From f5fb7a6f38afe210bb1ed1e77ca6f087f31e5321 Mon Sep 17 00:00:00 2001 From: G Adam Cox Date: Fri, 3 Feb 2023 10:54:32 -0800 Subject: [PATCH] Puts random sampler and nidaq sampler on equal footing. Moves common methods to base class. Only a _read_samples method and clock_rate should be implemeneted by subclasses. removes setting .running attribute in subclasses --- src/qt3utils/datagenerators/daqsamplers.py | 197 +++++++++++---------- 1 file changed, 106 insertions(+), 91 deletions(-) diff --git a/src/qt3utils/datagenerators/daqsamplers.py b/src/qt3utils/datagenerators/daqsamplers.py index d7466e45..4c3573d5 100644 --- a/src/qt3utils/datagenerators/daqsamplers.py +++ b/src/qt3utils/datagenerators/daqsamplers.py @@ -10,11 +10,12 @@ logger = logging.getLogger(__name__) class RateCounterBase(abc.ABC): - + """ + Subclasses must implement a clock_rate attribute or property. + """ def __init__(self): - self.clock_rate = 1 # default clock rate self.running = False - + self.clock_rate = 0 def stop(self): """ subclasses may override this for custom behavior @@ -34,27 +35,92 @@ def close(self): pass @abc.abstractmethod - def sample_counts(self, n_samples = 1) -> np.ndarray: + def _read_samples(self): """ - Should return a numpy array of size n_samples, with each row being - an array (or tuple) of two values, The first value is equal to the number of counts, - and the second value is the number of clock samples that were used to measure the counts. + subclasses must implement this method + + Should return total_counts, num_clock_samples + """ + pass + + def sample_counts(self, n_batches=1, sum_counts=True): + """ + Performs n_batches of batch reads from _read_samples method. + + This is useful when hardware (such as NIDAQ) is pre-configured to acquire a fixed number of samples + and the caller wishes to read more data than the number of samples acquired. + For example, if the NiDAQ is configured to acquire 1000 clock samples, but the caller + wishes to read 10000 samples, then this function may be called with n_batches=10. + + For each batch read (of size `num_data_samples_per_batch`), the + total counts are summed. Because it's possible (though unlikely) + for the hardware to return fewer than `num_data_samples_per_batch` measurements, + the actual number of data samples per batch are also recorded. + + If sum_counts is False, a numpy array of shape (n_batches, 2) is returned, where + the first element is the sum of the counts, and the second element is + the actual number of clock samples per batch. This may be useful for the caller if + they wish to perform their own averaging or other statistical analysis that may be time dependent. + + For example, if `num_data_samples_per_batch` is 5 and n_batches is 3, + (typical values are 100 and 10, 100 and 1, 1000 and 1, etc) - Example, if n_samples = 3 + reading counts from the NiDAQ may return + + #sample 1 + raw_counts_1 = [3,5,4,6,4] + sum_counts_1 = 22 + size_counts_1 = 5 + (22, 5) + #sample 2 + raw_counts_2 = [5,5,7,3,4] + sum_counts_2 = 24 + size_counts_2 = 5 + (24, 5) + #sample 3 + raw_counts_3 = [5,3,5,7] + sum_counts_3 = 20 + size_counts_2 = 4 + (20, 4) + + In this example, the numpy array is of shape (3, 2) and will be data = [ - [22, 5], # 22 counts were observed in 5 clock samples + [22, 5], [24, 5], - [20, 4] # this data indicates there was an error with data acquisition - 4 clock samples were observed. + [20, 4] ] + + If sum_counts is True, then will the total number of counts and total number of + clock samples read will be returned. + + np.sum(data, axis=0, keepdims=True). + + In the example above, this would be [[66, 14]]. + + With these data, and knowing the clock_rate, one can easily compute + the count rate. See sample_count_rate. """ - pass + + data = np.zeros((n_batches, 2)) + for i in range(n_batches): + data_sample, samples_read = self._read_samples() + if samples_read > 0: + data[i][0] = np.sum(data_sample[:samples_read]) + data[i][1] = samples_read + logger.info(f'batch data (sum counts, num clock cycles per batch): {data[i]}') + + if sum_counts: + return np.sum(data, axis=0, keepdims=True) + else: + return data def sample_count_rate(self, data_counts: np.ndarray): """ Converts the output of sample_counts to a count rate. Expects data_counts to be a 2d numpy array - of [[counts, clock_samples], [counts, clock_samples], ...] as is returned by sample_counts. + of [[counts, clock_samples], [counts, clock_samples], ...] or a 2d array with one row: [[counts, clock_samples]] + as is returned by sample_counts. - Under normal conditions, will return a single value + Returns the count rate in counts/second = clock_rate * total counts/ total clock_samples) If the sum of all clock_samples is 0, will return np.nan. """ @@ -64,7 +130,6 @@ def sample_count_rate(self, data_counts: np.ndarray): else: return np.nan - def yield_count_rate(self): while self.running: count_data = self.sample_counts() @@ -78,32 +143,41 @@ class RandomRateCounter(RateCounterBase): This is similar to a PL source moving in and out of focus. ''' - def __init__(self): + def __init__(self, simulate_single_light_source=False, num_data_samples_per_batch=10): super().