no real change

base.py

@@ -5,7 +5,6 @@ from collections import OrderedDict
 from datetime import datetime
 import getpass
 import h5py
-import inspect
 import logging
 import numpy as np
 import platform
@@ -58,6 +57,7 @@ CENTRAL_WIDGET_MINIMUM_WIDTH =  1240
 SLS_CENTRAL_WIDGET_MINIMUM_HEIGHT = 840
 SLS_CENTRAL_WIDGET_MINIMUM_WIDTH = 940
 
+
 class BaseWindow(QMainWindow):
     """ BaseWindow
     """
@@ -75,14 +75,15 @@ class BaseWindow(QMainWindow):
             QThread.__init__(self)
             self.parent = parent
             self.settings = self.parent.settings
+
             self.folder_name = folder_name
             self.time_in_seconds = time_in_seconds
             self.reanalysis_time = reanalysis_time
             self.all_data = self.parent.all_data
             self.all_data_2 = self.parent.all_data_2
 
-        #Causes QThread::wait: Thread tried to wait on itself
+        # Causes QThread::wait: Thread tried to wait on itself
-        #def __del__(self):
+        # def __del__(self):
         #    self.wait()
 
         def run(self):
@@ -94,7 +95,7 @@ class BaseWindow(QMainWindow):
                 reanalysis_time_in_seconds=self.reanalysis_time)
 
             def extract_and_attach(i, nfig, name, all_fig_data):
-                canvas = 'Canvas {0}'.format(i+1)
+                canvas = 'Canvas {0}'.format(i + 1)
                 name_base = name.replace(' ', '_').lower()
                 write_message_fired = False
 
@@ -109,17 +110,28 @@ class BaseWindow(QMainWindow):
 
                         name = name_base + "_{0}".format(
                             idx) if idx > 0 else name_base
+
                         save_dest = (folder_name + date_str + '_' + name +
                                      '.png')
 
-                      
-                        if not os.path.exists(save_dest):
-                            if all_fig_data[canvas][idx] is not None:
                         _dirname = os.path.dirname(save_dest)
 
+                        #print("DIRECTORY NAME IS ", _dirname)
+                        # print("exists?",  os.path.exists(_dirname),
+                        # os.path.exists(save_dest))
+
+                        if not os.path.isfile(save_dest):
+                            if all_fig_data[canvas][idx] is not None:
+
+                                if not os.path.exists(_dirname):
+
+                                    os.makedirs(_dirname)
+
                                 if os.access(_dirname, os.W_OK):
 
-                                    all_fig_data[canvas][idx].savefig(save_dest)
+                                    all_fig_data[canvas][idx].savefig(
+                                        save_dest)
+
                                 elif not write_message_fired:
 
                                     _mess = ("Do not have write permission " +
@@ -133,46 +145,41 @@ class BaseWindow(QMainWindow):
                                         _line(), _mess, {})
                                     write_message_fired = True
 
-                         
                         if not write_message_fired:
                             attach_files.append(save_dest)
 
-
-          
-
             try:
                 resultsSeq = self.settings.data["GUI"]["resultsSeq"]
                 titleSeq = self.settings.data["GUI"]["subResultsTabTitle"]
                 if self.all_data:
                     fig_data = self.all_data['Figure data']
-                    for i, (nfig, name) in enumerate(zip(resultsSeq, titleSeq)):
+                    for i, (nfig, name) in enumerate(
+                            zip(resultsSeq, titleSeq)):
                         print(i, nfig, name, flush=True)
                         print(fig_data, flush=True)
                         extract_and_attach(i, nfig, name, fig_data)
             except KeyError as ex:
                 pass
 
-
             try:
                 resultsSeq = self.settings.data["GUI2"]["resultsSeq"]
                 titleSeq = self.settings.data["GUI2"]["subResultsTabTitle"]
                 if self.all_data_2:
                     fig_data = self.all_data_2['Figure data']
-                    for i, (nfig, name) in enumerate(zip(resultsSeq, titleSeq)):
+                    for i, (nfig, name) in enumerate(
+                            zip(resultsSeq, titleSeq)):
                         extract_and_attach(i, nfig, name, fig_data)
             except KeyError as ex:
                 pass
 
-
+            # Not so nice.. send a signal instead?
-
-            #Not so nice.. send a signal instead?
             if attach_files:
                 self.parent.attach_files = attach_files
                 print(attach_files, flush=True)
                 print("All files attached", flush=True)
             else:
                 print("No files to attach", flush=True)
-            time.sleep(0.1) #avoid race condition
+            time.sleep(0.1)  # avoid race condition
 
     class HDFSave(QThread):
         """Thread for hdf analysis
@@ -181,11 +188,11 @@ class BaseWindow(QMainWindow):
         def __init__(self, parent, from_dialog):
             QThread.__init__(self)
             self.parent = parent
-            self.from_dialog=from_dialog
+            self.from_dialog = from_dialog
 
-        #Only a precaution, not experienced    
+        # Only a precaution, not experienced
-        #Causes QThread::wait: Thread tried to wait on itself
+        # Causes QThread::wait: Thread tried to wait on itself
-        #def __del__(self):
+        # def __del__(self):
         #    self.wait()
 
         def run(self):
@@ -194,7 +201,7 @@ class BaseWindow(QMainWindow):
             QApplication.processEvents(QEventLoop.ExcludeUserInputEvents, 5000)
 
             self.all_data = self.parent.all_data
-            #Reanalysis data
+            # Reanalysis data
 
             if self.all_data is not None:
                 try:
@@ -218,7 +225,7 @@ class BaseWindow(QMainWindow):
                             now_in_seconds = self.all_data['Processed data'][
                                 'Reanalysis time in seconds']
 
