🐛 Prevent DExTer and PyDex File IDs getting out of sync with long camera exposures

danielruttley · danielruttley · commit bca4831034fb · 2023-02-20T12:46:40.000Z
diff --git a/andorcamera/roi_1x1_larger_arrays.dat b/andorcamera/roi_1x1_larger_arrays.dat
@@ -0,0 +1,23 @@
+0 setPointT    = -60
+1 coolerMode   = 1
+2 shutterMode  = 1
+3 outamp       = 0
+4 hsspeed      = 2
+5 vsspeed      = 4
+6 preampgain   = 3
+7 EMgain       = 10
+8 hbin         = 1
+9 hstart       = 112
+10 hend        = 272
+11 vbin        = 1
+12 vstart      = 132
+13 vend        = 292
+14 cropMode    = 0
+15 readmode    = 4
+16 acqumode    = 5
+17 triggerMode = 7
+18 frameTransf = 0
+19 fastTrigger = 0
+20 expTime     = 10e-3
+21 verbosity   = 0
+22 numKinetics = 1
diff --git a/dds/dds/defaultDDS2.txt b/dds/dds/defaultDDS2.txt
@@ -1 +1 @@
-{"FTW": ["110.0", "80.5", "83.33", "110.0", "253.0"], "POW": ["0.0", "0.0", "0.0", "0.0", "0.0"], "AMW": ["1.0", "1.0", "1.0", "0.74", "0.906"], "fout": [["110.0", "100.105", "100.076", "100.059", "100.077", "100.0938", "100.1106", "99.995"], ["80.37", "80.0", "80.0", "110.0", "0.0", "110.0", "0.0", "0.0"], ["84.3", "80.0", "80.0", "84.28", "110.0", "110.0", "110.08", "110.0"], ["100.0", "82.0", "100.0", "79.46", "0.0", "0.0", "0.0", "99.948"], ["250.0", "252.0", "100.0166", "250.0", "100.01", "100.035", "100.06", "99.938"]], "tht": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "amp": [["0.0", "0.305", "0.305", "0.075", "0.075", "0.075", "0.075", "0.305"], ["0.5", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["1.0", "0.0", "1.0", "1.0", "0.0", "0.0", "0.0", "0.85"], ["0.0", "1.0", "0.0", "1.0", "0.0", "0.0", "0.0", "0.9"], ["0.0", "0.906", "0.82", "0.33", "0.33", "0.33", "0.33", "0.33"]], "Start_Address": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["3.0", "0.0", "6.0", "509.0", "0.0", "0.0", "1010.0", "509.0"], ["3.0", "0.0", "6.0", "509.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "499.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "1011.0", "0.0", "1011.0", "0.0", "0.0", "0.0", "0.0"]], "End_Address": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["4.0", "1.0", "505.0", "1008.0", "1.0", "1.0", "1021.0", "1008.0"], ["4.0", "1.0", "505.0", "1008.0", "0.0", "0.0", "0.0", "0.0"], ["1.0", "500.0", "1000.0", "1000.0", "1000.0", "1000.0", "1000.0", "1000.0"], ["1.0", "1022.0", "1.0", "1022.0", "0.0", "0.0", "0.0", "0.0"]], "Rate": [["1.0", "1.0", "1.0", "1.0", "1.0", "1.0", "1.0", "1.0"], ["0.004", "0.004", "0.3", "0.3", "0.004", "0.004", "0.6", "0.3"], ["0.004", "0.004", "0.3", "0.3", "0.0", "0.0", "0.0", "0.0"], ["1.0", "0.281", "0.004", "0.188", "0.224", "0.251", "0.272", "0.4"], ["0.004", "0.1", "0.004", "0.1", "0.0", "0.0", "0.0", "0.0"]], "No_dwell": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "Zero_crossing": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "RAM_playback_mode": [[["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "0.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"]]], "RAM_data_filename": ["", "STIRAP_cos4.csv", "STIRAP_cos4.csv", "", "STIRAP_cos4.csv"]}
+{"FTW": ["110.0", "80.5", "83.33", "110.0", "253.0"], "POW": ["0.0", "0.0", "0.0", "0.0", "0.0"], "AMW": ["1.0", "1.0", "1.0", "0.74", "0.906"], "fout": [["110.0", "100.105", "100.076", "100.059", "100.077", "100.0938", "100.1106", "99.995"], ["80.37", "80.0", "80.0", "110.0", "0.0", "110.0", "0.0", "0.0"], ["84.3", "80.0", "80.0", "84.28", "110.0", "110.0", "110.08", "110.0"], ["100.0", "82.0", "100.0", "79.46", "0.0", "0.0", "0.0", "99.948"], ["250.0", "252.0", "100.0166", "250.0", "100.01", "100.035", "100.06", "99.938"]], "tht": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "amp": [["0.0", "0.305", "0.305", "0.075", "0.075", "0.075", "0.075", "0.305"], ["0.5", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["1.0", "0.0", "1.0", "1.0", "0.0", "0.0", "0.0", "0.85"], ["0.0", "1.0", "0.0", "1.0", "0.0", "0.0", "0.0", "0.9"], ["0.0", "0.906", "0.82", "0.33", "0.33", "0.33", "0.33", "0.33"]], "Start_Address": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["3.0", "0.0", "6.0", "509.0", "0.0", "0.0", "1010.0", "509.0"], ["3.0", "0.0", "6.0", "509.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "499.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "1011.0", "0.0", "1011.0", "0.0", "0.0", "0.0", "0.0"]], "End_Address": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["4.0", "1.0", "505.0", "1008.0", "1.0", "1.0", "1021.0", "1008.0"], ["4.0", "1.0", "505.0", "1008.0", "0.0", "0.0", "0.0", "0.0"], ["1.0", "500.0", "1000.0", "1000.0", "1000.0", "1000.0", "1000.0", "1000.0"], ["1.0", "1022.0", "1.0", "1022.0", "0.0", "0.0", "0.0", "0.0"]], "Rate": [["1.0", "1.0", "1.0", "1.0", "1.0", "1.0", "1.0", "1.0"], ["0.004", "0.004", "0.3", "0.3", "0.004", "0.004", "0.6", "0.3"], ["0.004", "0.004", "0.3", "0.3", "0.0", "0.0", "0.0", "0.0"], ["1.0", "0.281", "0.004", "0.188", "0.224", "0.251", "0.272", "0.4"], ["0.004", "0.1", "0.004", "0.1", "0.0", "0.0", "0.0", "0.0"]], "No_dwell": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "Zero_crossing": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "RAM_playback_mode": [[["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "0.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"]]], "RAM_data_filename": ["", "", "", "", ""]}
diff --git a/imageanalysis/atomChecker2.py b/imageanalysis/atomChecker2.py
@@ -272,6 +272,7 @@ def set_rois(self, ROIlist, atom='Cs'):
         """Set the ROI list as the new ROIs"""
         self.rh[atom].create_rois(len(ROIlist), label=atom+' ')
         self.rh[atom].resize_rois(ROIlist)
+        self.create_new_rois(atom=atom) # populates the table widget
         self.display_rois()
 
