Commit 8bd94bac authored by Håkan Wennlöf's avatar Håkan Wennlöf Committed by Simon Spannagel
Browse files

Improved [DopingProfileReader]

parent cde27218

src/core/Allpix.cpp

+1 −1
Original line number Diff line number Diff line
@@ -284,7 +284,7 @@ void Allpix::set_style() { 


    // Title offset: distance between given text and axis

    style->SetLabelOffset(0.01f, "xyz");

    style->SetTitleOffset(1.6f, "yz");

    style->SetTitleOffset(1.4f, "yz");

    style->SetTitleOffset(1.4f, "x");



    // Set font settings

src/core/geometry/DetectorField.tpp

+0 −1
Original line number Diff line number Diff line
@@ -130,7 +130,6 @@ namespace allpix { 
            // Calculate the field from the configured function:

            ret_val = function_(ROOT::Math::XYZPoint(x, y, z));

        }



        // Flip vector if necessary

        flip_vector_components(ret_val, replica_x % 2, replica_y % 2);

        return ret_val;

src/modules/DopingProfileReader/DopingProfileReaderModule.cpp

+142 −2
Original line number Diff line number Diff line
@@ -12,6 +12,8 @@ 
#include <string>

#include <utility>



#include <TH2F.h>



#include "core/utils/log.h"



using namespace allpix;
@@ -54,7 +56,7 @@ void DopingProfileReaderModule::initialize() { 
                "shifting doping concentration map by more than one pixel (offset > 1.0) is not allowed");

        }

        LOG(DEBUG) << "Doping concentration map starts with offset " << offset << " to pixel boundary";

        std::array<double, 2> field_offset{{offset.x(), offset.y()}};

        std::array<double, 2> field_offset{{model->getPixelSize().x() * offset.x(), model->getPixelSize().y() * offset.y()}};



        auto field_data = read_field(field_scale);

        detector_->setDopingProfileGrid(
@@ -99,6 +101,11 @@ void DopingProfileReaderModule::initialize() { 


        detector_->setDopingProfileFunction(function, type);

    }



    // Produce doping_concentration_histograms if needed

    if(config_.get<bool>("output_plots", false)) {

        create_output_plots();

    }

}



/**
@@ -113,7 +120,7 @@ FieldData<double> DopingProfileReaderModule::read_field(std::array<double, 2> fi 
        // Get field from file

        auto field_data = field_parser_.getByFileName(config_.getPath("file_name", true), "/cm/cm/cm");



        // Check if electric field matches chip

        // Check if doping concentration profile matches chip

        check_detector_match(field_data.getSize(), field_scale);



        LOG(INFO) << "Set doping concentration map with " << field_data.getDimensions().at(0) << "x"
@@ -130,6 +137,139 @@ FieldData<double> DopingProfileReaderModule::read_field(std::array<double, 2> fi 
    }

}



void DopingProfileReaderModule::create_output_plots() {

    LOG(TRACE) << "Creating output plots";



    auto steps = config_.get<size_t>("output_plots_steps", 500);

    auto project = config_.get<char>("output_plots_project", 'x');



    if(project != 'x' && project != 'y' && project != 'z') {

        throw InvalidValueError(config_, "output_plots_project", "can only project on x, y or z axis");

    }



    auto model = detector_->getModel();



    // If we need to plot a single pixel, we use size and position of the pixel at the origin

    auto single_pixel = config_.get<bool>("output_plots_single_pixel", true);

    auto center = (single_pixel ? ROOT::Math::XYZPoint(model->getPixelCenter(0, 0).x(), model->getPixelCenter(0, 0).y(), 0)

                                : model->getSensorCenter());

    auto size =

        (single_pixel

             ? ROOT::Math::XYZVector(model->getPixelSize().x(), model->getPixelSize().y(), model->getSensorSize().z())

             : model->getSensorSize());



    double z_min = center.z() - size.z() / 2.0;

    double z_max = center.z() + size.z() / 2.0;



    // Determine minimum and maximum index depending on projection axis

    double min1 = NAN, max1 = NAN;

    double min2 = NAN, max2 = NAN;

    if(project == 'x') {

        min1 = center.y() - size.y() / 2.0;

        max1 = center.y() + size.y() / 2.0;

        min2 = z_min;

        max2 = z_max;

    } else if(project == 'y') {

        min1 = center.x() - size.x() / 2.0;

        max1 = center.x() + size.x() / 2.0;

        min2 = z_min;

        max2 = z_max;

    } else {

        min1 = center.x() - size.x() / 2.0;

        max1 = center.x() + size.x() / 2.0;

        min2 = center.y() - size.y() / 2.0;

        max2 = center.y() + size.y() / 2.0;

    }



    // Create 2D doping_concentration_histograms

    auto* doping_concentration_histogram = new TH2F("doping_concentration",

                                                    "Doping concentration (1/cm^{3})",

                                                    static_cast<int>(steps),

                                                    min1,

                                                    max1,

                                                    static_cast<int>(steps),

                                                    min2,

                                                    max2);

    doping_concentration_histogram->SetOption("colz");



    // Create 1D doping_concentration_histogram

    auto* doping_concentration_histogram1D = new TH1F("concentration1D_z",

                                                      "Doping concentration along z;z (mm);Doping concentration (1/cm^{3})",

                                                      static_cast<int>(steps),

                                                      min2,

                                                      max2);

    doping_concentration_histogram1D->SetOption("hist");



