Added support for adaptive orbit feedback and spectral analysis

app/__init__.py

@@ -1 +1,2 @@
 from .adaptiveorbit import AdaptiveOrbit
+from .spectralanalysis import SpectralAnalysis

app/adaptiveorbit.py

@@ -61,7 +61,13 @@ class AdaptiveOrbit:
                 name = pv[i].pvname
                 raise ValueError(f"PV-Channel {name} is not available")
         return pvs
-        
+
+    def flush(self):
+        with self.bsAR.pt.queue.mutex:
+            self.bsAR.pt.queue.queue.clear()       
+        with self.bsAT.pt.queue.mutex:
+            self.bsAT.pt.queue.queue.clear()       
+
     def terminate(self):
         print('Stopping BSStream Thread...')    
         self.bsAR.stop()

app/spectralanalysis.py

@@ -0,0 +1,51 @@
+import time
+import numpy as np
+
+from bstrd import BSCache
+from bstrd.bscache import make_channel_config, is_available
+from epics import PV
+
+class SpectralAnalysis:
+    """
+    Wrapper class to bundle all daq/io needed for adaptive orbit feedback.
+    """
+    def __init__(self):
+
+        self.bs = BSCache()
+        self.bs.stop()
+        
+        self.channel = ''
+        self.channels = ['SARFE10-PSSS059:SPECTRUM_Y',
+                         'SATOP21-PMOS127-2D:SPECTRUM_Y',
+                         'SATOP31-PMOS132-2D:SPECTRUM_Y']
+        self.isConnected = False
+
+    def connect(self,ich):
+        if ich < 0 or ich >= len(self.channels):
+            return False
+        self.channel = self.channels[ich]
+        print('Connecting to BS-Channel:',self.channel)
+        self.bs.channels.clear()
+        self.bs.get_var(self.channel)  # this starts the stream into the cache
+        self.pv = PV(self.channel.replace('_Y','_X'))
+        
+    def terminate(self):
+        print('Stopping BSStream Thread...')    
+        self.bs.stop()
+        self.bs.pt.running.clear() # for some reason I have to
+
+    def flush(self):
+        with self.bs.pt.queue.mutex:
+            self.bs.pt.queue.queue.clear()
+
+    def read(self):
+        data=self.bs.__next__()
+        return data['pid'],data[self.channel]
+
+    def readPV(self):
+        return self.pv.value
+
+    def getSpectrometerName(self):
+        return self.channel
+
+        

interface/__init__.py

@@ -0,0 +1,4 @@
+from .snap import getSnap
+from .save import saveDataset
+from .load import loadDataset
+from .elog import writeElog

interface/elog.py

@@ -1,6 +1,7 @@
+import os
 import elog
 
-def write(text, Title = 'Test', Application = 'SFBD-Module', Attachment = None):
+def writeElog(text, Title = 'Test', Application = 'SFBD-Module', Attachment = None):
     """
     Generates an entry in the electronic logbook of SwissFEL Commisisoning Data
     :param text:  The text to be placed in the log book
@@ -11,12 +12,11 @@ def write(text, Title = 'Test', Application = 'SFBD-Module', Attachment = None):
     """
 
     # supplemental  info
-    Author = 'sfop'
+    Author = os.getlogin()
     Category  = 'Measurement' # Info or Measurement
     System = 'Beamdynamics'  # Beamdynamics, Operation, Controls
 
     dict_att = {'Author': Author, 'Application': Application, 'Category': Category, 'Title': Title, 'System': System}
-    print('\nLog book entry generated')
 
     logbook = elog.open('https://elog-gfa.psi.ch/SwissFEL+commissioning+data/', user='robot', password='robot')
     return logbook.post(text, attributes=dict_att, attachments=Attachment)

interface/load.py

@@ -1,67 +1,51 @@
-import sys
-import os
-import datetime
 import h5py
 
-# add other classes
-#sys.path.append('/sf/bd/packages/SFBD/src')
 