     def make_roi_grid(self, toggle=True, method='', atom='Cs'):
diff --git a/imageanalysis/dataanalysis.py b/imageanalysis/dataanalysis.py
@@ -29,7 +29,7 @@ def __init__(self, directory=None):
     
     def load_from_directory(self,directory):
         maia_files = [x for x in os.listdir(directory) if x.split('.')[0] == 'MAIA']
-        # print(maia_files)
+        print(maia_files)
         
         self.analysers = {}
         for file in maia_files:
@@ -125,7 +125,8 @@ def convert_maia_data_to_df(self,maia_data):
     
         # use threshold data to calculate occupancy
         counts_df_occupancy_columns = [x+' occupancy' for x in roi_names]
-        for occupancy_col, counts_col, thresh_col in zip(counts_df_occupancy_columns,counts_df,threshold_df):
+        for occupancy_col, counts_col, thresh_col in zip(counts_df_occupancy_columns,counts_df_columns,threshold_df_columns):
+            # print(occupancy_col, counts_col, thresh_col)
             counts_df[occupancy_col] = np.where(counts_df[counts_col] > threshold_df[thresh_col][0],True,False)
         
         self.num_images = num_images
@@ -135,7 +136,9 @@ def convert_maia_data_to_df(self,maia_data):
         self.aux_df = pd.concat([threshold_df,roi_coords_df],axis=1)
         
