dataset correctphase update

correctphase returns a new object not correcting the old object

autodeer/FieldSweep.py

@@ -102,7 +102,7 @@ def __init__(self, dataset:DataArray) -> None:
             self.axis = dataset['X']
 
         self.data = dataset
-        self.data.epr.correctphasefull
+        self.data = self.data.epr.correctphasefull
 
         if 'LO' in dataset.attrs:
             self.LO = dataset.attrs['LO']

autodeer/Relaxation.py

@@ -32,7 +32,7 @@ def __init__(self, dataset, sequence: Sequence = None) -> None:
         else:
             self.axis = dataset['X']
 
-        dataset.epr.correctphasefull
+        dataset = dataset.epr.correctphasefull
         self.data = dataset.data
         self.dataset = dataset
         # if sequence is None and hasattr(dataset,'sequence'):
@@ -362,7 +362,7 @@ def __init__(self, dataset, sequence: Sequence = None) -> None:
             self.axis.append(dataset['Xt'])
             self.axis.append(dataset['Yt'])
 
-        dataset.epr.correctphasefull
+        dataset = dataset.epr.correctphasefull
         self.data = dataset.data
         self.dataset = dataset
 

autodeer/classes.py

@@ -113,7 +113,7 @@ def terminate_at(self, criterion, test_interval=2, keep_running=True, verbosity=
             try:
                 # nAvgs = data.num_scans.value
                 nAvgs = data.attrs['nAvgs']
-            except AttributeError:
+            except AttributeError or KeyError:
                 print("WARNING: Dataset missing number of averages(nAvgs)!")
                 nAvgs = 1
             finally:

autodeer/dataset.py

@@ -174,13 +174,13 @@ def save(self, filename,type='netCDF'):
 
     @property
     def correctphase(self):
-
+        new_obj = copy.deepcopy(self._obj)
         if np.iscomplexobj(self._obj.data):
                 corr_data = correctphase(self._obj.data)
-                self._obj.data = corr_data
+                new_obj.data = corr_data
         else:
             UserWarning("Data is not complex, phase correction not applied")
-        return self._obj
+        return new_obj
 
     @property
     def normalise(self):
@@ -189,13 +189,13 @@ def normalise(self):
 
     @property
     def correctphasefull(self):
-
+        new_obj = copy.deepcopy(self._obj)
         if np.iscomplexobj(self._obj.data):
                 Re,Im,_ = correctphase(self._obj.data,full_output=True)
-                self._obj.data = Re + 1j*Im
+                new_obj.data = Re + 1j*Im
         else:
             UserWarning("Data is not complex, phase correction not applied")
-        return self._obj
+        return new_obj
 
     @property
     def SNR(self):

autodeer/gui/autoDEER_worker.py

@@ -241,7 +241,7 @@ def run_2D_relax(self):
             pi_pulse=self.pulses['ref_pulse'], det_event=self.pulses['det_event'])
 
         self.interface.launch(seq,savename=self.savename("2D_DEC"),IFgain=2)
-        self.interface.terminate_at(SNRCriteria(10),test_interval=0.5)
+        self.interface.terminate_at(SNRCriteria(30),test_interval=0.5)
         while self.interface.isrunning():
             time.sleep(self.updaterate)
         self.signals.Relax2D_result.emit(self.interface.acquire_dataset())
@@ -388,11 +388,11 @@ def _build_methods(self):
 
         if (seq is None) or (seq == '5pDEER'):
             methods.append(self.run_CP_relax)
+            methods.append(self.run_T2_relax)
         elif (seq == '4pDEER') or (seq == 'Ref2D'):
             methods.append(self.run_CP_relax)
+            methods.append(self.run_T2_relax)
             methods.append(self.run_2D_relax)
-
-        methods.append(self.run_T2_relax)
 
         if seq == 'Ref2D':
             return methods

autodeer/gui/main.py

@@ -691,10 +691,15 @@ def create_relax_figure(self):
 
     def refresh_relax_figure(self):
 
