diff --git a/App/src/IsGISAXSTools.cpp b/App/src/IsGISAXSTools.cpp
index 5d3fa1d84b4592028e593854b6c56026aa4a54a0..ecc8d25960ce12e4a64a41bfb17c2a65bd81cb32 100644
--- a/App/src/IsGISAXSTools.cpp
+++ b/App/src/IsGISAXSTools.cpp
@@ -81,7 +81,7 @@ void IsGISAXSTools::drawOutputDataInPad(const OutputData<double>& output,
}
TH1 *hist(0);
- if(output.getNdimensions() == 2 ) {
+ if(output.getRank() == 2 ) {
hist = IsGISAXSTools::getOutputDataTH2D(output, "p_hist1D");
} else {
hist = IsGISAXSTools::getOutputDataTH123D(output, "p_hist1D");
@@ -120,15 +120,15 @@ TH2D *IsGISAXSTools::getOutputDataTH2D(const OutputData<double>& output,
const std::string& histo_name)
{
assert(&output);
- if (output.getNdimensions() !=2)
+ if (output.getRank() !=2)
throw( "IsGISAXSTools::getOutputDataTH2D() -> "
"Warning! Expected number of dimensiobs is 2.");
std::vector<AxisStructure > haxises;
- haxises.resize(output.getNdimensions());
+ haxises.resize(output.getRank());
// we assume variable bin size and prepare [nbins+1] array of left edges of each bin plus right edge of the last bin
- for(size_t i_axis=0; i_axis<output.getNdimensions(); ++i_axis) {
+ for(size_t i_axis=0; i_axis<output.getRank(); ++i_axis) {
const IAxis *axis = output.getAxis(i_axis);
if( !axis ) throw("IsGISAXSTools::getOutputDataTH123D() -> Error! Can't cast axis");
double dx(0);
@@ -192,16 +192,16 @@ TH2D *IsGISAXSTools::getOutputDataTH2D(const OutputData<double>& output,
TH1 *IsGISAXSTools::getOutputDataTH123D(const OutputData<double>& output, const std::string &histo_name)
{
assert(&output);
- if (output.getNdimensions() >3) {
+ if (output.getRank() >3) {
std::cout << "IsGISAXSTools::getOutputDataTH123D() -> Warning! Expected number of dimensions should be not more than 3" << std::endl;
return 0;
}
std::vector<AxisStructure > haxises;
- haxises.resize(output.getNdimensions());
+ haxises.resize(output.getRank());
// we assume variable bin size and prepare [nbins+1] array of left edges of each bin plus right edge of the last bin
- for(size_t i_axis=0; i_axis<output.getNdimensions(); ++i_axis) {
+ for(size_t i_axis=0; i_axis<output.getRank(); ++i_axis) {
const IAxis *axis = output.getAxis(i_axis);
if( !axis ) throw("IsGISAXSTools::getOutputDataTH123D() -> Error! Can't cast axis");
double dx(0);
@@ -240,16 +240,16 @@ TH1 *IsGISAXSTools::getOutputDataTH123D(const OutputData<double>& output, const
TH1D *hist1(0);
TH2D *hist2(0);
TH3D *hist3(0);
- if(output.getNdimensions() == 1) {
+ if(output.getRank() == 1) {
hist1 = new TH1D(histo_name.c_str(), histo_name.c_str(), (int)haxises[0].nbins, &haxises[0].xbins[0]);
hist1->GetXaxis()->SetTitle( haxises[0].name.c_str() );
hist = hist1;
- } else if(output.getNdimensions() == 2) {
+ } else if(output.getRank() == 2) {
hist2 = new TH2D(histo_name.c_str(), histo_name.c_str(), (int)haxises[0].nbins, &haxises[0].xbins[0], (int)haxises[1].nbins, &haxises[1].xbins[0]);
hist2->GetXaxis()->SetTitle( haxises[0].name.c_str() );
hist2->GetYaxis()->SetTitle( haxises[1].name.c_str() );
hist = hist2;
- } else if(output.getNdimensions() == 3) {
+ } else if(output.getRank() == 3) {
hist3 = new TH3D(histo_name.c_str(), histo_name.c_str(), (int)haxises[0].nbins, &haxises[0].xbins[0], (int)haxises[1].nbins, &haxises[1].xbins[0], (int)haxises[1].nbins, &haxises[1].xbins[0]);
hist3->GetXaxis()->SetTitle( haxises[0].name.c_str() );
hist3->GetYaxis()->SetTitle( haxises[1].name.c_str() );
@@ -478,7 +478,7 @@ TLine *IsGISAXSTools::getOutputDataScanLine(const OutputData<double> &data)
{
assert(&data);
- if(data.getNdimensions() != 2) throw LogicErrorException("IsGISAXSTools::getOutputDataScanLine() -> Error! Number of dimensions should be 2");
+ if(data.getRank() != 2) throw LogicErrorException("IsGISAXSTools::getOutputDataScanLine() -> Error! Number of dimensions should be 2");
double x1(0), x2(0), y1(0), y2(0);
if( data.getAxis("alpha_f") && data.getAxis("alpha_f")->getSize() == 1) {
// horizontal line
@@ -509,7 +509,7 @@ TH1D *IsGISAXSTools::getOutputDataScanHist(const OutputData<double> &data, const
{
assert(&data);
- if(data.getNdimensions() != 2) throw LogicErrorException("IsGISAXSTools::getOutputDataScanHist() -> Error! Number of dimensions should be 2");
+ if(data.getRank() != 2) throw LogicErrorException("IsGISAXSTools::getOutputDataScanHist() -> Error! Number of dimensions should be 2");
// one of axis should have dimension 1
if( (data.getAxis("alpha_f") && data.getAxis("alpha_f")->getSize() != 1) && (data.getAxis("phi_f") && data.getAxis("phi_f")->getSize() != 1))
{
diff --git a/App/src/TestIsGISAXS12.cpp b/App/src/TestIsGISAXS12.cpp
index 9996bc02cff8f15c53d59420b03e6b672792eb98..2f7341bf9f7107e1a05aa1373f4c35b00f22cc50 100644
--- a/App/src/TestIsGISAXS12.cpp
+++ b/App/src/TestIsGISAXS12.cpp