-                    #Double check 
+                    # Double check
                     if not from_hdf:
                         if 'from_hdf' in self.all_data['Processed data']:
                             from_hdf = bool(self.all_data['Processed data'][
@@ -229,8 +236,8 @@ class BaseWindow(QMainWindow):
 
                 self.parent.from_hdf = from_hdf
 
-                print("t=========================>", ts_in_seconds, " // ",  now_in_seconds)     
+                print("t", ts_in_seconds, now_in_seconds)
-                print("from hdf5=========================>", from_hdf) 
+                print("from hdf5, dialog=====>", from_hdf, self.from_dialog)
 
                 if self.parent.hdf_filename is None or not self.from_dialog:
                     self.parent.set_new_hdf_filename(ts_in_seconds,
@@ -239,19 +246,19 @@ class BaseWindow(QMainWindow):
                     print("FILENAME ==", self.parent.hdf_filename, flush=True)
                     with h5py.File(self.parent.hdf_filename, 'w') as dataH5:
 
-                        #experiment
+                        # experiment
                         if not from_hdf:
                             self.parent.add_pvs_to_hdf(
                                 dataH5, pv_list=self.parent.pv_machine_list,
                                 from_hdf=from_hdf)
 
-                        #general
+                        # general
-                        #if not from_hdf:
+                        # if not from_hdf:
                         self.parent.add_general_to_hdf(dataH5)
                         self.parent.add_to_hdf(dataH5, proc=True, raw=True)
                         self.parent.hdf_save_completed = True
 
-                        _mess = "Processed data saved to {}".format(
+                        _mess = "Data saved to {}".format(
                             self.parent.hdf_filename)
                         self.parent.trigger_log_message.emit(
                             MsgSeverity.INFO.name, _pymodule, _line(), _mess,
@@ -263,7 +270,6 @@ class BaseWindow(QMainWindow):
                         MsgSeverity.ERROR.name, _pymodule, _line(), _mess, {})
                     self.parent.hdf_save_completed = False
 
-
     class HDFThread(QThread):
         """Thread for hdf analysis
         """
@@ -276,9 +282,9 @@ class BaseWindow(QMainWindow):
             self.all_data = all_data
             self.hdf_filename_loaded = self.parent.hdf_filename_loaded
 
-        #Only a precaution, not experienced    
+        # Only a precaution, not experienced
-        #Causes QThread::wait: Thread tried to wait on itself   
+        # Causes QThread::wait: Thread tried to wait on itself
-        #def __del__(self):
+        # def __del__(self):
         #    self.wait()
 
         def run(self):
@@ -289,7 +295,7 @@ class BaseWindow(QMainWindow):
                 mess = ("Analysis not configured for HDF analysis! " +
                         "Missing method: load_hdf_file")
                 self.parent.trigger_log_message.emit(
-                    MsgSeverity.ERROR.name,_pymodule, _line(), mess, {})
+                    MsgSeverity.ERROR.name, _pymodule, _line(), mess, {})
                 self.parent.trigger_progressbar.emit(PROGRESS_THREAD_END)
                 return
 
@@ -313,7 +319,7 @@ class BaseWindow(QMainWindow):
                 expt_dict = None
                 pass
 
-            #Open hdf5file here and
+            # Open hdf5file here and
             mess = "HDF file {} analysis proceeding...".format(
                 self.hdf_filename_loaded)
             self.parent.trigger_log_message.emit(MsgSeverity.INFO.name,
@@ -339,14 +345,13 @@ class BaseWindow(QMainWindow):
                 self.parent.trigger_log_message.emit(
                     MsgSeverity.ERROR.name, _pymodule, _line(), mess, {})
 
-
     class AnalysisThread(QThread):
         """Analysis thread
         """
         trigger_thread_event = Signal(dict)
 
         def __init__(self, parent, analysis_procedure, input_parameters,
-                     messages: dict={
+                     messages: dict = {
                          "success": "Analysis completed", "fail":
                          "No data returned from analysis procedure"}):
 
@@ -367,13 +372,16 @@ class BaseWindow(QMainWindow):
         def run(self):
             """Run thread
             """
-            print("RUN IN BASE CLASS", flush=True)
+            print("RUN ANLYSIS THREAD FROM WITHIN IN BASE CLASS", flush=True)
+
+            # Reset all_data fro parent
+            self.parent.all_data = None
 
             all_dict = self.analysis_procedure.measure_and_analyze(
                 self.input_parameters)
 
             # Emit results
-            if all_dict:
+            if all_dict is not None:
                 self.trigger_thread_event.emit(all_dict)
                 mess = self.messages['success']
                 self.parent.trigger_log_message.emit(
@@ -383,7 +391,6 @@ class BaseWindow(QMainWindow):
                 self.parent.trigger_log_message.emit(
                     MsgSeverity.WARN.name, _pymodule, _line(), mess, {})
 
-
     def __init__(self, parent=None, pymodule=None, appversion=None, title="",
                  user_mode=UserMode.OPERATION, facility=Facility.SwissFEL,
                  extended=True, has_optics=True, has_procedure=True):
@@ -395,13 +402,11 @@ class BaseWindow(QMainWindow):
         self.appversion = appversion if appversion else _appversion
         self.source_file = None
         self.author = _author
-        self.appversion = _appversion
         self.title = title
         self.facility = facility
         self.user_mode = user_mode
         self.appname, self.appext = self.pymodule.split(".")
 
