Merge branch 'fieldAndDopingPlotting' into 'master' (5602a16e) · Commits · XRFLab109 / Allpix Squared

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

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		@@ -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

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		@@ -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]