@@ -199,7 +199,6 @@ void TestIsGISAXS12::plot_isgisaxs_fit_results()
c1->cd(6); leg3->Draw();
c1->Update();
-
}
@@ -532,7 +531,7 @@ void TestIsGISAXS12::print_axes(IsGISAXSData::DataSet_t &data)
{
for(size_t i_set=0; i_set<data.size(); ++i_set) {
std::cout << "scan #" << i_set << " ";
- for(size_t i_axis=0; i_axis<data[(int)i_set]->getNdimensions(); ++i_axis) {
+ for(size_t i_axis=0; i_axis<data[(int)i_set]->getRank(); ++i_axis) {
const IAxis *axis = data[(int)i_set]->getAxis(i_axis);
std::cout << "( " << axis->getName() << ", " << axis->getSize() << ", " << axis->getMin() << ", " << axis->getMax() << " ) ";
}
diff --git a/Core/Algorithms/inc/DWBASimulation.h b/Core/Algorithms/inc/DWBASimulation.h
index e3d04f808b423a96b112904522cda8bb62dece24..23524adc78cc14fd15d591164518960d21e29c39 100644
--- a/Core/Algorithms/inc/DWBASimulation.h
+++ b/Core/Algorithms/inc/DWBASimulation.h
@@ -38,7 +38,7 @@ class DWBASimulation : public ISimulation
virtual void setThreadInfo(const ThreadInfo& thread_info)
{ m_thread_info = thread_info; }
- //! return output data containing calculated intensity
+ //! Return output data containing calculated intensity
const OutputData<double>& getDWBAIntensity() const
{ return m_dwba_intensity; }
@@ -46,7 +46,6 @@ class DWBASimulation : public ISimulation
void addDWBAIntensity(const OutputData<double>& data_to_add)
{ m_dwba_intensity += data_to_add; }
- //! clone DWBA simulation
virtual DWBASimulation *clone() const;
// ---------------------------------
@@ -57,16 +56,16 @@ class DWBASimulation : public ISimulation
typedef OutputDataIterator<const double, const OutputData<double> >
const_iterator;
- //! return a read/write iterator that points to the first element
+ //! Return a read/write iterator that points to the first element
iterator begin();
- //! return a read-only iterator that points to the first element
+ //! Return a read-only iterator that points to the first element
const_iterator begin() const;
- //! return a read/write iterator that points to the one past last element
+ //! Return a read/write iterator that points to the one past last element
const iterator end() { return m_dwba_intensity.end(); }
- //! return a read-only iterator that points to the one past last element
+ //! Return a read-only iterator that points to the one past last element
const const_iterator end() const { return m_dwba_intensity.end(); }
protected:
diff --git a/Core/Algorithms/inc/DiffuseDWBASimulation.h b/Core/Algorithms/inc/DiffuseDWBASimulation.h
index e6da8b69fd24ec6d6c70c2c0c56f0e5040d7ad27..4fa7b781d20d737fd691e9a15d846379d1427285 100644
--- a/Core/Algorithms/inc/DiffuseDWBASimulation.h
+++ b/Core/Algorithms/inc/DiffuseDWBASimulation.h
@@ -24,15 +24,26 @@ class DiffuseDWBASimulation: public LayerDWBASimulation
public:
DiffuseDWBASimulation()
: m_refractive_index(1., 0.), m_surface_density(1.) {}
+
virtual ~DiffuseDWBASimulation() {}
virtual void run();
+
size_t getSize() const { return m_np_infos.size(); }
- void addParticleInfo(DiffuseParticleInfo *p_info);
+
+ void addParticleInfo(DiffuseParticleInfo *p_info)
+ { m_np_infos.push_back(p_info); }
+
void setRefractiveIndex(complex_t n) { m_refractive_index = n; }
+
void setSurfaceDensity(double surface_density)
{ m_surface_density = surface_density; }
- void rescaleAbundances(double factor);
+
+ void rescaleAbundances(double factor)
+ {
+ for (size_t np_index=0; np_index<m_np_infos.size(); ++np_index)
+ m_np_infos[np_index]->scaleAbundance(factor);
+ }
protected:
complex_t m_refractive_index;
@@ -41,7 +52,11 @@ class DiffuseDWBASimulation: public LayerDWBASimulation
struct DiffuseFormFactorTerm {
DiffuseFormFactorTerm()
: m_form_factors(), m_probabilities(), m_factor(0.) {}
- ~DiffuseFormFactorTerm();
+ ~DiffuseFormFactorTerm()
+ {
+ for (size_t i=0; i<m_form_factors.size(); ++i)
+ delete m_form_factors[i];
+ }
std::vector<IFormFactor*> m_form_factors;
std::vector<double> m_probabilities;
double m_factor;
diff --git a/Core/Algorithms/inc/Mask.h b/Core/Algorithms/inc/Mask.h
index dff929b3651a998cefb34df48c1a6350d35629b0..f30db9a997e83e615a1394990d6715c151be80c3 100644
--- a/Core/Algorithms/inc/Mask.h
+++ b/Core/Algorithms/inc/Mask.h
@@ -18,7 +18,7 @@
#include "MaskCoordinateFunction.h"
-//! Base class for masking OutputData elements
+//! Base class for masking OutputData elements.
class Mask : public ICloneable
{
@@ -46,7 +46,7 @@ class Mask : public ICloneable
size_t nextSubIndex(size_t total_index);
};
-//! Mask based on the index modulo a given number
+//! Mask based on the index modulo a given number.
class MaskIndexModulus : public Mask
{
@@ -64,7 +64,7 @@ class MaskIndexModulus : public Mask
size_t m_remainder;
};
-//! Mask based on the coordinates
+//! Mask based on the coordinates.