-       
         print("=============================================")
         print("Starting {0} at: {1}".format(self.appname, datetime.now()))
         print("User: {0} Host: {1}".format(os.getlogin(), os.uname()[1]))
@@ -409,7 +414,7 @@ class BaseWindow(QMainWindow):
 
         self.settings = ReadJSON(self.appname)
 
-        #Read out current_logbook
+        # Read out current_logbook
 
         self.cafe = PyCafe.CyCafe()
         self.cyca = PyCafe.CyCa()
@@ -425,8 +430,9 @@ class BaseWindow(QMainWindow):
         self.screenshot_items = []
 
         self.filename = None
-        self.hdf_filename_loaded = "NONE" #For loading into hdf dockwidget
+        self.hdf_filename_loaded = "NONE"  # For loading into hdf dockwidget
-        self.hdf_filename = None #For saving
+        self.hdf_filename = None  # For saving
+        self.hdf_user_dict = {}
         self.hdf_dialog = None
         self.from_hdf = False
 
@@ -441,9 +447,13 @@ class BaseWindow(QMainWindow):
 
         self.menu = self.menuBar()
 
-     
-
         self.elog_dest = self.settings.data["Elog"]["destination"]
+
+        try:
+            self.elog_add_date_to_dir = self.settings.data["Elog"]["addDateToDir"]
+        except KeyError:
+            self.elog_add_date_to_dir = True
+
         self.screenshot_dest = self.settings.data["screenshot"]["destination"]
         self.stdlog_dest = (self.settings.data["stdlog"]["destination"] +
                             self.appname + "-" + os.getlogin() + ".log")
@@ -482,16 +492,15 @@ class BaseWindow(QMainWindow):
 
         self.hdf_save_completed = False if self.autopost_hdf else True
 
+        self.all_input_parameters = {}  # gui
+        self.all_input_labels = {}  # gui
+        self.all_expert_parameters = {}  # gui
+        self.all_expert_labels = {}  # gui
 
-        self.all_input_parameters = {} #gui
+        self.input_parameters = {}  # analysis thread
-        self.all_input_labels = {} #gui
-        self.all_expert_parameters = {} #gui
-        self.all_expert_labels = {} #gui
-
-        self.input_parameters = {} #analysis thread
         self.input_labels = {}
         #self.input_value_dict = {}
-        self.expert_parameters = {} #added to input_parameters
+        self.expert_parameters = {}  # added to input_parameters
         self.expert_labels = {}
 
         self.read_input_parameters()
@@ -510,8 +519,8 @@ class BaseWindow(QMainWindow):
             print(("Base class without user supplied AnalysisProcedure class."
                    + " import Error:"), e, flush=True)
 
-        ##self.trigger_elog_entry.connect(self.receive_elog_notification)
+        # self.trigger_elog_entry.connect(self.receive_elog_notification)
-        ##self.trigger_hdf_save.connect(self.save_to_hdf)
+        # self.trigger_hdf_save.connect(self.save_to_hdf)
 
         self.msg_severity_qcolor = {
             MsgSeverity.FATAL: QColor(
@@ -540,7 +549,7 @@ class BaseWindow(QMainWindow):
                 self.settings.data["MsgSeverity"]["debug"])
         }
 
-        #QSetttings
+        # QSetttings
         self.restore_application_settings()
 
         self.init_toolbar()
@@ -599,7 +608,6 @@ class BaseWindow(QMainWindow):
         self.show_log_message(MsgSeverity.INFO.name, _pymodule, _line(),
                               "Application configured")
 
-
     def read_input_parameters(self):
 
         for key, dictval in self.settings.data["Parameters"].items():
@@ -643,7 +651,6 @@ class BaseWindow(QMainWindow):
             self.all_input_labels[key] = dictval["data"]["text"]
             #print(key, self.settings.data["Parameters"][key]["flag"])
 
-            
         if "Expert" not in self.settings.data:
             return
 
@@ -688,7 +695,6 @@ class BaseWindow(QMainWindow):
                 self.expert_labels[key] = dictval["data"]["text"]
             self.all_expert_labels[key] = dictval["data"]["text"]
 
-
     def init_toolbar(self):
         """ Prepare toolbar
         """
@@ -716,7 +722,7 @@ class BaseWindow(QMainWindow):
         #menu_daq = self.menu.addMenu("&DAQ")
         #menu_daq_actions = []
         #daq_toolbar = self.addToolBar("DAQ")
-        #daq_toolbar.setObjectName("ViewToolBar")
+        # daq_toolbar.setObjectName("ViewToolBar")
 
         help_toolbar = self.addToolBar("Help")
         help_toolbar.setObjectName("HelpToolBar")
@@ -786,7 +792,7 @@ class BaseWindow(QMainWindow):
             "Save&ALL", slot=self.write_to_destinations,
             shortcut="Ctrl+Z", icon="save_all", tip="Save All")
 
-         #toolbar
+        # toolbar
         # Place ExitWidget on the far right
         exit_toolbar = self.addToolBar("EXIT")
         exit_toolbar.setObjectName("ExitToolBar")
@@ -796,20 +802,21 @@ class BaseWindow(QMainWindow):
         exit_toolbar.addWidget(spacer_wgt)
         #_qsize = exit_toolbar.iconSize()
         #print("qsize", _qsize)
-        true_list = [self.autopost_epics, self.autopost_hdf, self.autopost_elog]
+        true_list = [
+            self.autopost_epics,
+            self.autopost_hdf,
+            self.autopost_elog]
 
         if true_list.count(True) > 1:
-            exit_toolbar.setIconSize(QSize(true_list.count(True)*30+10, 24))
+            exit_toolbar.setIconSize(
-            #exit_toolbar.setIconSize(_qsize)
+                QSize(true_list.count(True) * 30 + 10, 24))
+            # exit_toolbar.setIconSize(_qsize)
             self.add_actions(exit_toolbar, (
                 save_all_action, "Space", None, "Space", quit_action))
         else:
             self.add_actions(exit_toolbar, (quit_action,))
 
