Codespell: fix typos in modules

src/modules/Clustering4D/Clustering4D.cpp

@@ -17,7 +17,7 @@ using namespace std;
 Clustering4D::Clustering4D(Configuration& config, std::shared_ptr<Detector> detector)
     : Module(config, detector), m_detector(detector) {
 
-    // Backwards compatibilty: also allow timing_cut to be used for time_cut_abs
+    // Backwards compatibility: also allow timing_cut to be used for time_cut_abs
     config_.setAlias("time_cut_abs", "timing_cut", true);
     config_.setAlias("neighbor_radius_row", "neighbour_radius_row", true);
     config_.setAlias("neighbor_radius_col", "neighbour_radius_col", true);
@@ -262,7 +262,7 @@ void Clustering4D::calculateClusterCentre(Cluster* cluster) {
 
     // Loop over all pixels
     for(auto& pixel : pixels) {
-        // If charge == 0 (use epsilon to avoid errors in floating-point arithmetics):
+        // If charge == 0 (use epsilon to avoid errors in floating-point arithmetic):
         if(pixel->charge() < std::numeric_limits<double>::epsilon()) {
             // apply arithmetic mean if a pixel has zero charge
             found_charge_zero = true;

src/modules/ClusteringSpatial/ClusteringSpatial.cpp

@@ -210,7 +210,7 @@ void ClusteringSpatial::calculateClusterCentre(Cluster* cluster) {
 
     // Loop over all pixels
     for(auto& pixel : pixels) {
-        // If charge == 0 (use epsilon to avoid errors in floating-point arithmetics):
+        // If charge == 0 (use epsilon to avoid errors in floating-point arithmetic):
         if(pixel->charge() < std::numeric_limits<double>::epsilon()) {
             // apply arithmetic mean if a pixel has zero charge
             found_charge_zero = true;

src/modules/DUTAssociation/DUTAssociation.cpp

@@ -17,7 +17,7 @@ using namespace std;
 DUTAssociation::DUTAssociation(Configuration& config, std::shared_ptr<Detector> detector)
     : Module(config, detector), m_detector(detector) {
 
-    // Backwards compatibilty: also allow timing_cut to be used for time_cut_abs and spatial_cut for spatial_cut_abs
+    // Backwards compatibility: also allow timing_cut to be used for time_cut_abs and spatial_cut for spatial_cut_abs
     config_.setAlias("time_cut_abs", "timing_cut", true);
     config_.setAlias("spatial_cut_abs", "spatial_cut", true);
 
@@ -111,7 +111,7 @@ StatusCode DUTAssociation::run(const std::shared_ptr<Clipboard>& clipboard) {
 
     // Loop over all tracks
     for(auto& track : tracks) {
-        LOG(TRACE) << "Proccessing track with model " << track->getType() << ", chi2 of " << track->getChi2();
+        LOG(TRACE) << "Processing track with model " << track->getType() << ", chi2 of " << track->getChi2();
         int assoc_cls_per_track = 0;
         auto min_distance = std::numeric_limits<double>::max();
 

src/modules/EventLoaderCLICpix2/CLICpix2/clicpix2_frameDecoder.cpp

@@ -79,7 +79,7 @@ void clicpix2_frameDecoder::decodeHeader(const clicpix2_frameDecoder::WORD_TYPE
 void clicpix2_frameDecoder::extractColumns(std::vector<clicpix2_frameDecoder::WORD_TYPE>::const_iterator& data,
                                            std::vector<clicpix2_frameDecoder::WORD_TYPE>::const_iterator dataEnd) {
     std::array<std::array<pixelReadout, 8>, CLICPIX2_ROW * 2>
-        pixels_dc; // stores results of the processed doube columns (up to 8 if compression is enabled)
+        pixels_dc; // stores results of the processed double columns (up to 8 if compression is enabled)
     std::array<size_t, 8> row_index = {
         {0, 0, 0, 0, 0, 0, 0, 0}}; // 8 independent (in case of compression) counters navigating through the <pixels_dc>
     std::array<int, 8> row_slice = {{CLICPIX2_PIXEL_SIZE - 1,
@@ -248,7 +248,7 @@ void clicpix2_frameDecoder::processDCbit(std::array<std::array<pixelReadout, 8>,
         if(dc_counter ==
            static_cast<int>(2 * (CLICPIX2_ROW * CLICPIX2_PIXEL_SIZE + CLICPIX2_ROW / CLICPIX2_SUPERPIXEL_SIZE) + 1)) {
             if(data ||                             // not empty double-column
-               !DCandSuperPixelCompressionEnabled) // or collumn compression disabled
+               !DCandSuperPixelCompressionEnabled) // or column compression disabled
                 dc_counter = 0;
             else { // empty double-column
                 for(auto i = 0; i < static_cast<int>(2 * CLICPIX2_ROW); ++i)

src/modules/EventLoaderCLICpix2/CLICpix2/clicpix2_frameDecoder.hpp

@@ -62,10 +62,10 @@ namespace caribou {
         // current RCR register value
         uint8_t rcr;
 