-class Load:
+def loadDataset(filename):
-    def __init__(self, logger = None, program = 'SFBD', version = 'v1.0.0'):
+    hid = h5py.File(filename, "r")
-
+    snap = loadSnap(hid)
-        self.program = program
+    data = loadData(hid)
-        self.version = version
+    act = loadActuator(hid)
-        self.author ='S. Reiche'
+    hid.close()
-        self.file = None
+    return data,act,snap
-        
-
-        if logger == None:
-            logging.basicConfig(level=logging.INFO,
-                            format='%(levelname)-8s %(message)s')
-            self.logger = logging.getLogger(self.program)
-            self.logger.info('Load class started at %s' % datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S'))
-            self.logger.info('Version: %s ' % self.version)
-            self.logger.info('Host: %s' % socket.gethostname())
-        else:
-            self.logger = logger
-
-    
-    def open(self,filename):
-        self.file = h5py.File(filename, "r")
-
-    def close(self):
-        if self.file is not None:
-            self.file.close()
-        self.file = None
  
-    def loadSnap(self):
+def loadSnap(hid):
-        snap={}
+    snap={}
-        if not 'experiment' in self.file.keys():
+    if not 'experiment' in hid.keys():
-            return snap
+        return None
-        for key1 in self.file['experiment'].keys():
+    for key1 in hid['experiment'].keys():
-            for key2 in self.file['experiment'][key1].keys():
+        if isinstance(hid['experiment'][key1],h5py.Group):
-                val = self.file['experiment'][key1][key2][()]
+            for key2 in hid['experiment'][key1].keys():
-                snap[key1+':'+key2]={'val':val}
+                val = hid['experiment'][key1][key2][()]
-        return snap
+                snap[key1+':'+key2]=val
+        else:
+            snap[key1]=hid['experiment'][key1][()]
+    return snap
 
-    def loadData(self,scanrun=1):
+def loadData(hid,scanrun=1):
-        run='scan_%d' % scanrun
+    run='scan_%d' % scanrun
-        data = {} 
+    data = {} 
-        for key1 in self.file[run]['data'].keys():
+    for key1 in hid[run]['data'].keys():
-            for key2 in self.file[run]['data'][key1].keys():
+        if isinstance(hid[run]['data'][key1],h5py.Group):
-                val = self.file[run]['data'][key1][key2][()]
+            for key2 in hid[run]['data'][key1].keys():
+                val = hid[run]['data'][key1][key2][()]
                 data[key1+':'+key2]=val
-        return data
+        else:
+            data[key1]=hid[run]['data'][key1][()]
+    return data
 
-    def loadActuator(self,scanrun=1):
+def loadActuator(hid,scanrun=1):
-        run='scan_%d' % scanrun
+    run='scan_%d' % scanrun
-        data = {} 
+    data = {} 
-        if 'actuators' in self.file[run]['method'].keys():
+    if 'actuators' in hid[run]['method'].keys():
-            for key1 in self.file[run]['method']['actuators'].keys():
+        for key1 in hid[run]['method']['actuators'].keys():
-                for key2 in self.file[run]['method']['actuators'][key1].keys():
+            if isinstance(hid[run]['method']['actuators'],h5py.Group):
-                    val = self.file[run]['method']['actuators'][key1][key2][()]
+                for key2 in hid[run]['method']['actuators'][key1].keys():
+                    val = hid[run]['method']['actuators'][key1][key2][()]
                     data[key1+':'+key2]={'val':val}
-        return data
+        else:
+            data[key1]=hid[run]['method']['actuators'][key1][()]
+    return data
 
 
  

interface/save.py

@@ -2,147 +2,181 @@ import sys
 import os
 import datetime
 import h5py
-import logging
 import socket
+from PIL import Image
 
-# add other classes
+def getDatasetFileName(program='Unknown'):
-#sys.path.append('/sf/bd/packages/SFBD/src')
+    year = datetime.datetime.now().strftime('%Y')
+    month = datetime.datetime.now().strftime('%m')
+    day = datetime.datetime.now().strftime('%d')
 
-class Save:
+    path = '/sf/data/measurements/%s' % year
-    def __init__(self, logger = None, program = 'SFBD', version = 'v1.0.0'):
+    if not os.path.exists(path):
+        os.makedirs(path)
+    path = '%s/%s' % (path,month)
+    if not os.path.exists(path):
+        os.makedirs(path)
+    path = '%s/%s' % (path,day)
+    if not os.path.exists(path):
+        os.makedirs(path)
+    datetag = datetime.datetime.now().strftime('%Y_%m_%d_%H_%M_%S_%f')
+    filename=('%s/%s_%s' % (path, program.replace(' ','_'), datetag))
+    return filename
 