class MaskCoordinates : public Mask
{
diff --git a/Core/Algorithms/inc/ThreadInfo.h b/Core/Algorithms/inc/ThreadInfo.h
index bf2ac3ca62fb0eb5212ce51dccbeff7e564265e9..287fd03c3e04368197565d935fe42ad309af72e9 100644
--- a/Core/Algorithms/inc/ThreadInfo.h
+++ b/Core/Algorithms/inc/ThreadInfo.h
@@ -20,15 +20,9 @@
struct ThreadInfo
{
- ThreadInfo();
+ ThreadInfo() : n_threads(1), i_thread(0) {}
size_t n_threads;
size_t i_thread;
};
-inline ThreadInfo::ThreadInfo()
-: n_threads(1)
-, i_thread(0)
-{
-}
-
#endif /* THREADINFO_H_ */
diff --git a/Core/Algorithms/src/DWBASimulation.cpp b/Core/Algorithms/src/DWBASimulation.cpp
index 043f8eadb7d61e254820ca0f78b3dd38eedc535c..769efef08b4057017dad10f6e3e54cbd82ff6601 100644
--- a/Core/Algorithms/src/DWBASimulation.cpp
+++ b/Core/Algorithms/src/DWBASimulation.cpp
@@ -47,7 +47,6 @@ DWBASimulation *DWBASimulation::clone() const
p_result->m_thread_info = m_thread_info;
if (mp_simulation)
p_result->mp_simulation = mp_simulation->clone();
-
return p_result;
}
diff --git a/Core/Algorithms/src/DiffuseDWBASimulation.cpp b/Core/Algorithms/src/DiffuseDWBASimulation.cpp
index 806fabe168cbedf80587c6752fec849995f6e266..95967d9e42d4192dbcd5ba5c9af3fbf0b87fc583 100644
--- a/Core/Algorithms/src/DiffuseDWBASimulation.cpp
+++ b/Core/Algorithms/src/DiffuseDWBASimulation.cpp
@@ -16,30 +16,32 @@
#include "DiffuseDWBASimulation.h"
#include "FormFactorDWBAConstZ.h"
-// Run a simulation.
+#define SQR(x) ((x)*(x))
+
+//! Carry out one simulation thread.
void DiffuseDWBASimulation::run()
{
+ // Set diffuse terms.
std::vector<DiffuseFormFactorTerm*> diffuse_terms;
size_t nbr_heights = 50;
size_t samples_per_particle = 9;
initDiffuseFormFactorTerms(
diffuse_terms, nbr_heights, samples_per_particle);
- double wavevector_scattering_factor = M_PI/getWaveLength()/getWaveLength();
+
+ double wavevector_scattering_factor = M_PI/SQR(getWaveLength());
cvector_t k_ij = m_ki;
k_ij.setZ(-mp_kz_function->evaluate(-m_alpha_i));
- DWBASimulation::iterator it_intensity = begin();
- while ( it_intensity != end() ) {
+ for (DWBASimulation::iterator it_intensity =
+ begin(); it_intensity != end(); ++it_intensity ) {
Bin1D phi_bin = getDWBAIntensity().getBinOfAxis(
"phi_f", it_intensity.getIndex());
Bin1D alpha_bin = getDWBAIntensity().getBinOfAxis(
"alpha_f", it_intensity.getIndex());
double alpha_f = alpha_bin.getMidPoint();
- if (alpha_f<0) {
- ++it_intensity;
+ if (alpha_f<0)
continue;
- }
Bin1DCVector k_f_bin = getKfBin(getWaveLength(), alpha_bin, phi_bin);
double total_intensity = 0;
@@ -55,29 +57,23 @@ void DiffuseDWBASimulation::run()
intensity += p_diffuse_term->m_probabilities[j]*std::norm(amp);
}
total_intensity +=
- p_diffuse_term->m_factor*(intensity - std::norm(amplitude));
+ p_diffuse_term->m_factor * (intensity - std::norm(amplitude));
}
- *it_intensity = total_intensity*
- wavevector_scattering_factor*wavevector_scattering_factor;
- ++it_intensity;
+ *it_intensity = total_intensity * SQR(wavevector_scattering_factor);
}
for (size_t i=0; i<diffuse_terms.size(); ++i)
delete diffuse_terms[i];
}
-void DiffuseDWBASimulation::addParticleInfo(DiffuseParticleInfo *p_info)
-{
- m_np_infos.push_back(p_info);
-}
-
-void DiffuseDWBASimulation::rescaleAbundances(double factor)
-{
- for (size_t np_index=0; np_index<m_np_infos.size(); ++np_index) {
- m_np_infos[np_index]->scaleAbundance(factor);
- }
-}
+//! Initialize vector<DiffuseFormFactorTerm*> term.
+//! Called near beginning of this->run().
+//! Collect one entry (p_diffuse_term) per particle type and layer[?].
+//! For each entry, set
+//! - m_factor
+//! - m_form_factors <- vector<FormFactorDWBAConstZ*>
+//!