-        
+    def combine_save_icons(self):  # epics=False, hdf=False, elog=False):
-
-
-    def combine_save_icons(self): #epics=False, hdf=False, elog=False):
 
         epics = self.autopost_epics
         hdf = self.autopost_hdf
@@ -835,9 +842,9 @@ class BaseWindow(QMainWindow):
             elif hdf:
                 startx2 = 20
                 startx3 = 150
-        comboPixmap = QPixmap(130*true_list.count(True), 100) #420, 100
+        comboPixmap = QPixmap(130 * true_list.count(True), 100)  # 420, 100
-        #comboPixmap.fill(Qt.transparent)
+        # comboPixmap.fill(Qt.transparent)
-        comboPixmap.fill(QColor("#dcdcdc"))  #"#bcc6cc"
+        comboPixmap.fill(QColor("#dcdcdc"))  # "#bcc6cc"
         epicsImage = QPixmap(":/epics.png")
         hdfImage = QPixmap(":/hdfS.png")
         elogImage = QPixmap(":/elog.png")
@@ -852,8 +859,8 @@ class BaseWindow(QMainWindow):
         painter.end()
         return combinedIcon
 
+    # Actions
 
-    ################# Actions
     def add_actions(self, target, actions):
         """ Add to toolbar
         """
@@ -868,7 +875,7 @@ class BaseWindow(QMainWindow):
                 target.addAction(action)
 
     def create_action(self, text, slot=None, shortcut=None, icon=None, tip=None,
-                      checkable=False):# signal="triggered()"):
+                      checkable=False):  # signal="triggered()"):
         """ Helper fn
         """
         action = QAction(text, self)
@@ -888,8 +895,6 @@ class BaseWindow(QMainWindow):
             action.setCheckable(True)
         return action
 
-
-
     def verify_close_event(self):
         """ Overrides QMainWindow method
         """
@@ -930,13 +935,13 @@ class BaseWindow(QMainWindow):
     def closeEvent(self, event):
         """ Overrides QMainWindow method
         """
-        #Close all dock widgets
+        # Close all dock widgets
-        #self.removeDockWidget(self.hdf_dock_widget)
+        # self.removeDockWidget(self.hdf_dock_widget)
         self.logger.info("Closing Application")
         print("Closing Application", flush=True)
         self.save_application_settings()
         QApplication.processEvents()
-        #print( ("Stopping Monitors. This may on occasion lead to " + 
+        # print( ("Stopping Monitors. This may on occasion lead to " +
         #        "NO CYTHON CALLBACK MATCH FOUND notices"), flush=True)
         self.cafe.monitorStopAll()
         time.sleep(0.05)
@@ -1015,16 +1020,15 @@ class BaseWindow(QMainWindow):
         qdialog.setLayout(layout)
         qdialog.show()
 
-
+    # def save_to_hdf_started(self):
-    #def save_to_hdf_started(self):
     #    QApplication.processEvents()
-    #def save_to_hdf_finished(self):
+    # def save_to_hdf_finished(self):
     #    QApplication.processEvents()
 
     @Slot()
     def write_to_destinations(self):
-        #disable signal
+        # disable signal
-        #self.gui_frame.autopost_save.blockSignals(True)
+        # self.gui_frame.autopost_save.blockSignals(True)
         QApplication.processEvents()
         if self.autopost_epics:
             self.save_to_epics()
@@ -1037,9 +1041,8 @@ class BaseWindow(QMainWindow):
         if self.autopost_elog:
             self.send_to_elog()
         QApplication.processEvents()
-        #enable signal
+        # enable signal
-        #self.gui_frame.autopost_save.blockSignals(False)
+        # self.gui_frame.autopost_save.blockSignals(False)
-
 
     def set_new_hdf_filename(self, time_in_seconds=None,
                              reanalysis_time_in_seconds=None):
@@ -1047,7 +1050,6 @@ class BaseWindow(QMainWindow):
         self.hdf_filename = (self.hdf_dest + self.add_date_to_path(
             time_in_seconds, reanalysis_time_in_seconds) + ".h5")
 
-
     def add_date_to_path(self, time_in_seconds=None,
                          reanalysis_time_in_seconds=None):
 
@@ -1069,9 +1071,11 @@ class BaseWindow(QMainWindow):
             _month = when.strftime("%m")
             _day = when.strftime("%d")
 
+        if self.elog_add_date_to_dir:
             return str(_year + "/" + _month + "/" + _day + "/" + self.appname +
                        "_" + _date_label)
-
+        else:
+            return str(self.appname + "_" + _date_label)
 
     def verify_save_to_hdf(self):
         """ To be called by user from save_to_hdf
@@ -1103,7 +1107,6 @@ class BaseWindow(QMainWindow):
             QApplication.processEvents()
             return False
 
-
         if self.hdf_save_completed:
             _mess = "Data previously saved to hdf:\n{0}".format(
                 self.hdf_filename)
@@ -1114,7 +1117,6 @@ class BaseWindow(QMainWindow):
 
         return True
 
-
     def add_to_hdf(self, dataH5=None, proc=True, raw=False):
         """ Abstract method to be overwritten by user. Optional.
         """
@@ -1144,7 +1146,6 @@ class BaseWindow(QMainWindow):
         )
         QM.exec()
 