-        // firt column of the currently analyzed part of the package
+        // first column of the currently analyzed part of the package
         uint16_t firstColumn;
 
-        // Configutation
+        // Configuration
         bool pixelCompressionEnabled;
         bool DCandSuperPixelCompressionEnabled;
         std::map<size_t, std::map<size_t, bool>> counter_config; // [row][column]

src/modules/EventLoaderCLICpix2/EventLoaderCLICpix2.cpp

@@ -266,7 +266,7 @@ StatusCode EventLoaderCLICpix2::run(const std::shared_ptr<Clipboard>& clipboard)
                 tot = 1;
             }
 
-            // Time defaults ot rising shutter edge:
+            // Time defaults to rising shutter edge:
             double timestamp = shutterStartTime + (shutterStopTime - shutterStartTime) / 2;
 
             // Decide whether information is counter of ToA

src/modules/EventLoaderMuPixTelescope/EventLoaderMuPixTelescope.cpp

@@ -95,7 +95,7 @@ StatusCode EventLoaderMuPixTelescope::run(const std::shared_ptr<Clipboard>& clip
             double px_timestamp = 8 * static_cast<double>(((tf.timestamp() >> 2) & 0xFFFFF700) + h.timestamp_raw());
             auto p = std::make_shared<Pixel>(detectors.at(h.tag() / 4), h.column(), h.row(), 0, 0, px_timestamp);
 
-            // Select earlies and latest pixel:
+            // Select earliest and latest pixel:
             frame_start = (px_timestamp < frame_start ? px_timestamp : frame_start);
             frame_end = (px_timestamp > frame_end ? px_timestamp : frame_end);
 

src/modules/EventLoaderTimepix3/EventLoaderTimepix3.h

@@ -53,7 +53,7 @@ namespace corryvreckan {
         void loadCalibration(std::string path, char delim, std::vector<std::vector<float>>& dat);
         void maskPixels(std::string);
 
-        // configuration paramaters:
+        // configuration parameters:
         std::string m_inputDirectory;
 
         bool applyCalibration;

src/modules/FileReader/FileReader.cpp

@@ -72,7 +72,7 @@ template <typename T> static void add_creator(FileReader::ObjectCreatorMap& map)
             }
         }
 
-        // Store the ojects on the clipboard:
+        // Store the objects on the clipboard:
         if(detector.empty()) {
             clipboard->putData(std::move(data));
         } else {
@@ -190,7 +190,7 @@ void FileReader::initialize() {
             // Check tree structure and if object type matches name
             auto split_type = corryvreckan::split<std::string>(branch->GetClassName(), "<>");
             if(split_type.size() != 2 || split_type[1].size() <= 2) {
-                throw ModuleError("Tree is malformed and cannot be used for creating objetcs");
+                throw ModuleError("Tree is malformed and cannot be used for creating objects");
             }
             std::string class_name = split_type[1].substr(0, split_type[1].size() - 1);
             std::string corry_namespace = "corryvreckan::";

src/modules/ImproveReferenceTimestamp/ImproveReferenceTimestamp.cpp

@@ -33,7 +33,7 @@ void ImproveReferenceTimestamp::initialize() {
 
 StatusCode ImproveReferenceTimestamp::run(const std::shared_ptr<Clipboard>& clipboard) {
 
-    // Recieved triggers
+    // Received triggers
     std::vector<double> trigger_times;
 
     // Get trigger signals

src/modules/JSONWriter/JSONWriter.cpp

@@ -67,7 +67,7 @@ StatusCode JSONWriter::run(const std::shared_ptr<Clipboard>& clipboard) {
             auto class_name_full = corryvreckan::demangle(type_idx.name(), true);
             LOG(TRACE) << "Received objects of type \"" << class_name << "\"";
 
