issue #1

.clang-format

@@ -0,0 +1,67 @@
+# Copyright (C) 2015 Free Software Foundation, Inc.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# clang-format 7.0.1 is required
+#
+# To utilize the tool to lines just touched by a patch, use
+# clang-format-diff script that is usually also packaged with clang-format.
+#
+# Example of usage:
+# git diff -U0 --no-color | clang-format-diff -p1
+# (here the tool will generate a patch)
+# git diff -U0 --no-color | clang-format-diff -p1 -i
+# (modifications are applied)
+
+---
+Language: Cpp
+AccessModifierOffset: -2
+AlwaysBreakAfterReturnType: TopLevel
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
+  AfterClass: true
+  AfterControlStatement: true
+  AfterEnum: true
+  AfterFunction: true
+  AfterNamespace: false
+  AfterObjCDeclaration: true
+  AfterStruct: true
+  AfterUnion: true
+  BeforeCatch: true
+  BeforeElse: true
+  IndentBraces: true
+  SplitEmptyFunction: false
+BreakBeforeBinaryOperators: All
+BreakBeforeBraces: Custom
+BreakBeforeTernaryOperators: true
+ColumnLimit: 80
+ConstructorInitializerIndentWidth: 2
+ContinuationIndentWidth: 2
+ForEachMacros: []
+IndentCaseLabels: false
+NamespaceIndentation: None
+PenaltyBreakBeforeFirstCallParameter: 100
+PointerAlignment: Right
+SortIncludes: false
+SpaceAfterCStyleCast: true
+SpaceBeforeParens: Always
+SpacesBeforeTrailingComments: 1
+UseTab: Always
+AlignEscapedNewlines: Right
+AlignTrailingComments: true
+AllowShortFunctionsOnASingleLine: All
+AlwaysBreakTemplateDeclarations: MultiLine
+KeepEmptyLinesAtTheStartOfBlocks: false
+Standard: c++14

.gitignore

@@ -1,10 +1,26 @@
 *~
-#*
+
 *.o
 *.dylib
 *.so
+*.obj
+*.exe
 Makefile
 build/
-CMakeFiles/
+
 CMakeCache.txt
+CMakeFiles/
+CMakeScripts
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps
+
+# Jetbrains
+.idea/
+out/
+cmake-build-*/
 
+# VSCode
+.vscode/

include/goptical/core/common.hpp

@@ -38,12 +38,16 @@
 #include <vector>
 #include <deque>
 #include <functional>
+#include <algorithm>
+#include <memory>
 
 #include "goptical/core/vector_pool"
 #include "goptical/core/ref"    /* mkdoc:skip */
 #include "goptical/core/fstring"        /* mkdoc:skip */
 #include "goptical/core/vlarray"        /* mkdoc:skip */
 
+#include <gsl/gsl_math.h>
+
 #include <math.h>
 
 #include <limits>
@@ -624,7 +628,21 @@ namespace _goptical {
     class RayFan;
   }
 
+  namespace util {
+      class ArrayIndex2D {
+      public:
+          unsigned rowSize;
+          unsigned colSize;
+          unsigned operator()(unsigned row, unsigned col) {
+              return colSize * row + col;
+          }
+      };
+  }
+
 }
 
+extern "C" int find_first_bit_set (int i);
+extern double drand48();
+
 #endif
 

include/goptical/core/fstring

@@ -35,7 +35,7 @@
 
 /** @file @module{Formatted string} */
 
-#ifdef __GNUC__
+#ifndef __GNUC__
 # define _DPP_FORMAT_CHK(archetype, string_index, first_to_check)
 #else
 # define _DPP_FORMAT_CHK(archetype, string_index, first_to_check) \

include/goptical/core/math/vector.hpp

@@ -45,7 +45,7 @@ namespace _goptical {
      */
     template <int N, typename T> struct VectorBase
     {
-      template <int, typename> friend class VectorBase;
+      template <int, typename> friend struct VectorBase;
 