void DiffuseDWBASimulation::initDiffuseFormFactorTerms(
std::vector<DiffuseFormFactorTerm*>& terms,
size_t nbr_heights,
@@ -93,7 +89,7 @@ void DiffuseDWBASimulation::initDiffuseFormFactorTerms(
DiffuseFormFactorTerm *p_diffuse_term = new DiffuseFormFactorTerm;
p_diffuse_term->m_factor = density_per_height_per_particle;
double depth = p_diff_info->getDepth() -
- (double)j*p_diff_info->getHeightRange()/(nbr_heights-1.0);
+ j*p_diff_info->getHeightRange()/(nbr_heights-1.0);
std::vector<IFormFactor*> form_factors;
p_diff_info->getParticle()->getSimpleFormFactor()->createDistributedFormFactors(
form_factors, p_diffuse_term->m_probabilities,
@@ -113,9 +109,3 @@ void DiffuseDWBASimulation::initDiffuseFormFactorTerms(
}
}
-DiffuseDWBASimulation::DiffuseFormFactorTerm::~DiffuseFormFactorTerm()
-{
- for (size_t i=0; i<m_form_factors.size(); ++i) {
- delete m_form_factors[i];
- }
-}
diff --git a/Core/Algorithms/src/Instrument.cpp b/Core/Algorithms/src/Instrument.cpp
index 2ef9107b4d2ea8b4c91574844b5d7809d574fa02..572b4712ca7321f3bbac419fce6fb297411dd452 100644
--- a/Core/Algorithms/src/Instrument.cpp
+++ b/Core/Algorithms/src/Instrument.cpp
@@ -35,7 +35,7 @@ Instrument::Instrument(const Instrument& other)
void Instrument::matchDetectorParameters(const OutputData<double>& output_data)
{
m_detector.clear();
- for(size_t i_axis=0; i_axis<output_data.getNdimensions(); ++i_axis) {
+ for(size_t i_axis=0; i_axis<output_data.getRank(); ++i_axis) {
const IAxis *axis = output_data.getAxis(i_axis);
m_detector.addAxis(*axis);
}
diff --git a/Core/Fitting/src/MinimizerScan.cpp b/Core/Fitting/src/MinimizerScan.cpp
index d421337255dff9a253c264555695cb9e6c4d4479..4fb41264ea279296202995068dc0306efd299940 100644
--- a/Core/Fitting/src/MinimizerScan.cpp
+++ b/Core/Fitting/src/MinimizerScan.cpp
@@ -25,7 +25,7 @@ void MinimizerScan::minimize()
// scanning values of fit parameters
for(OutputData<double>::iterator it = m_fcnvalues_map->begin(); it!=m_fcnvalues_map->end(); ++it) {
- for(size_t i_axis=0; i_axis<m_fcnvalues_map->getNdimensions(); ++i_axis) {
+ for(size_t i_axis=0; i_axis<m_fcnvalues_map->getRank(); ++i_axis) {
size_t xbin = m_fcnvalues_map->toCoordinate(it.getIndex(), i_axis);
double value = (*m_fcnvalues_map->getAxis(i_axis))[xbin];
std::string parname = m_fcnvalues_map->getAxis(i_axis)->getName();
@@ -53,7 +53,7 @@ void MinimizerScan::construct_fcnvalues_map()
m_fcnvalues_map->addAxis(axis);
}
}
- if( !m_fcnvalues_map->getNdimensions() ) {
+ if( !m_fcnvalues_map->getRank() ) {
throw LogicErrorException("MinimizerScan::construct_parameter_map() -> Error! No parameters with TAttLimit::limited(left,right) attribute were found.");
}
m_fcnvalues_map->setAllTo(0.0);
@@ -64,7 +64,7 @@ void MinimizerScan::set_parvalues_to_minimum()
{
assert(m_fcnvalues_map);
OutputData<double>::iterator it = std::min_element(m_fcnvalues_map->begin(), m_fcnvalues_map->end());
- for(size_t i_axis=0; i_axis<m_fcnvalues_map->getNdimensions(); ++i_axis) {
+ for(size_t i_axis=0; i_axis<m_fcnvalues_map->getRank(); ++i_axis) {
size_t xbin = m_fcnvalues_map->toCoordinate(it.getIndex(), i_axis);
double value = (*m_fcnvalues_map->getAxis(i_axis))[xbin];
std::string parname = m_fcnvalues_map->getAxis(i_axis)->getName();
diff --git a/Core/FormFactors/inc/IFormFactor.h b/Core/FormFactors/inc/IFormFactor.h
index 6937e523f805a438148b9ed8652e5b041d665cc8..2657214d65192f0803f57078dcbab366776a1e33 100644
--- a/Core/FormFactors/inc/IFormFactor.h
+++ b/Core/FormFactors/inc/IFormFactor.h
@@ -3,7 +3,7 @@
// BornAgain: simulate and fit scattering at grazing incidence
//
//! @file FormFactors/inc/IFormFactor.h
-//! @brief Defines class IFormFactor.
+//! @brief Defines pure virtual interface class IFormFactor.
//!
//! @homepage http://apps.jcns.fz-juelich.de/BornAgain
//! @license GNU General Public License v3 or higher (see COPYING)
diff --git a/Core/FormFactors/inc/IFormFactorBornSeparable.h b/Core/FormFactors/inc/IFormFactorBornSeparable.h
index 865a060f4d77160308d98ff5b8c32edab5966be4..cf54933d5b4045628a28d7adc306ac7792336f74 100644
--- a/Core/FormFactors/inc/IFormFactorBornSeparable.h
+++ b/Core/FormFactors/inc/IFormFactorBornSeparable.h
@@ -3,7 +3,7 @@
// BornAgain: simulate and fit scattering at grazing incidence
//
//! @file FormFactors/inc/IFormFactorBornSeparable.h
-//! @brief Defines class IFormFactorBornSeparable.
+//! @brief Defines pure virtual interface class IFormFactorBornSeparable.
//!
//! @homepage http://apps.jcns.fz-juelich.de/BornAgain
//! @license GNU General Public License v3 or higher (see COPYING)
diff --git a/Core/FormFactors/inc/IFormFactorDecorator.h b/Core/FormFactors/inc/IFormFactorDecorator.h
index 66bb359bb34ebd9fe112865a27f8b05fdce53f08..15eac8d098eb80527cc555cad0708ac07ab67277 100644
--- a/Core/FormFactors/inc/IFormFactorDecorator.h
+++ b/Core/FormFactors/inc/IFormFactorDecorator.h
@@ -3,7 +3,7 @@
// BornAgain: simulate and fit scattering at grazing incidence
//
//! @file FormFactors/inc/IFormFactorDecorator.h
-//! @brief Defines class IFormFactorDecorator.
+//! @brief Defines pure vurtual interface class IFormFactorDecorator.
//!