-            // Check if these objects hsould be read
+            // Check if these objects should be read
             if((!include_.empty() && include_.find(class_name) == include_.end()) ||
                (!exclude_.empty() && exclude_.find(class_name) != exclude_.end())) {
                 LOG(TRACE) << "Ignoring object " << corryvreckan::demangle(type_idx.name())

src/modules/MaskCreator/MaskCreator.cpp

@@ -34,7 +34,7 @@ MaskCreator::MaskCreator(Configuration& config, std::shared_ptr<Detector> detect
 
 void MaskCreator::initialize() {
 
-    // adjust per-axis bandwith for pixel pitch along each axis such that the
+    // adjust per-axis bandwidth for pixel pitch along each axis such that the
     // covered area is approximately circular in metric coordinates.
     double scale = std::hypot(m_detector->getPitch().X(), m_detector->getPitch().Y()) / M_SQRT2;
     m_bandwidthCol = static_cast<int>(std::ceil(bandwidth * scale / m_detector->getPitch().X()));

src/modules/TextWriter/TextWriter.cpp

@@ -65,7 +65,7 @@ StatusCode TextWriter::run(const std::shared_ptr<Clipboard>& clipboard) {
             auto class_name_full = corryvreckan::demangle(type_idx.name(), true);
             LOG(TRACE) << "Received objects of type \"" << class_name << "\"";
 
-            // Check if these objects hsould be read
+            // Check if these objects should be read
             if((!include_.empty() && include_.find(class_name) == include_.end()) ||
                (!exclude_.empty() && exclude_.find(class_name) != exclude_.end())) {
                 LOG(TRACE) << "Ignoring object " << corryvreckan::demangle(type_idx.name())

src/modules/Tracking4D/README.md

@@ -16,7 +16,7 @@ The DUT plane can be excluded from the track finding.
 * `time_cut_abs`: Specifies an absolute value for the maximum time difference allowed between clusters and a track for association to the track. Absolute and relative time cuts are mutually exclusive. No default value.
 * `spatial_cut_rel`: Factor by which the `spatial_resolution` in x and y of each detector plane will be multiplied. These calculated value are defining an ellipse which is then used as the maximum distance in the XY plane allowed between clusters and a track for association to the track. This allows the spatial cuts between different planes to be detector appropriate. By default, a relative spatial cut is applied. Absolute and relative spatial cuts are mutually exclusive. Defaults to `3.0`.
 * `spatial_cut_abs`: Specifies a set of absolute value (x and y) which defines an ellipse for the maximum spatial distance in the XY plane between clusters and a track for association to the track. Absolute and relative spatial cuts are mutually exclusive. No default value.
-* `min_hits_on_track`: Minium number of associated clusters needed to create a track, equivalent to the minimum number of planes required for each track. Default value is `6`.
+* `min_hits_on_track`: Minimum number of associated clusters needed to create a track, equivalent to the minimum number of planes required for each track. Default value is `6`.
 * `exclude_dut`: Boolean to choose if the DUT plane is included in the track finding. Default value is `true`.
 * `require_detectors`: Names of detectors which are required to have a cluster on the track. If a track does not have a cluster from all detectors listed here, it is rejected. If empty, no detector is required. Default is empty.
 * `timestamp_from`: Defines the detector which provides the track timestamp. This detector is by default added to `required_detector`. If empty, the average timestamp of all clusters on the track will be used. Empty by default.

src/modules/Tracking4D/Tracking4D.cpp

@@ -21,7 +21,7 @@ using namespace std;
 Tracking4D::Tracking4D(Configuration& config, std::vector<std::shared_ptr<Detector>> detectors)
     : Module(config, std::move(detectors)) {
 
-    // Backwards compatibilty: also allow timing_cut to be used for time_cut_abs and spatial_cut for spatial_cut_abs
+    // Backwards compatibility: also allow timing_cut to be used for time_cut_abs and spatial_cut for spatial_cut_abs
     config_.setAlias("time_cut_abs", "timing_cut", true);
     config_.setAlias("spatial_cut_abs", "spatial_cut", true);
 

src/modules/TrackingSpatial/TrackingSpatial.cpp

@@ -29,7 +29,7 @@ reconstruction with a mostly colinear beam.
 TrackingSpatial::TrackingSpatial(Configuration& config, std::vector<std::shared_ptr<Detector>> detectors)
     : Module(config, std::move(detectors)) {
 
-    // Backwards compatibilty: also allow spatial_cut to be used for spatial_cut_abs
+    // Backwards compatibility: also allow spatial_cut to be used for spatial_cut_abs
     config_.setAlias("spatial_cut_abs", "spatial_cut", true);
 
     config_.setDefault<size_t>("min_hits_on_track", 6);