From 9c72b9ee8d584f4fd5729f496b7927fec8f55e4e Mon Sep 17 00:00:00 2001
From: Robert Twyman <robbietuk@gmail.com>
Date: Fri, 9 Oct 2020 16:25:26 +0100
Subject: [PATCH 1/3] Generate prior factory

This isn't working...
---
 src/swig/stir.i | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/swig/stir.i b/src/swig/stir.i
index b727d6805..30c92702a 100644
--- a/src/swig/stir.i
+++ b/src/swig/stir.i
@@ -1579,6 +1579,10 @@ namespace stir {
 #undef elemT
 #endif
 
+%newobject *::get_prior_ptr;
+%factory(stir::GeneralisedPrior *stir::GeneralisedObjectiveFunction::get_prior_ptr, stir::QuadraticPrior, stir::PLSPrior, stir::RelativeDifferencePrior);
+//%factory(stir::GeneralisedPrior<TargetT> *stir::GeneralisedObjectiveFunction< TargetT >::get_prior_ptr, stir::QuadraticPrior<elemT>, stir::PLSPrior<elemT>, stir::RelativeDifferencePrior<elemT>);
+
 %include "stir/recon_buildblock/GeneralisedObjectiveFunction.h"
 %include "stir/recon_buildblock/GeneralisedObjectiveFunction.h"
 %include "stir/recon_buildblock/PoissonLogLikelihoodWithLinearModelForMean.h"

From c6fbe6f14f96ea58b2606bb6ee8deb77f3b13ffc Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Sun, 18 Oct 2020 00:04:14 +0000
Subject: [PATCH 2/3] [SWIG] sort-out factory for get_prior

tell SWIG about the prior hierarchy such that get_prior() returns instances of the actual prior (not just the base class)
---
 src/swig/stir.i | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/src/swig/stir.i b/src/swig/stir.i
index 30c92702a..ef9e0e73e 100644
--- a/src/swig/stir.i
+++ b/src/swig/stir.i
@@ -472,6 +472,7 @@
 #endif
 
 %include "attribute.i"
+%include "factory.i"
 
 %init %{
 #if defined(SWIGPYTHON)
@@ -1575,14 +1576,24 @@ namespace stir {
 %shared_ptr(stir::FBP2DReconstruction);
 %shared_ptr(stir::FBP3DRPReconstruction);
 
+// tell SWIG to convert the return of get_prior_ptr etc to the appropriate object
+/* This currently fails, so is still commented out
+
+%newobject *::get_objective_function;
+%factory(
+         stir::GeneralisedObjectiveFunction<TargetT >& stir::IterativeReconstruction<TargetT >::get_objective_function,
+         %arg(stir::PoissonLogLikelihoodWithLinearModelForMeanAndProjData<TargetT >));
+*/       
+%newobject *::get_prior_ptr;
+%factory(stir::GeneralisedPrior<TargetT> *stir::GeneralisedObjectiveFunction< TargetT >::get_prior_ptr,
+         stir::QuadraticPrior<elemT>,
+         stir::PLSPrior<elemT>,
+         stir::RelativeDifferencePrior<elemT>);
+
 #undef TargetT
 #undef elemT
 #endif
 
-%newobject *::get_prior_ptr;
-%factory(stir::GeneralisedPrior *stir::GeneralisedObjectiveFunction::get_prior_ptr, stir::QuadraticPrior, stir::PLSPrior, stir::RelativeDifferencePrior);
-//%factory(stir::GeneralisedPrior<TargetT> *stir::GeneralisedObjectiveFunction< TargetT >::get_prior_ptr, stir::QuadraticPrior<elemT>, stir::PLSPrior<elemT>, stir::RelativeDifferencePrior<elemT>);
-
 %include "stir/recon_buildblock/GeneralisedObjectiveFunction.h"
 %include "stir/recon_buildblock/GeneralisedObjectiveFunction.h"
 %include "stir/recon_buildblock/PoissonLogLikelihoodWithLinearModelForMean.h"

From fd15a8b7ae410643d945a7b8d02741e0a7bb5891 Mon Sep 17 00:00:00 2001
From: Robert Twyman <robbietuk@gmail.com>
Date: Tue, 20 Oct 2020 18:09:39 +0100
Subject: [PATCH 3/3] Clean up comments [ci skip]

---
 src/swig/stir.i | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/swig/stir.i b/src/swig/stir.i
index ef9e0e73e..441c89425 100644
--- a/src/swig/stir.i
+++ b/src/swig/stir.i
@@ -1576,14 +1576,14 @@ namespace stir {
 %shared_ptr(stir::FBP2DReconstruction);
 %shared_ptr(stir::FBP3DRPReconstruction);
 
-// tell SWIG to convert the return of get_prior_ptr etc to the appropriate object
 /* This currently fails, so is still commented out
-
 %newobject *::get_objective_function;
 %factory(
          stir::GeneralisedObjectiveFunction<TargetT >& stir::IterativeReconstruction<TargetT >::get_objective_function,
          %arg(stir::PoissonLogLikelihoodWithLinearModelForMeanAndProjData<TargetT >));
-*/       
+*/
+
+// tell SWIG to convert the return of get_prior_ptr etc to the appropriate object
 %newobject *::get_prior_ptr;
 %factory(stir::GeneralisedPrior<TargetT> *stir::GeneralisedObjectiveFunction< TargetT >::get_prior_ptr,
          stir::QuadraticPrior<elemT>,