       /** Set the whole vector to the specified value */
       inline void set(T value);

include/goptical/core/vlarray

@@ -166,9 +166,16 @@ namespace dpp {
 	buffer array of integers along with a @ref vlarray object and
 	pass the buffer array as storage space to the @ref vlarray
 	constructor. @hidecontent */
+#ifndef _MSC_VER
 #define DPP_VLARRAY(type, size, name)		\
   uint64_t _##name[sizeof(type) * size / 8 + 1];	\
   ::dpp::vlarray<type> name(_##name, size); /* FIXME size alignment */
+#else
+#define DPP_VLARRAY(type, size, name)		\
+  auto _##name_ptr = std::unique_ptr<uint64_t>(new uint64_t[sizeof(type) * size / 8 + 1]); \
+  uint64_t *_##name = _##name_ptr.get(); \
+  ::dpp::vlarray<type> name(_##name, size); /* FIXME size alignment */
+#endif
 
     typedef X value_type;
     typedef X & reference;

src/core/curve_conic.cpp

@@ -161,7 +161,10 @@ namespace _goptical {
 
     double Conic::fit(const Rotational &c, double radius, unsigned int count)
     {
-      double X[count], Y[count];
+//      double X[count], Y[count];
+      double *X, *Y;
+      X = (double *) calloc(count, sizeof(double));
+      Y = (double *) calloc(count, sizeof(double));
 
       double step = radius / (double)count;
       double y = step / 2.0;
@@ -185,6 +188,9 @@ namespace _goptical {
       _sh = -c1;
       _roc = c0 / 2.0;
 
+      free(X);
+      free(Y);
+
       return sqrt(chisq / count); // FIXME bad rms error
     }
 

src/core/curve_conic_base.cpp

@@ -94,7 +94,10 @@ namespace _goptical {
 
     double ConicBase::fit_roc(const Rotational &c, double radius, unsigned int count)
     {
-      double X[count], Y[count];
+      //double X[count], Y[count];
+      double *X, *Y;
+      X = (double *) calloc(count, sizeof(double));
+      Y = (double *) calloc(count, sizeof(double));
 
       double step = radius / (double)count;
       double y = step / 2.0;
@@ -133,6 +136,8 @@ namespace _goptical {
           _roc = 2.0 * c1;
         }
 
+      free(X);
+      free(Y);
       return sqrt(chisq / count); // FIXME bad rms error
     }
 

src/core/data_grid.cpp

@@ -325,23 +325,27 @@ namespace _goptical {
     {
       unsigned int n = _size[v];
 
-      double eq[n][3];
-      double dd[n];
+      //double eq[n][3];
+      double *eq = (double*)calloc(n * 3, sizeof(double));
+      _goptical::util::ArrayIndex2D _ = { n, 3 };
+
+      //double dd[n];
+      double* dd = (double*)calloc(n, sizeof(double));
 
       // tridiag system equations
       dd[0  ] = dd[n-1] = 0.0;
-      eq[0  ][1] = eq[n-1][1] = 1.0;
-      eq[1  ][0] = eq[n-2][2] = -1.0;
+      eq[_(0,1)] = eq[_(n-1,1)] = 1.0;
+      eq[_(1,0)] = eq[_(n-2,2)] = -1.0;
 
       int i, j = 0;
 
       for (i = 1; i < (int)n - 1; i++)
         {
           j = o + i * w;
 
