Merge branch 'main' into 2D_I_GUI

autodeer/FieldSweep.py

@@ -104,7 +104,7 @@ 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

@@ -33,7 +33,7 @@ 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'):
@@ -363,7 +363,7 @@ 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 +113,8 @@ 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:
                 self.log.warning("WARNING: Dataset missing number of averages(nAvgs)!")
                 nAvgs = 1
             finally:

autodeer/colors.py

@@ -1,3 +1,3 @@
-primary_colors=['#D95B6F','#42A399','E1AE38']
+primary_colors=['#D95B6F','#42A399','#E1AE38']
 ReIm_colors = ['#D61B00','#00BBD6']
 shade_colors=[]

autodeer/dataset.py

@@ -173,13 +173,13 @@ 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):
@@ -188,13 +188,13 @@ 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

@@ -80,7 +80,7 @@ def __init__(self, interface, wait:QtCore.QWaitCondition, mutex:QtCore.QMutex,pu
         self.stop_flag = False
         self.quick_deer_state = True
 
-        self.max_tau = 5
+        self.max_tau = 3.5
 
         if (self.project is None) or (self.project == ''):
             def savename(exp, suffix=""):
@@ -190,7 +190,7 @@ def run_CP_relax(self,dt=200):
         gyro = self.gyro
         reptime = self.reptime
         relax = DEERSequence(
-            B=LO/gyro, LO=LO,reptime=reptime,averages=10,shots=int(10*self.noise_mode),
+            B=LO/gyro, LO=LO,reptime=reptime,averages=10,shots=int(20*self.noise_mode),
             tau1=0.5, tau2=0.5, tau3=0.2, dt=15,
             exc_pulse=self.pulses['exc_pulse'], ref_pulse=self.pulses['ref_pulse'],
             pump_pulse=self.pulses['pump_pulse'], det_event=self.pulses['det_event']
@@ -217,7 +217,7 @@ def run_T2_relax(self,dt=60):
         reptime = self.reptime
 
         seq = T2RelaxationSequence(
-            B=LO/gyro, LO=LO,reptime=reptime,averages=10,shots=int(20*self.noise_mode),
+            B=LO/gyro, LO=LO,reptime=reptime,averages=10,shots=int(40*self.noise_mode),
             step=dt,dim=200,pi2_pulse=self.pulses['exc_pulse'],
             pi_pulse=self.pulses['ref_pulse'], det_event=self.pulses['det_event'])
 
@@ -236,12 +236,12 @@ def run_2D_relax(self):
         reptime = self.reptime
 
         seq = RefocusedEcho2DSequence(
-            B=LO/gyro, LO=LO,reptime=reptime,averages=10,shots=int(20*self.noise_mode),
+            B=LO/gyro, LO=LO,reptime=reptime,averages=10,shots=int(50*self.noise_mode),
             tau=self.max_tau, pi2_pulse=self.pulses['exc_pulse'],
             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/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)
 
@@ -152,6 +152,10 @@ def extract_date_time(str):
                     data = uwb_eval_match(Matfile, exp,verbosity=verbosity,filter_type='cheby2',filter_width=0.01)
                 else:
                     data = uwb_eval_match(Matfile, exp,verbosity=verbosity)
+
+                if np.all(data.data == 0+0j):
+                    time.sleep(10)
+                    continue
             except OSError:
                 time.sleep(10)
             except IndexError:
@@ -254,10 +258,11 @@ 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 +323,7 @@ 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 +472,7 @@ 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 +815,7 @@ def terminate(self):
             self.engine.dig_interface('terminate', nargout=0)
             self.stop_flag.set()
             self.bg_thread = None
-            self.bg_data = None
+
         pass
 
 
@@ -879,7 +884,7 @@ def set_params_by_uuid(new_seq, progTable,uuid,index):
             while bool(interface.engine.dig_interface('savenow')):
                 if stop_flag.is_set():
                     break
-                time.sleep(1)
+                time.sleep(10)
 
             if reduced:
                 single_scan_data = interface.acquire_dataset_from_matlab(cur_exp=tmp_seq).data
@@ -888,4 +893,5 @@ 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