-
     def add_pvs_to_hdf(self, dataH5, top_group="experiment", pv_list=None,
                        from_hdf=False):
 
@@ -1172,7 +1173,6 @@ class BaseWindow(QMainWindow):
                             {})
             return isOK
 
-                                
         if from_hdf:
             return isOK
 
@@ -1198,20 +1198,23 @@ class BaseWindow(QMainWindow):
                     MsgSeverity.WARN.name, _pymodule, _line(), _mess, {})
         return isOK
 
-
-
     def add_general_to_hdf(self, dataH5):
         isOK = True
         user_dict = {}
 
-        user_dict['Comment'] = self.hdf_dialog.user_dict[
+        #user_dict['Comment'] is prefilled in  get_data in savehdf.py
-            'Comment'] if self.hdf_dialog is not None else str(
+        # user_dict['Comment'] = self.hdf_dialog.user_dict[
-                "HDF file generated via Save All button")
+        #    'Comment'] if self.hdf_dialog is not None else str(
-
+        #        "HDF file generated via Save All button")
+        #user_dict['Comment'] = self.hdf_dialog.comment.document().toPlainText()
+        if self.hdf_user_dict:
+            user_dict['Comment'] = self.hdf_user_dict['Comment']
+        else:
+            user_dict['Comment'] = "HDF file generated via Save All button"
         user_dict['Author'] = self.author
         user_dict['Application'] = self.pymodule
         user_dict['Version'] = self.appversion
-        #user_dict['Comment'] = comment if comment is not None else str(
+        # user_dict['Comment'] = comment if comment is not None else str(
         #    "HDF file generated via Save All button")
         user_dict['Filepath'] = self.source_file
         #user_dict['Process'] = os.getpid()
@@ -1245,13 +1248,12 @@ class BaseWindow(QMainWindow):
                     MsgSeverity.WARN.name, _pymodule, _line(), _mess, {})
         return isOK
 
-
     @Slot()
     def save_to_hdf_dialog(self):
         """ This uses the widget interface to allow the user to enter
         additional meta-data
         """
-       
+        print("save_to_hdf_dialog==>", flush=True)
         if not self.verify_save_to_hdf():
             return False
 
@@ -1274,7 +1276,6 @@ class BaseWindow(QMainWindow):
         self.hdf_dialog = QSaveHDF(self, input_options=input_options,
                                    from_dialog=True)
 
-
     def verify_send_to_elog(self):
 
         if self.analysis_thread is not None:
@@ -1324,20 +1325,18 @@ class BaseWindow(QMainWindow):
 
         #_elog_sf = ElogSwissFEL()
         _logbook = None
-        _category_idx = 0 #_elog_sf.category.MEASUREMENT=1
+        _category_idx = 0  # _elog_sf.category.MEASUREMENT=1
-        _domain_idx = 0 #_elog_sf.system.NONE
+        _domain_idx = 0  # _elog_sf.system.NONE
-        _section_idx = 0 #_elog_sf.system.BEAMDYNAMICS=1
+        _section_idx = 0  # _elog_sf.system.BEAMDYNAMICS=1
         _attach_files = []
         _message = ""
 
-        
         QSendToELOG(self, logbook=_logbook, categoryIdx=_category_idx,
                     domainIdx=_domain_idx, sectionIdx=_section_idx,
                     title=self.title, message=_message,
                     attachFile=_attach_files)
         QApplication.processEvents()
 
-
     def initiate_cycling(self, pv_list=[]):
         if not pv_list:
             return False
@@ -1395,7 +1394,7 @@ class BaseWindow(QMainWindow):
         while self.is_cycling(pv_cycle_quads):
             time.sleep(0.005)
             QApplication.processEvents()
-            if time.time()-start > timeout:
+            if time.time() - start > timeout:
                 _mess = ("Timeout ({0}s) reached for Cycling. " +
                          "\nPlease check set points for " +
                          "\nDeflector: {1} " +
@@ -1406,7 +1405,6 @@ class BaseWindow(QMainWindow):
                 qm.warning(self, "Set Optics", _mess, QMessageBox.Ok)
                 break
 
-
     @Slot()
     def set_optics(self):
         """ Abstract method to be overwritten by user
@@ -1429,12 +1427,11 @@ class BaseWindow(QMainWindow):
         )
         QM.exec()
 
-
     def verify_save_to_epics(self):
         """ To be called by user from save_to_epics
         """
         if self.all_data:
-            #Data from hdf analysis - do not save to epics
+            # Data from hdf analysis - do not save to epics
             if 'Reanalysis time' in self.all_data['Processed data']:
                 if self.all_data['Processed data']['Reanalysis time']:
                     print("HDF RUN - data not written to epics")
@@ -1484,7 +1481,6 @@ class BaseWindow(QMainWindow):
         )
         QM.exec()
 
-
     def send_to_log_window(self, pv_list: list = [], status: int = 1,
                            status_list: list = [], operation: str = 'set/get',
                            pymodule=_pymodule, line: int = _line()):
@@ -1504,11 +1500,9 @@ class BaseWindow(QMainWindow):
                      "See Log window").format(ibad, len(status_list))
             self.statusbar.showMessage(_mess)
 
-
     def send_to_epics(self, pv_dict: dict = None, pv_names: list = None,
                       pv_values: list = None) -> (int, list):
 
