Merge pull request #19 from cl-fontana/master

Adding the TSpectrum one-dimensional background estimation with SNIP algorithm

doc/data.rst

@@ -637,11 +637,24 @@ and functions:
     Calculates Shirley background
     (useful in X-ray photoelectron spectroscopy).
 
+``snip_bg(@n, window_width, direction, filter_order, estimate_compton)``
+    Calculates the spectrum background applying a Sensitive Nonlinear Iterative Peak clipping algorithm (SNIP) (useful in gamma-ray spectroscopy).
+    This SNIP algorithm is taken from the `TSpectrum <https://root.cern.ch/doc/v608/classTSpectrum.html>`_ class of `ROOT <http://root.cern.ch>`_.
+    It requires the parameters:
+    1. ``window_width``: maximal width of clipping window;
+    2. ``direction``:  direction of change of clipping window, if it is a positive number the window will be increasing;
+    3. ``filter_order``:  order of clipping filter, possible values are 2, 4, 6 or 8;
+    4. ``estimate_compton``:  if a positive number the algorithm will try to estimate the Compton edge.
+    Active points are modified according to the SNIP algorithm.
+    Inactive points are left as they are, assuming that they are already considered background.
+    Subtracting the calculated background from the initial spectrum gives zero in all inactive points.
+
 Examples::
 
   @+ = @0 # duplicate the dataset
   @+ = @0 and @1 # create a new dataset from @0 and @1
   @0 = @0 - shirley_bg(@0) # remove Shirley background 
+  @0 = @0 - snip_bg(@0, 30, 1, 2, 0) # remove gamma background 
   @0 = @0 - @1 # subtract @1 from @0
   @0 = @0 - 0.28*@1 # subtract scaled dataset @1 from @0
 

fityk/Makefile.am

@@ -13,13 +13,15 @@ libfityk_la_SOURCES = logic.cpp view.cpp lexer.cpp eparser.cpp cparser.cpp \
 		 runner.cpp info.cpp common.cpp data.cpp var.cpp mgr.cpp \
 		 tplate.cpp func.cpp udf.cpp bfunc.cpp f_fcjasym.cpp ast.cpp \
 		 vm.cpp transform.cpp settings.cpp ui.cpp ui_api.cpp \
+		 root/background.cpp \
 		 luabridge.cpp GAfit.cpp LMfit.cpp guess.cpp NMfit.cpp \
 		 model.cpp fit.cpp voigt.cpp numfuncs.cpp fityk.cpp \
 		 \
                  logic.h view.h lexer.h eparser.h cparser.h \
 		 runner.h info.h common.h data.h var.h mgr.h \
 		 tplate.h func.h udf.h bfunc.h f_fcjasym.h ast.h \
 		 vm.h transform.h settings.h ui.h luabridge.h \
+		 root/background.hpp \
 		 GAfit.h LMfit.h guess.h NMfit.h \
 		 model.h fit.h voigt.h numfuncs.h \
 		 swig/fityk_lua.cpp swig/luarun.h \

fityk/eparser.cpp

@@ -79,6 +79,7 @@ const char* function_name(int op)
         case OP_DT_SUM_SAME_X: return "sum_same_x";
         case OP_DT_AVG_SAME_X: return "avg_same_x";
         case OP_DT_SHIRLEY_BG: return "shirley_bg";
+        case OP_DT_SNIP_BG: return "snip_bg";
         // 2-args functions
         case OP_MOD: return "mod";
         case OP_MIN2: return "min2";
@@ -138,6 +139,8 @@ int get_function_narg(int op)
         case OP_RANDNORM:
         case OP_RANDU:
             return 2;
+        case OP_DT_SNIP_BG:
+            return 5;
         // Fityk functions
         case OP_FUNC:
         case OP_SUM_F:
@@ -819,6 +822,8 @@ void ExpressionParser::parse_expr(Lexer& lex, int default_ds,
                         put_function(OP_DT_AVG_SAME_X);
                     else if (mode == kDatasetTrMode && word == "shirley_bg")
                         put_function(OP_DT_SHIRLEY_BG);
+                    else if (mode == kDatasetTrMode && word == "snip_bg")
+                        put_function(OP_DT_SNIP_BG);
 
                     else
                         lex.throw_syntax_error("unknown function: " + word);