-        self.program = program
-        self.version = version
-        self.author ='S. Reiche'
-        self.filename=None
-        self.file = None
-        
-
-        if logger == None:
-            logging.basicConfig(level=logging.INFO,
-                            format='%(levelname)-8s %(message)s')
-            self.logger = logging.getLogger(self.program)
-            self.logger.info('Save class started at %s' % datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S'))
-            self.logger.info('Version: %s ' % self.version)
-            self.logger.info('Host: %s' % socket.gethostname())
-        else:
-            self.logger = logger
 
+def saveDataset(program,data,actuator=None,snap=None,analysis=None,figures=None):
+    hid,filename = openDataset(program)
+    if not hid:
+        return None
+    # check if scan is multiple instances of a scan
+    if isinstance(data,list):
+        for iscan,singledata in enumerate(data):
+            writeData(hid,singledata,iscan)
+    else:
+        writeData(hid,data,1)
+    # same for actuator
+    if isinstance(actuator,list):
+        for iscan,singleactuator in enumerate(actuator):
+            writeActuator(hid,singleactuator,iscan)
+    else:
+        writeActuator(hid,actuator,1)
+    # and same for analysis
+    if isinstance(analysis,list):
+        for iscan,singleana in enumerate(analysis):
+            writeAnalysis(hid,singleana,iscan)
+    else:
+        writeAnalysis(hid,analysis,1)
+    # write aux data
+    writeSnap(hid,snap)
+    hid.close()
     
-
+    writeFigure(filename,figures)
-    def open(self):
+    return filename
-        year = datetime.datetime.now().strftime('%Y')
-        month = datetime.datetime.now().strftime('%m')
-        day = datetime.datetime.now().strftime('%d')
-
-        path = '/sf/data/measurements/%s' % year
-        if not os.path.exists(path):
-            os.makedirs(path)
-        path = '%s/%s' % (path,month)
-        if not os.path.exists(path):
-            os.makedirs(path)
-        path = '%s/%s' % (path,day)
-        if not os.path.exists(path):
-            os.makedirs(path)
-        datetag = datetime.datetime.now().strftime('%Y_%m_%d_%H_%M_%S_%f')
-        self.filename=('%s/%s_%s' % (path, self.program.replace(' ','_'), datetag))
-        self.file = h5py.File(self.filename+'.h5', "w")
-
-        # meta data header               
-        dt = h5py.special_dtype(vlen=bytes)
-        dset=self.file.create_dataset('general/user',(1,),dtype=dt)
-        dset[0]=os.getlogin()
-        dset=self.file.create_dataset('general/application',(1,),dtype=dt)
-        dset[0]=self.program
-        dset=self.file.create_dataset('general/author',(1,),dtype=dt)
-        dset[0]=self.author
-        dset=self.file.create_dataset('general/version',(1,),dtype=dt)
-        dset[0]=self.version
-        dset=self.file.create_dataset('general/created',(1,),dtype=dt)
-        dset[0]=str(datetime.datetime.now())
 
