE_DIR
  8 +# Cutil library: CUDA_CUT_LIBRARY
  9 +##############################################################################
  10 +#
  11 +#
  12 +# CUDA_SDK_ROOT_DIR -- Path to the CUDA SDK. Use this to find files in the
  13 +# SDK. This script will not directly support finding
  14 +# specific libraries or headers, as that isn't
  15 +# supported by NVIDIA. If you want to change
  16 +# libraries when the path changes see the
  17 +# FindCUDA.cmake script for an example of how to clear
  18 +# these variables. There are also examples of how to
  19 +# use the CUDA_SDK_ROOT_DIR to locate headers or
  20 +# libraries, if you so choose (at your own risk).
  21 +#
  22 +# This code is licensed under the MIT License. See the FindCUDASDK.cmake script
  23 +# for the text of the license.
  24 +
  25 +# The MIT License
  26 +#
  27 +# License for the specific language governing rights and limitations under
  28 +# Permission is hereby granted, free of charge, to any person obtaining a
  29 +# copy of this software and associated documentation files (the "Software"),
  30 +# to deal in the Software without restriction, including without limitation
  31 +# the rights to use, copy, modify, merge, publish, distribute, sublicense,
  32 +# and/or sell copies of the Software, and to permit persons to whom the
  33 +# Software is furnished to do so, subject to the following conditions:
  34 +#
  35 +# The above copyright notice and this permission notice shall be included
  36 +# in all copies or substantial portions of the Software.
  37 +#
  38 +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
  39 +# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  40 +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
  41 +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  42 +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  43 +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  44 +# DEALINGS IN THE SOFTWARE.
  45 +#
  46 +###############################################################################
  47 +
  48 +# FindCUDASDK.cmake
  49 +
  50 +# # Check to see if the CUDA_SDK_ROOT_DIR has changed,
  51 +# # if it has then clear the cache variable, so that it will be detected again.
  52 +# if(NOT "${CUDA_SDK_ROOT_DIR}" STREQUAL "${CUDA_SDK_ROOT_DIR_INTERNAL}")
  53 +# # No specific variables to catch. Use this kind of code before calling
  54 +# # find_package(CUDA) to clean up any variables that may depend on this path.
  55 +#
  56 +# # unset(MY_SPECIAL_CUDA_SDK_INCLUDE_DIR CACHE)
  57 +# # unset(MY_SPECIAL_CUDA_SDK_LIBRARY CACHE)
  58 +# endif()
  59 +#
  60 +# ########################
  61 +# # Look for the SDK stuff
  62 +# find_path(CUDA_SDK_ROOT_DIR cutil.h
  63 +# PATH_SUFFIXES "common/inc" "C/common/inc"
  64 +# "$ENV{NVSDKCUDA_ROOT}"
  65 +# "[HKEY_LOCAL_MACHINE\\SOFTWARE\\NVIDIA Corporation\\Installed Products\\NVIDIA SDK 10\\Compute;InstallDir]"
  66 +# "/Developer/GPU\ Computing/C"
  67 +# )
  68 +#
  69 +# # fallback method for determining CUDA_SDK_ROOT_DIR in case the previous one failed!
  70 +# if (NOT CUDA_SDK_ROOT_DIR)
  71 +# find_path(CUDA_SDK_ROOT_DIR C/common/inc/cutil.h
  72 +# "$ENV{NVSDKCUDA_ROOT}"
  73 +# "[HKEY_LOCAL_MACHINE\\SOFTWARE\\NVIDIA Corporation\\Installed Products\\NVIDIA SDK 10\\Compute;InstallDir]"
  74 +# "/Developer/GPU\ Computing/C"
  75 +# )
  76 +# endif()
  77 +
  78 +# Keep the CUDA_SDK_ROOT_DIR first in order to be able to override the
  79 +# environment variables.
