]> sigrok.org Git - pulseview.git/blobdiff - pv/data/decodesignal.cpp
Session: Fix issue #67 by improving error handling
[pulseview.git] / pv / data / decodesignal.cpp
index f1995dcae4f48c03b65f5efb6646fdf9dd24368f..9c695a1baa8247dfa09be12c8cdd9b2ee5956d34 100644 (file)
  * along with this program; if not, see <http://www.gnu.org/licenses/>.
  */
 
+#include "config.h"
+
+#include <cstring>
+#include <forward_list>
 #include <limits>
 
 #include <QDebug>
+#if QT_VERSION >= QT_VERSION_CHECK(6, 0, 0)
+#include <QRegularExpression>
+#endif
 
 #include "logic.hpp"
 #include "logicsegment.hpp"
 #include "decodesignal.hpp"
 #include "signaldata.hpp"
 
-#include <pv/binding/decoder.hpp>
 #include <pv/data/decode/decoder.hpp>
 #include <pv/data/decode/row.hpp>
 #include <pv/globalsettings.hpp>
 #include <pv/session.hpp>
 
+using std::dynamic_pointer_cast;
 using std::lock_guard;
-using std::make_pair;
 using std::make_shared;
 using std::min;
 using std::out_of_range;
 using std::shared_ptr;
 using std::unique_lock;
-using pv::data::decode::Annotation;
-using pv::data::decode::Decoder;
-using pv::data::decode::Row;
+using pv::data::decode::AnnotationClass;
+using pv::data::decode::DecodeChannel;
 
 namespace pv {
 namespace data {
@@ -68,29 +73,54 @@ DecodeSignal::~DecodeSignal()
        reset_decode(true);
 }
 
+void DecodeSignal::set_name(QString name)
+{
+       SignalBase::set_name(name);
+
+       update_output_signals();
+}
+
+void DecodeSignal::set_color(QColor color)
+{
+       SignalBase::set_color(color);
+
+       update_output_signals();
+}
+
 const vector< shared_ptr<Decoder> >& DecodeSignal::decoder_stack() const
 {
        return stack_;
 }
 
-void DecodeSignal::stack_decoder(const srd_decoder *decoder)
+void DecodeSignal::stack_decoder(const srd_decoder *decoder, bool restart_decode)
 {
        assert(decoder);
-       const shared_ptr<Decoder> dec = make_shared<decode::Decoder>(decoder);
 
-       stack_.push_back(dec);
+       // Set name if this decoder is the first in the list or the name is unchanged
+       const srd_decoder* prev_dec = stack_.empty() ? nullptr : stack_.back()->get_srd_decoder();
+       const QString prev_dec_name = prev_dec ? QString::fromUtf8(prev_dec->name) : QString();
 
-       // Set name if this decoder is the first in the list
-       if (stack_.size() == 1)
+       if ((stack_.empty()) || ((stack_.size() > 0) && (name() == prev_dec_name)))
                set_name(QString::fromUtf8(decoder->name));
 
+       const shared_ptr<Decoder> dec = make_shared<Decoder>(decoder, stack_.size());
+       stack_.push_back(dec);
+
+       connect(dec.get(), SIGNAL(annotation_visibility_changed()),
+               this, SLOT(on_annotation_visibility_changed()));
+
        // Include the newly created decode channels in the channel lists
        update_channel_list();
 
        stack_config_changed_ = true;
        auto_assign_signals(dec);
        commit_decoder_channels();
-       begin_decode();
+       update_output_signals();
+
+       decoder_stacked((void*)dec.get());
+
+       if (restart_decode)
+               begin_decode();
 }
 
 void DecodeSignal::remove_decoder(int index)
@@ -99,9 +129,12 @@ void DecodeSignal::remove_decoder(int index)
        assert(index < (int)stack_.size());
 
        // Find the decoder in the stack
-       auto iter = stack_.begin();
-       for (int i = 0; i < index; i++, iter++)
-               assert(iter != stack_.end());
+       auto iter = stack_.begin() + index;
+       assert(iter != stack_.end());
+
+       shared_ptr<Decoder> dec = *iter;
+
+       decoder_removed(dec.get());
 
        // Delete the element
        stack_.erase(iter);
@@ -123,8 +156,8 @@ bool DecodeSignal::toggle_decoder_visibility(int index)
        // Toggle decoder visibility
        bool state = false;
        if (dec) {
-               state = !dec->shown();
-               dec->show(state);
+               state = !dec->visible();
+               dec->set_visible(state);
        }
 
        return state;
@@ -132,6 +165,8 @@ bool DecodeSignal::toggle_decoder_visibility(int index)
 
 void DecodeSignal::reset_decode(bool shutting_down)
 {
+       resume_decode();  // Make sure the decode thread isn't blocked by pausing
+
        if (stack_config_changed_ || shutting_down)
                stop_srd_session();
        else
@@ -149,15 +184,18 @@ void DecodeSignal::reset_decode(bool shutting_down)
                logic_mux_thread_.join();
        }
 
-       class_rows_.clear();
        current_segment_id_ = 0;
        segments_.clear();
 
+       for (const shared_ptr<decode::Decoder>& dec : stack_)
+               if (dec->has_logic_output())
+                       output_logic_[dec->get_srd_decoder()]->clear();
+
        logic_mux_data_.reset();
        logic_mux_data_invalid_ = true;
 
        if (!error_message_.isEmpty()) {
-               error_message_ = QString();
+               error_message_.clear();
                // TODO Emulate noquote()
                qDebug().nospace() << name() << ": Error cleared";
        }
@@ -196,38 +234,18 @@ void DecodeSignal::begin_decode()
        // Make sure that all assigned channels still provide logic data
        // (can happen when a converted signal was assigned but the
        // conversion removed in the meanwhile)
-       for (data::DecodeChannel &ch : channels_)
+       for (decode::DecodeChannel& ch : channels_)
                if (ch.assigned_signal && !(ch.assigned_signal->logic_data() != nullptr))
                        ch.assigned_signal = nullptr;
 
        // Check that all decoders have the required channels
-       for (const shared_ptr<decode::Decoder> &dec : stack_)
+       for (const shared_ptr<Decoder>& dec : stack_)
                if (!dec->have_required_channels()) {
                        set_error_message(tr("One or more required channels "
                                "have not been specified"));
                        return;
                }
 
-       // Map out all the annotation classes
-       for (const shared_ptr<decode::Decoder> &dec : stack_) {
-               assert(dec);
-               const srd_decoder *const decc = dec->decoder();
-               assert(dec->decoder());
-
-               for (const GSList *l = decc->annotation_rows; l; l = l->next) {
-                       const srd_decoder_annotation_row *const ann_row =
-                               (srd_decoder_annotation_row *)l->data;
-                       assert(ann_row);
-
-                       const Row row(decc, ann_row);
-
-                       for (const GSList *ll = ann_row->ann_classes;
-                               ll; ll = ll->next)
-                               class_rows_[make_pair(decc,
-                                       GPOINTER_TO_INT(ll->data))] = row;
-               }
-       }
-
        // Free the logic data and its segment(s) if it needs to be updated
        if (logic_mux_data_invalid_)
                logic_mux_data_.reset();
@@ -238,13 +256,8 @@ void DecodeSignal::begin_decode()
                logic_mux_data_ = make_shared<Logic>(ch_count);
        }
 
-       // Receive notifications when new sample data is available
-       connect_input_notifiers();
-
-       if (get_input_segment_count() == 0) {
+       if (get_input_segment_count() == 0)
                set_error_message(tr("No input data"));
-               return;
-       }
 
        // Make sure the logic output data is complete and up-to-date
        logic_mux_interrupt_ = false;
@@ -255,13 +268,26 @@ void DecodeSignal::begin_decode()
        decode_thread_ = std::thread(&DecodeSignal::decode_proc, this);
 }
 
-QString DecodeSignal::error_message() const
+void DecodeSignal::pause_decode()
 {
-       lock_guard<mutex> lock(output_mutex_);
-       return error_message_;
+       decode_paused_ = true;
 }
 
-const vector<data::DecodeChannel> DecodeSignal::get_channels() const
+void DecodeSignal::resume_decode()
+{
+       // Manual unlocking is done before notifying, to avoid waking up the
+       // waiting thread only to block again (see notify_one for details)
+       decode_pause_mutex_.unlock();
+       decode_pause_cond_.notify_one();
+       decode_paused_ = false;
+}
+
+bool DecodeSignal::is_paused() const
+{
+       return decode_paused_;
+}
+
+const vector<decode::DecodeChannel> DecodeSignal::get_channels() const
 {
        return channels_;
 }
@@ -270,8 +296,11 @@ void DecodeSignal::auto_assign_signals(const shared_ptr<Decoder> dec)
 {
        bool new_assignment = false;
 
+       // Disconnect all input signal notifications so we don't have duplicate connections
+       disconnect_input_notifiers();
+
        // Try to auto-select channels that don't have signals assigned yet
-       for (data::DecodeChannel &ch : channels_) {
+       for (decode::DecodeChannel& ch : channels_) {
                // If a decoder is given, auto-assign only its channels
                if (dec && (ch.decoder_ != dec))
                        continue;
@@ -279,19 +308,55 @@ void DecodeSignal::auto_assign_signals(const shared_ptr<Decoder> dec)
                if (ch.assigned_signal)
                        continue;
 