 
-    def close(self):
+def openDataset(program):
-        if self.file is not None:
+    if isinstance(program,str):
-            self.file.close()
+        program={'Name':program,'Author':'Unknown','Version':'Unknown'}
-        self.file = None
+    if not isinstance(program,dict):
+        return None,None
+    if not 'Author' in program.keys():
+        program['Author']='Unknown'
+    if not 'Version' in program.keys():
+        program['Version']='Unknown'
+    filename=getDatasetFileName(program['Name'])
+    hid= h5py.File(filename+'.h5', "w")
+
+    # meta data header               
+    dt = h5py.special_dtype(vlen=bytes)
+    dset=hid.create_dataset('general/user',(1,),dtype=dt)
+    dset[0]=os.getlogin()
+    dset=hid.create_dataset('general/application',(1,),dtype=dt)
+    dset[0]=program['Name']
+    dset=hid.create_dataset('general/author',(1,),dtype=dt)
+    dset[0]=program['Author']
+    dset=hid.create_dataset('general/version',(1,),dtype=dt)
+    dset[0]=program['Version']
+    dset=hid.create_dataset('general/created',(1,),dtype=dt)
+    dset[0]=str(datetime.datetime.now())
+    return hid,filename
+
+
+
+def writeData(hid, data, scanrun=1):
+    if not 'pid' in data.keys():
+        return
+    shape = data['pid'].shape
+    ndim = len(shape)
+    nsam = shape[-1]
+    nrec = 0
+    if ndim > 1:
+        nrec = shape[:-1][0]
+    hid.create_dataset("scan_%d/method/records" % scanrun,data=[nrec])
+    hid.create_dataset("scan_%d/method/samples" % scanrun,data=[nsam])
+    hid.create_dataset("scan_%d/method/dimension" % scanrun,data=[ndim])
+    hid.create_dataset("scan_%d/method/reducedData" % scanrun,data=[0])  # indicating that there is at least a 2D array for scalar data
+    # write the sensor raw value
+    for ele in data.keys():
+        name=ele.split(':')
+        if len(name)>1:
+            dset=hid.create_dataset('scan_%d/data/%s/%s' % (scanrun, name[0], name[1]), data=data[ele])
+        else:
+            dset=hid.create_dataset('scan_%d/data/%s' % (scanrun, name[0]), data=data[ele])
+        dset.attrs['system'] = getDatasetSystem(name[0])
+        dset.attrs['units'] = 'unknown'
+
+def writeActuator(hid,act,scanrun=1):
+    if not act:
+        return
+    dt = h5py.special_dtype(vlen=bytes)
+    dset=hid.create_dataset("scan_%d/method/type" % scanrun,(1,),dtype=dt)
+    nact = len(act.keys())
+    if nact>0:
+        dset[0]='Scan'        
+    else:
+        dset[0]='Time Recording'
+    for ele in act.keys():
+        name=ele.split(':')
+        if len(name)>1:
+            dset=hid.create_dataset("scan_%d/method/actuators/%s/%s" % (scanrun,name[0],name[1]),data=act[ele])
+        else:
+            dset=hid.create_dataset("scan_%d/method/actuators/%s" % (scanrun,name[0]),data=act[ele])
+        dset.attrs['system']=getDatasetSystem(name[0])
+        dset.attrs['units']='unknown'
+
+def writeSnap(hid,val):
+    if not val:
+        return
+    for key in val.keys():
+        name=key.split(':')
+        if len(name)>1:
+            dset=hid.create_dataset('experiment/%s/%s' % (name[0],name[1]),data=val[key])
+        else:
+            dset=hid.create_dataset('experiment/%s/%s' % (name[0]),data=val[key])
+        dset.attrs['system']=getDatasetSystem(name[0])
+        dset.attrs['units']='unknown'
+
+
+def writeAnalysis(hid,data,scanrun=1):
+    if not data:
+        return
+    for key in data.keys():
+        name=key.split(':')
+        if len(name)>1:
+            dset=hid.create_dataset('scan_%d/analysis/%s/%s' % (scanrun, name[0], name[1]), data=data[key])
+        else:
+            dset=hid.create_dataset('scan_%d/analysis/%s/%s' % (scanrun, name[0]), data=data[key])
+        dset.attrs['system']='analysis'
+        dset.attrs['units']='unknown'
+
+def writeFigure(filename,figs):
+    for i,ele in enumerate(figs):
+        plotname='%s_Fig%d.png' % (filename,(i+1))
+        im = Image.open(ele)
+        im.save(plotname)
+    return None
  