-
         if pv_dict is not None:
             pv_values = []
             pv_names = list(pv_dict.keys())
@@ -1538,15 +1532,15 @@ class BaseWindow(QMainWindow):
         status = self.cyca.ICAFE_NORMAL
         status_list = []
         try:
-            status, status_list = self.cafe.setCompoundList(pv_names, pv_values)
+            status, status_list = self.cafe.setCompoundList(
-        except:
+                pv_names, pv_values)
+        except BaseException:
             print("Exception raised in cafe.setCompoundList", flush=True)
             status = self.cyca.ECAFE_BADTYPE
             for pv, val in zip(pv_names, pv_values):
                 print("pv/val", pv, val, flush=True)
                 status_list.append(self.ECAFE_BADTYPE)
 
-
         if status != self.cyca.ICAFE_NORMAL:
             ibad = 0
             for _status, _pv in zip(status_list, pv_names):
@@ -1589,7 +1583,7 @@ class BaseWindow(QMainWindow):
                               self.printer.paperRect().y() +
                               self.printer.pageRect().height() / 2)
             painter.scale(scale, scale)
-            painter.translate(-w.width()/2, -w.height()/2)
+            painter.translate(-w.width() / 2, -w.height() / 2)
             w.render(painter)
 
     @Slot()
@@ -1648,7 +1642,7 @@ class BaseWindow(QMainWindow):
             self.screenshot_titles.clear()
             self.screenshot_items.clear()
 
-    ############################### Init
+    # Init
     def init_statusbar_wgt(self):
         """ Configure statusbar
         """
@@ -1675,7 +1669,7 @@ class BaseWindow(QMainWindow):
                                         layout="Hor")
         self.hdf_dock_widget.setObjectName("hdfDockWidget")
         self.hdf_dock_widget.setVisible(False)
-        #hdfDockWidget.setFloating(True)
+        # hdfDockWidget.setFloating(True)
         self.hdf_dock_widget.setContentsMargins(9, 9, 9, 9)
         self.h5_groupbox.analyze_h5_widget.clicked.connect(
             self.start_hdf_thread)
@@ -1707,7 +1701,7 @@ class BaseWindow(QMainWindow):
         settings.setValue("BaseWindow/Geometry", (self.saveGeometry()))
         settings.setValue("BaseWindow/State", (self.saveState()))
 
-    #To be overloaded by user
+    # To be overloaded by user
     def load_hdf_file(self):
         """ load_hdf5 file into analysis dictionary
         """
@@ -1737,31 +1731,31 @@ class BaseWindow(QMainWindow):
                                         _mess, QMessageBox.Ok)
                 return
 
-        #self.hdf_thread_started()
+        # self.hdf_thread_started()
         self.statusbar.showMessage("Loading {0}".format(
             self.hdf_filename_loaded))
         self.trigger_progressbar_str.emit(
             5, "Loading HDF file for analysis")
-        #Fill all data from HDF file
+        # Fill all data from HDF file
         ###hdf_all_data = self.load_hdf_file()
 
-        ###if not hdf_all_data:
+        # if not hdf_all_data:
-        ###    self.hdf_thread_finished()
+        # self.hdf_thread_finished()
-        ###    return
+        # return
 
         self.hdf_thread = self.HDFThread(
-            self, self.analysis_procedure, all_data=None) #=hdf_all_data
+            self, self.analysis_procedure, all_data=None)  # =hdf_all_data
         self.hdf_thread.trigger_thread_event.connect(
             self.receive_analysis_results)
-        #procedure moved above
+        # procedure moved above
         self.hdf_thread.started.connect(self.hdf_thread_started)
         self.hdf_thread.finished.connect(self.hdf_thread_finished)
 
         self.hdf_thread.start()
         QApplication.processEvents()
 
+    # To be overloaded by user
 
-    #To be overloaded by user
     def verify_analysis_preconditions(self):
         return True
 
@@ -1792,7 +1786,6 @@ class BaseWindow(QMainWindow):
         if not self.verify_analysis_preconditions():
             return
 
-      
         self.analysis_thread = self.AnalysisThread(
             self, self.analysis_procedure, self.input_parameters)
 
@@ -1802,11 +1795,9 @@ class BaseWindow(QMainWindow):
         self.analysis_thread.started.connect(self.analysis_thread_started)
         self.analysis_thread.finished.connect(self.analysis_thread_finished)
 
-       
         self.analysis_thread.start()
         QApplication.processEvents()
 
-   
     @Slot()
     def analysis_thread_started(self):
         """ Change state of widgets when measuring
@@ -1830,7 +1821,6 @@ class BaseWindow(QMainWindow):
         self.gui_frame.in_hdf_measurement_procedure()
         QApplication.processEvents()
 
-
     @Slot()
     def hdf_thread_finished(self):
         """ Reset widgets to intial pre-measurement state
@@ -1839,7 +1829,6 @@ class BaseWindow(QMainWindow):
         QApplication.processEvents()
         #print("Thread Finished")
 
-
     @Slot(dict)
     def receive_analysis_results(self, all_dict):
         self.all_data = all_dict
@@ -1854,21 +1843,25 @@ class BaseWindow(QMainWindow):
             try:
                 results_data = all_dict['Processed data']['Results']
                 self.gui_frame.send_to_results_output_wgt(results_data)
-            except:
+            except BaseException:
                 pass
 
         #print("IDX+++", self.gui_frame.central_tab_widget.indexOf('Emittance'), flush=True)
         #print("IDX+++", self.gui_frame.level2_tab_wgt[0].indexOf('Plots'))
-        #self.gui_frame.central_tab_widget.setCurrentIndex(1)
+        # self.gui_frame.central_tab_widget.setCurrentIndex(1)
 
         self.gui_frame.results_tab_wgt.setCurrentIndex(0)
 
         if "GUITree" in self.settings.data:
 
