Merge branch 'polMesoTransformed' into develop

.cproject

@@ -163,7 +163,7 @@
 		<buildTargets>
 			<target name="CMake Release" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>cmake</buildCommand>
-				<buildArguments>-E chdir ../BornAgain_cmake_release/ cmake -G "Unix Makefiles" ../BornAgain/ -DCMAKE_BUILD_TYPE=Release</buildArguments>
+				<buildArguments>-E chdir ../BornAgain_cmake_release/ cmake -G "Unix Makefiles" ../BornAgain/ -DCMAKE_BUILD_TYPE=Release -DBORNAGAIN_APP=ON</buildArguments>
 				<buildTarget/>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>
@@ -171,7 +171,7 @@
 			</target>
 			<target name="CMake Debug" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 				<buildCommand>cmake</buildCommand>
-				<buildArguments>-E chdir ../BornAgain_cmake_debug/ cmake -G "Unix Makefiles" ../BornAgain/ -DCMAKE_BUILD_TYPE=Debug</buildArguments>
+				<buildArguments>-E chdir ../BornAgain_cmake_debug/ cmake -G "Unix Makefiles" ../BornAgain/ -DCMAKE_BUILD_TYPE=Debug -DBORNAGAIN_APP=ON</buildArguments>
 				<buildTarget/>
 				<stopOnError>true</stopOnError>
 				<useDefaultCommand>false</useDefaultCommand>

Core/FormFactors/inc/FormFactorCrystal.h

@@ -48,6 +48,8 @@ public:
 
     virtual double getVolume() const;
 
+    void setTransformation(const Geometry::PTransform3D& P_transform);
+
 private:
     void calculateLargestReciprocalDistance();
 
@@ -58,6 +60,8 @@ private:
     IFormFactor *mp_meso_form_factor;
     const IMaterial *mp_ambient_material;
     double m_max_rec_length;
+    Geometry::PTransform3D mP_transform;
+    Geometry::PTransform3D mP_inverse_transform;
 };
 
 #endif /* FORMFACTORCRYSTAL_H_ */

Core/FormFactors/src/FormFactorCrystal.cpp

@@ -47,6 +47,9 @@ FormFactorCrystal* FormFactorCrystal::clone() const
             *mp_meso_form_factor, mp_ambient_material,
             m_wavevector_scattering_factor);
     result->setName(getName());
+    if (mP_transform.get()) {
+        result->setTransformation(mP_transform);
+    }
     return result;
 }
 
@@ -67,7 +70,16 @@ complex_t FormFactorCrystal::evaluate(const cvector_t& k_i,
         const Bin1DCVector& k_f_bin, Bin1D alpha_f_bin) const
 {
     // construct a real reciprocal vector
-    Bin1DCVector q_bin(k_i - k_f_bin.m_q_lower, k_i - k_f_bin.m_q_upper);
+    cvector_t q_bin_lower = k_i - k_f_bin.m_q_lower;
+    cvector_t q_bin_upper = k_i - k_f_bin.m_q_upper;
+    Bin1DCVector q_bin;
+    if (mP_inverse_transform.get()) {
+        q_bin = Bin1DCVector(mP_inverse_transform->transformed(q_bin_lower),
+                mP_inverse_transform->transformed(q_bin_upper));
+    } else {
+        q_bin = Bin1DCVector(q_bin_lower, q_bin_upper);
+    }
+
     cvector_t q = q_bin.getMidPoint();
     kvector_t q_real(q.x().real(), q.y().real(), q.z().real());
     cvector_t k_zero;
@@ -101,7 +113,16 @@ Eigen::Matrix2cd FormFactorCrystal::evaluatePol(const cvector_t& k_i,
         const Bin1DCVector& k_f_bin, Bin1D alpha_f_bin, Bin1D phi_f_bin) const
 {
     // construct a real reciprocal vector
-    Bin1DCVector q_bin(k_i - k_f_bin.m_q_lower, k_i - k_f_bin.m_q_upper);
+    cvector_t q_bin_lower = k_i - k_f_bin.m_q_lower;
+    cvector_t q_bin_upper = k_i - k_f_bin.m_q_upper;
+    Bin1DCVector q_bin;
+    if (mP_inverse_transform.get()) {
+        q_bin = Bin1DCVector(mP_inverse_transform->transformed(q_bin_lower),
+                mP_inverse_transform->transformed(q_bin_upper));
+    } else {
+        q_bin = Bin1DCVector(q_bin_lower, q_bin_upper);
+    }
+
     cvector_t q = q_bin.getMidPoint();
     kvector_t q_real(q.x().real(), q.y().real(), q.z().real());
     cvector_t k_zero;
@@ -119,6 +140,7 @@ Eigen::Matrix2cd FormFactorCrystal::evaluatePol(const cvector_t& k_i,
         cvector_t q_i((*it).x(), (*it).y(), (*it).z());
         Bin1DCVector min_q_i_zero_bin(-q_i, -q_i);
         Bin1DCVector q_i_min_q(q_i - q_bin.m_q_lower, q_i - q_bin.m_q_upper);
+        //TODO: transform the matrix amplitude back!
         Eigen::Matrix2cd basis_factor = mp_basis_form_factor->evaluatePol(
                 k_zero, min_q_i_zero_bin, alpha_f_bin, phi_f_bin);
         complex_t meso_factor = mp_meso_form_factor->evaluate(
@@ -136,6 +158,13 @@ double FormFactorCrystal::getVolume() const
     return mp_meso_form_factor->getVolume();
 }
 