     def load_dfs_from_file(self,filename):
-        self.aux_df = pd.read_csv(filename,nrows=2)
+        print(filename)
+        self.aux_df = pd.read_csv(filename,nrows=1)
+        print(self.aux_df)
         self.counts_df = pd.read_csv(filename,skiprows=2,index_col='File ID')
         roi_names = [x[:-7] for x in self.counts_df.columns if ' counts' in x]
         
diff --git a/imageanalysis/imagerGUI.py b/imageanalysis/imagerGUI.py
@@ -438,6 +438,7 @@ def recieve_image(self,image,file_id=None,image_num=None):
         MAIA. The file ID and image number can be manually specified 
         or can just be left as None to let the MAIA assign the file ID 
         and image number."""
+        print('iGUI recieved image: file_id, image_num =',file_id,image_num)
         self.signal_send_maia_image.emit(image,file_id,image_num)
 
     def get_draw_image_num(self):
diff --git a/imageanalysis/multiAtomImageAnalyser.py b/imageanalysis/multiAtomImageAnalyser.py
@@ -194,8 +194,6 @@ def recieve_image(self,image,file_id=None,image_num=None):
             file_id = self.file_id
         if image_num is None:
             image_num = self.next_image
-        image_num = self.next_image
-        file_id = self.file_id
         self.queue.append([image,file_id,image_num])
         self.signal_status_message.emit('Recieved ID {} Im {} and placed in queue'.format(file_id,image_num))
         self.signal_draw_image.emit(image,image_num)
@@ -276,9 +274,15 @@ def process_next_image(self):
             image = image - self.emccd_bias # don't edit in place because this seemed to cause an issue with images not showing in GUI. Maybe not thread safe?
             # print('image min',np.min(image))
             # print('image max',np.max(image))
+            image_num_too_big = False
             for group in self.roi_groups:
                 for roi in group.rois:
-                    roi.counts[image_num][file_id] = image[roi.x:roi.x+roi.w,roi.y:roi.y+roi.h].sum()
+                    try:
+                        roi.counts[image_num][file_id] = image[roi.x:roi.x+roi.w,roi.y:roi.y+roi.h].sum()
+                    except IndexError: # image_num was not valid for the number of images that MAIA is expecting
+                        image_num_too_big = True
+            if image_num_too_big:
+                self.signal_status_message.emit('Image number {} is greater than max expected images, so this image has been ignored (most likely cause is rearrangement toggle).')
             self.signal_status_message.emit('Finished processing ID {} Im {}'.format(file_id,image_num))
             self.calculate_thresholds()
 
@@ -303,8 +307,8 @@ def calculate_thresholds(self):
         for group in self.roi_groups:
             for roi in group.rois:
                 for image in range(len(roi.counts)):
-                    print(roi.autothreshs)
-                    print('image',image)
+                    # print(roi.autothreshs)
+                    # print('image',image)
                     if roi.autothreshs[image]:
                         values = np.fromiter(roi.counts[image].values(), dtype=float)
                         roi.thresholds[image] = self.calculate_threshold(values)
@@ -416,13 +420,15 @@ def save(self):
         self.should_save to true, but this will only be done once the image 
         queue is empty."""
         if (self.should_save) and (not self.queue): # only save if should_save is True and queue is empty
-            # filename = self.results_path+'\{}\MAIA.{}.csv'.format(self.measure_prefix,self.hist_id) # TODO might need to add hist ID in here
-            filename = self.results_path+'\MAIA.{}.csv'.format(self.hist_id) # TODO might need to add hist ID in here
+            self.signal_status_message.emit('Beginning save process')
+            filename = self.results_path+'\MAIA.{}.csv'.format(self.hist_id)
             data = self.get_analyser_data()
+            self.signal_status_message.emit('Extracted analyser data')
             analyser = Analyser(data)
             additional_data = self.get_user_variable_dict()
             additional_data['Hist ID'] = self.hist_id
             additional_data['EMCCD bias'] = self.emccd_bias
+            self.signal_status_message.emit('Created Analyser, requesting data save')
             try:
                 analyser.save_data(filename,additional_data)
                 self.signal_status_message.emit('Saved data to {}'.format(filename))
diff --git a/master.py b/master.py
@@ -333,6 +333,7 @@ def init_UI(self, startn=0):
             'Resync DExTer', 'Start acquisition'])
         self.actions.resize(self.actions.sizeHint())
         self.centre_widget.layout.addWidget(self.actions, 2,0,1,1)
+
         