-            #for j in range(len(self.gui_frame.level1_tab_wgt)):
+            # for j in range(len(self.gui_frame.level1_tab_wgt)):
             j = self.gui_frame.central_tab_widget.currentIndex()
             for i in range(self.gui_frame.level1_tab_wgt[j].count()):
-                print(j, i, self.gui_frame.level1_tab_wgt[j].tabText(i), flush=True)
+                print(
+                    j,
+                    i,
+                    self.gui_frame.level1_tab_wgt[j].tabText(i),
+                    flush=True)
                 if self.gui_frame.level1_tab_wgt[j].tabText(i) == "Plots":
                     self.gui_frame.level1_tab_wgt[j].setCurrentIndex(i)
                 else:
@@ -1876,14 +1869,20 @@ class BaseWindow(QMainWindow):
         else:
 
             for i in range(self.gui_frame.central_tab_widget.count()):
-                print(i, self.gui_frame.central_tab_widget.tabText(i), flush=True)
+                print(
+                    i,
+                    self.gui_frame.central_tab_widget.tabText(i),
+                    flush=True)
                 if self.gui_frame.central_tab_widget.tabText(i) == "Plots":
                     self.gui_frame.central_tab_widget.setCurrentIndex(i)
                 else:
                     pass
 
             for i in range(self.gui_frame.measurement_tab_wgt.count()):
-                print(i, self.gui_frame.measurement_tab_wgt.tabText(i), flush=True)
+                print(
+                    i,
+                    self.gui_frame.measurement_tab_wgt.tabText(i),
+                    flush=True)
                 if self.gui_frame.measurement_tab_wgt.tabText(i) == "Plots":
                     self.gui_frame.measurement_tab_wgt.setCurrentIndex(i)
                 else:
@@ -1907,10 +1906,9 @@ class BaseWindow(QMainWindow):
         self.gui_frame.in_abort_procedure()
         # Trigger abort signal to the analysis thread
         self.analysis_procedure.trigger_abort.emit()
-        #self.trigger_progressbar.emit(PROGRESS_THREAD_ABORTING)
+        # self.trigger_progressbar.emit(PROGRESS_THREAD_ABORTING)
         QApplication.processEvents()
 
-
     @Slot(str, str, int, str, dict)
     def receive_log_message(self, severity, module, line, message, options={}):
         '''Receive message from thread for routing to log window'''
@@ -1925,7 +1923,7 @@ class BaseWindow(QMainWindow):
         '''Receives update of message'''
         self.progressbar.setVisible(True)
         try:
-            if self.input_parameters["simulation"] :
+            if self.input_parameters["simulation"]:
                 self.progressbar_color = self.progressbar_simulation
         except KeyError:
             pass
@@ -1954,7 +1952,7 @@ class BaseWindow(QMainWindow):
             mess = "Aborting measurement procedure"
             self.show_log_message(
                 MsgSeverity.WARN.name, _pymodule, _line(), mess)
-            #self.statusbar.showMessage(mess)
+            # self.statusbar.showMessage(mess)
         elif value == PROGRESS_THREAD_ABORTED:
             self.progressbar.setFormat("Procedure aborted")
             self.progressbar.setObjectName(self.progressbar_abort)
@@ -1989,7 +1987,6 @@ class BaseWindow(QMainWindow):
         QApplication.processEvents()
         time.sleep(0.0001)
 
-
     def initialize_application(self, appname=_appname, delay=None,
                                facility=Facility.SwissFEL):
         """
@@ -2033,10 +2030,10 @@ class BaseWindow(QMainWindow):
         parser.add_argument("-f", "--facility")
         parser.add_argument("-u", "--user")
         #result, unknown = parser.parse_known_args(["--qss", ":/sfop.qss"])
-        #result, unknown = parser.parse_known_args(["--qss", ":/sfop.qss",
+        # result, unknown = parser.parse_known_args(["--qss", ":/sfop.qss",
-        #"-c", "--facility", "--user"])
+        # "-c", "--facility", "--user"])
-        #print(result)
+        # print(result)
-        #print(unknown)
+        # print(unknown)
         result = parser.parse_args()
         if result.qss:
             print("qss file {0} supplied by user".format(result.qss))
@@ -2068,21 +2065,20 @@ class BaseWindow(QMainWindow):
                 <p style='color:black; font-weight:bold;
                 font-size:20px; margin-right:22px;'>
                 This message will self-destruct in {1} seconds<br></p>
-                """.format(appname, round(delay)), Qt.AlignCenter | Qt.AlignTop)
+                """.format(appname, round(delay)),
-            width = 860 + (len(appname)-10)*15
+                Qt.AlignmentFlag(Qt.AlignCenter | Qt.AlignTop))
+            width = 860 + (len(appname) - 10) * 15
             height = 220
             self.splash_screen.resize(width, height)
 
-            #Maybe useful at some point
+            # Maybe useful at some point
             #pSplashNotice = QCheckBox(self.splash_screen);
-            #pSplashNotice.setChecked(Qt.Checked)
+            # pSplashNotice.setChecked(Qt.Checked)
-
 
             self.splash_progressbar = QProgressBar(self.splash_screen)
             self.splash_timer = QTimer()
             self.splash_screen.show()
 