-
+def getDatasetSystem(name):
-    def writeSnap(self,val):
+    if len(name) > 11:
-        for key in val.keys():
+        tag=name[8:9]
-            name=key.split(':')
+        fulltag=name[8:12]
-            if 'value' in val[key].keys():
+    else:
-                data=val[key]['value']
+        tag=''
-            elif 'val' in val[key].keys():
+        fulltag=''
-                data=val[key]['val']
+    sys='Unknown'
-            else:
+    if tag =='P':
-                continue
+        sys='Photonics'
-            dset=self.file.create_dataset('experiment/%s/%s' % (name[0],name[1]),data=[data])
+    if tag =='D':
-            dset.attrs['system']=self.getSystem(name[0])
+        sys='Diagnostics'
-            dset.attrs['units']='unknown'
+    if fulltag =='DSCR':
-
+        sys='Camera'
-    def writeAnalysis(self,data,scanrun=1):
+    if tag == 'R':
-        for key1 in data.keys():
+        sys='RF'
-            for key2 in data[key1].keys():
+    if tag == 'M':
-                dset=self.file.create_dataset('scan_%d/analysis/%s/%s' % (scanrun, key1, key2), 
+        sys='Magnets'
-                                              data=data[key1][key2])
+    if tag == 'U':
-
+        sys='Undulator'
-    def writeData(self, data, scanrun=1):
+    return sys
-        if not 'Shot:ID' in data.keys():
-            return
-        shape = data['Shot:ID'].shape
-        ndim = len(shape)
-        nsam = shape[-1]
-        nrec = 0
-        if ndim > 1:
-            nrec = shape[:-1][0]
-        self.file.create_dataset("scan_%d/method/records" % scanrun,data=[nrec])
-        self.file.create_dataset("scan_%d/method/samples" % scanrun,data=[nsam])
-        self.file.create_dataset("scan_%d/method/dimension" % scanrun,data=[ndim])
-        self.file.create_dataset("scan_%d/method/reducedData" % scanrun,data=[0])  # indicating that there is at least a 2D array for scalar data
-        # write the sensor raw value
-        for ele in data.keys():
-            name=ele.split(':')
-            dset=self.file.create_dataset('scan_%d/data/%s/%s' % (scanrun, name[0], name[1]), data=data[ele])
-            dset.attrs['system'] = self.getSystem(name[0])
-            dset.attrs['units'] = 'unknown'
-
-
-    def writeActuator(self,act,scanrun=1):
-        dt = h5py.special_dtype(vlen=bytes)
-        dset=self.file.create_dataset("scan_%d/method/type" % scanrun,(1,),dtype=dt)
-        if act.isActuator:
-            dset[0]='Scan'        
-        else:
-            dset[0]='Time Recording'
-        for ele in act.actuators.keys():
-            name=ele.split(':')
-            dset=self.file.create_dataset("scan_%d/method/actuators/%s/%s" % (scanrun,name[0],name[1]),data=act.actuators[ele]['val'])
-            dset.attrs['system']=self.getSystem(name[0])
-            dset.attrs['units']='unknown'
-
-        
-    def getSystem(self,name):
-        if len(name) > 11:
-            tag=name[8:9]
-            fulltag=name[8:12]
-        else:
-            tag=''
-            fulltag=''
-        sys='Unknown'
-        if tag =='P':
-            sys='Photonics'
-        if tag =='D':
-            sys='Diagnostics'
-        if fulltag =='DSCR':
-            sys='Camera'
-        if tag == 'R':
-            sys='RF'
-        if tag == 'M':
-            sys='Magnets'
-        if tag == 'U':
-            sys='Undulator'
-        return sys
 
 
 

interface/snap.py

@@ -1,261 +1,71 @@
-import datetime
-import re
 import numpy as np
 import yaml 
 import os
-import json
-
-import copy
-
-from threading import Thread
 
 import epics
 
-class Snap:
+# things to do:
-    def __init__(self,filename='/sf/data/applications/snapshot/req/op/SF_settings.yaml'):
+# 1. Read a snapshot file (not request file)
+# 2. Save a snapshot file
+# 3. add parameters and performance channels (e.g. AT photon energies)
 
-        self.pvs = self.parseYAML(filename)
+def parseSnapShotReqYAML(filename):
-        self.doAbort = False
+# read the snapshot request file
+# returns a list of PV names
+    if not filename:
+        filename =  '/sf/data/applications/snapshot/req/op/SF_settings.yaml'
+    pvs = []
+    path = os.path.dirname(filename)
+    with open(filename) as f:
+        try:
+            content = yaml.load(f, Loader=yaml.SafeLoader)
+            if 'include' in content.keys():
+                if len(content['include']) > 0:
+                    for cont in content['include']:
+                        retpv = parseSnapShotReqYAML(path+'/'+cont['name'])
+                        if 'macros' in cont.keys():
+                            retpv = applyReqMacro(retpv,cont['macros'])
+                        pvs =  pvs + retpv
+            if 'pvs' in content.keys():
+                if 'list' in content['pvs']:
+                    for pv in content['pvs']['list']:
+                        pvs.append(pv['name'])
+                return pvs
+            return None
+        except yaml.YAMLError as e:
+            print(e)
+            return None
+    return None
 