//! @homepage http://apps.jcns.fz-juelich.de/BornAgain
//! @license GNU General Public License v3 or higher (see COPYING)
diff --git a/Core/PythonAPI/src/PythonOutputData.cpp b/Core/PythonAPI/src/PythonOutputData.cpp
index 205afd51a97b37ef16046e1c6468da9ec2d9b52e..d83f6eae85022e56b58a7a2fd4de5b70a5385250 100644
--- a/Core/PythonAPI/src/PythonOutputData.cpp
+++ b/Core/PythonAPI/src/PythonOutputData.cpp
@@ -38,7 +38,7 @@ PyObject *ExportOutputDataAxis(const OutputData<double > &output, int naxis);
int GetOutputDataNdimensions(const Simulation &simulation)
{
const OutputData<double > *data = simulation.getOutputData();
- int ndims = data->getNdimensions();
+ int ndims = data->getRank();
return ndims;
}
@@ -66,7 +66,7 @@ PyObject *ExportOutputData(const OutputData<double > &output_data)
{
// getting size of dimensions from output_data
std::vector<int > dimensions;
- for(size_t i=0; i<output_data.getNdimensions(); i++) {
+ for(size_t i=0; i<output_data.getRank(); i++) {
//const AxisDouble *axis = output_data.getAxis(i);
const IAxis *axis = output_data.getAxis(i);
dimensions.push_back( axis->getSize() );
@@ -106,7 +106,7 @@ PyObject *ExportOutputDataAxis(const OutputData<double > &output_data, int naxis
{
// getting size of dimensions from output_data
std::vector<int > dimensions;
- for(size_t i=0; i<output_data.getNdimensions(); i++) {
+ for(size_t i=0; i<output_data.getRank(); i++) {
const IAxis *axis = output_data.getAxis(i);
dimensions.push_back( axis->getSize() );
}
diff --git a/Core/Tools/inc/ICloneable.h b/Core/Tools/inc/ICloneable.h
index 9c3880bb6acf26aa30ae6a8a8c51ade1f1da42c4..944b724408c62399a25a5f9da2c6e71ca41bc009 100644
--- a/Core/Tools/inc/ICloneable.h
+++ b/Core/Tools/inc/ICloneable.h
@@ -18,7 +18,7 @@
#include "Exceptions.h"
-//! Disable copy constructor and = operator; child classes must provide clone().
+//! Disable copy constructor and operator=; child classes should provide clone().
class ICloneable
{
@@ -28,8 +28,10 @@ class ICloneable
virtual ICloneable *clone() const = 0;
private:
- ICloneable(const ICloneable &) { throw NotImplementedException("ICloneable(const ICloneable &) -> Error: not implemented."); }
- ICloneable &operator=(const ICloneable &) { throw NotImplementedException("ICloneable &operator=(const ICloneable &) -> Error: not implemented."); }
+ ICloneable(const ICloneable &) { throw NotImplementedException(
+ "ICloneable(const ICloneable &) -> Error: not implemented."); }
+ ICloneable &operator=(const ICloneable &) { throw NotImplementedException(
+ "ICloneable &operator=(const ICloneable &) -> Error: not implemented."); }
};
#endif // ICLONEABLE_H
diff --git a/Core/Tools/inc/IFactory.h b/Core/Tools/inc/IFactory.h
index 1f586cf9305de39d7ec89bc24b5d02f8b86b9232..a19f21f9e01ceb287668488b7191a4f5822f220b 100644
--- a/Core/Tools/inc/IFactory.h
+++ b/Core/Tools/inc/IFactory.h
@@ -3,7 +3,7 @@
// BornAgain: simulate and fit scattering at grazing incidence
//
//! @file Tools/inc/IFactory.h
-//! @brief Defines class IFactory.
+//! @brief Defines interface class IFactory.
//!
//! @homepage http://apps.jcns.fz-juelich.de/BornAgain
//! @license GNU General Public License v3 or higher (see COPYING)
diff --git a/Core/Tools/inc/INamed.h b/Core/Tools/inc/INamed.h
index a2ff2cb0cf666b68f58deca51f87f032e442a2da..98e6bd64e4af1b6487789c9c8666e224a5092583 100644
--- a/Core/Tools/inc/INamed.h
+++ b/Core/Tools/inc/INamed.h
@@ -3,7 +3,7 @@
// BornAgain: simulate and fit scattering at grazing incidence
//
//! @file Tools/inc/INamed.h
-//! @brief Defines class INamed.
+//! @brief Defines the standard mix-in INamed.
//!
//! @homepage http://apps.jcns.fz-juelich.de/BornAgain
//! @license GNU General Public License v3 or higher (see COPYING)
diff --git a/Core/Tools/inc/OutputData.h b/Core/Tools/inc/OutputData.h
index cca0cdbbb85b16a49a2bd8dd65348e949acd0e40..e7a4558c8533336956d2861fd28e7f238b631051 100644
--- a/Core/Tools/inc/OutputData.h
+++ b/Core/Tools/inc/OutputData.h
@@ -17,23 +17,20 @@
#define OUTPUTDATA_H
#include "AxisDouble.h"
-//#include "Exceptions.h"
#include "Types.h"
#include "LLData.h"
#include "OutputDataIterator.h"
#include "SafePointerVector.h"
-//#include <string>
#include <sstream>
-//! Store data of any type in multi-dimensional space
+//! Store data of any type in multi-dimensional space.
template <class T> class OutputData
{
public:
OutputData();
~OutputData();
- //! make object clone
OutputData* clone() const;
void copyFrom(const OutputData<T> &x);
@@ -49,29 +46,19 @@ template <class T> class OutputData
// retrieve basic info
// ---------------------------------
- //! return number of dimensions
+ //! Return number of dimensions.
size_t getRank() const { return m_value_axes.size(); }
- //! return number of dimensions (same as above)
- size_t getNdimensions() const { return getRank(); }
-
- //! return total size of data buffer (product of bin number in every dimension)
+ //! Return total size of data buffer (product of bin number in every dimension).
size_t getAllocatedSize() const {
if (mp_ll_data) return mp_ll_data->getTotalSize();
return 0;
}
- //! return total size of data buffer (product of bin number in every dimension)
- //!
