Diff: main.cpp

Revision:

3:3888b5ecad7e

Parent:

2:b46d53a5f931

Child:

4:629ca12c04f4

--- a/main.cpp	Fri Aug 30 14:51:08 2019 +0000
+++ b/main.cpp	Thu Sep 05 08:28:26 2019 +0000
@@ -7,9 +7,11 @@
 #include <vector>
 #include <iterator>
 
-MODSERIAL pc(PA_9, PA_10, 512); //mcu TX, RX, 512 byte TX and RX buffers
+#define BUFFER_SIZE 4096
 
-uint8_t buffer[512];
+MODSERIAL pc(PA_9, PA_10, BUFFER_SIZE); //mcu TX, RX, BUFFER_SIZE byte TX and RX buffers
+
+uint8_t buffer[BUFFER_SIZE];
 size_t message_length;
 bool status;
 int i = 0;
@@ -17,15 +19,59 @@
 memspcr_ExperimentConfiguration exp_config = memspcr_ExperimentConfiguration_init_zero;
 int buffer_length;
 int n_points;
+//int logging_interval_ms = 100;  // typical for experimental testing 
+//int logging_interval_ms = 1000; // for drive electronics resistance measurement calibration
+//int logging_interval_ms = 5000; // for consumable temperature calibration
+int logging_interval_ms = 500;  // for melt curve measurement
 
 std::vector<memspcr_ThermalStep> profile;
 
+//Parameters for test ramp
+//float resistance[9]     = {  0.45, 0.525, 0.525, 0.535, 0.545, 0.555, 0.555};
+//int elapsed_time_ms[9]  = {     0,  1000,  2000,  3000,  4000,  5000,  6000};
+//int camera_offset_ms[9] = {     0,   500,   500,   500,   500,   500,   500};
 
-//Parameters
-float resistance[9] = {0.45,0.525,0.525,0.555,0.555,0.525,0.525,0.555};
-int elapsed_time_ms[9] = {0,5000,10000,10001,15000,15001,20000};
-int camera_offset_ms[9] = {0,0,250,0,100,100,100,200};
-        
+//Parameters for drive electronics resistance measurement calibration
+//float resistance[2]       = {     0,     0};
+//int elapsed_time_ms[2]    = {     0, 20000};
+//int camera_offset_ms[2]   = {     0,     0};
+
+//Parameters for consumable temperature calibration
+//float resistance[2]       = {     0,       0};
+//int elapsed_time_ms[2]    = {     0, 3600000};
+//int camera_offset_ms[2]   = {     0,       0};
+  
+//Melt curve programmed later  
+//float melt_resistance_start = 0.525;
+//float melt_resistance_end = 0.550;
+//float resistance[103];
+//int elapsed_time_ms[103];
+//int camera_offset_ms[103];    
+
+//RT-PCR temperature profile programmed later
+float resistance[165];
+float elapsed_time_ms[165];
+float camera_offset_ms[165];
+
+int RT_ramp_time_ms =        1000;
+int RT_hold_time_ms =        4000;
+float RT_resistance =       0.500;
+
+
+int hotstart_ramp_time_ms =  1000;
+int hotstart_hold_time_ms =  4000;
+float hotstart_resistance = 0.550;
+
+int low_ramp_time_ms =       2000;
+int low_hold_time_ms =       3000;
+float low_resistance =      0.520;
+
+int high_ramp_time_ms =      2000;
+int high_hold_time_ms =       500;
+float high_resistance =     0.550;
+
+int n_cycles =                 40;
+int camera_time_ms =         1000;
 
 void write_message()
 {
@@ -71,20 +117,94 @@
 
 int main()
 {
+    float melt_resistance_step;
+    
     /* This is the buffer where we will store our message. */
     pc.baud(115200);
     n_points = sizeof(resistance)/sizeof(float);
     buffer_length = sizeof(buffer)/sizeof(uint8_t);
 