-               for (shared_ptr<data::SignalBase> s : session_.signalbases()) {
-                       const QString ch_name = ch.name.toLower();
-                       const QString s_name = s->name().toLower();
+               QString ch_name = ch.name.toLower();
+#if QT_VERSION >= QT_VERSION_CHECK(6, 0, 0)
+               ch_name = ch_name.replace(QRegularExpression("[-_.]"), " ");
+#else
+               ch_name = ch_name.replace(QRegExp("[-_.]"), " ");
+#endif
+
+               shared_ptr<data::SignalBase> match;
+               for (const shared_ptr<data::SignalBase>& s : session_.signalbases()) {
+                       if (!s->enabled())
+                               continue;
+
+                       QString s_name = s->name().toLower();
+#if QT_VERSION >= QT_VERSION_CHECK(6, 0, 0)
+                       s_name = s_name.replace(QRegularExpression("[-_.]"), " ");
+#else
+                       s_name = s_name.replace(QRegExp("[-_.]"), " ");
+#endif
 
                        if (s->logic_data() &&
                                ((ch_name.contains(s_name)) || (s_name.contains(ch_name)))) {
-                               ch.assigned_signal = s.get();
-                               new_assignment = true;
+                               if (!match)
+                                       match = s;
+                               else {
+                                       // Only replace an existing match if it matches more characters
+                                       int old_unmatched = ch_name.length() - match->name().length();
+                                       int new_unmatched = ch_name.length() - s->name().length();
+                                       if (abs(new_unmatched) < abs(old_unmatched))
+                                               match = s;
+                               }
                        }
                }
+
+               // Prevent using a signal more than once as D1 would match e.g. D1 and D10
+               bool signal_not_already_used = true;
+               for (decode::DecodeChannel& ch : channels_)
+                       if (ch.assigned_signal && (ch.assigned_signal == match))
+                               signal_not_already_used = false;
+
+               if (match && signal_not_already_used) {
+                       ch.assigned_signal = match;
+                       new_assignment = true;
+               }
        }
 
        if (new_assignment) {
+               // Receive notifications when new sample data is available
+               connect_input_notifiers();
+
                logic_mux_data_invalid_ = true;
                stack_config_changed_ = true;
                commit_decoder_channels();
@@ -299,14 +364,20 @@ void DecodeSignal::auto_assign_signals(const shared_ptr<Decoder> dec)
        }
 }
 
-void DecodeSignal::assign_signal(const uint16_t channel_id, const SignalBase *signal)
+void DecodeSignal::assign_signal(const uint16_t channel_id, shared_ptr<const SignalBase> signal)
 {
-       for (data::DecodeChannel &ch : channels_)
+       // Disconnect all input signal notifications so we don't have duplicate connections
+       disconnect_input_notifiers();
+
+       for (decode::DecodeChannel& ch : channels_)
                if (ch.id == channel_id) {
                        ch.assigned_signal = signal;
                        logic_mux_data_invalid_ = true;
                }
 
+       // Receive notifications when new sample data is available
+       connect_input_notifiers();
+
        stack_config_changed_ = true;
        commit_decoder_channels();
        channels_updated();
@@ -317,12 +388,68 @@ int DecodeSignal::get_assigned_signal_count() const
 {
        // Count all channels that have a signal assigned to them
        return count_if(channels_.begin(), channels_.end(),
-               [](data::DecodeChannel ch) { return ch.assigned_signal; });
+               [](decode::DecodeChannel ch) { return ch.assigned_signal.get(); });
+}
+
+void DecodeSignal::update_output_signals()
+{
+       for (const shared_ptr<decode::Decoder>& dec : stack_) {
+               assert(dec);
+
+               if (dec->has_logic_output()) {
+                       const vector<decode::DecoderLogicOutputChannel> logic_channels =
+                               dec->logic_output_channels();
+
+                       // All signals of a decoder share the same LogicSegment, so it's
+                       // sufficient to check for only the first channel
+                       const decode::DecoderLogicOutputChannel& first_ch = logic_channels[0];
+
+                       bool ch_exists = false;
+                       for (const shared_ptr<SignalBase>& signal : output_signals_)
+                               if (signal->internal_name() == first_ch.id)
+                                       ch_exists = true;
+
+                       if (!ch_exists) {
+                               shared_ptr<Logic> logic_data = make_shared<Logic>(logic_channels.size());
+                               logic_data->set_samplerate(get_samplerate());
+                               output_logic_[dec->get_srd_decoder()] = logic_data;
+                               output_logic_muxed_data_[dec->get_srd_decoder()] = vector<uint8_t>();
+
+                               shared_ptr<LogicSegment> logic_segment = make_shared<data::LogicSegment>(
+                                       *logic_data, 0, (logic_data->num_channels() + 7) / 8, get_samplerate());
+                               logic_data->push_segment(logic_segment);
+
+                               uint index = 0;
+                               for (const decode::DecoderLogicOutputChannel& logic_ch : logic_channels) {
+                                       shared_ptr<data::SignalBase> signal =
+                                               make_shared<data::SignalBase>(nullptr, LogicChannel);
+                                       signal->set_internal_name(logic_ch.id);
+                                       signal->set_index(index);
+                                       signal->set_data(logic_data);
+                                       output_signals_.push_back(signal);
+                                       session_.add_generated_signal(signal);
+                                       index++;
+                               }
+                       } else {
+                               shared_ptr<Logic> logic_data = output_logic_[dec->get_srd_decoder()];
+                               logic_data->set_samplerate(get_samplerate());
+                               for (shared_ptr<LogicSegment>& segment : logic_data->logic_segments())
+                                       segment->set_samplerate(get_samplerate());
+                       }
+               }
+       }
+
+       for (shared_ptr<SignalBase> s : output_signals_) {
+               s->set_name(s->internal_name() + " (" + name() + ")");
+               s->set_color(color());
+       }
+
+       // TODO Assert that all sample rates are the same as the session's
 }
 
 void DecodeSignal::set_initial_pin_state(const uint16_t channel_id, const int init_state)
 {
-       for (data::DecodeChannel &ch : channels_)
+       for (decode::DecodeChannel& ch : channels_)
                if (ch.id == channel_id)
                        ch.initial_pin_state = init_state;
 
@@ -331,7 +458,7 @@ void DecodeSignal::set_initial_pin_state(const uint16_t channel_id, const int in
        begin_decode();
 }
 
-double DecodeSignal::samplerate() const
+double DecodeSignal::get_samplerate() const
 {
        double result = 0;
 
@@ -362,92 +489,264 @@ int64_t DecodeSignal::get_working_sample_count(uint32_t segment_id) const
        int64_t count = std::numeric_limits<int64_t>::max();
        bool no_signals_assigned = true;
 
-       for (const data::DecodeChannel &ch : channels_)
+       for (const decode::DecodeChannel& ch : channels_)
                if (ch.assigned_signal) {
+                       if (!ch.assigned_signal->logic_data())
+                               return 0;
+
                        no_signals_assigned = false;
 
                        const shared_ptr<Logic> logic_data = ch.assigned_signal->logic_data();
-                       if (!logic_data || logic_data->logic_segments().empty())
+                       if (logic_data->logic_segments().empty())
                                return 0;
 
-                       try {
-                               const shared_ptr<LogicSegment> segment = logic_data->logic_segments().at(segment_id);
-                               count = min(count, (int64_t)segment->get_sample_count());
-                       } catch (out_of_range&) {
+                       if (segment_id >= logic_data->logic_segments().size())
                                return 0;
-                       }
+
+                       const shared_ptr<const LogicSegment> segment = logic_data->logic_segments()[segment_id]->get_shared_ptr();
+                       if (segment)
+                               count = min(count, (int64_t)segment->get_sample_count());
                }
 
        return (no_signals_assigned ? 0 : count);
 }
 
-int64_t DecodeSignal::get_decoded_sample_count(uint32_t segment_id) const
+int64_t DecodeSignal::get_decoded_sample_count(uint32_t segment_id,
+       bool include_processing) const
 {
        lock_guard<mutex> decode_lock(output_mutex_);
 
        int64_t result = 0;
 
-       try {
-               const DecodeSegment *segment = &(segments_.at(segment_id));
-               result = segment->samples_decoded;
-       } catch (out_of_range&) {
-               // Do nothing
-       }
+       if (segment_id >= segments_.size())
+               return result;
+
+       if (include_processing)
+               result = segments_[segment_id].samples_decoded_incl;
+       else
+               result = segments_[segment_id].samples_decoded_excl;
 
        return result;
 }
 
-vector<Row> DecodeSignal::visible_rows() const
+vector<Row*> DecodeSignal::get_rows(bool visible_only)
 {
-       lock_guard<mutex> lock(output_mutex_);
-
-       vector<Row> rows;
+       vector<Row*> rows;
 
-       for (const shared_ptr<decode::Decoder> &dec : stack_) {
+       for (const shared_ptr<Decoder>& dec : stack_) {
                assert(dec);
-               if (!dec->shown())
+               if (visible_only && !dec->visible())
                        continue;
 
-               const srd_decoder *const decc = dec->decoder();
-               assert(dec->decoder());
+               for (Row* row : dec->get_rows())
+                       rows.push_back(row);
+       }
+
+       return rows;
+}
+
+vector<const Row*> DecodeSignal::get_rows(bool visible_only) const
+{
+       vector<const Row*> rows;
 