- //! copy of getAllocatedSize() for use in OutputDataIterator
- size_t size() const {
- return getAllocatedSize();
- }
-
- //! return all sizes of its axes
+ //! Return all sizes of its axes
std::vector<size_t> getAllSizes() const;
- //! return copy of raw data vector
+ //! Return copy of raw data vector
std::vector<T> getRawDataVector() const;
//! fill raw array with data
@@ -87,22 +74,22 @@ template <class T> class OutputData
friend class OutputDataIterator<T, OutputData<T> >;
friend class OutputDataIterator<const T, const OutputData<T> >;
- //! read/write iterator type
+ //! Read/write iterator type
typedef OutputDataIterator<T, OutputData<T> > iterator;
- //! read-only iterator type
+ //! Read-only iterator type
typedef OutputDataIterator<const T, const OutputData<T> > const_iterator;
- //! return a read/write iterator that points to the first element
+ //! Return a read/write iterator that points to the first element
iterator begin();
- //! return a read-only iterator that points to the first element
+ //! Return a read-only iterator that points to the first element
const_iterator begin() const;
- //! return a read/write iterator that points to the one past last element
+ //! Return a read/write iterator that points to the one past last element
iterator end() { return iterator(this, getAllocatedSize()); }
- //! return a read-only iterator that points to the one past last element
+ //! Return a read-only iterator that points to the one past last element
const_iterator end() const { return const_iterator(this, getAllocatedSize()); }
//! get mask that will be used by iterators
@@ -114,29 +101,29 @@ template <class T> class OutputData
//! add mask that will be used by iterators
void addMask(const Mask &mask);
- //! remove all masks
+ //! Remove all masks
void removeAllMasks();
// ---------------------------------
// coordinate and index functions
// ---------------------------------
- //! return vector of coordinates for given index
+ //! Return vector of coordinates for given index
std::vector<int> toCoordinates(size_t index) const;
- //! return coordinate for given index and axis number
+ //! Return coordinate for given index and axis number
int toCoordinate(size_t index, size_t i_selected_axis) const;
- //! return index for specified coordinates
+ //! Return index for specified coordinates
size_t toIndex(std::vector<int> coordinates) const;
- //! return index of axis with given name for given total index
+ //! Return index of axis with given name for given total index
size_t getIndexOfAxis(const std::string &axis_name, size_t total_index) const;
- //! return value of axis with given name at given index
+ //! Return value of axis with given name at given index
double getValueOfAxis(const std::string &axis_name, size_t index) const;
- //! return bin of axis with given name and index
+ //! Return bin of axis with given name and index
Bin1D getBinOfAxis(const std::string &axis_name, size_t index) const;
// ---------
@@ -173,7 +160,7 @@ template <class T> class OutputData
//! multiplication-assignment operator for two output data
const OutputData<T> &operator*=(const OutputData<T> &right);
- //! indexed accessor
+ //! indexed accessor
T &operator[](size_t index) {
if (mp_ll_data) return (*mp_ll_data)[index];
throw ClassInitializationException("Low-level data object was not yet initialized");
@@ -189,10 +176,10 @@ template <class T> class OutputData
// helpers
// --------
- //! return true if object have same dimensions
+ //! Return true if object have same dimensions
bool hasSameDimensions(const OutputData<T> &right) const;
- //! return true if object have same dimensions and shape of axises
+ //! Return true if object have same dimensions and shape of axises
bool hasSameShape(const OutputData<T> &right) const;
private:
//! disabled copy constructor and assignment operators
@@ -256,9 +243,12 @@ template <class T> void OutputData<T>::copyFrom(const OutputData<T> &other)
template <class T> void OutputData<T>::addAxis(const IAxis &new_axis)
{
- if( getAxis(new_axis.getName()) ) throw LogicErrorException("OutputData<T>::addAxis(const IAxis &new_axis) -> Error! Attempt to add axis with already existing name '"+ new_axis.getName()+std::string("'"));
- if (new_axis.getSize()>0)
- {
+ if( getAxis(new_axis.getName()) )
+ throw LogicErrorException(
+ "OutputData<T>::addAxis(const IAxis &new_axis) -> "
+ "Error! Attempt to add axis with already existing name '" +
+ new_axis.getName() + "'");
+ if (new_axis.getSize()>0) {
m_value_axes.push_back(new_axis.clone());
allocate();
}
@@ -279,10 +269,8 @@ template <class T> const IAxis *OutputData<T>::getAxis(size_t index) const
template <class T> const IAxis *OutputData<T>::getAxis(const std::string &label) const
{
- for (size_t i = 0; i < m_value_axes.size(); ++i)
- {
- if (m_value_axes[i]->getName() == label)
- {
+ for (size_t i = 0; i < m_value_axes.size(); ++i) {
+ if (m_value_axes[i]->getName() == label) {
return m_value_axes[i];
}
}
@@ -359,7 +347,9 @@ template <class T> void OutputData<T>::setMask(const Mask &mask)
template <class T> void OutputData<T>::addMask(const Mask &mask)
{
if (mask.mp_submask) {
- throw RuntimeErrorException("OutputData<T>::addMask() -> Error! One can only add single masks to OutputDataIterator at a time");
+ throw RuntimeErrorException(