-    def my_caget_many(self):
+def applyReqMacro(pvs_in,macros):    
-        # this skips quite some channels - don't know why?
+    pvs = []
+    for macro in macros:
+        for key in macro:
+            tag='$('+key+')'
+            for pv in pvs_in:
+                if tag in pv:
+                    pvs.append(pv.replace(tag,macro[key]))
+    for pv in pvs_in:   # copy the ones without macro
+        if not '$(' in pv:
+            pvs.append(pv)
+    return pvs
 
-        pvdata = {}
+def getSnap(pvs=None):  
-        pvchids = []
+    if not isinstance(pvs,list):
-        # create, don't connect or create callbacks
+        pvs = parseSnapShotReqYAML(pvs)
-        for name in self.pvs:
+    if not pvs:
-            chid = epics.ca.create_channel(name, connect=False, auto_cb=False) # note 1
+        return
-            pvchids.append(chid)
+    ret={}
-
+    val = epics.caget_many(pvs)
-        # connect
+    for i,pv in enumerate(pvs):
-        for chid in pvchids:
+        if val[i]:      # filter out None values
-            print(epics.ca.name(chid))
+            ret[pv]=float(val[i]) 
-            epics.ca.connect_channel(chid)
+    epics.ca.clear_cache()
-
+    return ret
-        # request get, but do not wait for result
-        epics.ca.poll()
-        for chid in pvchids:
-            print(epics.ca.name(chid))
-            epics.ca.get(chid, wait=False)  # note 2
-
-        # now wait for get() to complete
-        epics.ca.poll()
-        for chid in pvchids:
-            print(epics.ca.name(chid))
-            val = epics.ca.get_complete(chid,timeout=0.5)
-            if not val:
-                pvdata[epics.ca.name(chid)] = np.array([val])
-        epics.ca.clear_cache()
-        return pvdata
-
-    def abort(self):
-        self.doAbort=True
-        print('Aborting Snap')
-
-    def getSnapValues(self,force=True):
-        self.doAbort=False
-        ret={}
-        if self.pvs:
-#            ret=self.my_caget_many()
-            val = epics.caget_many(self.pvs)
-            for i,pv in enumerate(self.pvs):
-                if val[i]:      # filter out None values
-                    ret[pv]={'val':float(val[i])} 
-        epics.ca.clear_cache()
-        return ret,{}
-
-    #-------------
-    # routines to parse the OP YAML file
-
-    def applyMacro(self,pvs_in,macros):    
-        pvs = []
-        for macro in macros:
-            for key in macro:
-                tag='$('+key+')'
-                for pv in pvs_in:
-                    if tag in pv:
-                        pvs.append(pv.replace(tag,macro[key]))
-        for pv in pvs_in:   # copy the ones without macro
-            if not '$(' in pv:
-                pvs.append(pv)
-        return pvs
-
-    def parseYAML(self,filename='/sf/data/applications/snapshot/req/op/SF_settings.yaml'):
-        pvs = []
-        path = os.path.dirname(filename)
-        with open(filename) as f:
-            try:
-                content = yaml.load(f, Loader=yaml.SafeLoader)
-                if 'include' in content.keys():
-                    if len(content['include']) > 0:
-                        for cont in content['include']:
-                            retpv = self.parseYAML(path+'/'+cont['name'])
-                            if 'macros' in cont.keys():
-                                retpv = self.applyMacro(retpv,cont['macros'])
-                            pvs =  pvs + retpv
-                if 'pvs' in content.keys():
-                    if 'list' in content['pvs']:
-                        for pv in content['pvs']['list']:
-                            pvs.append(pv['name'])
-                    return pvs
-                return None
-
-            except yaml.YAMLError as e:
-                print(e)
-                return None
-        return None
 
 
 