-               // Add a row for the decoder if it doesn't have a row list
-               if (!decc->annotation_rows)
-                       rows.emplace_back(decc);
+       for (const shared_ptr<Decoder>& dec : stack_) {
+               assert(dec);
+               if (visible_only && !dec->visible())
+                       continue;
 
-               // Add the decoder rows
-               for (const GSList *l = decc->annotation_rows; l; l = l->next) {
-                       const srd_decoder_annotation_row *const ann_row =
-                               (srd_decoder_annotation_row *)l->data;
-                       assert(ann_row);
-                       rows.emplace_back(decc, ann_row);
-               }
+               for (const Row* row : dec->get_rows())
+                       rows.push_back(row);
        }
 
        return rows;
 }
 
-void DecodeSignal::get_annotation_subset(
-       vector<pv::data::decode::Annotation> &dest,
-       const decode::Row &row, uint32_t segment_id, uint64_t start_sample,
+uint64_t DecodeSignal::get_annotation_count(const Row* row, uint32_t segment_id) const
+{
+       if (segment_id >= segments_.size())
+               return 0;
+
+       const DecodeSegment* segment = &(segments_.at(segment_id));
+
+       auto row_it = segment->annotation_rows.find(row);
+
+       const RowData* rd;
+       if (row_it == segment->annotation_rows.end())
+               return 0;
+       else
+               rd = &(row_it->second);
+
+       return rd->get_annotation_count();
+}
+
+void DecodeSignal::get_annotation_subset(deque<const Annotation*> &dest,
+       const Row* row, uint32_t segment_id, uint64_t start_sample,
        uint64_t end_sample) const
 {
        lock_guard<mutex> lock(output_mutex_);
 
-       try {
-               const DecodeSegment *segment = &(segments_.at(segment_id));
-               const map<const decode::Row, decode::RowData> *rows =
-                       &(segment->annotation_rows);
-
-               const auto iter = rows->find(row);
-               if (iter != rows->end())
-                       (*iter).second.get_annotation_subset(dest,
-                               start_sample, end_sample);
-       } catch (out_of_range&) {
-               // Do nothing
+       if (segment_id >= segments_.size())
+               return;
+
+       const DecodeSegment* segment = &(segments_.at(segment_id));
+
+       auto row_it = segment->annotation_rows.find(row);
+
+       const RowData* rd;
+       if (row_it == segment->annotation_rows.end())
+               return;
+       else
+               rd = &(row_it->second);
+
+       rd->get_annotation_subset(dest, start_sample, end_sample);
+}
+
+void DecodeSignal::get_annotation_subset(deque<const Annotation*> &dest,
+       uint32_t segment_id, uint64_t start_sample, uint64_t end_sample) const
+{
+       for (const Row* row : get_rows())
+               get_annotation_subset(dest, row, segment_id, start_sample, end_sample);
+}
+
+uint32_t DecodeSignal::get_binary_data_chunk_count(uint32_t segment_id,
+       const Decoder* dec, uint32_t bin_class_id) const
+{
+       if ((segments_.size() == 0) || (segment_id >= segments_.size()))
+               return 0;
+
+       const DecodeSegment *segment = &(segments_[segment_id]);
+
+       for (const DecodeBinaryClass& bc : segment->binary_classes)
+               if ((bc.decoder == dec) && (bc.info->bin_class_id == bin_class_id))
+                       return bc.chunks.size();
+
+       return 0;
+}
+
+void DecodeSignal::get_binary_data_chunk(uint32_t segment_id,
+       const  Decoder* dec, uint32_t bin_class_id, uint32_t chunk_id,
+       const vector<uint8_t> **dest, uint64_t *size)
+{
+       if (segment_id >= segments_.size())
+               return;
+
+       const DecodeSegment *segment = &(segments_[segment_id]);
+
+       for (const DecodeBinaryClass& bc : segment->binary_classes)
+               if ((bc.decoder == dec) && (bc.info->bin_class_id == bin_class_id)) {
+                       if (dest) *dest = &(bc.chunks.at(chunk_id).data);
+                       if (size) *size = bc.chunks.at(chunk_id).data.size();
+                       return;
+               }
+}
+
+void DecodeSignal::get_merged_binary_data_chunks_by_sample(uint32_t segment_id,
+       const Decoder* dec, uint32_t bin_class_id, uint64_t start_sample,
+       uint64_t end_sample, vector<uint8_t> *dest) const
+{
+       assert(dest != nullptr);
+
+       if (segment_id >= segments_.size())
+               return;
+
+       const DecodeSegment *segment = &(segments_[segment_id]);
+
+       const DecodeBinaryClass* bin_class = nullptr;
+       for (const DecodeBinaryClass& bc : segment->binary_classes)
+               if ((bc.decoder == dec) && (bc.info->bin_class_id == bin_class_id))
+                       bin_class = &bc;
+
+       // Determine overall size before copying to resize dest vector only once
+       uint64_t size = 0;
+       uint64_t matches = 0;
+       for (const DecodeBinaryDataChunk& chunk : bin_class->chunks)
+               if ((chunk.sample >= start_sample) && (chunk.sample < end_sample)) {
+                       size += chunk.data.size();
+                       matches++;
+               }
+       dest->resize(size);
+
+       uint64_t offset = 0;
+       uint64_t matches2 = 0;
+       for (const DecodeBinaryDataChunk& chunk : bin_class->chunks)
+               if ((chunk.sample >= start_sample) && (chunk.sample < end_sample)) {
+                       memcpy(dest->data() + offset, chunk.data.data(), chunk.data.size());
+                       offset += chunk.data.size();
+                       matches2++;
+
+                       // Make sure we don't overwrite memory if the array grew in the meanwhile
+                       if (matches2 == matches)
+                               break;
+               }
+}
+
+void DecodeSignal::get_merged_binary_data_chunks_by_offset(uint32_t segment_id,
+       const Decoder* dec, uint32_t bin_class_id, uint64_t start, uint64_t end,
+       vector<uint8_t> *dest) const
+{
+       assert(dest != nullptr);
+
+       if (segment_id >= segments_.size())
+               return;
+
+       const DecodeSegment *segment = &(segments_[segment_id]);
+
+       const DecodeBinaryClass* bin_class = nullptr;
+       for (const DecodeBinaryClass& bc : segment->binary_classes)
+               if ((bc.decoder == dec) && (bc.info->bin_class_id == bin_class_id))
+                       bin_class = &bc;
+
+       // Determine overall size before copying to resize dest vector only once
+       uint64_t size = 0;
+       uint64_t offset = 0;
+       for (const DecodeBinaryDataChunk& chunk : bin_class->chunks) {
+               if (offset >= start)
+                       size += chunk.data.size();
+               offset += chunk.data.size();
+               if (offset >= end)
+                       break;
+       }
+       dest->resize(size);
+
+       offset = 0;
+       uint64_t dest_offset = 0;
+       for (const DecodeBinaryDataChunk& chunk : bin_class->chunks) {
+               if (offset >= start) {
+                       memcpy(dest->data() + dest_offset, chunk.data.data(), chunk.data.size());
+                       dest_offset += chunk.data.size();
+               }
+               offset += chunk.data.size();
+               if (offset >= end)
+                       break;
        }
 }
 
+const DecodeBinaryClass* DecodeSignal::get_binary_data_class(uint32_t segment_id,
+       const Decoder* dec, uint32_t bin_class_id) const
+{
+       if (segment_id >= segments_.size())
+               return nullptr;
+
+       const DecodeSegment *segment = &(segments_[segment_id]);
+
+       for (const DecodeBinaryClass& bc : segment->binary_classes)
+               if ((bc.decoder == dec) && (bc.info->bin_class_id == bin_class_id))
+                       return &bc;
+
+       return nullptr;
+}
+
+const deque<const Annotation*>* DecodeSignal::get_all_annotations_by_segment(
+       uint32_t segment_id) const
+{
+       if (segment_id >= segments_.size())
+               return nullptr;
+
+       const DecodeSegment *segment = &(segments_[segment_id]);
+
+       return &(segment->all_annotations);
+}
+
 void DecodeSignal::save_settings(QSettings &settings) const
 {
        SignalBase::save_settings(settings);
@@ -456,20 +755,25 @@ void DecodeSignal::save_settings(QSettings &settings) const
 
        // Save decoder stack
        int decoder_idx = 0;
-       for (shared_ptr<decode::Decoder> decoder : stack_) {
+       for (const shared_ptr<Decoder>& decoder : stack_) {
                settings.beginGroup("decoder" + QString::number(decoder_idx++));
 
-               settings.setValue("id", decoder->decoder()->id);
+#if QT_VERSION >= QT_VERSION_CHECK(6, 0, 0)
+               settings.setValue("id", (const char *)decoder->get_srd_decoder()->id);
+#else
+               settings.setValue("id", decoder->get_srd_decoder()->id);
+#endif
+               settings.setValue("visible", decoder->visible());
 
                // Save decoder options
                const map<string, GVariant*>& options = decoder->options();
 
                settings.setValue("options", (int)options.size());
 
-               // Note: decode::Decoder::options() returns only the options
+               // Note: Decoder::options() returns only the options
                // that differ from the default. See binding::Decoder::getter()
                int i = 0;
-               for (auto option : options) {
+               for (auto& option : options) {
                        settings.beginGroup("option" + QString::number(i));
                        settings.setValue("name", QString::fromStdString(option.first));
                        GlobalSettings::store_gvariant(settings, option.second);
@@ -477,6 +781,24 @@ void DecodeSignal::save_settings(QSettings &settings) const
                        i++;
                }
 