+ "OutputData<T>::addMask() -> "
+ "Error! One can only add single masks to OutputDataIterator at a time");
}
Mask *p_old_mask = getMask();
mp_mask = mask.clone();
@@ -380,13 +370,15 @@ template<class T> std::vector<int> OutputData<T>::toCoordinates(size_t index) co
result.resize(mp_ll_data->getRank());
for (size_t i=0; i<mp_ll_data->getRank(); ++i)
{
- result[mp_ll_data->getRank()-1-i] = (int)(remainder % m_value_axes[mp_ll_data->getRank()-1-i]->getSize());
+ result[mp_ll_data->getRank()-1-i] =
+ (int)(remainder % m_value_axes[mp_ll_data->getRank()-1-i]->getSize());
remainder /= m_value_axes[mp_ll_data->getRank()-1-i]->getSize();
}
return result;
}
-template<class T> int OutputData<T>::toCoordinate(size_t index, size_t i_selected_axis) const
+template<class T> int OutputData<T>::toCoordinate(
+ size_t index, size_t i_selected_axis) const
{
size_t remainder(index);
for (size_t i=0; i<mp_ll_data->getRank(); ++i)
@@ -396,15 +388,16 @@ template<class T> int OutputData<T>::toCoordinate(size_t index, size_t i_selecte
if(i_selected_axis == i_axis ) return result;
remainder /= m_value_axes[i_axis]->getSize();
}
- throw LogicErrorException("OutputData<T>::toCoordinate() -> Error! No axis with given number");
+ throw LogicErrorException("OutputData<T>::toCoordinate() -> "
+ "Error! No axis with given number");
}
-
template <class T> size_t OutputData<T>::toIndex(std::vector<int> coordinates) const
{
- if (coordinates.size() != mp_ll_data->getRank()) {
- throw LogicErrorException("size_t OutputData<T>::toIndex() -> Error! Number of coordinates must match rank of data structure");
- }
+ if (coordinates.size() != mp_ll_data->getRank())
+ throw LogicErrorException(
+ "size_t OutputData<T>::toIndex() -> "
+ "Error! Number of coordinates must match rank of data structure");
size_t result = 0;
int step_size = 1;
for (size_t i=mp_ll_data->getRank(); i>0; --i)
@@ -415,7 +408,8 @@ template <class T> size_t OutputData<T>::toIndex(std::vector<int> coordinates) c
return result;
}
-template <class T> size_t OutputData<T>::getIndexOfAxis(const std::string &axis_name, size_t total_index) const
+template <class T> size_t OutputData<T>::getIndexOfAxis(
+ const std::string &axis_name, size_t total_index) const
{
std::vector<int> coordinates = toCoordinates(total_index);
for (size_t i=0; i<m_value_axes.size(); ++i) {
@@ -423,10 +417,11 @@ template <class T> size_t OutputData<T>::getIndexOfAxis(const std::string &axis_
return coordinates[i];
}
}
- throw LogicErrorException("OutputData<T>::getIndexOfAxis() -> Error! Axis with given name not found '"+std::string(axis_name)+std::string("'"));
+ throw LogicErrorException(
+ "OutputData<T>::getIndexOfAxis() -> "
+ "Error! Axis with given name not found '" + axis_name+"'");
}
-
template <class T>
double OutputData<T>::getValueOfAxis(const std::string &axis_name, size_t index) const
{
@@ -436,7 +431,9 @@ double OutputData<T>::getValueOfAxis(const std::string &axis_name, size_t index)
return (*m_value_axes[i])[axis_index];
}
}
- throw LogicErrorException("OutputData<T>::getValueOfAxis() -> Error! Axis with given name not found '"+std::string(axis_name)+std::string("'"));
+ throw LogicErrorException(
+ "OutputData<T>::getValueOfAxis() -> "
+ "Error! Axis with given name not found '" + axis_name + "'");
}
template <class T>
@@ -448,7 +445,9 @@ Bin1D OutputData<T>::getBinOfAxis(const std::string &axis_name, size_t index) co
return m_value_axes[i]->getBin(axis_index);
}
}
- throw LogicErrorException("OutputData<T>::getBinOfAxis() -> Error! Axis with given name not found '"+std::string(axis_name)+std::string("'"));
+ throw LogicErrorException(
+ "OutputData<T>::getBinOfAxis() -> "
+ "Error! Axis with given name not found '" + axis_name + "'");
}
template<class T>
@@ -543,21 +542,25 @@ template<class T> inline void OutputData<T>::setRawDataArray(const T *source)
}
-//! return true if object have same dimensions
-template<class T> inline bool OutputData<T>::hasSameDimensions(const OutputData<T> &right) const
+//! Return true if object have same dimensions
+template<class T> inline bool OutputData<T>::hasSameDimensions(
+ const OutputData<T> &right) const
{
if(!mp_ll_data || !right.mp_ll_data ) return false;
return HaveSameDimensions(*mp_ll_data, *right.mp_ll_data);
}
-//! return true if object have same dimensions and shape of axis
+//! Return true if object have same dimensions and shape of axis
template<class T>
bool OutputData<T>::hasSameShape(const OutputData<T> &right) const
{
if(!hasSameDimensions(right)) return false;
- if( (mp_ll_data->getRank() != m_value_axes.size()) || (right.mp_ll_data->getRank() != right.m_value_axes.size()) ) {
- throw LogicErrorException("OutputData<T>::hasSameShape() -> Panic! Inconsistent dimensions in LLData and axes");
+ if( (mp_ll_data->getRank() != m_value_axes.size()) ||
+ (right.mp_ll_data->getRank() != right.m_value_axes.size()) ) {
+ throw LogicErrorException(
+ "OutputData<T>::hasSameShape() -> "
+ "Panic! Inconsistent dimensions in LLData and axes");
}
for (size_t i=0; i<m_value_axes.size(); ++i) {
const IAxis *p_axis_left = m_value_axes[i];
diff --git a/Core/Tools/inc/OutputDataIterator.h b/Core/Tools/inc/OutputDataIterator.h
index 9318fb4a0daad0ef1032c90ed8234cf40a85674c..66fe55e104a27544f29c56ffc1bed3dfd00a6c6c 100644
