Corr: add DataUtils

Device/Data/DataUtils.cpp

+//  ************************************************************************************************
+//
+//  BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @file      Device/Data/DataUtils.cpp
+//! @brief     Implements namespace DataUtils.
+//!
+//! @homepage  http://www.bornagainproject.org
+//! @license   GNU General Public License v3 or higher (see COPYING)
+//! @copyright Forschungszentrum Jülich GmbH 2018
+//! @authors   Scientific Computing Group at MLZ (see CITATION, AUTHORS)
+//
+//  ************************************************************************************************
+
+#include "Device/Data/DataUtils.h"
+#include "Base/Math/FourierTransform.h"
+#include "Base/Math/Numeric.h"
+#include <iostream>
+
+namespace {
+
+std::vector<std::vector<double>> FT2DArray(const std::vector<std::vector<double>>& signal) {
+    FourierTransform ft;
+    std::vector<std::vector<double>> ret;
+    ft.fft(signal, ret);
+    ft.fftshift(ret); // low frequency to center of array
+    return ret;
+}
+
+} // namespace
+
+//! Returns relative difference between two data sets sum(dat[i] - ref[i])/ref[i]).
+double DataUtils::getRelativeDifference(const OutputData<double>& dat,
+                                        const OutputData<double>& ref) {
+    if (!dat.hasSameDimensions(ref))
+        throw std::runtime_error("OutputData dimension differs from reference");
+
+    double diff = 0.0;
+    for (size_t i = 0; i < dat.getAllocatedSize(); ++i)
+        diff += Numeric::GetRelativeDifference(dat[i], ref[i]);
+    diff /= dat.getAllocatedSize();
+    if (std::isnan(diff))
+        throw std::runtime_error("diff=NaN!");
+    return diff;
+}
+
+//! Returns true is relative difference is below threshold; prints informative output
+bool DataUtils::checkRelativeDifference(const OutputData<double>& dat,
+                                        const OutputData<double>& ref, const double threshold) {
+    const double diff = getRelativeDifference(dat, ref);
+    if (diff > threshold) {
+        std::cerr << "FAILED: relative deviation of dat from ref is " << diff
+                  << ", above given threshold " << threshold << "\n";
+        return false;
+    }
+    if (diff)
+        std::cerr << "- OK: relative deviation of dat from ref is " << diff
+                  << ", within given threshold " << threshold << "\n";
+    else
+        std::cout << "- OK: dat = ref\n";
+    return true;
+}
+
+std::unique_ptr<OutputData<double>>
+DataUtils::createRelativeDifferenceData(const OutputData<double>& data,
+                                        const OutputData<double>& reference) {
+    if (!data.hasSameDimensions(reference))
+        throw std::runtime_error("DataUtils::createRelativeDifferenceData() -> "
+                                 "Error. Different dimensions of data and reference.");
+    std::unique_ptr<OutputData<double>> result(reference.clone());
+    for (size_t i = 0; i < result->getAllocatedSize(); ++i)
+        (*result)[i] = Numeric::GetRelativeDifference(data[i], reference[i]);
+    return result;
+}
+
+std::unique_ptr<OutputData<double>>
+DataUtils::createRearrangedDataSet(const OutputData<double>& data, int n) {
+    if (data.rank() != 2)
+        throw std::runtime_error("DataUtils::rotateDataByN90Deg()"
+                                 " -> Error! Works only on two-dimensional data");
+    n = (4 + n % 4) % 4;
+    if (n == 0)
+        return std::unique_ptr<OutputData<double>>(data.clone());
+    std::unique_ptr<OutputData<double>> output(new OutputData<double>());
+
+    // swapping axes if necessary
+    const IAxis& x_axis = data.axis(0);
+    const IAxis& y_axis = data.axis(1);
+    output->addAxis(n == 2 ? x_axis : y_axis);
+    output->addAxis(n == 2 ? y_axis : x_axis);
+
+    // creating index mapping
+    std::function<void(std::vector<int>&)> index_mapping;
+    if (n == 2) {
+        const int end_bin_x = static_cast<int>(x_axis.size()) - 1;
+        const int end_bin_y = static_cast<int>(y_axis.size()) - 1;
+        index_mapping = [end_bin_x, end_bin_y](std::vector<int>& inds) {
+            inds[0] = end_bin_x - inds[0];
+            inds[1] = end_bin_y - inds[1];
+        };
+    } else {
+        const size_t rev_axis_i = n % 3;
+        const size_t end_bin = data.axis(rev_axis_i).size() - 1;