+               // Save row properties
+               i = 0;
+               for (const Row* row : decoder->get_rows()) {
+                       settings.beginGroup("row" + QString::number(i));
+                       settings.setValue("visible", row->visible());
+                       settings.endGroup();
+                       i++;
+               }
+
+               // Save class properties
+               i = 0;
+               for (const AnnotationClass* ann_class : decoder->ann_classes()) {
+                       settings.beginGroup("ann_class" + QString::number(i));
+                       settings.setValue("visible", ann_class->visible());
+                       settings.endGroup();
+                       i++;
+               }
+
                settings.endGroup();
        }
 
@@ -485,7 +807,7 @@ void DecodeSignal::save_settings(QSettings &settings) const
 
        for (unsigned int channel_id = 0; channel_id < channels_.size(); channel_id++) {
                auto channel = find_if(channels_.begin(), channels_.end(),
-                       [&](data::DecodeChannel ch) { return ch.id == channel_id; });
+                       [&](decode::DecodeChannel ch) { return ch.id == channel_id; });
 
                if (channel == channels_.end()) {
                        qDebug() << "ERROR: Gap in channel index:" << channel_id;
@@ -502,6 +824,8 @@ void DecodeSignal::save_settings(QSettings &settings) const
 
                settings.endGroup();
        }
+
+       // TODO Save logic output signal settings
 }
 
 void DecodeSignal::restore_settings(QSettings &settings)
@@ -524,10 +848,13 @@ void DecodeSignal::restore_settings(QSettings &settings)
                                continue;
 
                        if (QString::fromUtf8(dec->id) == id) {
-                               shared_ptr<decode::Decoder> decoder =
-                                       make_shared<decode::Decoder>(dec);
+                               shared_ptr<Decoder> decoder = make_shared<Decoder>(dec, stack_.size());
+
+                               connect(decoder.get(), SIGNAL(annotation_visibility_changed()),
+                                       this, SLOT(on_annotation_visibility_changed()));
 
                                stack_.push_back(decoder);
+                               decoder->set_visible(settings.value("visible", true).toBool());
 
                                // Restore decoder options that differ from their default
                                int options = settings.value("options").toInt();
@@ -542,6 +869,25 @@ void DecodeSignal::restore_settings(QSettings &settings)
 
                                // Include the newly created decode channels in the channel lists
                                update_channel_list();
+
+                               // Restore row properties
+                               int i = 0;
+                               for (Row* row : decoder->get_rows()) {
+                                       settings.beginGroup("row" + QString::number(i));
+                                       row->set_visible(settings.value("visible", true).toBool());
+                                       settings.endGroup();
+                                       i++;
+                               }
+
+                               // Restore class properties
+                               i = 0;
+                               for (AnnotationClass* ann_class : decoder->ann_classes()) {
+                                       settings.beginGroup("ann_class" + QString::number(i));
+                                       ann_class->set_visible(settings.value("visible", true).toBool());
+                                       settings.endGroup();
+                                       i++;
+                               }
+
                                break;
                        }
                }
@@ -553,12 +899,12 @@ void DecodeSignal::restore_settings(QSettings &settings)
        // Restore channel mapping
        unsigned int channels = settings.value("channels").toInt();
 
-       const unordered_set< shared_ptr<data::SignalBase> > signalbases =
+       const vector< shared_ptr<data::SignalBase> > signalbases =
                session_.signalbases();
 
        for (unsigned int channel_id = 0; channel_id < channels; channel_id++) {
                auto channel = find_if(channels_.begin(), channels_.end(),
-                       [&](data::DecodeChannel ch) { return ch.id == channel_id; });
+                       [&](decode::DecodeChannel ch) { return ch.id == channel_id; });
 
                if (channel == channels_.end()) {
                        qDebug() << "ERROR: Non-existant channel index:" << channel_id;
@@ -569,28 +915,50 @@ void DecodeSignal::restore_settings(QSettings &settings)
 
                QString assigned_signal_name = settings.value("assigned_signal_name").toString();
 
-               for (shared_ptr<data::SignalBase> signal : signalbases)
-                       if (signal->name() == assigned_signal_name)
-                               channel->assigned_signal = signal.get();
+               for (const shared_ptr<data::SignalBase>& signal : signalbases)
+                       if ((signal->name() == assigned_signal_name) && (signal->type() != SignalBase::DecodeChannel))
+                               channel->assigned_signal = signal;
 
                channel->initial_pin_state = settings.value("initial_pin_state").toInt();
 
                settings.endGroup();
        }
 
+       connect_input_notifiers();
+
        // Update the internal structures
        stack_config_changed_ = true;
        update_channel_list();
        commit_decoder_channels();
+       update_output_signals();
+
+       // TODO Restore logic output signal settings
 
        begin_decode();
 }
 
-void DecodeSignal::set_error_message(QString msg)
+bool DecodeSignal::all_input_segments_complete(uint32_t segment_id) const
 {
-       error_message_ = msg;
-       // TODO Emulate noquote()
-       qDebug().nospace() << name() << ": " << msg;
+       bool all_complete = true;
+
+       for (const decode::DecodeChannel& ch : channels_)
+               if (ch.assigned_signal) {
+                       if (!ch.assigned_signal->logic_data())
+                               continue;
+
+                       const shared_ptr<Logic> logic_data = ch.assigned_signal->logic_data();
+                       if (logic_data->logic_segments().empty())
+                               return false;
+
+                       if (segment_id >= logic_data->logic_segments().size())
+                               return false;
+
+                       const shared_ptr<const LogicSegment> segment = logic_data->logic_segments()[segment_id]->get_shared_ptr();
+                       if (segment && !segment->is_complete())
+                               all_complete = false;
+               }
+
+       return all_complete;
 }
 
 uint32_t DecodeSignal::get_input_segment_count() const
@@ -598,7 +966,7 @@ uint32_t DecodeSignal::get_input_segment_count() const
        uint64_t count = std::numeric_limits<uint64_t>::max();
        bool no_signals_assigned = true;
 
-       for (const data::DecodeChannel &ch : channels_)
+       for (const decode::DecodeChannel& ch : channels_)
                if (ch.assigned_signal) {
                        no_signals_assigned = false;
 
@@ -614,19 +982,21 @@ uint32_t DecodeSignal::get_input_segment_count() const
        return (no_signals_assigned ? 0 : count);
 }
 
-uint32_t DecodeSignal::get_input_samplerate(uint32_t segment_id) const
+double DecodeSignal::get_input_samplerate(uint32_t segment_id) const
 {
        double samplerate = 0;
 
-       for (const data::DecodeChannel &ch : channels_)
+       for (const decode::DecodeChannel& ch : channels_)
                if (ch.assigned_signal) {
                        const shared_ptr<Logic> logic_data = ch.assigned_signal->logic_data();
                        if (!logic_data || logic_data->logic_segments().empty())
                                continue;
 
                        try {
-                               const shared_ptr<LogicSegment> segment = logic_data->logic_segments().at(segment_id);
-                               samplerate = segment->samplerate();
+                               const shared_ptr<const LogicSegment> segment =
+                                       logic_data->logic_segments().at(segment_id)->get_shared_ptr();
+                               if (segment)
+                                       samplerate = segment->samplerate();
                        } catch (out_of_range&) {
                                // Do nothing
                        }
@@ -636,25 +1006,34 @@ uint32_t DecodeSignal::get_input_samplerate(uint32_t segment_id) const
        return samplerate;
 }
 
+Decoder* DecodeSignal::get_decoder_by_instance(const srd_decoder *const srd_dec)
+{
+       for (shared_ptr<Decoder>& d : stack_)
+               if (d->get_srd_decoder() == srd_dec)
+                       return d.get();
+
+       return nullptr;
+}
+
 void DecodeSignal::update_channel_list()
 {
-       vector<data::DecodeChannel> prev_channels = channels_;
+       vector<decode::DecodeChannel> prev_channels = channels_;
        channels_.clear();
 
        uint16_t id = 0;
 
        // Copy existing entries, create new as needed
-       for (shared_ptr<Decoder> decoder : stack_) {
-               const srd_decoder* srd_d = decoder->decoder();
+       for (shared_ptr<Decoder>& decoder : stack_) {
+               const srd_decoder* srd_dec = decoder->get_srd_decoder();
                const GSList *l;
 
                // Mandatory channels
-               for (l = srd_d->channels; l; l = l->next) {
+               for (l = srd_dec->channels; l; l = l->next) {
                        const struct srd_channel *const pdch = (struct srd_channel *)l->data;
                        bool ch_added = false;
 
                        // Copy but update ID if this channel was in the list before
-                       for (data::DecodeChannel &ch : prev_channels)
+                       for (decode::DecodeChannel& ch : prev_channels)
                                if (ch.pdch_ == pdch) {
                                        ch.id = id++;
                                        channels_.push_back(ch);
@@ -664,7 +1043,7 @@ void DecodeSignal::update_channel_list()
 
                        if (!ch_added) {
                                // Create new entry without a mapped signal
-                               data::DecodeChannel ch = {id++, 0, false, nullptr,
+                               decode::DecodeChannel ch = {id++, 0, false, nullptr,
                                        QString::fromUtf8(pdch->name), QString::fromUtf8(pdch->desc),
                                        SRD_INITIAL_PIN_SAME_AS_SAMPLE0, decoder, pdch};
                                channels_.push_back(ch);
@@ -672,12 +1051,12 @@ void DecodeSignal::update_channel_list()
                }
 
