- Modified how analog input sample times are computed by the Data_logger, to only use the chunk's timestamp if the sample time computed based on the previous sample time and sampling rate does not match the chunk timestamp. This avoids jumps in sample times at chunk boundaries that otherwise occured when sampling rate is > 1KHz.

- Changed the order of function calls at run start in framework.py to ensure that the run_start methods of hardware objects are called as late as possible in the sequence, ensuring sample times for analog inputs are as well aligned as possible with event/state timestamps.

Author: ThomasAkam

com/data_logger.py

@@ -132,6 +132,7 @@ def open_data_files(self, session_filepath):
         self.d_tempfile_path = self.path_stem + f'.data.1{self.data_type}.temp'
         self.time_tempfile  = open(self.t_tempfile_path, 'wb')
         self.data_tempfile = open(self.d_tempfile_path, 'wb')
+        self.next_chunk_start_time = 0
 
     def close_files(self):
         '''Close data files. Convert temp files to numpy.'''
@@ -148,9 +149,14 @@ def close_files(self):
 
     def save_analog_chunk(self, timestamp, data_array):
         '''Save a chunk of analog data to .pca data file.'''
+        if np.abs(self.next_chunk_start_time - timestamp/1000)<0.001:
+            chunk_start_time = self.next_chunk_start_time
+        else:
+            chunk_start_time = timestamp/1000
         times = (np.arange(len(data_array), dtype='float64') 
-                 / self.sampling_rate) + timestamp/1000 # Seconds
+                 / self.sampling_rate) + chunk_start_time # Seconds
         self.time_tempfile.write(times.tobytes())
         self.data_tempfile.write(data_array.tobytes())
         self.time_tempfile.flush()
-        self.data_tempfile.flush()
+        self.data_tempfile.flush()
+        self.next_chunk_start_time = chunk_start_time+len(data_array)/self.sampling_rate

pyControl/framework.py

@@ -126,15 +126,15 @@ def run():
     event_queue.reset()
     data_output_queue.reset()
     if not hw.initialised: hw.initialise()
+    usb_serial.setinterrupt(-1) # Disable 'ctrl+c' on serial raising KeyboardInterrupt.
     current_time = 0
     ut.print_variables(when='t')
-    hw.run_start()
     start_time = pyb.millis()
     clock.init(freq=1000)
-    clock.callback(_clock_tick)
-    usb_serial.setinterrupt(-1) # Disable 'ctrl+c' on serial raising KeyboardInterrupt.
-    running = True
+    clock.callback(_clock_tick) 
     sm.start()
+    hw.run_start()
+    running = True
     # Run
     while running:
         # Priority 1: Process hardware interrupts.

pyControl/hardware.py

@@ -235,10 +235,12 @@ def __init__(self, pin, name, sampling_rate, threshold=None, rising_event=None,
         assign_ID(self)
 
     def _run_start(self):
+        # Start sampling timer, initialise threshold, aquire first sample.
         self.timer.init(freq=self.Analog_channel.sampling_rate)
         self.timer.callback(self._timer_ISR)
         if self.threshold:
             self.threshold.run_start(self.read_sample())
+        self._timer_ISR(0)
 
     def _run_stop(self):
         self.timer.deinit()