  80 +set(CUDA_SDK_SEARCH_PATH
  81 + "${CUDA_SDK_ROOT_DIR}"
  82 + "${CUDA_TOOLKIT_ROOT_DIR}/local/NVSDK0.2"
  83 + "${CUDA_TOOLKIT_ROOT_DIR}/NVSDK0.2"
  84 + "${CUDA_TOOLKIT_ROOT_DIR}/NV_SDK"
  85 + "${CUDA_TOOLKIT_ROOT_DIR}/NV_CUDA_SDK"
  86 + "$ENV{HOME}/NVIDIA_CUDA_SDK"
  87 + "$ENV{HOME}/NVIDIA_CUDA_SDK_MACOSX"
  88 + "$ENV{HOME}/NVIDIA_GPU_Computing_SDK"
  89 + "/Developer/CUDA"
  90 + )
  91 +
  92 +# Find include file from the CUDA_SDK_SEARCH_PATH
  93 +
  94 +find_path(CUDA_CUT_INCLUDE_DIR
  95 + cutil.h
  96 + PATHS ${CUDA_SDK_SEARCH_PATH}
  97 + PATH_SUFFIXES "common/inc" "C/common/inc"
  98 + DOC "Location of cutil.h"
  99 + NO_DEFAULT_PATH
  100 + )
  101 +# Now search system paths
  102 +find_path(CUDA_CUT_INCLUDE_DIR cutil.h DOC "Location of cutil.h")
  103 +
  104 +# mark_as_advanced(CUDA_CUT_INCLUDE_DIR)
  105 +
  106 +
  107 +# Example of how to find a library in the CUDA_SDK_ROOT_DIR
  108 +
  109 +# cutil library is called cutil64 for 64 bit builds on windows. We don't want
  110 +# to get these confused, so we are setting the name based on the word size of
  111 +# the build.
  112 +
  113 +# New library might be called cutil_x86_64 !
  114 +
  115 +if(CMAKE_SIZEOF_VOID_P EQUAL 8)
  116 + set(cuda_cutil_name cutil64)
  117 +else(CMAKE_SIZEOF_VOID_P EQUAL 8)
  118 + set(cuda_cutil_name cutil32)
  119 +endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
  120 +
  121 +find_library(CUDA_CUT_LIBRARY
  122 + NAMES ${cuda_cutil_name} cutil cutil_x86_64 cutil_i386
  123 + PATHS ${CUDA_SDK_SEARCH_PATH}
  124 + # The new version of the sdk shows up in common/lib, but the old one is in lib
  125 + # The very newest installation Path of the SDK is in subdirectory 'C'. Please add this Path to the possible suffixes.
  126 + PATH_SUFFIXES "C/lib" "common/lib" "lib" "C/common/lib" "common/lib"
  127 + DOC "Location of cutil library"
  128 + NO_DEFAULT_PATH
  129 + )
  130 +# # Now search system paths
  131 +# find_library(CUDA_CUT_LIBRARY NAMES cutil ${cuda_cutil_name} DOC "Location of cutil library")
  132 +mark_as_advanced(CUDA_CUT_LIBRARY)
  133 +set(CUDA_CUT_LIBRARIES ${CUDA_CUT_LIBRARY})
  134 +
  135 +#############################
  136 +# Check for required components
  137 +if(CUDA_CUT_INCLUDE_DIR)
  138 + set(CUDASDK_FOUND TRUE)
  139 +endif(CUDA_CUT_INCLUDE_DIR)
  140 +
  141 +# set(CUDA_SDK_ROOT_DIR_INTERNAL "${CUDA_SDK_ROOT_DIR}" CACHE INTERNAL
  142 +# "This is the value of the last time CUDA_SDK_ROOT_DIR was set successfully." FORCE)
FindFFTW.cmake 0 → 100644
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  1 +++ a/FindFFTW.cmake
  1 +# - Find the native FFTW includes and library
  2 +#
  3 +# This module defines
  4 +#
  5 +# FFTW_INCLUDE_DIR, where to find fftw3.h, etc.
  6 +# FFTW_LIBRARY, the libraries to link against to use FFTW.