    // Determine the coordinate to use for projection

    double x = 0, y = 0, z = 0;

    if(project == 'x') {

        x = center.x() - size.x() / 2.0 + config_.get<double>("output_plots_projection_percentage", 0.5000001) * size.x();

        doping_concentration_histogram->GetXaxis()->SetTitle("y (mm)");

        doping_concentration_histogram->GetYaxis()->SetTitle("z (mm)");

        doping_concentration_histogram->SetTitle(

            ("Doping concentration (1/cm^{3}) at x=" + std::to_string(x) + " mm").c_str());

    } else if(project == 'y') {

        y = center.y() - size.y() / 2.0 + config_.get<double>("output_plots_projection_percentage", 0.5000001) * size.y();

        doping_concentration_histogram->GetXaxis()->SetTitle("x (mm)");

        doping_concentration_histogram->GetYaxis()->SetTitle("z (mm)");

        doping_concentration_histogram->SetTitle(

            ("Doping concentration (1/cm^{3}) at y=" + std::to_string(y) + " mm").c_str());

    } else {

        z = z_min + config_.get<double>("output_plots_projection_percentage", 0.5000001) * size.z();

        doping_concentration_histogram->GetXaxis()->SetTitle("x (mm)");

        doping_concentration_histogram->GetYaxis()->SetTitle("y (mm)");

        doping_concentration_histogram->SetTitle(

            ("Doping concentration (1/cm^{3}) at z=" + std::to_string(z) + " mm").c_str());

    }



    // set z axis tile

    doping_concentration_histogram->GetZaxis()->SetTitle("Concentration");



    // Find the doping concentration at every index, scan axes in local coordinates!

    for(size_t j = 0; j < steps; ++j) {

        if(project == 'x') {

            y = center.y() - size.y() / 2.0 + ((static_cast<double>(j) + 0.5) / static_cast<double>(steps)) * size.y();

        } else if(project == 'y') {

            x = center.x() - size.x() / 2.0 + ((static_cast<double>(j) + 0.5) / static_cast<double>(steps)) * size.x();

        } else {

            x = center.x() - size.x() / 2.0 + ((static_cast<double>(j) + 0.5) / static_cast<double>(steps)) * size.x();

        }

        for(size_t k = 0; k < steps; ++k) {

            if(project == 'x') {

                z = z_min + ((static_cast<double>(k) + 0.5) / static_cast<double>(steps)) * size.z();

            } else if(project == 'y') {

                z = z_min + ((static_cast<double>(k) + 0.5) / static_cast<double>(steps)) * size.z();

            } else {

                y = center.y() - size.y() / 2.0 + ((static_cast<double>(k) + 0.5) / static_cast<double>(steps)) * size.y();

            }



            // Get doping concentration from detector - directly convert to double

            // and 1/cm3 to fill root doping_concentration_histograms

            auto concentration = static_cast<double>(

                Units::convert(detector_->getDopingConcentration(ROOT::Math::XYZPoint(x, y, z)), "/cm/cm/cm"));

            // Fill the main doping_concentration_histogram

            if(project == 'x') {

                doping_concentration_histogram->Fill(y, z, concentration);

            } else if(project == 'y') {

                doping_concentration_histogram->Fill(x, z, concentration);

            } else {

                doping_concentration_histogram->Fill(x, y, concentration);

            }

            // Fill the 1d doping_concentration_histogram, in the middle of the range

            if(j == steps / 2) {

                doping_concentration_histogram1D->Fill(z, concentration);

            }

        }

    }



    // Write the doping_concentration_histograms to module file

    doping_concentration_histogram->Write();

    doping_concentration_histogram1D->Write();



    LOG(DEBUG) << "Maximum doping concentration within plotted cut: " << doping_concentration_histogram->GetMaximum()

               << " 1/cm3";

}



/**

 * @brief Check if the detector matches the file header

 */

src/modules/DopingProfileReader/DopingProfileReaderModule.hpp

+5 −0
Original line number Diff line number Diff line
@@ -56,6 +56,11 @@ namespace allpix { 
        FieldData<double> read_field(std::array<double, 2> field_scale);

        static FieldParser<double> field_parser_;



        /**

         * @brief Create output plots of the doping profile

         */

        void create_output_plots();



        /**

         * @brief Compare the dimensions of the detector with the field, print warnings

         * @param dimensions Dimensions of the field read from file

src/modules/DopingProfileReader/README.md

+7 −0
Original line number Diff line number Diff line
@@ -27,6 +27,13 @@ Only used if the *model* parameter has the value **mesh**. 
* `doping_depth` : Thickness of the doping profile region. The doping profile is extrapolated in the region below the `doping_depth`.

Only used if the *model* parameter has the value **mesh**.



### Plotting parameters

* `output_plots` : Determines if output plots should be generated. Disabled by default.

* `output_plots_steps` : Number of bins in both x- and y-direction in the 2D histogram used to plot the doping concentration in the detectors. Only used if `output_plots` is enabled.

* `output_plots_project` : Axis to project the doping concentration on to create the 2D histogram. Either **x**, **y** or **z**. Only used if `output_plots` is enabled. Default is **x** (i.e. producing a slice of the **yz** plane).

* `output_plots_projection_percentage` : Percentage on the projection axis to plot the doping concentration profile. For example if *output_plots_project* is **x** and this parameter is set to 0.5, the profile is plotted in the **yz** plane at the x-coordinate in the middle of the sensor. Default is 0.5.

* `output_plots_single_pixel`: Determines if the whole sensor has to be plotted or only a single pixel. Defaults to true (plotting a single pixel).



### Usage

```toml

[DopingProfileReader]