Merge pull request #90 from qt3uw/fix-cwodmr-bug-when-returning-summe…

…d-raw-trace

Fixes issue with converting list of heterogeneous type to numpy array. 

Tested locally on QLM

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "qt3utils"
-version = "1.0.2.dev0"
+version = "1.0.2.dev1"
 
 description = "A package for performing experiments in the QT3 lab at UW."
 readme = "README.md"

src/qt3utils/experiments/cwodmr.py

@@ -88,10 +88,10 @@ def experimental_conditions(self):
     def run(self, N_cycles = 500000,
                   post_process_function = simple_measure_contrast,
                   random_order = False):
-        '''
-        Performs the CWODMR scan over the specificed range of frequencies.
+        """
+        Performs the CWODMR scan over the specified range of frequencies.
 
-        For each frequency, some number of cycles of data are acquired. A cycle
+        For each frequency, the specified number of cycles of data are acquired. A cycle
         is one full sequence of the pulse train used in the experiment. For CWODMR,
         a cycle is {RF on for pulser.rf_pulse_duration time, RF off for pulser.rf_pulse_duration time}.
 
@@ -109,7 +109,7 @@ def run(self, N_cycles = 500000,
         which is useful to reduce the required memory to hold the raw data.
 
         After data acquisition for each frequency in the scan,
-        the post_process_function function is called and takes two arguments:
+        the post_process_function is called and takes two arguments:
             1) data_buffer: the full trace of data acquired
             2) self: a reference to an instance of this object
 
@@ -118,15 +118,18 @@ def run(self, N_cycles = 500000,
 
         If post_process_function = None, the full raw data trace will be kept.
 
-        The return from this function is a list. Each element of the list
+        The return from this function is a numpy array. Each element of the array
         is a list of the following values
-            RF Frequency,
-            data_post_processing_output (or raw data trace)
+            RF Frequency (float),
+            data_post_processing_output, or raw data trace (typically of type numpy array(dtype = float))
+
+        Because of the mixed types in this array, the numpy array data type returned
+        here is an 'object'.
 
         The remaining (fixed) values for analysis can be obtained from the
         self.experimental_conditions function.
 
-        '''
+        """
 
         self.N_cycles = int(N_cycles)
 
@@ -203,7 +206,7 @@ def run(self, N_cycles = 500000,
                 logger.error(f'in finally.close. {type(e)}: {e}')
 
             self.rfsynth.rf_off(self.rfsynth_channel)
-            data = np.array(data)
+            data = np.array(data, dtype=object)
             data = data[data[:,0].argsort()] #sorts the data by values in zeroth column... this is necessary if random_order = True
             return data
 

src/qt3utils/experiments/podmr.py

@@ -96,7 +96,7 @@ def _stop_and_close_daq_tasks(self):
     def run(self, N_cycles = 500000,
                   post_process_function = simple_measure_contrast,
                   random_order = False):
-        '''
+        """
         Performs the PulsedODMR scan over the specificed range of frequencies.
 
         For each frequency, some number of cycles of data are acquired. A cycle
@@ -117,7 +117,7 @@ def run(self, N_cycles = 500000,
         which is useful to reduce the required memory to hold the raw data.
 
         After data acquisition for each frequency in the scan,
-        the post_process_function function is called and takes two arguments:
+        the post_process_function is called and takes two arguments:
             1) data_buffer: the full trace of data acquired
             2) self: a reference to an instance of this object
 
@@ -126,16 +126,19 @@ def run(self, N_cycles = 500000,
 
         If post_process_function = None, the full raw data trace will be kept.
 
-        The return from this function is a list. Each element of the list
+        The return from this function is a numpy array. Each element of the array
         is a list of the following values
-            RF Frequency,
-            data_post_processing_output (or raw data trace)
+            RF Frequency (float),
+            data_post_processing_output, or raw data trace (typically of type numpy array(dtype = float))
+
+        Because of the mixed types in this array, the numpy array data type returned
+        here is an 'object'.
 
         The remaining (fixed) values for analysis can be obtained from the
         self.experimental_conditions function.
 
 
-        '''
+        """
 
         self.N_cycles = int(N_cycles)
 
@@ -210,7 +213,7 @@ def run(self, N_cycles = 500000,
             except Exception as e:
                 logger.error(f'in finally.close. {type(e)}: {e}')
             #rfsynth.rf_off(self.rfsynth_channel)
-            data = np.array(data)
+            data = np.array(data, dtype=object)
             data = data[data[:,0].argsort()] #sorts the data by values in zeroth column... this is necessary if random_order = True
 
             return data

src/qt3utils/experiments/rabi.py

@@ -188,7 +188,7 @@ def _acquire_data_at_parameter(self, rf_pulse_duration, N_cycles = 10000,
 
     def run(self, N_cycles = 50000,
                   post_process_function = qt3utils.experiments.podmr.simple_measure_contrast):
-        '''
+        """
         Performs the scan over the specificed range of RF widths.
 