                // Optional channels
-               for (l = srd_d->opt_channels; l; l = l->next) {
+               for (l = srd_dec->opt_channels; l; l = l->next) {
                        const struct srd_channel *const pdch = (struct srd_channel *)l->data;
                        bool ch_added = false;
 
                        // Copy but update ID if this channel was in the list before
-                       for (data::DecodeChannel &ch : prev_channels)
+                       for (decode::DecodeChannel& ch : prev_channels)
                                if (ch.pdch_ == pdch) {
                                        ch.id = id++;
                                        channels_.push_back(ch);
@@ -687,7 +1066,7 @@ void DecodeSignal::update_channel_list()
 
                        if (!ch_added) {
                                // Create new entry without a mapped signal
-                               data::DecodeChannel ch = {id++, 0, true, nullptr,
+                               decode::DecodeChannel ch = {id++, 0, true, nullptr,
                                        QString::fromUtf8(pdch->name), QString::fromUtf8(pdch->desc),
                                        SRD_INITIAL_PIN_SAME_AS_SAMPLE0, decoder, pdch};
                                channels_.push_back(ch);
@@ -702,8 +1081,8 @@ void DecodeSignal::update_channel_list()
        } else {
                // Same number but assignment may still differ, so compare all channels
                for (size_t i = 0; i < channels_.size(); i++) {
-                       const data::DecodeChannel &p_ch = prev_channels[i];
-                       const data::DecodeChannel &ch = channels_[i];
+                       const decode::DecodeChannel& p_ch = prev_channels[i];
+                       const decode::DecodeChannel& ch = channels_[i];
 
                        if ((p_ch.pdch_ != ch.pdch_) ||
                                (p_ch.assigned_signal != ch.assigned_signal)) {
@@ -720,10 +1099,10 @@ void DecodeSignal::update_channel_list()
 void DecodeSignal::commit_decoder_channels()
 {
        // Submit channel list to every decoder, containing only the relevant channels
-       for (shared_ptr<decode::Decoder> dec : stack_) {
-               vector<data::DecodeChannel*> channel_list;
+       for (shared_ptr<Decoder> dec : stack_) {
+               vector<decode::DecodeChannel*> channel_list;
 
-               for (data::DecodeChannel &ch : channels_)
+               for (decode::DecodeChannel& ch : channels_)
                        if (ch.decoder_ == dec)
                                channel_list.push_back(&ch);
 
@@ -732,7 +1111,7 @@ void DecodeSignal::commit_decoder_channels()
 
        // Channel bit IDs must be in sync with the channel's apperance in channels_
        int id = 0;
-       for (data::DecodeChannel &ch : channels_)
+       for (decode::DecodeChannel& ch : channels_)
                if (ch.assigned_signal)
                        ch.bit_id = id++;
 }
@@ -744,23 +1123,28 @@ void DecodeSignal::mux_logic_samples(uint32_t segment_id, const int64_t start, c
                return;
 
        // Fetch the channel segments and their data
-       vector<shared_ptr<LogicSegment> > segments;
+       vector<shared_ptr<const LogicSegment> > segments;
        vector<const uint8_t*> signal_data;
        vector<uint8_t> signal_in_bytepos;
        vector<uint8_t> signal_in_bitpos;
 
-       for (data::DecodeChannel &ch : channels_)
+       for (decode::DecodeChannel& ch : channels_)
                if (ch.assigned_signal) {
                        const shared_ptr<Logic> logic_data = ch.assigned_signal->logic_data();
 
-                       shared_ptr<LogicSegment> segment;
-                       try {
-                               segment = logic_data->logic_segments().at(segment_id);
-                       } catch (out_of_range&) {
+                       shared_ptr<const LogicSegment> segment;
+                       if (segment_id < logic_data->logic_segments().size()) {
+                               segment = logic_data->logic_segments().at(segment_id)->get_shared_ptr();
+                       } else {
                                qDebug() << "Muxer error for" << name() << ":" << ch.assigned_signal->name() \
                                        << "has no logic segment" << segment_id;
+                               logic_mux_interrupt_ = true;
                                return;
                        }
+
+                       if (!segment)
+                               return;
+
                        segments.push_back(segment);
 
                        uint8_t* data = new uint8_t[(end - start) * segment->unit_size()];
@@ -772,7 +1156,6 @@ void DecodeSignal::mux_logic_samples(uint32_t segment_id, const int64_t start, c
                        signal_in_bitpos.push_back(bitpos % 8);
                }
 
-
        shared_ptr<LogicSegment> output_segment;
        try {
                output_segment = logic_mux_data_->logic_segments().at(segment_id);
@@ -780,6 +1163,7 @@ void DecodeSignal::mux_logic_samples(uint32_t segment_id, const int64_t start, c
                qDebug() << "Muxer error for" << name() << ": no logic mux segment" \
                        << segment_id << "in mux_logic_samples(), mux segments size is" \
                        << logic_mux_data_->logic_segments().size();
+               logic_mux_interrupt_ = true;
                return;
        }
 
@@ -787,7 +1171,9 @@ void DecodeSignal::mux_logic_samples(uint32_t segment_id, const int64_t start, c
        uint8_t* output = new uint8_t[(end - start) * output_segment->unit_size()];
        unsigned int signal_count = signal_data.size();
 
-       for (int64_t sample_cnt = 0; sample_cnt < (end - start); sample_cnt++) {
+       for (int64_t sample_cnt = 0; !logic_mux_interrupt_ && (sample_cnt < (end - start));
+               sample_cnt++) {
+
                int bitpos = 0;
                uint8_t bytepos = 0;
 
@@ -821,64 +1207,88 @@ void DecodeSignal::mux_logic_samples(uint32_t segment_id, const int64_t start, c
 
 void DecodeSignal::logic_mux_proc()
 {
-       uint32_t segment_id = 0;
+       uint32_t input_segment_count;
+       do {
+               input_segment_count = get_input_segment_count();
+               if (input_segment_count == 0) {
+                       // Wait for input data
+                       unique_lock<mutex> logic_mux_lock(logic_mux_mutex_);
+                       logic_mux_cond_.wait(logic_mux_lock);
+               }
+       } while ((!logic_mux_interrupt_) && (input_segment_count == 0));
+
+       if (logic_mux_interrupt_)
+               return;
 
        assert(logic_mux_data_);
 
+       uint32_t segment_id = 0;
+
        // Create initial logic mux segment
        shared_ptr<LogicSegment> output_segment =
-               make_shared<LogicSegment>(*logic_mux_data_, segment_id,
-                       logic_mux_unit_size_, 0);
+               make_shared<LogicSegment>(*logic_mux_data_, segment_id, logic_mux_unit_size_, 0);
        logic_mux_data_->push_segment(output_segment);
 
        output_segment->set_samplerate(get_input_samplerate(0));
 
+       // Logic mux data is being updated
+       logic_mux_data_invalid_ = false;
+
+       uint64_t samples_to_process;
        do {
-               const uint64_t input_sample_count = get_working_sample_count(segment_id);
-               const uint64_t output_sample_count = output_segment->get_sample_count();
+               do {
+                       const uint64_t input_sample_count = get_working_sample_count(segment_id);
+                       const uint64_t output_sample_count = output_segment->get_sample_count();
 
-               const uint64_t samples_to_process =
-                       (input_sample_count > output_sample_count) ?
-                       (input_sample_count - output_sample_count) : 0;
+                       samples_to_process =
+                               (input_sample_count > output_sample_count) ?
+                               (input_sample_count - output_sample_count) : 0;
 
-               // Process the samples if necessary...
-               if (samples_to_process > 0) {
-                       const uint64_t unit_size = output_segment->unit_size();
-                       const uint64_t chunk_sample_count = DecodeChunkLength / unit_size;
+                       if (samples_to_process > 0) {
+                               const uint64_t unit_size = output_segment->unit_size();
+                               const uint64_t chunk_sample_count = DecodeChunkLength / unit_size;
 
-                       uint64_t processed_samples = 0;
-                       do {
-                               const uint64_t start_sample = output_sample_count + processed_samples;
-                               const uint64_t sample_count =
-                                       min(samples_to_process - processed_samples,     chunk_sample_count);
+                               uint64_t processed_samples = 0;
+                               do {
+                                       const uint64_t start_sample = output_sample_count + processed_samples;
+                                       const uint64_t sample_count =
+                                               min(samples_to_process - processed_samples,     chunk_sample_count);
 
-                               mux_logic_samples(segment_id, start_sample, start_sample + sample_count);
-                               processed_samples += sample_count;
+                                       mux_logic_samples(segment_id, start_sample, start_sample + sample_count);
+                                       processed_samples += sample_count;
 
-                               // ...and process the newly muxed logic data
-                               decode_input_cond_.notify_one();
-                       } while (processed_samples < samples_to_process);
-               }
+                                       // ...and process the newly muxed logic data
+                                       decode_input_cond_.notify_one();
+                               } while (!logic_mux_interrupt_ && (processed_samples < samples_to_process));
+                       }
+               } while (!logic_mux_interrupt_ && (samples_to_process > 0));
 
-               if (samples_to_process == 0) {
-                       // TODO Optimize this by caching the input segment count and only
-                       // querying it when the cached value was reached
-                       if (segment_id < get_input_segment_count() - 1) {
-                               // Process next segment
-                               segment_id++;
+               if (!logic_mux_interrupt_) {
+                       // samples_to_process is now 0, we've exhausted the currently available input data
 