         # shortcuts
         self.shortcuts=[QShortcut('F2', self)]
@@ -359,6 +360,9 @@ def init_UI(self, startn=0):
         self.action_button.resize(self.action_button.sizeHint())
         self.centre_widget.layout.addWidget(self.action_button, 2,1, 1,1)
 
+        self.sync_label = QLabel('')
+        self.centre_widget.layout.addWidget(self.sync_label, 3,0, 1,3)
+
         #### choose main window position, dimensions: (xpos,ypos,width,height)
         self.setWindowTitle('PyDex controller')
         self.setWindowIcon(QIcon('docs/pydexicon.png'))
@@ -556,11 +560,13 @@ def start_action(self, action_text=''):
             if 'Run sequence' in action_text:
                 # queue up messages: start acquisition, check run number
                 self.action_button.setEnabled(False) # only process 1 run at a time
-                self.rn._k = 0 # reset image per run count 
+                self.rn._k = 0 # reset image per run count
+                self.rn.set_n('0')
                 self.rn.server.add_message(TCPENUM['TCP read'], 'start acquisition\n'+'0'*2000) 
                 self.rn.monitor.add_message(self.rn._n, 'update run number')
             elif 'Multirun run' in action_text:
                 if self.rn.seq.mr.check_table():
+                    self.rn.set_n('0')
                     if not self.sync_toggle.isChecked():
                         self.sync_toggle.setChecked(True) # it's better to multirun in synced mode
                         warning('Multirun has changed the "sync with DExTer" setting.')
@@ -590,6 +596,7 @@ def start_action(self, action_text=''):
                     self.rn.seq.mr.ind = 0
                     self.rn.seq.mr.reset_sequence(self.rn.seq.tr.copy())
                     self.rn.iGUI.clear_data_and_queue()
+                    self.sync_file_id_with_dexter(True)
             elif 'Skip multirun histogram' in action_text:
                 if self.rn.seq.mr.multirun:
                     self.rn.skip_mr_hist()
@@ -644,6 +651,14 @@ def sync_mode(self, toggle=True):
         reset_slot(self.rn.cam.AcquireEnd, self.rn.receive, toggle) 
         reset_slot(self.rn.cam.AcquireEnd, self.rn.unsync_receive, not toggle)
 
+    def sync_file_id_with_dexter(self, toggle):
+        """Toggles whether the PyDex File ID should be synced with Dexter."""
+        if toggle:
+            self.sync_label.setText('Sync File ID with DExTer: on')
+        else:
+            self.sync_label.setText('Sync File ID with DExTer: off')
+        reset_slot(self.rn.server.dxnum,self.rn.set_n,toggle)
+
     def set_inflxdb_toggle(self, toggle=False):
         """Whether to send data to influxdb database"""
         # self.rn.sw.send_data = toggle
@@ -699,6 +714,7 @@ def respond(self, msg=''):
             else: warning('Run %s started without camera acquisition.'%(self.rn._n))
             if 'restart' not in msg: self.rn.multirun_go(msg) # might be resuming multirun instead of starting a new one
         elif 'multirun run' in msg:
+            self.sync_file_id_with_dexter(False)
             if self.check_rois.isChecked(): # start experiment when ROIs have atoms
                 reset_slot(self.rn.check.rh['Cs'].trigger, self.trigger_exp_start, True) 
                 self.rn.atomcheck_go() # start camera in internal trigger mode
@@ -763,6 +779,9 @@ def end_run(self, msg=''):
         #         for im in unprocessed:
         #             # image dimensions: (# kscans, width pixels, height pixels)
         #             self.rn.receive(im[0]) 
+        
+        print('===reset ID slot===')
+        self.sync_file_id_with_dexter(True)
         self.idle_state()
         
