Merge pull request #32 from Fluorescence-Tools/development

Fix issues with confocor3 header

examples/correlation/plot_confocor3_two_ch_correlation.py

@@ -116,6 +116,6 @@
     label="Corr(2,2)"
 )
 
-plt.ylim(1.032, 1.050)
+plt.ylim(0.98, 1.30)
 plt.show()
 

include/TTTRHeader.h

@@ -14,6 +14,8 @@
 #include <array>
 #include <memory>
 #include <numeric>
+#include <iostream>
+#include <iomanip> /* std::setfill */
 #include <fstream> /* ifstream */
 
 #include <any>

include/TTTRHeaderTypes.h

@@ -145,9 +145,15 @@ typedef union cz_confocor3_settings{
     struct{
         char Ident[52];
         char dummy1[11];
-        unsigned channel        :8;
-        unsigned TagHead_Idx    :32;
-        unsigned sync_rate      :32;
+        unsigned channel               :8;
+        // 64 byte
+        uint32_t measure_id[4];  // 16
+        uint32_t measurement_position; // 8
+        uint32_t kinetic_index; // 8
+        uint32_t repetition_number; // 8
+        uint32_t frequency; // 8
+        char dummy2[32]; //32
+        // 64 + 64 byte
     } bits;
 } cz_confocor3_settings_t;
 

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-version = "0.24.1"
+version = "0.24.2"
 name = "tttrlib"
 requires-python = ">=3.8"
 description = "Read, write & process time-tagged time-resolved (TTTR) data."

src/TTTRHeader.cpp

@@ -152,22 +152,45 @@ size_t TTTRHeader::read_cz_confocor3_header(
     if(rewind) std::fseek(fpin, 0, SEEK_SET);
     cz_confocor3_settings_t rec;
     fread(&rec, sizeof(rec),1, fpin);
-    fseek(fpin, 68, 0);
-    float sync_rate;
-    fread(&sync_rate, sizeof(float), 1, fpin);
-    double mt_clk = 1. / (1000. * sync_rate);
+
+    float frequency_float = rec.bits.frequency;
+    double mt_clk = 1. / frequency_float;
+
+    // Convert each element to hexadecimal and concatenate them
+    std::stringstream ss;
+    for (int i = 0; i < 4; i++) {
+        ss << std::hex << std::setw(8) << std::setfill('0') << rec.bits.measure_id[i];
+    }
+    size_t total_length = ss.str().length() + 1;
+    char* hex_measure_id = new char[total_length];
+    std::strcpy(hex_measure_id, ss.str().c_str());
+
+    int measurement_position = rec.bits.measurement_position;
+    int kinetic_index = rec.bits.kinetic_index;
+    int repetition_number = rec.bits.repetition_number;
+    int channel_nbr = rec.bits.channel - 48;
 
     add_tag(data, TTTRTagGlobRes, mt_clk, tyFloat8);
     // Convert ASCII channel number to int
-    add_tag(data, "channel", rec.bits.channel - 48, tyInt8);
-    add_tag(data, TTTRTagBits, 32, tyInt8);
     add_tag(data, TTTRRecordType, (int) CZ_RECORD_TYPE_CONFOCOR3, tyInt8);
+    add_tag(data, "channel", channel_nbr, tyInt8);
+    add_tag(data, "measure_id", hex_measure_id, tyAnsiString);
+    add_tag(data, "measurement_position", measurement_position + 1, tyInt8);
+    add_tag(data, "kinetic_index", kinetic_index + 1, tyInt8);
+    add_tag(data, "repetition_number", repetition_number + 1, tyInt8);
+    add_tag(data, TTTRTagBits, 32, tyInt8);
 #ifdef VERBOSE_TTTRLIB
     std::clog << "-- Confocor3 header reader " << std::endl;
+    std::clog << "-- frequency_float: " << frequency_float << std::endl;
+    std::clog << "-- measure_id_string: " << hex_measure_id << std::endl;
     std::clog << "-- macro_time_resolution: " << mt_clk << std::endl;
-    std::clog << "-- macro_time_resolution: " << sync_rate << std::endl;
+    std::clog << "-- channel_nbr: " << channel_nbr << std::endl;
+    std::clog << "-- measurement_position: " << measurement_position << std::endl;
+    std::clog << "-- kinetic_index: " << kinetic_index << std::endl;
+    std::clog << "-- repetition_number: " << repetition_number << std::endl;
+    std::clog << "-- header bytes: " << sizeof(rec) << std::endl;
 #endif
-    return 80;
+    return sizeof(rec);
 }
 
 

src/TTTRRecordReader.cpp

@@ -291,30 +291,27 @@ bool ProcessSPC600_256(
         ){
     bh_spc600_256_record_t rec;
     rec.allbits = TTTRRecord;
-
     if(!rec.bits.mtov && !rec.bits.invalid){
         // normal record
         true_nsync = rec.bits.mt + overflow_counter * 4096;
         micro_time = (uint16_t) (255 - rec.bits.adc);
         channel = (uint16_t) (rec.bits.rout);
         return true;
-    } else{
-        if(!rec.bits.invalid && rec.bits.mtov){
-            // valid record with a single macro time overflow
-            overflow_counter += 1;
-            true_nsync = rec.bits.mt + overflow_counter * 65536; // 65536 = 2**16 (16 bits for macro time counter)
-            micro_time = (uint16_t) (255 - rec.bits.adc);
-            channel = (uint16_t) (rec.bits.rout);
-            return true;
-        } else{
-            if(rec.bits.invalid && rec.bits.mtov){
-                bh_overflow_t ovf;
-                ovf.allbits = TTTRRecord;
-                overflow_counter += ovf.bits.cnt;
-                return false;
-            }
-        }
     }
+    if(!rec.bits.invalid && rec.bits.mtov){
+        // valid record with a single macro time overflow
+        overflow_counter += 1;
+        true_nsync = rec.bits.mt + overflow_counter * 65536; // 65536 = 2**16 (16 bits for macro time counter)
+        micro_time = (uint16_t) (255 - rec.bits.adc);
+        channel = (uint16_t) (rec.bits.rout);
+        return true;
+    }
+    if(rec.bits.invalid && rec.bits.mtov){
+            bh_overflow_t ovf;
+            ovf.allbits = TTTRRecord;
+            overflow_counter += ovf.bits.cnt;
+            return false;
+        }
     return false;
 }