--- a/Core/Tools/inc/OutputDataIterator.h
+++ b/Core/Tools/inc/OutputDataIterator.h
@@ -173,7 +173,7 @@ template<class TValue, class TContainer> OutputDataIterator<TValue, TContainer>
m_current_index = mp_mask->getNextIndex(m_current_index);
}
else {
- if (m_current_index<mp_output_data->size()) {
+ if (m_current_index<mp_output_data->getAllocatedSize()) {
++m_current_index;
}
}
@@ -203,7 +203,7 @@ template<class TValue, class TContainer> void OutputDataIterator<TValue, TContai
if (mp_mask != &mask) {
delete mp_mask;
mp_mask = mask.clone();
- mp_mask->setMaxIndex(mp_output_data->size());
+ mp_mask->setMaxIndex(mp_output_data->getAllocatedSize());
}
m_current_index = mp_mask->getFirstValidIndex();
}
@@ -216,7 +216,7 @@ template<class TValue, class TContainer> void OutputDataIterator<TValue, TContai
Mask *p_old_mask = getMask();
mp_mask = mask.clone();
mp_mask->mp_submask = p_old_mask;
- mp_mask->setMaxIndex(mp_output_data->size());
+ mp_mask->setMaxIndex(mp_output_data->getAllocatedSize());
m_current_index = mp_mask->getFirstValidIndex();
}
diff --git a/Core/Tools/inc/Units.h b/Core/Tools/inc/Units.h
index 0d699601024a211b0d4b65066422edc9183d5402..ace56137b9489784a7657fda3dd21cab6eeb7c6c 100644
--- a/Core/Tools/inc/Units.h
+++ b/Core/Tools/inc/Units.h
@@ -53,5 +53,4 @@ static const double PI_SQR = 9.86960440108935861883449099987615114f;
}
-
#endif // UNITS_H
diff --git a/Core/Tools/src/OutputDataFunctions.cpp b/Core/Tools/src/OutputDataFunctions.cpp
index 3a1618201028b99b60b477f5b59fbb0b35b5ca48..bf06f0873d6ef29bae5667f865313e8db9bafa70 100644
--- a/Core/Tools/src/OutputDataFunctions.cpp
+++ b/Core/Tools/src/OutputDataFunctions.cpp
@@ -212,7 +212,7 @@ OutputData<double>* OutputDataFunctions::sliceAccrossOneAxis(
const OutputData<double > &data, const std::string &fixed_axis_name,
double fixed_axis_value)
{
- if (data.getNdimensions() != 2) {
+ if (data.getRank() != 2) {
throw LogicErrorException("OutputDataFunctions::sliceAccrossOneAxis() -> Error! It was checked only with number of dimensions equal 2.");
}
if( !data.getAxis(fixed_axis_name) ) {
@@ -223,7 +223,7 @@ OutputData<double>* OutputDataFunctions::sliceAccrossOneAxis(
const IAxis *fixed_axis(0);
int fixed_axis_index(-1);
- for(size_t i_axis=0; i_axis<data.getNdimensions(); i_axis++) {
+ for(size_t i_axis=0; i_axis<data.getRank(); i_axis++) {
const IAxis *axis = data.getAxis(i_axis);
if( axis->getName() != fixed_axis_name ) {
sliced_data->addAxis(*axis);
@@ -261,7 +261,7 @@ OutputData<double>* OutputDataFunctions::selectRangeOnOneAxis(
const OutputData<double > &data, const std::string &selected_axis_name,
double axis_value1, double axis_value2)
{
- if (data.getNdimensions() != 2) {
+ if (data.getRank() != 2) {
throw LogicErrorException("OutputDataFunctions::selectRangeOnOneAxis() -> Error! It was checked only with number of dimensions equal 2.");
}
@@ -282,7 +282,7 @@ OutputData<double>* OutputDataFunctions::selectRangeOnOneAxis(
// preparing new data with modified axes
OutputData<double > *new_data = new OutputData<double >;
- for(size_t i_axis=0; i_axis<data.getNdimensions(); i_axis++) {
+ for(size_t i_axis=0; i_axis<data.getRank(); i_axis++) {
const IAxis *axis = data.getAxis(i_axis);
if( axis->getName() != selected_axis_name ) {
new_data->addAxis(*axis);
diff --git a/Tests/UnitTests/TestCore/SimulationTest.h b/Tests/UnitTests/TestCore/SimulationTest.h
index b9c8ab1a68715fd8a370e8b01cf188d5078c895e..765bda383d044abcce0d72eef8e58828a389fd39 100644
--- a/Tests/UnitTests/TestCore/SimulationTest.h
+++ b/Tests/UnitTests/TestCore/SimulationTest.h
@@ -36,12 +36,10 @@ SimulationTest::SimulationTest()
test_data.addAxis("phi_f", 10, 0., 10.);
test_data.addAxis("theta_f", 20, 0., 20.);
test_data.setAllTo(2.0);
-
}
SimulationTest::~SimulationTest()
{
-
}
@@ -49,8 +47,8 @@ TEST_F(SimulationTest, SimulationInitialState)
{
EXPECT_EQ( NULL, emptySimulation.getSample());
EXPECT_EQ( size_t(1), emptySimulation.getOutputData()->getAllocatedSize());
- EXPECT_EQ( size_t(0), emptySimulation.getOutputData()->getNdimensions());
- EXPECT_TRUE(emptySimulation.getOutputData()->getNdimensions() == emptySimulation.getInstrument().getDetectorDimension() );
+ EXPECT_EQ( size_t(0), emptySimulation.getOutputData()->getRank());
+ EXPECT_TRUE(emptySimulation.getOutputData()->getRank() == emptySimulation.getInstrument().getDetectorDimension() );
}
@@ -83,8 +81,8 @@ TEST_F(SimulationTest, SimulationInitialStateOfClone)
Simulation *emptyClonedSimulation = emptySimulation.clone();
EXPECT_EQ( NULL, emptyClonedSimulation->getSample());
EXPECT_EQ( size_t(1), emptyClonedSimulation->getOutputData()->getAllocatedSize());
- EXPECT_EQ( size_t(0), emptyClonedSimulation->getOutputData()->getNdimensions());
- EXPECT_TRUE(emptyClonedSimulation->getOutputData()->getNdimensions() == emptyClonedSimulation->getInstrument().getDetector().getDimension() );
+ EXPECT_EQ( size_t(0), emptyClonedSimulation->getOutputData()->getRank());
+ EXPECT_TRUE(emptyClonedSimulation->getOutputData()->getRank() == emptyClonedSimulation->getInstrument().getDetector().getDimension() );
EXPECT_EQ( double(1), emptyClonedSimulation->getInstrument().getIntensity());
delete emptyClonedSimulation;
}
@@ -107,5 +105,4 @@ TEST_F(SimulationTest, SimulationClone)
delete clonedSimulation;
}
-
#endif // SIMULATIONTEST_H