         For each RF width, some number of cycles of data are acquired. A cycle
@@ -221,14 +221,17 @@ def run(self, N_cycles = 50000,
 
         If post_process_function = None, the full raw data trace will be kept.
 
-        The return from this function is a list. Each element of the list
+        The return from this function is a numpy array. Each element of the array
         is a list of the following values
-            RF width,
-            data_post_processing_output (or raw data trace)
+            RF width (float),
+            data_post_processing_output, or raw data trace (typically of type numpy array(dtype = float))
+
+        Because of the mixed types in this array, the numpy array data type returned
+        here is an 'object'.
 
         The remaining (fixed) values for analysis can be obtained from the
         self.experimental_conditions function.
-        '''
+        """
 
         #first check that the pulser width is large enough
         try:
@@ -267,8 +270,7 @@ def run(self, N_cycles = 50000,
             except Exception as e:
                 pass
             #rfsynth.rf_off(self.rfsynth_channel)
-            data = np.array(data)
+            data = np.array(data, dtype=object)
 
             return data
 
-        return data

src/qt3utils/experiments/ramsey.py

@@ -26,7 +26,7 @@ def __init__(self, ramsey_pulser, rfsynth, edge_counter_config,
         of an experiment and the hardware system setup.
 
         Hardware Settings
-            ramsey_pulser - a qt3utils.experiments.pulsers.pulseblaster.PulseBlasterRamHahnDD object
+            ramsey_pulser - a qt3utils.pulsers.pulseblaster.PulseBlasterRamHahnDD object
             rfsynth - a qt3rfsynthcontrol.Pulser object
             edge_counter_config - a qt3utils.nidaq.config.EdgeCounter object
 
@@ -101,27 +101,24 @@ def experimental_conditions(self):
 
     def run(self, N_cycles = 50000,
                   post_process_function = qt3utils.experiments.podmr.simple_measure_contrast):
-        '''
+        """
         Performs the scan over the specificed range of free precession times.
 
-        For each RF width, some number of cycles of data are acquired. A cycle
-        is one full sequence of the pulse train used in the experiment.
-        For Rabi, a cycle is {AOM on, AOM off/RF on, AOM on, AOM off/RF off}.
+        For each RF pulse delay, tau, some number of cycles of data are acquired. A cycle
+        is one full sequence of the pulse train used in the experiment as specified
+        by the supplied ramsey_pulser object.
 
         The N_cycles specifies the total number of these cycles to
         acquire. Your choice depends on your desired resolution or signal-to-noise
         ratio, your post-data acquisition processing choices, and the amount of memory
         available on your computer.
 
-        For each width, the number of data read from the NI DAQ will be
+        For each free precession time, tau, the number of data read from the NI DAQ will be
         N_clock_ticks_per_cycle * N_cycles, where N_clock_ticks_per_cycle
         is the value returned by self.set_pulser_state(tau).
 
-        Given the way our pulser is configured, N_clock_ticks_per_cycle will
-        grow linearly by tau.
-
         The acquired data are stored in a data_buffer within this method. They
-        may be analyzed with a function passed to post_process_function,
+        may be processed with a function passed to post_process_function,
         which is useful to reduce the required memory to hold the raw data.
 
         After data acquisition for each width in the scan,
@@ -134,14 +131,17 @@ def run(self, N_cycles = 50000,
 
         If post_process_function = None, the full raw data trace will be kept.
 
-        The return from this function is a list. Each element of the list
+        The return from this function is a numpy array. Each element of the array
         is a list of the following values
-            RF width,
-            data_post_processing_output (or raw data trace)
+            RF Frequency (float),
+            data_post_processing_output, or raw data trace (typically of type numpy array(dtype = float))
+
+        Because of the mixed types in this array, the numpy array data type returned
+        here is an 'object'.
 
         The remaining (fixed) values for analysis can be obtained from the
         self.experimental_conditions function.
-        '''
+        """
 
         #first check that the pulser width is large enough
         try:
@@ -228,8 +228,7 @@ def run(self, N_cycles = 50000,
             except Exception as e:
                 logger.error(f'in finally.close. {type(e)}: {e}')
             #rfsynth.rf_off(self.rfsynth_channel)
-            data = np.array(data)
+            data = np.array(data, dtype=object)
 
             return data
 
-        return data