     def print_times(self, keys=['waiting', 'blocking']):
diff --git a/monitor/DEoptimiseConfig.dat b/monitor/DEoptimiseConfig.dat
@@ -1,11 +1,11 @@
-n=16633
+n=0
 config_file=Z:/Tweezer/Code/Python 3.5/PyDex/monitor/DEoptimiseConfig.dat
 trace_file=DAQtrace.csv
 graph_file=99.2MHz.csv
-save_dir=Z:\Tweezer\Experimental Results\2023\January\13\Measure9
+save_dir=Z:\Tweezer\Experimental Results\2023\February\17\Measure0
 Sample Rate (kS/s)=50.0
-Duration (ms)=250.0
+Duration (ms)=600.0
 Trigger Channel=/Dev4/PFI0
 Trigger Level (V)=1.0
 Trigger Edge=rising
-channels=[[Dev4/ai0, STIRAP, 1.0, 0.0, 10.0, 0, 0], [Dev4/ai1, RB4, 1.0, 0.0, 1.0, 1, 1], [Dev4/ai2, bias coils, 1.0, 0.0, 10.0, 0, 0], [Dev4/ai3, RB2, 1.0, 0.0, 1.0, 1, 1], [Dev4/ai4, jump coils, 1.0, 0.0, 10.0, 0, 0], [Dev4/ai5, 1013, 1.0, 0.0, 5.0, 0, 0], [Dev4/ai6, RB1, 1.0, 0.0, 5.0, 1, 1], [Dev4/ai7, 817, 1.0, 0.0, 5.0, 0, 0]]
+channels=[[Dev4/ai0, Cs MOT, 1.0, 0.0, 10.0, 1, 1], [Dev4/ai1, RB4, 1.0, 0.0, 1.0, 0, 0], [Dev4/ai2, 1065 power, 1.0, 0.0, 10.0, 0, 0], [Dev4/ai3, RB2, 1.0, 0.0, 1.0, 0, 0], [Dev4/ai4, jump coils, 1.0, 0.0, 10.0, 0, 0], [Dev4/ai5, 1013, 1.0, 0.0, 5.0, 0, 0], [Dev4/ai6, RB1, 1.0, 0.0, 5.0, 0, 0], [Dev4/ai7, 817, 1.0, 0.0, 5.0, 0, 0]]
diff --git a/mythread.py b/mythread.py
@@ -8,7 +8,7 @@
  - if the queue is empty, keep refreshing.
  - stop the thread by calling close()
 """
-from PyQt5.QtCore import QThread, pyqtSignal
+from PyQt5.QtCore import QThread, pyqtSignal, pyqtSlot
 from PyQt5.QtWidgets import QApplication 
 enco = 'mbcs' # TCP message encoding
 
@@ -31,6 +31,7 @@ def __init__(self):
         super().__init__()
         self.app = QApplication.instance()
 
+    @pyqtSlot(object)
     def add_item(self, new_item, *args, **kwargs):
         """Append a new item to the queue for processing."""
         self.queue.append(new_item)
diff --git a/networking/runid.py b/networking/runid.py
diff --git a/saveimages/imsaver.py b/saveimages/imsaver.py
diff --git a/sequences/multirunEditor.py b/sequences/multirunEditor.py
diff --git a/state_last_closed.pds b/state_last_closed.pds