  7 +#
  8 +# FFTW_FOUND
  9 +#
  10 +# Was borrowed from http://houdini-ocean-toolkit.googlecode.com
  11 +#
  12 +
  13 +find_path(FFTW_INCLUDE_DIR fftw3.h
  14 + PATHS ${CMAKE_SOURCE_DIR}/../3rdparty/include;
  15 + ${CMAKE_SOURCE_DIR}/3rdparty/include)
  16 +
  17 +find_library(FFTW_LIBRARY fftw3
  18 + PATHS ${CMAKE_SOURCE_DIR}/../3rdparty/lib;
  19 + ${CMAKE_SOURCE_DIR}/3rdparty/lib)
  20 +
  21 +if (FFTW_INCLUDE_DIR AND FFTW_LIBRARY)
  22 + set(FFTW_FOUND TRUE)
  23 +else (FFTW_INCLUDE_DIR AND FFTW_LIBRARY)
  24 + set(FFTW_FOUND FALSE)
  25 +endif (FFTW_INCLUDE_DIR AND FFTW_LIBRARY)
FindRTS.cmake 0 → 100644
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  1 +++ a/FindRTS.cmake
  1 +# Tries to find the RTS include directory
  2 +
  3 + FIND_PATH( RTS_INCLUDE_DIR NAMES rts_glShaderProgram.h
  4 + PATHS
  5 + ${CMAKE_CURRENT_SOURCE_DIR}/rts
  6 + ${RTS_ROOT_PATH}
  7 +)
  8 +
  9 +IF (RTS_FOUND)
  10 + #The following deprecated settings are for backwards compatibility with CMake1.4
  11 + SET (RTS_INCLUDE_PATH ${RTS_INCLUDE_DIR})
  12 +ENDIF(RTS_FOUND)
  13 +
  14 +FIND_PACKAGE_HANDLE_STANDARD_ARGS(RTS REQUIRED_VARS TRUE RTS_INCLUDE_DIR)
README.md 0 → 100644
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  1 +++ a/README.md
  1 +Computes the dispersion of a material given material properties. For example, given an absorbance spectrum, this software can estimate the complex refractive index and Chi values.
  2 +
  3 +A Windows 32 executable is provided in the Win32 directory. All of the necessary runtime libraries are included. Start by running 'ricalc -h' for command-line options.
  4 +
  5 +This software is designed to be used with CMake, so we recommend using it to build the application.
  6 +
  7 +This software requires the following libraries for compiling:
  8 +
  9 +FFTW - Fast Fourier Transform library -- http://www.fftw.org
  10 + or
  11 +CUDA - NVidia's GPU programming toolkit -- https://developer.nvidia.com/
  12 +
  13 +RTS - Real-Time Scraps C++ library (my codebase) -- https://github.com/dmayerich/RTS
  14 +
  15 +
  16 +
  17 +
  18 +
  19 +
Win32/libfftw3-3.dll 0 → 100644
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Win32/ricalc.exe 0 → 100644
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etaPolyethylene.txt 0 → 100644
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  1 +++ a/etaPolyethylene.txt
  1 +#nu n k
  2 +898.666 1.54119 0.00042801
  3 +902.523 1.54118 0.00038246
  4 +906.38 1.541 0.00040294
  5 +910.237 1.54094 0.00039488
  6 +914.094 1.54085 0.00037618
  7 +917.95 1.54084 0.0003536
  8 +921.807 1.54082 0.0003278
  9 +925.664 1.54081 0.0003156
  10 +929.521 1.54084 0.00028804
  11 +933.378 1.54084 0.00032099
  12 +937.235 1.54084 0.00031952
  13 +941.092 1.54084 0.00033633
  14 +944.949 1.54087 0.00036991
  15 +948.806 1.54083 0.00040887
  16 +952.663 1.54078 0.00044517
  17 +956.52 1.54076 0.00043966
  18 +960.377 1.54073 0.00044863
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  20 +968.091 1.54065 0.00045241
  21 +971.948 1.54062 0.00043188
  22 +975.804 1.54052 0.00039329
  23 +979.661 1.54055 0.00034324
  24 +983.518 1.54054 0.00027772
  25 +987.375 1.54053 0.00024005
  26 +991.232 1.54061 0.00018819
  27 +995.089 1.54062 0.00017644
  28 +998.946 1.54068 0.0001743
  29 +1002.8 1.5407 0.0001892
  30 +1006.66 1.54073 0.00022698
  31 +1010.52 1.54072 0.00025522
  32 +1014.37 1.54074 0.00027914
  33 +1018.23 1.54071 0.00028447
  34 +1022.09 1.54068 0.00030539