-                               output_segment =
-                                       make_shared<LogicSegment>(*logic_mux_data_, segment_id,
-                                               logic_mux_unit_size_, 0);
-                               logic_mux_data_->push_segment(output_segment);
+                       // If the input segments are complete, we've completed this segment
+                       if (all_input_segments_complete(segment_id)) {
+                               if (!output_segment->is_complete())
+                                       output_segment->set_complete();
 
-                               output_segment->set_samplerate(get_input_samplerate(segment_id));
+                               if (segment_id < get_input_segment_count() - 1) {
 
-                       } else {
-                               // All segments have been processed
-                               logic_mux_data_invalid_ = false;
+                                       // Process next segment
+                                       segment_id++;
 
-                               // Wait for more input
+                                       output_segment =
+                                               make_shared<LogicSegment>(*logic_mux_data_, segment_id,
+                                                       logic_mux_unit_size_, 0);
+                                       logic_mux_data_->push_segment(output_segment);
+
+                                       output_segment->set_samplerate(get_input_samplerate(segment_id));
+                               } else {
+                                       // Wait for more input data if we're processing the currently last segment
+                                       unique_lock<mutex> logic_mux_lock(logic_mux_mutex_);
+                                       logic_mux_cond_.wait(logic_mux_lock);
+                               }
+                       } else {
+                               // Input segments aren't all complete yet but samples_to_process is 0, wait for more input data
                                unique_lock<mutex> logic_mux_lock(logic_mux_mutex_);
                                logic_mux_cond_.wait(logic_mux_lock);
                        }
@@ -888,7 +1298,7 @@ void DecodeSignal::logic_mux_proc()
 
 void DecodeSignal::decode_data(
        const int64_t abs_start_samplenum, const int64_t sample_count,
-       const shared_ptr<LogicSegment> input_segment)
+       const shared_ptr<const LogicSegment> input_segment)
 {
        const int64_t unit_size = input_segment->unit_size();
        const int64_t chunk_sample_count = DecodeChunkLength / unit_size;
@@ -900,6 +1310,12 @@ void DecodeSignal::decode_data(
                const int64_t chunk_end = min(i + chunk_sample_count,
                        abs_start_samplenum + sample_count);
 
+               {
+                       lock_guard<mutex> lock(output_mutex_);
+                       // Update the sample count showing the samples including currently processed ones
+                       segments_.at(current_segment_id_).samples_decoded_incl = chunk_end;
+               }
+
                int64_t data_size = (chunk_end - i) * unit_size;
                uint8_t* chunk = new uint8_t[data_size];
                input_segment->get_samples(i, chunk_end, chunk);
@@ -907,20 +1323,25 @@ void DecodeSignal::decode_data(
                if (srd_session_send(srd_session_, i, chunk_end, chunk,
                                data_size, unit_size) != SRD_OK) {
                        set_error_message(tr("Decoder reported an error"));
-                       delete[] chunk;
-                       break;
+                       decode_interrupt_ = true;
                }
 
                delete[] chunk;
 
                {
                        lock_guard<mutex> lock(output_mutex_);
-                       segments_.at(current_segment_id_).samples_decoded = chunk_end;
+                       // Now that all samples are processed, the exclusive sample count catches up
+                       segments_.at(current_segment_id_).samples_decoded_excl = chunk_end;
                }
 
                // Notify the frontend that we processed some data and
                // possibly have new annotations as well
                new_annotations();
+
+               if (decode_paused_) {
+                       unique_lock<mutex> pause_wait_lock(decode_pause_mutex_);
+                       decode_pause_cond_.wait(pause_wait_lock);
+               }
        }
 }
 
@@ -929,16 +1350,20 @@ void DecodeSignal::decode_proc()
        current_segment_id_ = 0;
 
        // If there is no input data available yet, wait until it is or we're interrupted
-       if (logic_mux_data_->logic_segments().size() == 0) {
-               unique_lock<mutex> input_wait_lock(input_mutex_);
-               decode_input_cond_.wait(input_wait_lock);
-       }
+       do {
+               if (logic_mux_data_->logic_segments().size() == 0) {
+                       // Wait for input data
+                       unique_lock<mutex> input_wait_lock(input_mutex_);
+                       decode_input_cond_.wait(input_wait_lock);
+               }
+       } while ((!decode_interrupt_) && (logic_mux_data_->logic_segments().size() == 0));
 
        if (decode_interrupt_)
                return;
 
-       shared_ptr<LogicSegment> input_segment = logic_mux_data_->logic_segments().front();
-       assert(input_segment);
+       shared_ptr<const LogicSegment> input_segment = logic_mux_data_->logic_segments().front()->get_shared_ptr();
+       if (!input_segment)
+               return;
 
        // Create the initial segment and set its sample rate so that we can pass it to SRD
        create_decode_segment();
@@ -947,63 +1372,75 @@ void DecodeSignal::decode_proc()
 
        start_srd_session();
 
-       uint64_t sample_count = 0;
+       uint64_t samples_to_process = 0;
        uint64_t abs_start_samplenum = 0;
        do {
                // Keep processing new samples until we exhaust the input data
                do {
-                       lock_guard<mutex> input_lock(input_mutex_);
-                       sample_count = input_segment->get_sample_count() - abs_start_samplenum;
+                       samples_to_process = input_segment->get_sample_count() - abs_start_samplenum;
 
-                       if (sample_count > 0) {
-                               decode_data(abs_start_samplenum, sample_count, input_segment);
-                               abs_start_samplenum += sample_count;
+                       if (samples_to_process > 0) {
+                               decode_data(abs_start_samplenum, samples_to_process, input_segment);
+                               abs_start_samplenum += samples_to_process;
                        }
-               } while (error_message_.isEmpty() && (sample_count > 0) && !decode_interrupt_);
-
-               if (error_message_.isEmpty() && !decode_interrupt_ && sample_count == 0) {
-                       if (current_segment_id_ < logic_mux_data_->logic_segments().size() - 1) {
-                               // Process next segment
-                               current_segment_id_++;
-
-                               try {
-                                       input_segment = logic_mux_data_->logic_segments().at(current_segment_id_);
-                               } catch (out_of_range&) {
-                                       qDebug() << "Decode error for" << name() << ": no logic mux segment" \
-                                               << current_segment_id_ << "in decode_proc(), mux segments size is" \
-                                               << logic_mux_data_->logic_segments().size();
-                                       return;
+               } while (!decode_interrupt_ && (samples_to_process > 0));
+
+               if (!decode_interrupt_) {
+                       // samples_to_process is now 0, we've exhausted the currently available input data
+
+                       // If the input segment is complete, we've exhausted this segment
+                       if (input_segment->is_complete()) {
+#if defined HAVE_SRD_SESSION_SEND_EOF && HAVE_SRD_SESSION_SEND_EOF
+                               // Tell protocol decoders about the end of
+                               // the input data, which may result in more
+                               // annotations being emitted
+                               (void)srd_session_send_eof(srd_session_);
+                               new_annotations();
+#endif
+
+                               if (current_segment_id_ < (logic_mux_data_->logic_segments().size() - 1)) {
+                                       // Process next segment
+                                       current_segment_id_++;
+
+                                       try {
+                                               input_segment = logic_mux_data_->logic_segments().at(current_segment_id_);
+                                       } catch (out_of_range&) {
+                                               qDebug() << "Decode error for" << name() << ": no logic mux segment" \
+                                                       << current_segment_id_ << "in decode_proc(), mux segments size is" \
+                                                       << logic_mux_data_->logic_segments().size();
+                                               decode_interrupt_ = true;
+                                               return;
+                                       }
+                                       abs_start_samplenum = 0;
+
+                                       // Create the next segment and set its metadata
+                                       create_decode_segment();
+                                       segments_.at(current_segment_id_).samplerate = input_segment->samplerate();
+                                       segments_.at(current_segment_id_).start_time = input_segment->start_time();
+
+                                       // Reset decoder state but keep the decoder stack intact
+                                       terminate_srd_session();
+                               } else {
+                                       // All segments have been processed
+                                       if (!decode_interrupt_)
+                                               decode_finished();
+
+                                       // Wait for more input data
+                                       unique_lock<mutex> input_wait_lock(input_mutex_);
+                                       decode_input_cond_.wait(input_wait_lock);
                                }
-                               abs_start_samplenum = 0;
-
-                               // Create the next segment and set its metadata
-                               create_decode_segment();
-                               segments_.at(current_segment_id_).samplerate = input_segment->samplerate();
-                               segments_.at(current_segment_id_).start_time = input_segment->start_time();
-
-                               // Reset decoder state but keep the decoder stack intact
-                               terminate_srd_session();
                        } else {
-                               // All segments have been processed
-                               decode_finished();
-
-                               // Wait for new input data or an interrupt was requested
+                               // Input segment isn't complete yet but samples_to_process is 0, wait for more input data
                                unique_lock<mutex> input_wait_lock(input_mutex_);
                                decode_input_cond_.wait(input_wait_lock);
                        }
-               }
-       } while (error_message_.isEmpty() && !decode_interrupt_);
 
-       // Potentially reap decoders when the application no longer is
-       // interested in their (pending) results.
-       if (decode_interrupt_)
-               terminate_srd_session();
+               }
+       } while (!decode_interrupt_);
 }
 
 void DecodeSignal::start_srd_session()
 {
-       uint64_t samplerate;
-
        // If there were stack changes, the session has been destroyed by now, so if
        // it hasn't been destroyed, we can just reset and re-use it
        if (srd_session_) {
@@ -1014,23 +1451,33 @@ void DecodeSignal::start_srd_session()
                // and) construction of another decoder stack.
 