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		-{"FTW": ["110.0", "80.5", "83.33", "110.0", "253.0"], "POW": ["0.0", "0.0", "0.0", "0.0", "0.0"], "AMW": ["1.0", "1.0", "1.0", "0.74", "0.906"], "fout": [["110.0", "100.105", "100.076", "100.059", "100.077", "100.0938", "100.1106", "99.995"], ["80.37", "80.0", "80.0", "110.0", "0.0", "110.0", "0.0", "0.0"], ["84.3", "80.0", "80.0", "84.28", "110.0", "110.0", "110.08", "110.0"], ["100.0", "82.0", "100.0", "79.46", "0.0", "0.0", "0.0", "99.948"], ["250.0", "252.0", "100.0166", "250.0", "100.01", "100.035", "100.06", "99.938"]], "tht": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "amp": [["0.0", "0.305", "0.305", "0.075", "0.075", "0.075", "0.075", "0.305"], ["0.5", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["1.0", "0.0", "1.0", "1.0", "0.0", "0.0", "0.0", "0.85"], ["0.0", "1.0", "0.0", "1.0", "0.0", "0.0", "0.0", "0.9"], ["0.0", "0.906", "0.82", "0.33", "0.33", "0.33", "0.33", "0.33"]], "Start_Address": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["3.0", "0.0", "6.0", "509.0", "0.0", "0.0", "1010.0", "509.0"], ["3.0", "0.0", "6.0", "509.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "499.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "1011.0", "0.0", "1011.0", "0.0", "0.0", "0.0", "0.0"]], "End_Address": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["4.0", "1.0", "505.0", "1008.0", "1.0", "1.0", "1021.0", "1008.0"], ["4.0", "1.0", "505.0", "1008.0", "0.0", "0.0", "0.0", "0.0"], ["1.0", "500.0", "1000.0", "1000.0", "1000.0", "1000.0", "1000.0", "1000.0"], ["1.0", "1022.0", "1.0", "1022.0", "0.0", "0.0", "0.0", "0.0"]], "Rate": [["1.0", "1.0", "1.0", "1.0", "1.0", "1.0", "1.0", "1.0"], ["0.004", "0.004", "0.3", "0.3", "0.004", "0.004", "0.6", "0.3"], ["0.004", "0.004", "0.3", "0.3", "0.0", "0.0", "0.0", "0.0"], ["1.0", "0.281", "0.004", "0.188", "0.224", "0.251", "0.272", "0.4"], ["0.004", "0.1", "0.004", "0.1", "0.0", "0.0", "0.0", "0.0"]], "No_dwell": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "Zero_crossing": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "RAM_playback_mode": [[["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "0.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"]]], "RAM_data_filename": ["", "STIRAP_cos4.csv", "STIRAP_cos4.csv", "", "STIRAP_cos4.csv"]}
	`1`	+{"FTW": ["110.0", "80.5", "83.33", "110.0", "253.0"], "POW": ["0.0", "0.0", "0.0", "0.0", "0.0"], "AMW": ["1.0", "1.0", "1.0", "0.74", "0.906"], "fout": [["110.0", "100.105", "100.076", "100.059", "100.077", "100.0938", "100.1106", "99.995"], ["80.37", "80.0", "80.0", "110.0", "0.0", "110.0", "0.0", "0.0"], ["84.3", "80.0", "80.0", "84.28", "110.0", "110.0", "110.08", "110.0"], ["100.0", "82.0", "100.0", "79.46", "0.0", "0.0", "0.0", "99.948"], ["250.0", "252.0", "100.0166", "250.0", "100.01", "100.035", "100.06", "99.938"]], "tht": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "amp": [["0.0", "0.305", "0.305", "0.075", "0.075", "0.075", "0.075", "0.305"], ["0.5", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["1.0", "0.0", "1.0", "1.0", "0.0", "0.0", "0.0", "0.85"], ["0.0", "1.0", "0.0", "1.0", "0.0", "0.0", "0.0", "0.9"], ["0.0", "0.906", "0.82", "0.33", "0.33", "0.33", "0.33", "0.33"]], "Start_Address": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["3.0", "0.0", "6.0", "509.0", "0.0", "0.0", "1010.0", "509.0"], ["3.0", "0.0", "6.0", "509.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "499.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "1011.0", "0.0", "1011.0", "0.0", "0.0", "0.0", "0.0"]], "End_Address": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["4.0", "1.0", "505.0", "1008.0", "1.0", "1.0", "1021.0", "1008.0"], ["4.0", "1.0", "505.0", "1008.0", "0.0", "0.0", "0.0", "0.0"], ["1.0", "500.0", "1000.0", "1000.0", "1000.0", "1000.0", "1000.0", "1000.0"], ["1.0", "1022.0", "1.0", "1022.0", "0.0", "0.0", "0.0", "0.0"]], "Rate": [["1.0", "1.0", "1.0", "1.0", "1.0", "1.0", "1.0", "1.0"], ["0.004", "0.004", "0.3", "0.3", "0.004", "0.004", "0.6", "0.3"], ["0.004", "0.004", "0.3", "0.3", "0.0", "0.0", "0.0", "0.0"], ["1.0", "0.281", "0.004", "0.188", "0.224", "0.251", "0.272", "0.4"], ["0.004", "0.1", "0.004", "0.1", "0.0", "0.0", "0.0", "0.0"]], "No_dwell": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "Zero_crossing": [["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0", "0.0"]], "RAM_playback_mode": [[["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "0.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"]], [["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "1.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"], ["0.0", "0.0", "0.0"]]], "RAM_data_filename": ["", "", "", "", ""]}