+        index_mapping = [rev_axis_i, end_bin](std::vector<int>& inds) {
+            const int tm_index = inds[rev_axis_i];
+            inds[rev_axis_i] = inds[rev_axis_i ^ 1];
+            inds[rev_axis_i ^ 1] = static_cast<int>(end_bin) - tm_index;
+        };
+    }
+
+    for (size_t index = 0, size = data.getAllocatedSize(); index < size; ++index) {
+        std::vector<int> axis_inds = data.getAxesBinIndices(index);
+        index_mapping(axis_inds);
+        size_t output_index = output->toGlobalIndex(
+            {static_cast<unsigned>(axis_inds[0]), static_cast<unsigned>(axis_inds[1])});
+        (*output)[output_index] = data[index];
+    }
+    return output;
+}
+
+std::unique_ptr<OutputData<double>>
+DataUtils::createClippedDataSet(const OutputData<double>& origin, double x1, double y1, double x2,
+                                double y2) {
+    if (origin.rank() != 2)
+        throw std::runtime_error("DataUtils::createClippedData()"
+                                 " -> Error! Works only on two-dimensional data");
+
+    std::unique_ptr<OutputData<double>> result(new OutputData<double>);
+    for (size_t i_axis = 0; i_axis < origin.rank(); i_axis++) {
+        const IAxis& axis = origin.axis(i_axis);
+        IAxis* new_axis;
+        if (i_axis == 0)
+            new_axis = axis.createClippedAxis(x1, x2);
+        else
+            new_axis = axis.createClippedAxis(y1, y2);
+        result->addAxis(*new_axis);
+        delete new_axis;
+    }
+    result->setAllTo(0.0);
+
+    OutputData<double>::const_iterator it_origin = origin.begin();
+    OutputData<double>::iterator it_result = result->begin();
+    while (it_origin != origin.end()) {
+        double x = origin.getAxisValue(it_origin.getIndex(), 0);
+        double y = origin.getAxisValue(it_origin.getIndex(), 1);
+        if (result->axis(0).contains(x) && result->axis(1).contains(y)) {
+            *it_result = *it_origin;
+            ++it_result;
+        }
+        ++it_origin;
+    }
+
+    return result;
+}
+
+// For axis FixedBinAxis("axis", 8, -5.0, 3.0) the coordinate x=-4.5 (center of bin #0) will
+// be converted into 0.5 (which is a bin center expressed in bin fraction coordinates).
+// The coordinate -5.0 (outside of axis definition) will be converted to -0.5
+// (center of non-existing bin #-1).
+// Used for Mask conversion.
+
+double DataUtils::coordinateToBinf(double coordinate, const IAxis& axis) {
+    size_t index = axis.findClosestIndex(coordinate);
+    Bin1D bin = axis.bin(index);
+    double f = (coordinate - bin.m_lower) / bin.binSize();
+    return static_cast<double>(index) + f;
+}
+
+double DataUtils::coordinateFromBinf(double value, const IAxis& axis) {
+    int index = static_cast<int>(value);
+
+    double result(0);
+    if (index < 0) {
+        Bin1D bin = axis.bin(0);
+        result = bin.m_lower + value * bin.binSize();
+    } else if (index >= static_cast<int>(axis.size())) {
+        Bin1D bin = axis.bin(axis.size() - 1);
+        result = bin.m_upper + (value - axis.size()) * bin.binSize();
+    } else {
+        Bin1D bin = axis.bin(static_cast<size_t>(index));
+        result = bin.m_lower + (value - static_cast<double>(index)) * bin.binSize();
+    }
+
+    return result;
+}
+
+void DataUtils::coordinateToBinf(double& x, double& y, const OutputData<double>& data) {
+    x = coordinateToBinf(x, data.axis(0));
+    y = coordinateToBinf(y, data.axis(1));
+}
+
+void DataUtils::coordinateFromBinf(double& x, double& y, const OutputData<double>& data) {
+    x = coordinateFromBinf(x, data.axis(0));
+    y = coordinateFromBinf(y, data.axis(1));
+}
+
+std::vector<std::vector<double>>
+DataUtils::create2DArrayfromOutputData(const OutputData<double>& data) {
+    if (data.rank() != 2)
+        throw std::runtime_error("DataUtils::create2DArrayfromOutputData() -> "
+                                 "Error! Works only on two-dimensional data");
+
+    std::vector<std::vector<double>> array_2d;
+    std::vector<double> row_vec; // row vector for constructing each row of 2D array
+
+    size_t nrows = data.axis(0).size();
+    size_t ncols = data.axis(1).size();
+
+    size_t it = 0; // iterator of 'data'
+    for (size_t row = 0; row < nrows; row++) {
+        row_vec.clear();
+        for (size_t col = 0; col < ncols; col++) {