  35 +1025.94 1.54067 0.00030134
  36 +1029.8 1.54064 0.00030709
  37 +1033.66 1.54061 0.00030649
  38 +1037.52 1.54057 0.00027764
  39 +1041.37 1.54054 0.00024089
  40 +1045.23 1.54051 0.00017639
  41 +1049.09 1.54056 0.00013155
  42 +1052.94 1.54056 7.972e-005
  43 +1056.8 1.54061 4.678e-005
  44 +1060.66 1.54065 2.414e-005
  45 +1064.51 1.54066 6.56e-006
  46 +1068.37 1.54075 4.52e-006
  47 +1072.23 1.54077 1.86e-006
  48 +1076.08 1.54081 3.15e-005
  49 +1079.94 1.54086 5.205e-005
  50 +1083.8 1.54083 9.191e-005
  51 +1087.66 1.54083 0.00012551
  52 +1091.51 1.54082 0.00013487
  53 +1095.37 1.54082 0.0001366
  54 +1099.23 1.54081 0.00012324
  55 +1103.08 1.54082 0.00011624
  56 +1106.94 1.5408 9.228e-005
  57 +1110.8 1.54081 7.841e-005
  58 +1114.65 1.54084 5.534e-005
  59 +1118.51 1.54084 3.409e-005
  60 +1122.37 1.54087 1.855e-005
  61 +1126.22 1.54091 0
  62 +1130.08 1.54097 7.19e-006
  63 +1133.94 1.54103 1.989e-005
  64 +1137.8 1.54105 5.403e-005
  65 +1141.65 1.54112 8.195e-005
  66 +1145.51 1.54112 0.00012699
  67 +1149.37 1.54114 0.0001768
  68 +1153.22 1.54114 0.00021147
  69 +1157.08 1.54112 0.00025829
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  75 +1180.22 1.54101 0.00035023
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  77 +1187.94 1.541 0.00032161
  78 +1191.79 1.54104 0.00032158
  79 +1195.65 1.54104 0.00031863
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  97 +1265.07 1.54086 0.00038579
  98 +1268.93 1.54086 0.00037209
  99 +1272.79 1.54091 0.00037321
  100 +1276.65 1.54089 0.00036889
  101 +1280.5 1.54092 0.00038267
  102 +1284.36 1.54093 0.00039353
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  104 +1292.07 1.54092 0.00042425
  105 +1295.93 1.54088 0.0004231
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  108 +1307.5 1.54081 0.00038994
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  110 +1315.21 1.54081 0.00031839
  111 +1319.07 1.54081 0.00027074
  112 +1322.93 1.54083 0.00022097
  113 +1326.79 1.54089 0.00019314
  114 +1330.64 1.54091 0.00016466
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  206 +1685.48 1.54125 0.0005006
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etaTeflon.txt 0 → 100644
  Show/Hide comments   View file @1b0b5c1
  1 +++ a/etaTeflon.txt
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  768 +3853.08 1.30121 0.0729197
etaToluene.txt 0 → 100644
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  1 +++ a/etaToluene.txt
  1 +#nu n k
  2 +800 1.441201025 0.002370971
  3 +802 1.442449524 0.002279499
  4 +804 1.443622415 0.002218164
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main.cpp 0 → 100644
  Show/Hide comments   View file @1b0b5c1
  1 +++ a/main.cpp
  1 +#include <iostream>
  2 +#include <vector>
  3 +#include <complex>
  4 +#include <fstream>
  5 +#include <stdio.h>
  6 +#include <string.h>
  7 +using namespace std;
  8 +
  9 +//fftw fourier transform library
  10 +#ifdef FFTW_AVAILABLE
  11 +#include <fftw3.h>
  12 +#endif
  13 +
  14 +#include "rts/material.h"
  15 +//#include "options.h"
  16 +
  17 +#include <boost/program_options.hpp>
  18 +namespace po = boost::program_options;
  19 +
  20 +
  21 +typedef double ptype;
  22 +typedef complex<ptype> pcomplex;
  23 +
  24 +rts::material<ptype> M;
  25 +
  26 +#define PI 3.14159
  27 +
  28 +int main(int argc, char* argv[])
  29 +{
  30 + po::options_description desc("Allowed options");
  31 + desc.add_options()
  32 + ("help,h", "Display this help message.")