+void FormFactorCrystal::setTransformation(
+        const Geometry::PTransform3D& P_transform)
+{
+    mP_transform = P_transform;
+    mP_inverse_transform = mP_transform->inverse();
+}
+
 void FormFactorCrystal::calculateLargestReciprocalDistance()
 {
     kvector_t a1 = m_lattice.getBasisVectorA();

Core/Samples/inc/Crystal.h

@@ -43,7 +43,8 @@ public:
     virtual IFormFactor *createTotalFormFactor(
         const IFormFactor& meso_crystal_form_factor,
         const IMaterial *p_ambient_material,
-        complex_t wavevector_scattering_factor) const;
+        complex_t wavevector_scattering_factor,
+        const Geometry::PTransform3D& transform) const;
 
     Lattice getLattice() const { return m_lattice; }
     LatticeBasis *createBasis() const { return mp_lattice_basis->clone(); }

Core/Samples/inc/IClusteredParticles.h

@@ -59,11 +59,13 @@ public:
     virtual IFormFactor *createTotalFormFactor(
            const IFormFactor& meso_crystal_form_factor,
            const IMaterial *p_ambient_material,
-           complex_t wavevector_scattering_factor) const
+           complex_t wavevector_scattering_factor,
+           const Geometry::PTransform3D& transform) const
     {
         (void)meso_crystal_form_factor;
         (void)p_ambient_material;
         (void)wavevector_scattering_factor;
+        (void)transform;
         throw NotImplementedException(
                 "IClusteredParticles::createTotalFormFactor() "
                 "-> NotImplementedException");

Core/Samples/src/Crystal.cpp

@@ -52,11 +52,15 @@ Crystal* Crystal::cloneInvertB() const
 IFormFactor* Crystal::createTotalFormFactor(
         const IFormFactor& meso_crystal_form_factor,
         const IMaterial *p_ambient_material,
-        complex_t wavevector_scattering_factor) const
+        complex_t wavevector_scattering_factor,
+        const Geometry::PTransform3D& P_transform) const
 {
-    IFormFactor *p_ff_crystal =
+    FormFactorCrystal *p_ff_crystal =
         new FormFactorCrystal(*this, meso_crystal_form_factor,
                 p_ambient_material, wavevector_scattering_factor);
+    if (P_transform.get()) {
+        p_ff_crystal->setTransformation(P_transform);
+    }
     if (m_dw_factor>0.0) {
         return new FormFactorDecoratorDebyeWaller(p_ff_crystal, m_dw_factor);
     }

Core/Samples/src/MesoCrystal.cpp

@@ -70,18 +70,9 @@ void MesoCrystal::setAmbientMaterial(const IMaterial* p_material)
 IFormFactor* MesoCrystal::createFormFactor(
         complex_t wavevector_scattering_factor) const
 {
-    IFormFactor *p_result;
-    IFormFactor *p_crystal_ff = mp_particle_structure->createTotalFormFactor(
+    return mp_particle_structure->createTotalFormFactor(
             *mp_meso_form_factor, mp_ambient_material,
-            wavevector_scattering_factor);
-    if(mP_transform.get()) {
-        p_result = new FormFactorDecoratorTransformation(
-                p_crystal_ff, mP_transform);
-    }
-    else {
-        p_result = p_crystal_ff;
-    }
-    return p_result;
+            wavevector_scattering_factor, mP_transform);
 }
 
 void MesoCrystal::setSimpleFormFactor(IFormFactor* p_form_factor)