-          eq[i-1][2] = _step[v] / 6.0;
-          eq[i  ][1] = _step[v] * 2.0 / 3.0;
-          eq[i+1][0] = _step[v] / 6.0;
+          eq[_(i-1,2)] = _step[v] / 6.0;
+          eq[_(i,1)] = _step[v] * 2.0 / 3.0;
+          eq[_(i+1,0)] = _step[v] / 6.0;
           dd[i] = (_y_data[j+w] - _y_data[j]) / _step[v]
                 - (_y_data[j] - _y_data[j-w]) / _step[v];
         }
@@ -350,20 +354,22 @@ namespace _goptical {
       // forward substitution
       for (i = 1; i < (int)n; i++)
         {
-          double f = eq[i-1][2] / eq[i-1][1];
-          eq[i][1] -= f * eq[i][0];
+          double f = eq[_(i-1,2)] / eq[_(i-1,1)];
+          eq[_(i,1)] -= f * eq[_(i,0)];
           dd[i]    -= f * dd[i-1];
         }
 
       // backward substitution
       double k = 0;
       for (i = n - 1; i >= 0; i--)
         {
-          double ddi = (dd[i] - k) / eq[i][1];
+          double ddi = (dd[i] - k) / eq[_(i,1)];
           dd[i] = ddi;
-          k = eq[i][0] * ddi;
+          k = eq[_(i,0)] * ddi;
         }
 
+      free(eq);
+
       // here with have the continuous second derivative in dd[],
       // compute smooth 1st derivative
       double dt = _step[v];
@@ -379,6 +385,8 @@ namespace _goptical {
       d[j + w][v] =
         + (_y_data[j+w] - _y_data[j])
         + (dt * dt) * ((dd[i] + dt * (0.5 * (dd[i+1] - dd[i]) / dt)) - (dd[i+1] / 6.0 + dd[i] / 3.0));
+
+      free(dd);
     }
 
     void Grid::update_bicubic(unsigned int x[2], const math::Vector2 & v) const
@@ -391,7 +399,8 @@ namespace _goptical {
       const unsigned int s0 = _size[0] - 1;
       this_->_poly.resize(s0 * (_size[1] - 1));
 
-      double cd[_size[0] * _size[1]];
+      //double cd[_size[0] * _size[1]];
+      double *cd = (double *)calloc(_size[0] * _size[1], sizeof(double));
       get_cross_deriv_diff(cd);
 
       const unsigned int w = _size[0];
@@ -436,7 +445,7 @@ namespace _goptical {
       this_->_lookup = &Grid::lookup_interval;
       this_->_interpolate_y = &Grid::interpolate_bicubic_y;
       this_->_interpolate_d = &Grid::interpolate_bicubic_d;
-
+      free(cd);
       return lookup_interval(x, v);
     }
 
@@ -450,7 +459,9 @@ namespace _goptical {
       const unsigned int s0 = _size[0] - 1;
       this_->_poly.resize(s0 * (_size[1] - 1));
 
-      double cd[_size[0] * _size[1]];
+      //double cd[_size[0] * _size[1]];
+      double *cd = (double *)calloc(_size[0] * _size[1], sizeof(double));
+
       get_cross_deriv_diff(cd);
 
       DPP_VLARRAY(math::Vector2, _size[0] * _size[1], d);
@@ -489,7 +500,7 @@ namespace _goptical {
       this_->_lookup = &Grid::lookup_interval;
       this_->_interpolate_y = &Grid::interpolate_bicubic_y;
       this_->_interpolate_d = &Grid::interpolate_bicubic_d;
-
+      free(cd);
       return lookup_interval(x, v);
     }
 
@@ -503,7 +514,9 @@ namespace _goptical {
       const unsigned int s0 = _size[0] - 1;
       this_->_poly.resize(s0 * (_size[1] - 1));
 
-      double cd[_size[0] * _size[1]];
+      //double cd[_size[0] * _size[1]];
+      double *cd = (double *)calloc(_size[0] * _size[1], sizeof(double));
+
       get_cross_deriv_diff(cd);
 
       const unsigned int w = _size[0];
@@ -539,7 +552,7 @@ namespace _goptical {
       this_->_lookup = &Grid::lookup_interval;
       this_->_interpolate_y = &Grid::interpolate_bicubic_y;
       this_->_interpolate_d = &Grid::interpolate_bicubic_d;
-
+      free(cd);
       return lookup_interval(x, v);
     }