  33 + ("input-file,i", po::value<string>(), "Input file containing material information.")
  34 + ("input-format,f", po::value<string>()->default_value("wavenumber,n,k"), "Format string identifying the order of material properties in the input file. Options include: microns, wavenumber, n (real RI), k (imaginary RI), A (absorbance), Xp (real Chi), Xpp (imaginary Chi).\n\nThe default [microns,n,k] will load a material file with columns representing the wavelength in microns, followed by the real and imaginary parts of the refractive index.")
  35 + ("output-file,o", po::value<string>()->default_value("out.txt"), "Output file containing the processed material information.")
  36 + ("output-format,t", po::value<string>()->default_value("wavenumber,n,k"), "Format string for the output file (similar to --input-format).")
  37 + ("scaling,s", po::value<ptype>()->default_value(1.0), "Scaling value for the absorbance parameter. This value gives the thickness (in microns) of the measured material.")
  38 + ("n0,n", po::value<ptype>()->default_value(1.48), "Average effective refractive index. This is required when computing the real refractive index from the absorption.")
  39 + ("padding,p", po::value<int>()->default_value(2), "Padding factor used to remove edge artifacts in the Kramers-Kronig computation for computing the real RI from absorption. The default value of p=2 is sufficient in most cases.")
  40 + ("resolution,r", po::value<int>(), "Resolution of the spectrum. The default value is based on the number of spectral samples provided in the input file.");
  41 +
  42 + po::positional_options_description pos;
  43 + pos.add("input-file", 1);
  44 + pos.add("output-file", 1);
  45 +
  46 + po::variables_map vm;
  47 + po::store(po::command_line_parser(argc, argv).options(desc).positional(pos).run(), vm);
  48 + po::notify(vm);
  49 +
  50 + if(vm.count("help"))
  51 + {
  52 + cout<<desc<<endl;
  53 + return 1;
  54 + }
  55 +
  56 + //if the input file is given, load it, otherwise exit
  57 + if(vm.count("input-file"))
  58 + {
  59 + M.fromFile(vm["input-file"].as<string>(),
  60 + vm["input-format"].as<string>(),
  61 + vm["scaling"].as<ptype>());
  62 + }
  63 + else
  64 + {
  65 + cout<<"No input file was provided."<<endl;
  66 + exit(1);
  67 + }
  68 +
  69 + //the default sample rate of the spectrum is given by the number of samples in the input file
  70 + int R = M.nSamples();
  71 + if(vm.count("resolution"))
  72 + R = vm["resolution"].as<int>();
  73 +
  74 + //compute the real refractive index
  75 + rts::material<ptype> N = M.computeN(vm["n0"].as<ptype>(),
  76 + R,
  77 + vm["padding"].as<int>());
  78 +
  79 + //output the file using the standard format
  80 + N.save(vm["output-file"].as<string>(), vm["output-format"].as<string>());
  81 +
  82 + return 0;
  83 +}