-    //Prepare message
-    for (i = 0; i < n_points; i++)
-    {
-        memspcr_ThermalStep step = memspcr_ThermalStep_init_zero;
-        step.resistance = resistance[i];
-        step.elapsed_time_ms = elapsed_time_ms[i];
-        step.camera_offset_ms = camera_offset_ms[i];
-        profile.push_back(step);
-    }
+//    //Prepare temperature profile for melt curve with 100 images
+//    melt_resistance_step = (melt_resistance_end - melt_resistance_start)/100;
+//
+//    //Initial setpoint
+//    resistance[0] = 0.450;
+//    elapsed_time_ms[0] = 0;
+//    camera_offset_ms[0] = 0;
+//    
+//    //Ramp to start of melt curve
+//    resistance[1] = melt_resistance_start;
+//    elapsed_time_ms[1] = 2500;
+//    camera_offset_ms[1] = 0;
+//   
+//    //Hold at start of melt curve
+//    resistance[2] = melt_resistance_start;
+//    elapsed_time_ms[2] = 5000;
+//    camera_offset_ms[2] = 0;
+//    
+//    //Ramp temperature and obtain 100 images
+//    for (i = 0; i < 100; i++)
+//    {
+//        resistance[i+3] = resistance[i+2] + melt_resistance_step;
+//        elapsed_time_ms[i+3] = elapsed_time_ms[i+2] + logging_interval_ms;
+//        camera_offset_ms[i+3] = 10;
+//    }
+//
+//    for (i = 0; i < n_points; i++)
+//    {
+//        memspcr_ThermalStep step = memspcr_ThermalStep_init_zero;
+//        step.resistance = resistance[i];
+//        step.elapsed_time_ms = elapsed_time_ms[i];
+//        step.camera_offset_ms = camera_offset_ms[i];
+//        profile.push_back(step);
+//    }
+ 
+//Prepare temperature profile for RT-PCR with hotstart and 40 cycles
+
+//RT
+resistance[0] = 0.450;
+elapsed_time_ms[0] = 0;
+camera_offset_ms[0] = 0;
+
+resistance[1] = RT_resistance;
+elapsed_time_ms[1] = RT_ramp_time_ms;
+camera_offset_ms[1] = 0;
+
+resistance[2] = RT_resistance;
+elapsed_time_ms[2] = elapsed_time_ms[1] + RT_hold_time_ms;
+camera_offset_ms[2] = 0;
+
+//Hotstart
+resistance[3] = RT_resistance;
+elapsed_time_ms[3] = elapsed_time_ms[2] + hotstart_ramp_time_ms;
+camera_offset_ms[3] = 0;
+
+resistance[4] = RT_resistance;
+elapsed_time_ms[4] = elapsed_time_ms[3] + hotstart_hold_time_ms;
+camera_offset_ms[4] = 0;
+
+//Thermocycle
+for (i = 0; i < 4*n_cycles; i=i+4)
+{
+    // ramp high
+    resistance[i+4] = high_resistance;
+    elapsed_time_ms[i+4] = elapsed_time_ms[i+3] + high_ramp_time_ms;
+    camera_offset_ms[i+4] = 0;
+    // hold high
+    resistance[i+5] = high_resistance;
+    elapsed_time_ms[i+5] = elapsed_time_ms[i+4] + high_hold_time_ms;
+    camera_offset_ms[i+5] = 0;
+    // ramp low
+    resistance[i+6] = low_resistance;
+    elapsed_time_ms[i+6] = elapsed_time_ms[i+5] + low_ramp_time_ms;
+    camera_offset_ms[i+6] = 0;
+    // hold low
+    resistance[i+7] = low_resistance;
+    elapsed_time_ms[i+7] = elapsed_time_ms[i+6] + low_hold_time_ms;
+    camera_offset_ms[i+7] = low_hold_time_ms - camera_time_ms;
+}   
+
+ 
     //Set set points  
     exp_config.profile.arg = &profile;
     exp_config.profile.funcs.encode = encode_callback;
@@ -98,11 +218,9 @@
     exp_config.optics.led_pwm = 0.5;
     exp_config.fluidics.pressure_setpoint = 0.4;
     exp_config.fluidics.pressure_hysterisis = 0.01;
-    exp_config.logging_interval_ms = 100;
+    exp_config.logging_interval_ms = logging_interval_ms;
     exp_config.selected_heater = memspcr_ExperimentConfiguration_Heater_MAIN;
 
-    
-    
     encode_message();
     write_message();