-
-        if 'relax2D' in self.current_results:
+        if isinstance(self.relax_ax, np.ndarray):
             self.relax_ax[0].cla()
             self.relax_ax[1].cla()
+        else:
+            self.relax_ax.cla()
+
+
+        if 'relax2D' in self.current_results:
+
             fig, axs  = plt.subplots(2,1,figsize=(12.5, 6.28),layout='constrained',height_ratios=[2,1])
             relax_canvas = FigureCanvas(fig)
             self.relax_canvas.figure.clear()
@@ -705,7 +710,6 @@ def refresh_relax_figure(self):
             self.current_results['relax2D'].plot2D(axs=self.relax_ax[0],fig=fig)
             self.current_results['relax2D'].plot1D(axs=self.relax_ax[1],fig=fig)        
         else:
-            self.relax_ax.cla()
             fig = self.relax_canvas.figure
             axs = self.relax_ax
             relax1D_results = []

autodeer/hardware/Bruker_AWG.py

@@ -253,7 +253,7 @@ def tune_rectpulse(self,*,tp, LO, B, reptime, shots=400):
         while self.isrunning():
             time.sleep(10)
         dataset = self.acquire_dataset()
-        dataset.epr.correctphase
+        dataset = dataset.epr.correctphase
 
         data = np.abs(dataset.data)
         scale = np.around(dataset.pulse0_scale[data.argmax()].data,2)
@@ -358,7 +358,7 @@ def tune_pulse(self, pulse, mode, LO, B , reptime, shots=400):
             while self.isrunning():
                 time.sleep(10)
             dataset = self.acquire_dataset()
-            dataset.epr.correctphase
+            dataset = dataset.epr.correctphase
             data = dataset.data
             axis = dataset.pulse0_scale
             # data = correctphase(dataset.data)

autodeer/hardware/ETH_awg.py

@@ -105,7 +105,7 @@ def acquire_dataset(self,verbosity=0):
         if self.bg_data is None:
             data = self.acquire_dataset_from_matlab(verbosity=verbosity)
         else:
-            data = create_dataset_from_sequence(self.bg_data, self.cur_exp)
+            data = self.bg_data
 
         return super().acquire_dataset(data)
 
@@ -254,10 +254,11 @@ def launch_long(self, sequence , savename: str, IFgain: int = 0, axID=-1):
                 for item in p.dim:
                     dim.append(item)
         self.cur_exp = sequence
+        init_data = np.zeros(dim,dtype=np.complex128)
+        self.bg_data = create_dataset_from_sequence(init_data,self.cur_exp,extra_params={'nAvgs':0})
+
         self.stop_flag = threading.Event()
         self.bg_thread = threading.Thread(target=bg_thread,args=[self,sequence,savename,IFgain,axID,self.stop_flag])
-        self.bg_data = np.zeros(dim,dtype=np.complex128)
-
         self.bg_thread.start()
         log.debug('Background thread starting')
 
@@ -318,7 +319,7 @@ def tune_rectpulse(self,*,tp, LO, B, reptime, shots=400):
         while self.isrunning():
             time.sleep(10)
         dataset = self.acquire_dataset()
-        dataset.epr.correctphase
+        dataset = dataset.epr.correctphase
 
         data = np.abs(dataset.data)
         scale = np.around(dataset.pulse0_scale[data.argmax()].data,2)
@@ -467,7 +468,7 @@ def tune_pulse(self, pulse, mode, LO, B , reptime, shots=400):
             while self.isrunning():
                 time.sleep(10)
             dataset = self.acquire_dataset()
-            dataset.epr.correctphase
+            dataset = dataset.epr.correctphase
             data = dataset.data
             axis = dataset.pulse0_scale
             # data = correctphase(dataset.data)
@@ -810,7 +811,7 @@ def terminate(self):
             self.engine.dig_interface('terminate', nargout=0)
             self.stop_flag.set()
             self.bg_thread = None
-            self.bg_data = None
+
         pass
 
 
@@ -888,4 +889,5 @@ def set_params_by_uuid(new_seq, progTable,uuid,index):
 
         if stop_flag.is_set():
             break
-        interface.bg_data += single_scan_data
+        interface.bg_data.data += single_scan_data
+        interface.bg_data.attrs['nAvgs'] = iavg+1