+            row_vec.push_back(data[it]);
+            it++;
+        }
+        array_2d.push_back(row_vec);
+    }
+
+    return array_2d;
+}
+
+std::unique_ptr<OutputData<double>>
+DataUtils::createOutputDatafrom2DArray(const std::vector<std::vector<double>>& array_2d) {
+    std::unique_ptr<OutputData<double>> result(new OutputData<double>);
+    size_t nrows = array_2d.size();
+    size_t ncols = array_2d[0].size();
+
+    result->addAxis("x", nrows, 0.0, double(nrows));
+    result->addAxis("y", ncols, 0.0, double(ncols));
+    std::vector<unsigned> axes_indices(2);
+    for (unsigned row = 0; row < nrows; row++) {
+        for (unsigned col = 0; col < ncols; col++) {
+            axes_indices[0] = row;
+            axes_indices[1] = col;
+            size_t global_index = result->toGlobalIndex(axes_indices);
+            (*result)[global_index] = array_2d[row][col];
+        }
+    }
+
+    return result;
+}
+
+std::unique_ptr<OutputData<double>> DataUtils::createFFT(const OutputData<double>& data) {
+    auto array_2d = DataUtils::create2DArrayfromOutputData(data);
+    auto fft_array_2d = FT2DArray(array_2d);
+    return DataUtils::createOutputDatafrom2DArray(fft_array_2d);
+}

Device/Data/DataUtils.h

+//  ************************************************************************************************
+//
+//  BornAgain: simulate and fit scattering at grazing incidence
+//
+//! @file      Device/Data/DataUtils.h
+//! @brief     Defines namespace DataUtils.
+//!
+//! @homepage  http://www.bornagainproject.org
+//! @license   GNU General Public License v3 or higher (see COPYING)
+//! @copyright Forschungszentrum Jülich GmbH 2018
+//! @authors   Scientific Computing Group at MLZ (see CITATION, AUTHORS)
+//
+//  ************************************************************************************************
+
+#ifndef BORNAGAIN_DEVICE_DATA_DATAUTILS_H
+#define BORNAGAIN_DEVICE_DATA_DATAUTILS_H
+
+#include "Device/Data/OutputData.h"
+#include <memory>
+
+namespace DataUtils {
+
+//! Returns true is relative difference is below threshold; prints informative output
+bool checkRelativeDifference(const OutputData<double>& dat, const OutputData<double>& ref,
+                             const double threshold);
+
+//! Transforms coordinate on axis into the bin-fraction-coordinate.
+double coordinateToBinf(double coordinate, const IAxis& axis);
+
+//! Transforms bin-fraction-coordinate into axis coordinate.
+double coordinateFromBinf(double value, const IAxis& axis);
+
+//! Transforms x,y coordinate from OutputData axes coordinates to bin-fraction-coordinates.
+void coordinateToBinf(double& x, double& y, const OutputData<double>& data);
+
+//! Transforms x,y coordinate from bin-fraction-coordinates to OutputData's axes coordinates.
+void coordinateFromBinf(double& x, double& y, const OutputData<double>& data);
+
+//! Creates a vector of vectors of double (2D Array) from OutputData.
+std::vector<std::vector<double>> create2DArrayfromOutputData(const OutputData<double>& data);
+
+#ifndef SWIG
+
+//! Returns relative difference between two data sets sum(dat[i] - ref[i])/ref[i]).
+double getRelativeDifference(const OutputData<double>& dat, const OutputData<double>& ref);
+
+std::unique_ptr<OutputData<double>>
+createRelativeDifferenceData(const OutputData<double>& data, const OutputData<double>& reference);
+
+//! Returns new object with input data rotated by
+//! n*90 deg counterclockwise (n > 0) or clockwise (n < 0)
+//! Axes are swapped if the data is effectively rotated by 90 or 270 degrees
+//! Applicable to 2D arrays only
+std::unique_ptr<OutputData<double>> createRearrangedDataSet(const OutputData<double>& data, int n);
+
+//! Returns new IntensityData objects which axes clipped to represent the specified rectangle.
+std::unique_ptr<OutputData<double>>
+createClippedDataSet(const OutputData<double>& origin, double x1, double y1, double x2, double y2);
+
+//! Creates OutputData from a 2D Array.
+std::unique_ptr<OutputData<double>>
+createOutputDatafrom2DArray(const std::vector<std::vector<double>>& array_2d);
+
+//! Creates Fourier Transform (OutputData format) of intensity map (OutputData format).
+std::unique_ptr<OutputData<double>> createFFT(const OutputData<double>& data);
+
+#endif // USER_API
+
+} // namespace DataUtils
+
+#endif // BORNAGAIN_DEVICE_DATA_DATAUTILS_H