                // TODO Reduce redundancy, use a common code path for
-               // the meta/cb/start sequence?
+               // the meta/start sequence?
                terminate_srd_session();
-               srd_session_metadata_set(srd_session_, SRD_CONF_SAMPLERATE,
-                       g_variant_new_uint64(segments_.at(current_segment_id_).samplerate));
-               srd_pd_output_callback_add(srd_session_, SRD_OUTPUT_ANN,
-                       DecodeSignal::annotation_callback, this);
+
+               // Metadata is cleared also, so re-set it
+               uint64_t samplerate = 0;
+               if (segments_.size() > 0)
+                       samplerate = segments_.at(current_segment_id_).samplerate;
+               if (samplerate)
+                       srd_session_metadata_set(srd_session_, SRD_CONF_SAMPLERATE,
+                               g_variant_new_uint64(samplerate));
+               for (const shared_ptr<Decoder>& dec : stack_)
+                       dec->apply_all_options();
                srd_session_start(srd_session_);
+
                return;
        }
 
+       // Update the samplerates for the output logic channels
+       update_output_signals();
+
        // Create the session
        srd_session_new(&srd_session_);
        assert(srd_session_);
 
        // Create the decoders
        srd_decoder_inst *prev_di = nullptr;
-       for (const shared_ptr<decode::Decoder> &dec : stack_) {
+       for (const shared_ptr<Decoder>& dec : stack_) {
                srd_decoder_inst *const di = dec->create_decoder_inst(srd_session_);
 
                if (!di) {
@@ -1047,14 +1494,19 @@ void DecodeSignal::start_srd_session()
        }
 
        // Start the session
-       samplerate = segments_.at(current_segment_id_).samplerate;
-       if (samplerate)
+       if (segments_.size() > 0)
                srd_session_metadata_set(srd_session_, SRD_CONF_SAMPLERATE,
-                       g_variant_new_uint64(samplerate));
+                       g_variant_new_uint64(segments_.at(current_segment_id_).samplerate));
 
        srd_pd_output_callback_add(srd_session_, SRD_OUTPUT_ANN,
                DecodeSignal::annotation_callback, this);
 
+       srd_pd_output_callback_add(srd_session_, SRD_OUTPUT_BINARY,
+               DecodeSignal::binary_callback, this);
+
+       srd_pd_output_callback_add(srd_session_, SRD_OUTPUT_LOGIC,
+               DecodeSignal::logic_output_callback, this);
+
        srd_session_start(srd_session_);
 
        // We just recreated the srd session, so all stack changes are applied now
@@ -1068,8 +1520,22 @@ void DecodeSignal::terminate_srd_session()
        // have completed their operation, and reduces response time for
        // those stacks which still are processing data while the
        // application no longer wants them to.
-       if (srd_session_)
+       if (srd_session_) {
+#if defined HAVE_SRD_SESSION_SEND_EOF && HAVE_SRD_SESSION_SEND_EOF
+               (void)srd_session_send_eof(srd_session_);
+#endif
                srd_session_terminate_reset(srd_session_);
+
+               // Metadata is cleared also, so re-set it
+               uint64_t samplerate = 0;
+               if (segments_.size() > 0)
+                       samplerate = segments_.at(current_segment_id_).samplerate;
+               if (samplerate)
+                       srd_session_metadata_set(srd_session_, SRD_CONF_SAMPLERATE,
+                               g_variant_new_uint64(samplerate));
+               for (const shared_ptr<Decoder>& dec : stack_)
+                       dec->apply_all_options();
+       }
 }
 
 void DecodeSignal::stop_srd_session()
@@ -1080,58 +1546,62 @@ void DecodeSignal::stop_srd_session()
                srd_session_ = nullptr;
 
                // Mark the decoder instances as non-existant since they were deleted
-               for (const shared_ptr<decode::Decoder> &dec : stack_)
+               for (const shared_ptr<Decoder>& dec : stack_)
                        dec->invalidate_decoder_inst();
        }
 }
 
 void DecodeSignal::connect_input_notifiers()
 {
-       // Disconnect the notification slot from the previous set of signals
-       disconnect(this, SLOT(on_data_cleared()));
-       disconnect(this, SLOT(on_data_received()));
-
        // Connect the currently used signals to our slot
-       for (data::DecodeChannel &ch : channels_) {
+       for (decode::DecodeChannel& ch : channels_) {
                if (!ch.assigned_signal)
                        continue;
+               const data::SignalBase *signal = ch.assigned_signal.get();
 
-               const data::SignalBase *signal = ch.assigned_signal;
                connect(signal, SIGNAL(samples_cleared()),
-                       this, SLOT(on_data_cleared()));
+                       this, SLOT(on_data_cleared()), Qt::UniqueConnection);
                connect(signal, SIGNAL(samples_added(uint64_t, uint64_t, uint64_t)),
-                       this, SLOT(on_data_received()));
+                       this, SLOT(on_data_received()), Qt::UniqueConnection);
+
+               if (signal->logic_data())
+                       connect(signal->logic_data().get(), SIGNAL(segment_completed()),
+                               this, SLOT(on_input_segment_completed()), Qt::UniqueConnection);
+       }
+}
+
+void DecodeSignal::disconnect_input_notifiers()
+{
+       // Disconnect the notification slot from the previous set of signals
+       for (decode::DecodeChannel& ch : channels_) {
+               if (!ch.assigned_signal)
+                       continue;
+               const data::SignalBase *signal = ch.assigned_signal.get();
+               disconnect(signal, nullptr, this, SLOT(on_data_cleared()));
+               disconnect(signal, nullptr, this, SLOT(on_data_received()));
+
+               if (signal->logic_data())
+                       disconnect(signal->logic_data().get(), nullptr, this, SLOT(on_input_segment_completed()));
        }
 }
 
 void DecodeSignal::create_decode_segment()
 {
        // Create annotation segment
-       segments_.emplace_back(DecodeSegment());
+       segments_.emplace_back();
 
        // Add annotation classes
-       for (const shared_ptr<decode::Decoder> &dec : stack_) {
-               assert(dec);
-               const srd_decoder *const decc = dec->decoder();
-               assert(dec->decoder());
-
-               // Add a row for the decoder if it doesn't have a row list
-               if (!decc->annotation_rows)
-                       (segments_.back().annotation_rows)[Row(decc)] =
-                               decode::RowData();
+       for (const shared_ptr<Decoder>& dec : stack_)
+               for (Row* row : dec->get_rows())
+                       segments_.back().annotation_rows.emplace(row, RowData(row));
 
-               // Add the decoder rows
-               for (const GSList *l = decc->annotation_rows; l; l = l->next) {
-                       const srd_decoder_annotation_row *const ann_row =
-                               (srd_decoder_annotation_row *)l->data;
-                       assert(ann_row);
+       // Prepare our binary output classes
+       for (const shared_ptr<Decoder>& dec : stack_) {
+               uint32_t n = dec->get_binary_class_count();
 
-                       const Row row(decc, ann_row);
-
-                       // Add a new empty row data object
-                       (segments_.back().annotation_rows)[row] =
-                               decode::RowData();
-               }
+               for (uint32_t i = 0; i < n; i++)
+                       segments_.back().binary_classes.push_back(
+                               {dec.get(), dec->get_binary_class(i), deque<DecodeBinaryDataChunk>()});
        }
 }
 
@@ -1143,39 +1613,221 @@ void DecodeSignal::annotation_callback(srd_proto_data *pdata, void *decode_signa
        DecodeSignal *const ds = (DecodeSignal*)decode_signal;
        assert(ds);
 
+       if (ds->decode_interrupt_)
+               return;
+
+       if (ds->segments_.empty())
+               return;
+
        lock_guard<mutex> lock(ds->output_mutex_);
 
-       // Find the row
+       // Get the decoder and the annotation data
        assert(pdata->pdo);
        assert(pdata->pdo->di);
-       const srd_decoder *const decc = pdata->pdo->di->decoder;
-       assert(decc);
+       const srd_decoder *const srd_dec = pdata->pdo->di->decoder;
+       assert(srd_dec);
 
-       const srd_proto_data_annotation *const pda =
-               (const srd_proto_data_annotation*)pdata->data;
+       const srd_proto_data_annotation *const pda = (const srd_proto_data_annotation*)pdata->data;
        assert(pda);
 
-       auto row_iter = ds->segments_.at(ds->current_segment_id_).annotation_rows.end();
+       // Find the row
+       Decoder* dec = ds->get_decoder_by_instance(srd_dec);
+       assert(dec);
+
+       AnnotationClass* ann_class = dec->get_ann_class_by_id(pda->ann_class);
+       if (!ann_class) {
+               qWarning() << "Decoder" << ds->display_name() << "wanted to add annotation" <<
+                       "with class ID" << pda->ann_class << "but there are only" <<
+                       dec->ann_classes().size() << "known classes";
+               return;
+       }
 