__init__() self.default_offset = 100 - self.signal_noise_amp = 0.2 - self.possible_offset_values = np.arange(0, 1000, 50) + self.signal_noise_amp = 0.2 self.current_offset = self.default_offset self.current_direction = 1 - self.running = False + self.clock_rate = 0.9302010 # a totally random number :P + self.simulate_single_light_source = simulate_single_light_source + self.possible_offset_values = np.arange(5000, 100000, 1000) # these create the "bright" positions + self.num_data_samples_per_batch = num_data_samples_per_batch - def sample_counts(self, n_samples = 1): + def _read_samples(self): """ Returns a random number of counts """ - if np.random.random(1)[0] < 0.05: - if np.random.random(1)[0] < 0.1: - self.current_direction = -1 * self.current_direction - self.current_offset += self.current_direction*np.random.choice(self.possible_offset_values) + if self.simulate_single_light_source: + if np.random.random(1)[0] < 0.005: + self.current_offset = np.random.choice(self.possible_offset_values) + else: + self.current_offset = self.default_offset + + else: + if np.random.random(1)[0] < 0.05: + if np.random.random(1)[0] < 0.1: + self.current_direction = -1 * self.current_direction + self.current_offset += self.current_direction*np.random.choice(self.possible_offset_values) - if self.current_offset < self.default_offset: - self.current_offset = self.default_offset - self.current_direction = 1 + if self.current_offset < self.default_offset: + self.current_offset = self.default_offset + self.current_direction = 1 - counts = self.signal_noise_amp*self.current_offset*np.random.random(n_samples) + self.current_offset - count_size = np.ones(n_samples) - return np.column_stack((counts, count_size)) + counts = self.signal_noise_amp * self.current_offset * np.random.random(self.num_data_samples_per_batch) + self.current_offset + + return counts, self.num_data_samples_per_batch class NiDaqDigitalInputRateCounter(RateCounterBase): @@ -126,7 +200,6 @@ def __init__(self, daq_name = 'Dev1', self.read_write_timeout = read_write_timeout self.num_data_samples_per_batch = num_data_samples_per_batch self.trigger_terminal = trigger_terminal - self.running = False self.read_lock = False @@ -188,7 +261,6 @@ def _read_samples(self): self.read_lock = False return data_buffer, samples_read - def start(self): if self.running: self.stop() @@ -208,12 +280,12 @@ def _burn_and_log_exception(self, f): def stop(self): if self.running: while self.read_lock: - time.sleep(0.1) #wait for current read to complete + time.sleep(0.1) # wait for current read to complete if self.nidaq_config.clock_task: self._burn_and_log_exception(self.nidaq_config.clock_task.stop) - self._burn_and_log_exception(self.nidaq_config.clock_task.close) #close the task to free resource on NIDAQ - #self._burn_and_log_exception(self.nidaq_config.counter_task.stop) #will need to stop task if we move to continuous buffered acquisition + self._burn_and_log_exception(self.nidaq_config.clock_task.close) # close the task to free resource on NIDAQ + # self._burn_and_log_exception(self.nidaq_config.counter_task.stop) # will need to stop task if we move to continuous buffered acquisition self._burn_and_log_exception(self.nidaq_config.counter_task.close) self.running = False @@ -221,63 +293,6 @@ def stop(self): def close(self): self.stop() - def sample_counts(self, n_samples = 1): - ''' - Performs n_samples of batch reads from the NiDAQ. - - For each batch read (of size `num_data_samples_per_batch`), the - total counts are summed. Additionally, because it's possible (though unlikely) - for the NiDAQ to return fewer than `num_data_samples_per_batch` measurements, - the actual number of data samples per batch are also recorded. - - Finally, a numpy array of shape (n_samples, 2) is returned, where - the first element is the sum of the counts, and the second element is - the actual number of data samples per batch. - - For example, if `num_data_samples_per_batch` is 5 and n_samples is 3, - (typical values are 100 and 10, 100 and 1, 1000 and 1, etc) - - reading counts from the NiDAQ may return - - #sample 1 - raw_counts_1 = [3,5,4,6,4] - sum_counts_1 = 22 - size_counts_1 = 5 - (22, 5) - #sample 2 - raw_counts_2 = [5,5,7,3,4] - sum_counts_2 = 24 - size_counts_2 = 5 - (24, 5) - #sample 3 - raw_counts_3 = [5,3,5,7] - sum_counts_3 = 20 - size_counts_2 = 4 - (20, 4) - - In this example, the numpy array is of shape (3, 2) and will be - data = [ - [22, 5], - [24, 5], - [20, 4] - ] - - With these data, and knowing the clock_rate, one can easily compute - the count rate - #removes rows where num samples per batch were zero (which would be a bug in the code) - data = data[np.where(data[:,1] > 0)] - #count rate is the mean counts per clock cycle multiplied by the clock rate. - count_rate = clock_rate * data[:,0]/data[:,1] - ''' - - data = np.zeros((n_samples, 2)) - for i in range(n_samples): - data_sample, samples_read = self._read_samples() - if samples_read > 0: - data[i][0] = np.sum(data_sample[:samples_read]) - data[i][1] = samples_read - logger.info(f'batch data (sum counts, num clock cycles per batch): {data[i]}') - return data