-
             # Custom progress bar stylesheet
             progressbar_stylesheet = """
             QProgressBar:horizontal {
@@ -2104,9 +2100,9 @@ class BaseWindow(QMainWindow):
 
             def show_time():
                 now = time.time()
-                val = (now-start1)*100/delay
+                val = (now - start1) * 100 / delay
-                val = 5 * round(val/5)
+                val = 5 * round(val / 5)
-                int_seconds_remaining = int(delay - (now-start1))
+                int_seconds_remaining = int(delay - (now - start1))
                 seconds_remaining = '{:2d}'.format(int_seconds_remaining)
                 self.splash_progressbar.setValue(val)
                 self.processEvents()
@@ -2122,21 +2118,21 @@ class BaseWindow(QMainWindow):
                 {1:>2} second{2} remaining<br></p>
                 """.format(self.splash_appname, seconds_remaining, sec_str)
 
-                self.splash_screen.showMessage(mess, Qt.AlignCenter|Qt.AlignTop)
+                self.splash_screen.showMessage(
+                    mess, Qt.AlignmentFlag(Qt.AlignCenter | Qt.AlignTop))
                 self.processEvents()
                 #print(val, seconds_remaining)
 
             self.splash_timer.timeout.connect(show_time)
-            self.splash_timer.start(200) #ms with 10 samples per sec.
+            self.splash_timer.start(200)  # ms with 10 samples per sec.
 
         return self.splash_screen
 
-
     def initialize_finished(self, myapp):
         self.splash_timer.stop()
         self.splash_progressbar.setValue(100)
-        time.sleep(1.5)
+        time.sleep(0.4)
-        #app.processEvents()
+        # app.processEvents()
         self.splash_screen.showMessage(
             """
             <br><p style='color:black; font-weight:bold;
@@ -2148,11 +2144,10 @@ class BaseWindow(QMainWindow):
             Ready.... &nbsp;  &nbsp;  &nbsp; &nbsp;
             &nbsp; &nbsp; &nbsp;  &nbsp;  &nbsp;  &nbsp;
             <br></p>
-            """.format(self.splash_appname), Qt.AlignCenter | Qt.AlignTop)
+            """.format(self.splash_appname),
+            Qt.AlignmentFlag(Qt.AlignCenter | Qt.AlignTop))
         self.splash_screen.finish(myapp)
 
-
-
     def check_status_list(self, pymodule: str = _pymodule,
                           operation: str = "channel access",
                           pv_list: list = None, status_list: list = None,
@@ -2171,7 +2166,6 @@ class BaseWindow(QMainWindow):
                 if stat is None:
                     status_list[i] = self.cafe.getStatus(pv)
 
-
         brk = ("------------------------------------------------------" +
                "------------------------------------------------------")
         self.trigger_log_message.emit(
@@ -2201,15 +2195,14 @@ class BaseWindow(QMainWindow):
 
         return status_list
 
-
     def check_status(self, pymodule: str = _pymodule,
                      operation: str = "channel access",
                      pv: str = None, stat: int = None,
-                     line: int =_line()):
+                     line: int = _line()):
 
         if not pv:
             return
-        if stat == None:
+        if stat is None:
             stat = self.cafe.getStatus(pv)
 
         if stat != self.cyca.ICAFE_NORMAL:

savehdf.py

@@ -38,7 +38,6 @@ class QSaveHDF(QDialog):
         self.user_dict = {}
         self.user_dict['Comment'] = None
         #self.file_name = None
-
         #self.excluded_input = ['Year', 'Month', 'Date']
 
         if 'Time in seconds' in input_options.keys():
@@ -244,6 +243,7 @@ class QSaveHDF(QDialog):
 
     def save(self):
         self.get_data()
+        self.parent.hdf_user_dict = self.user_dict
         self.parent.hdf_filename = self.user_dict['Destination']
         self.parent.save_to_hdf(from_dialog=self.from_dialog)
         self.close()

sendelog.py

@@ -9,22 +9,13 @@ from qtpy.QtWidgets import (QComboBox, QDialog, QFileDialog, QHBoxLayout,
                             QVBoxLayout)
 
 import elog  # https://github.com/paulscherrerinstitute/py_elog
-from pyqtacc.bdbase.enumkind import MsgSeverity
+from apps4ops.bdbase.enumkind import MsgSeverity
+from apps4ops.bdbase.utils import _line
 
 _version = "1.0.0"
 _pymodule = os.path.basename(__file__)
 _appname, _appext = _pymodule.split(".")
 
-def _line():
-    """Macro to return the current line number.
-
-    The current line number within the file is used when
-    reporting messages to the message logging window.
-
-    Returns:
-        int: Current line number.
-    """
-    return inspect.currentframe().f_back.f_lineno
 
 class QSendToELOG(QDialog):
     """ Graphical interface to elog

sendelogframe.py

@@ -9,22 +9,14 @@ from qtpy.QtWidgets import (
     QLineEdit, QPushButton, QTextEdit, QVBoxLayout)
 
 import elog  # https://github.com/paulscherrerinstitute/py_elog
-from pyqtacc.bdbase.enumkind import MsgSeverity
+
+from apps4ops.bdbase.enumkind import MsgSeverity
+from apps4ops.bdbase.utils import _line
 
 _version = "1.0.0"
 _pymodule = os.path.basename(__file__)
 _appname, _appext = _pymodule.split(".")
 
-def _line():
-    """Macro to return the current line number.
-
-    The current line number within the file is used when
-    reporting messages to the message logging window.
-
-    Returns:
-        int: Current line number.
-    """
-    return inspect.currentframe().f_back.f_lineno
 
 class QSendToELOGFrame(QDialog):
     """ Graphical interface to elog