-       // Try looking up the sub-row of this class
-       const auto format = pda->ann_class;
-       const auto r = ds->class_rows_.find(make_pair(decc, format));
-       if (r != ds->class_rows_.end())
-               row_iter = ds->segments_.at(ds->current_segment_id_).annotation_rows.find((*r).second);
-       else {
-               // Failing that, use the decoder as a key
-               row_iter = ds->segments_.at(ds->current_segment_id_).annotation_rows.find(Row(decc));
+       const Row* row = ann_class->row;
+
+       if (!row)
+               row = dec->get_row_by_id(0);
+
+       RowData& row_data = ds->segments_[ds->current_segment_id_].annotation_rows.at(row);
+
+       // Add the annotation to the row
+       const Annotation* ann = row_data.emplace_annotation(pdata);
+
+       // We insert the annotation into the global annotation list in a way so that
+       // the annotation list is sorted by start sample and length. Otherwise, we'd
+       // have to sort the model, which is expensive
+       deque<const Annotation*>& all_annotations =
+               ds->segments_[ds->current_segment_id_].all_annotations;
+
+       if (all_annotations.empty()) {
+               all_annotations.emplace_back(ann);
+       } else {
+               const uint64_t new_ann_len = (pdata->end_sample - pdata->start_sample);
+               bool ann_has_earlier_start = (pdata->start_sample < all_annotations.back()->start_sample());
+               bool ann_is_longer = (new_ann_len >
+                       (all_annotations.back()->end_sample() - all_annotations.back()->start_sample()));
+
+               if (ann_has_earlier_start && ann_is_longer) {
+                       bool ann_has_same_start;
+                       auto it = all_annotations.end();
+
+                       do {
+                               it--;
+                               ann_has_earlier_start = (pdata->start_sample < (*it)->start_sample());
+                               ann_has_same_start = (pdata->start_sample == (*it)->start_sample());
+                               ann_is_longer = (new_ann_len > (*it)->length());
+                       } while ((ann_has_earlier_start || (ann_has_same_start && ann_is_longer)) && (it != all_annotations.begin()));
+
+                       // Allow inserting at the front
+                       if (it != all_annotations.begin())
+                               it++;
+
+                       all_annotations.emplace(it, ann);
+               } else
+                       all_annotations.emplace_back(ann);
+       }
+
+       // When emplace_annotation() inserts instead of appends an annotation,
+       // the pointers in all_annotations that follow the inserted annotation and
+       // point to annotations for this row are off by one and must be updated
+       if (&(row_data.annotations().back()) != ann) {
+               // Search backwards until we find the annotation we just added
+               auto row_it = row_data.annotations().end();
+               auto all_it = all_annotations.end();
+               do {
+                       all_it--;
+                       if ((*all_it)->row_data() == &row_data)
+                               row_it--;
+               } while (&(*row_it) != ann);
+
+               // Update the annotation addresses for this row's annotations until the end
+               do {
+                       if ((*all_it)->row_data() == &row_data) {
+                               *all_it = &(*row_it);
+                               row_it++;
+                       }
+                       all_it++;
+               } while (all_it != all_annotations.end());
        }
+}
+
+void DecodeSignal::binary_callback(srd_proto_data *pdata, void *decode_signal)
+{
+       assert(pdata);
+       assert(decode_signal);
+
+       DecodeSignal *const ds = (DecodeSignal*)decode_signal;
+       assert(ds);
 
-       if (row_iter == ds->segments_.at(ds->current_segment_id_).annotation_rows.end()) {
-               qDebug() << "Unexpected annotation: decoder = " << decc <<
-                       ", format = " << format;
-               assert(false);
+       if (ds->decode_interrupt_)
+               return;
+
+       // Get the decoder and the binary data
+       assert(pdata->pdo);
+       assert(pdata->pdo->di);
+       const srd_decoder *const srd_dec = pdata->pdo->di->decoder;
+       assert(srd_dec);
+
+       const srd_proto_data_binary *const pdb = (const srd_proto_data_binary*)pdata->data;
+       assert(pdb);
+
+       // Find the matching DecodeBinaryClass
+       DecodeSegment* segment = &(ds->segments_.at(ds->current_segment_id_));
+
+       DecodeBinaryClass* bin_class = nullptr;
+       for (DecodeBinaryClass& bc : segment->binary_classes)
+               if ((bc.decoder->get_srd_decoder() == srd_dec) &&
+                       (bc.info->bin_class_id == (uint32_t)pdb->bin_class))
+                       bin_class = &bc;
+
+       if (!bin_class) {
+               qWarning() << "Could not find valid DecodeBinaryClass in segment" <<
+                               ds->current_segment_id_ << "for binary class ID" << pdb->bin_class <<
+                               ", segment only knows" << segment->binary_classes.size() << "classes";
                return;
        }
 
-       // Add the annotation
-       (*row_iter).second.emplace_annotation(pdata);
+       // Add the data chunk
+       bin_class->chunks.emplace_back();
+       DecodeBinaryDataChunk* chunk = &(bin_class->chunks.back());
+
+       chunk->sample = pdata->start_sample;
+       chunk->data.resize(pdb->size);
+       memcpy(chunk->data.data(), pdb->data, pdb->size);
+
+       Decoder* dec = ds->get_decoder_by_instance(srd_dec);
+
+       ds->new_binary_data(ds->current_segment_id_, (void*)dec, pdb->bin_class);
+}
+
+void DecodeSignal::logic_output_callback(srd_proto_data *pdata, void *decode_signal)
+{
+       assert(pdata);
+       assert(decode_signal);
+
+       DecodeSignal *const ds = (DecodeSignal*)decode_signal;
+       assert(ds);
+
+       if (ds->decode_interrupt_)
+               return;
+
+       lock_guard<mutex> lock(ds->output_mutex_);
+
+       assert(pdata->pdo);
+       assert(pdata->pdo->di);
+       const srd_decoder *const decc = pdata->pdo->di->decoder;
+       assert(decc);
+
+       const srd_proto_data_logic *const pdl = (const srd_proto_data_logic*)pdata->data;
+       assert(pdl);
+
+       // FIXME Only one group supported for now
+       if (pdl->logic_group > 0) {
+               qWarning() << "Received logic output state change for group" << pdl->logic_group << "from decoder" \
+                       << QString::fromUtf8(decc->name) << "but only group 0 is currently supported";
+               return;
+       }
+
+       shared_ptr<Logic> output_logic = ds->output_logic_.at(decc);
+
+       vector< shared_ptr<Segment> > segments = output_logic->segments();
+
+       shared_ptr<LogicSegment> last_segment;
+
+       if (!segments.empty())
+               last_segment = dynamic_pointer_cast<LogicSegment>(segments.back());
+       else {
+               // Happens when the data was cleared - all segments are gone then
+               // segment_id is always 0 as it's the first segment
+               last_segment = make_shared<data::LogicSegment>(
+                       *output_logic, 0, (output_logic->num_channels() + 7) / 8, output_logic->get_samplerate());
+               output_logic->push_segment(last_segment);
+       }
+
+       if (pdata->start_sample < pdata->end_sample) {
+               vector<uint8_t> data;
+               const unsigned int unit_size = last_segment->unit_size();
+               data.resize(unit_size * (1 + pdl->repeat_count));
+
+               if (unit_size == 1)
+                       for (unsigned int i = 0; i <= pdl->repeat_count; i++)
+                               data.data()[i * unit_size] = *((uint8_t*)pdl->data);
+               else if (unit_size == 2)
+                       for (unsigned int i = 0; i <= pdl->repeat_count; i++)
+                               data.data()[i * unit_size] = *((uint16_t*)pdl->data);
+               else if (unit_size <= 4)
+                       for (unsigned int i = 0; i <= pdl->repeat_count; i++)
+                               data.data()[i * unit_size] = *((uint32_t*)pdl->data);
+               else if (unit_size <= 8)
+                       for (unsigned int i = 0; i <= pdl->repeat_count; i++)
+                               data.data()[i * unit_size] = *((uint64_t*)pdl->data);
+               else
+                       for (unsigned int i = 0; i <= pdl->repeat_count; i++)
+                               memcpy((void*)&data.data()[i * unit_size], (void*)pdl->data, unit_size);
+
+               last_segment->append_payload(data.data(), data.size());
+       } else
+               qWarning() << "Ignoring malformed logic output state change for group" << pdl->logic_group << "from decoder" \
+                       << QString::fromUtf8(decc->name) << "from" << pdata->start_sample << "to" << pdata->end_sample;
 }
 
 void DecodeSignal::on_capture_state_changed(int state)
@@ -1194,11 +1846,34 @@ void DecodeSignal::on_data_cleared()
 
 void DecodeSignal::on_data_received()
 {
+       // If we detected a lack of input data when trying to start decoding,
+       // we have set an error message. Bail out if we still don't have data
+       // to work with
+       if ((!error_message_.isEmpty()) && (get_input_segment_count() == 0))
+               return;
+
+       if (!error_message_.isEmpty()) {
+               error_message_.clear();
+               // TODO Emulate noquote()
+               qDebug().nospace() << name() << ": Input data available, error cleared";
+       }
+
        if (!logic_mux_thread_.joinable())
                begin_decode();
        else
                logic_mux_cond_.notify_one();
 }
 
+void DecodeSignal::on_input_segment_completed()
+{
+       if (!logic_mux_thread_.joinable())
+               logic_mux_cond_.notify_one();
+}
+
+void DecodeSignal::on_annotation_visibility_changed()
+{
+       annotation_visibility_changed();
+}
+
 } // namespace data
 } // namespace pv