Python Interface for MaCh3

CMakeLists.txt

@@ -210,24 +210,12 @@ add_subdirectory(samplePDF)
 add_subdirectory(mcmc)
 add_subdirectory(Diagnostics)
 add_subdirectory(plotting)
-
-################################# pybind11 stuff ##################################
-
-if( MaCh3_PYTHON_ENABLED )
-  ## EM: make a module target out of all the python*Module.cpp files (currently just one...)
-  pybind11_add_module(
-    pyMaCh3 MODULE
-    pyMaCh3.cpp
-    plotting/plottingUtils/pythonPlottingModule.cpp
-  )
-  ## EM: only works with code compiled with -fPIC enabled.. I think this flag can things slightly slower
-  ## so would be good to find a way around this.
-  set_property( TARGET pyMaCh3 PROPERTY POSITION_INDEPENDENT_CODE ON )
-  target_link_libraries( pyMaCh3 PUBLIC Plotting )
-  install( TARGETS pyMaCh3 DESTINATION pyMaCh3/)
+if (MaCh3_PYTHON_ENABLED)
+  add_subdirectory(python)
 endif()
 
 
+
 #This is to export the target properties of MaCh3
 #Anything that links to "MaCh3" will get all of these target properties
 add_library(MaCh3 INTERFACE)

Doc/sphinx/requirements.txt

@@ -1,4 +1,5 @@
 sphinx
 sphinx-rtd-theme
 sphinx-automodapi
-sphinx-mdinclude
+sphinx-mdinclude
+enum-tools[sphinx]

Doc/sphinx/source/conf.py

@@ -17,7 +17,8 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     "sphinx_automodapi.automodapi",
-    'sphinx_mdinclude'
+    "sphinx_mdinclude",
+    "enum_tools.autoenum"
     ]
 
 templates_path = ['_templates']

Doc/sphinx/source/covariance.rst

@@ -0,0 +1,10 @@
+Covariance
+==========
+
+This module contains the covariance objetcs which Mach3 uses to deal with systematic parameters. It also includes
+the :py:class:`pyMaCh3.covariance.CovarianceBase` class which you can use to implement your own!
+
+.. automodapi:: pyMaCh3.covariance
+   :members:
+   :undoc-members:
+   :show-inheritance:

Doc/sphinx/source/fitter.rst

@@ -0,0 +1,10 @@
+Fitter
+======
+
+This module contains the various MaCh3 fitter algorithms which are available, as well as 
+the :py:class:`pyMaCh3.fitter.FitterBase` class which you can use to implement your own!
+
+.. automodapi:: pyMaCh3.fitter
+   :members:
+   :undoc-members:
+   :show-inheritance:

Doc/sphinx/source/manager.rst

@@ -0,0 +1,51 @@
+Manager
+=======
+
+This module handles the high level stuff like config options and YAML stuff. The main class is the :py:class:`pyMaCh3.manager.Manager` class. \
+You can read more about the manager and config files on `the wiki page <https://github.com/mach3-software/MaCh3/wiki/01.-Manager-and-config-handling>`_. \
+YAML stuff works essentially the same as in the c++ version but with some caveats. 
+The main difference is that in the python version, the way that you access the actual data of a yaml node is different due to the way the python binding of the c++ code works. 
+
+Lets take the following YAML snippet as an example ::
+
+   Example: 
+      Int: 1234
+      Str: 'TestString'
+      IntArray: ['0', '1', '2'] 
+      StrArray: ['val1', 'val2', 'val3'] 
+
+In the c++ version you would access these by doing ::
+
+   // for the integer 
+   int testInt = node['Int'].as<int>() 
+   // for the string 
+   std::string testStr = node['Str'].as<std::string>() 
+   // for the integer array 
+   ... = node['IntArray'].as<std::vector<int>>() 
+   // and for the string array 
+   ... = node['StrArray'].as<std::vector<std::string>>() 
+
+In the python version however things are different. Arrays are interpreted as arrays of YAML nodes and all of the underlying data are stored as strings. \
+So to access the data as above you would need to do ::
+
+   test_int = int(node['Int'].data()) 
+   test_str = node['Str'].data() 
+   ## then for the arrays 
+   int1 = int(node['IntArray'][0].data()) 
+   int2 = int(node['IntArray'][1].data()) 
+   int3 = int(node['IntArray'][2].data()) 
+
+   str1 = node['StrArray'][0].data() 
+   str2 = node['StrArray'][1].data() 
+   str3 = node['StrArray'][2].data() 
+
+Parsing arrays can be made a bit less painful using list comprehension ::
+
+   int_list = [int(i.data()) for i in node['IntArray']] 
+   str_list = [i.data() for i in node['StrArray']] 
+
+
+.. automodapi:: pyMaCh3.manager
+   :members:
+   :undoc-members:
+   :show-inheritance:

Doc/sphinx/source/plotting.rst

@@ -1,7 +1,26 @@
 plotting
 ========
 
-.. mdinclude:: plotting.md
+The plotting module can be used to make beautiful plots. See the `plotting wiki page <https://github.com/mach3-software/MaCh3/wiki/15.-Plotting>`_ for information on how to configure the plotting library to work with your MaCh3 output files and other non-MaCh3 based fitters so you can compare results.
+
+The main class to worry about is :py:class:`pyMaCh3.plotting.PlottingManager` which provides the 
+high level functionality and gives you access to everything else you should need. 
+
+To use this in your plotting script simply do ::
+
+   ## import the plotting module
+   from pyMach3 import plotting
+   ## need sys to read command line arguments
+   import sys
+
+   man = plotting.PlottingManager()
+   ## give the command line arguments to the manager
+   manager.parse_inputs(sys.argv)
+
+   ## Now plot stuff!!
+   ## ...
+
+
 
 .. automodapi:: pyMaCh3.plotting
    :members:

Doc/sphinx/source/pyMaCh3.rst

@@ -4,4 +4,9 @@ pyMaCh3
 .. toctree::
    :maxdepth: 4
 
+   manager.rst
+   sample-pdf.rst
+   splines.rst
+   fitter.rst
+   covariance.rst
    plotting.rst

Doc/sphinx/source/sample-pdf.rst

@@ -0,0 +1,15 @@
+Sample PDF
+==========
+
+This module deals with sampling from the posterior density function of your 
+particular experimental model at different points, given your data. 
+
+In order to do this, you will generally need to create a SamplePDF object derived from :py:class:`pyMaCh3.fitter.SamplePDFFDBase` 
+for each sample of events for your experiment. For some more details on this you can see `the wiki page <https://github.com/mach3-software/MaCh3/wiki/04.-Making-a-samplePDF-experiment-class>`_ on this. 
+The code examples there are written using c++ however the general ideas are the same. 
+Happy sampling!
+
+.. automodapi:: pyMaCh3.sample_pdf
+   :members:
+   :undoc-members:
+   :show-inheritance:

Doc/sphinx/source/splines.rst

@@ -0,0 +1,68 @@
+Splines
+=======
+
+This module provides the utility for dealing with spline parameters. For some background reading se the `Splines wiki page <https://github.com/mach3-software/MaCh3/wiki/05.-Splines>`_.
+
+The main class which represents individual spline functions is :py:class:`pyMaCh3.splines.ResponseFunction`. 
+This is an abstract representation which covers multiple different types of interpolation, where the type of interpolation is specified at the time of construction.
+The available interpolation types are defined by :py:class:`pyMaCh3.splines.InterpolationType`. Here are some examples
+
+.. image:: spline-examples.png
+  :width: 400
+  :alt: Examples of linear, TSpline3 and monotonic interpolation
+
+To construct a ResponseFunction you must specify the x and y positions of the knots, and the interpolation type like in the following example::
+
+    from pyMaCh3 import splines
+
+    TSpline3_response_1 = splines.ResponseFunction([0.0, 1.0, 2.0], [1.0, 0.5, 2.0], splines.InterpolationType.Cubic_TSpline3)
+    linear_response_1 = splines.ResponseFunction([10.0, 11.0, 12.0], [6.0, 0.0, 0.5], splines.InterpolationType.Linear)
+
+    TSpline3_response_2 = splines.ResponseFunction([0.0, 1.0, 2.0], [2.0, 3.0, 0.0], splines.InterpolationType.Cubic_TSpline3)
+    linear_response_2 = splines.ResponseFunction([10.0, 11.0, 12.0], [3.0, 0.0, 4.5], splines.InterpolationType.Linear)
+
+Another important part of this module is the :py:class:`pyMaCh3.splines.EventSplineMonolith` class which allows you to easily and speedily deal with event-by-event splines in your analysis.
+To build this you first need to construct a response function for each event-by-event spline parameter for each of your events as in the example above.
+
+Let's take those example responses and build a simple EventSplineMonolith::
+
+    monolith = splines.EventSplineMonolith([[TSpline3_response_1, linear_response_1], [TSpline3_response_2, linear_response_2]])
+
+This will create an EventSplineMonolith which can deal with the reweighting of two events with two spline parameters.
+We now need to be able to set the values of the parameters so that we can calculate event weights. 
+This is done using the :py:func:`pyMaCh3.splines.EventSplineMonolith.set_param_value_array` function. 
+This allows us to bind a numpy array to our EventSplineMonolith, whose values we can change, and this will set the values of the parameters inside of the monolith.
+This works as follows::
+
+    # we need to keep track of how many parameters we have
+    # in our case this is two
+    n_parameters = 2
+
+    # we initialise the array, the initial values don't matter too much so we'll make them zero
+    param_array = np.zeros((n_parameters,))
+
+    # now we bind this array to the monolith we made above
+    monolith.set_param_value_array(param_array)
+
+    # now changes made in the param_array will be propagated to the monolith
+    param_array[0] = 0.5
+    param_array[1] = 11.042
+
+.. warning::
+    Once your array has been bound to your spline monolith that you keep it safe and don't overwrite it by doing something like::
+
+        param_array = np.array([0.5, 11.0])
+
+    as this will mean the original array (the one that is bound to your monolith will be lost forever and you will no longer be able to set parameter values!).
+    You need to set the values using indexes as above, or if you want to set them all at once you use slicing like::
+
+        param_array[...] = [0.5, 11.0]
+
+    This may seem a bit faffy but it is intended to avoid unneccessary copying from python to c++ so we can keep things nice and speedy.
+
+Happy splining!
+
+.. automodapi:: pyMaCh3.splines
+   :members:
+   :undoc-members:
+   :show-inheritance:

covariance/covarianceBase.h

@@ -178,6 +178,10 @@ class covarianceBase {
   /// element of a new array. There must be a clever C++ way to be careful
   inline const double* retPointer(const int iParam) {return &(_fPropVal.data()[iParam]);}
 
+  /// @brief Get a reference to the proposed parameter values
+  /// Can be useful if you want to track these without having to copy values using getProposed()
+  inline const std::vector<double> &getParPropVec() {return _fPropVal;}
+
   //Some Getters
   /// @brief Get total number of parameters
   inline int  GetNumParams() {return _fNumPar;}

covariance/covarianceXsec.h

@@ -32,6 +32,9 @@ class covarianceXsec : public covarianceBase {
     /// @brief Get interpolation type for a given parameter
     /// @param i spline parameter index, not confuse with global index
     inline SplineInterpolation GetParSplineInterpolation(const int i) {return SplineParams.at(i)._SplineInterpolationType;}
+    /// @brief Get the name of the spline associated with the spline at index i
+    /// @param i spline parameter index, not to be confused with global index
+    std::string GetParSplineName(const int i) {return _fSplineNames[i];}
 
     //DB Get spline parameters depending on given DetID
     const std::vector<int> GetGlobalSystIndexFromDetID(const int DetID, const SystType Type);

python/CMakeLists.txt

@@ -0,0 +1,21 @@
+
+################################# pybind11 stuff ##################################
+
+if( MaCh3_PYTHON_ENABLED )
+  ## EM: make a module target out of all the python*Module.cpp files (currently just one...)
+  pybind11_add_module( 
+    pyMaCh3 MODULE 
+    pyMaCh3.cpp 
+    plotting.cpp
+    fitter.cpp
+    samplePDF.cpp
+    manager.cpp
+    covariance.cpp
+    splines.cpp
+  )
+  ## EM: only works with code compiled with -fPIC enabled.. I think this flag can make things slightly slower
+  ## so would be good to find a way around this. 
+  set_property( TARGET pyMaCh3 PROPERTY POSITION_INDEPENDENT_CODE ON )
+  target_link_libraries( pyMaCh3 PUBLIC MaCh3::All )
+  install( TARGETS pyMaCh3 DESTINATION pyMaCh3/)
+endif()