 
-class Old:
-
-    def __init__(self):
-        self.filename = filename
-        print('Estbalishing snapshot with request file:', filename,flush=True)
-        self.savepath = savepath
-        self.tolerance = 0.0005
-        self.pvnames = []
-        self.pvs = []
-        self.mppvnames = []
-        self.mppvs = []
-        self.machinepar = []
-        self.message = ''
-        if self.filename:
-            self.openRequestFile(self.filename)
-
-    def openRequestFile(self, filename):
-        self.filename = filename
-        self.rootname = self.filename.split('/')[-1]
-
-        isReq = True
-        if '.yaml' in filename:
-            isReq = False
-#        req_file = SnapshotReqFile(path=str(self.filename))
-
-        if newVersion:
-            if '.yaml' in filename:
-                req_file = SnapshotJsonFile(path=str(self.filename))
-            else:
-                req_file = SnapshotReqFile(path=str(self.filename))
-            pvs_list= req_file.read()[0]
-            print('PV List:-------------------------')
-            for i in range(len(pvs_list)):
-                print(pvs_list[i])
-            print(req_file.read()[1])
-        else:
-            if '.yaml' in filename:
-                self.filename=None
-                self.rootname = None
-                print('YAML files not supported')
-                return
-            req_file = SnapshotReqFile(str(self.filename))
-            pvs_list = req_file.read()
 
 
-        self.pvnames.clear()
-        self.machinepar.clear()
-        for ele in pvs_list:
-            if isinstance(ele, list):
-                self.pvnames = ele
-            elif isinstance(ele, dict):
-                if 'machine_params' in ele.keys():
-                    self.machinepar = ele['machine_params']
-        Thread(target=self.connectPVs).start()
-
-    def connectPVs(self):
-        self.pvs = [PV(pv, auto_monitor=False) for pv in self.pvnames]
-        con = [pv.wait_for_connection(timeout=0.2) for pv in self.pvs]
-        pvscon=[]
-        for i, val in enumerate(con):
-            if val is False:
-                print('Cannot connect to PV:', self.pvs[i].pvname,flush=True)
-            else:
-                pvscon.append(self.pvs[i])
-        self.pvs = copy.deepcopy(pvscon)
-        if isinstance(self.machinepar,list):
-            self.mppvs = [PV(self.machinepar[key], auto_monitor=False) for key in self.machinepar]
-        else:
-            self.mppvs = [PV(self.machinepar[key], auto_monitor=False) for key in self.machinepar.keys()]
-        con = [pv.wait_for_connection(timeout=0.2) for pv in self.mppvs]
-        pvscon.clear()
-        for i, val in enumerate(con):
-            if val is False:
-                print('Cannot connect to mPV:', self.mppvs[i].pvname,flush=True)
-            else:
-                pvscon.append(self.mppvs[i])
-        self.mppvs=copy.deepcopy(pvscon)
-
-    def getSnapValues(self, force=True):
-        values = {}
-        val = [pv.get(timeout=0.6, use_monitor=False) for pv in self.pvs]
-        for i, pv in enumerate(self.pvs):
-            if val[i] is None:
-                if force:
-                    continue
-                else:
-                    return False
-            else:
-                values[pv.pvname] = {
-                    "raw_name": pv.pvname, "val": val[i], "EGU": pv.units, "prec": pv.precision}
-        mvalues = {}
-        val = [pv.get(timeout=0.6, use_monitor=False) for pv in self.mppvs]
-        for i, pv in enumerate(self.mppvs):
-            if val[i] is None:
-                if force:
-                    continue
-                else:
-                    return False
-            else:
-                mvalues[pv.pvname] = {"value": val[i],
-                                      "units": pv.units, "precision": pv.precision}
-        return values, mvalues
-
-    def save(self, labels=[], comment="Generated by SFBD-Package", force=True):
-        if self.filename is None:
-            self.message = 'No Request File Loaded'
-            return False
-
-        val, mval = self.getSnapValues(force)
-        if isinstance(val, bool) and val == False:
-            self.message = 'Unsuccesful reading of PV channels (unforced access)'
-            return False
-
-        # construct file name
-        datetag = datetime.datetime.now().strftime('%Y%m%d_%H%M%S')
-        root = self.rootname.split('.req')[0]
-        files = self.savepath+root+'_'+datetag+'.snap'
-        filel = self.savepath+root+'_latest.snap'
-
-        # reshuffle from mval to keyword based machine values
-        mmval = {}
-        for key in self.machinepar.keys():
-            if self.machinepar[key] in mval.keys():
-                mmval[key] = mval[self.machinepar[key]]
-        # save file
-        parse_to_save_file(
-            val, files, macros=None, symlink_path=filel, comment=comment,
-            labels=[],
-            req_file_name=self.rootname, machine_params=mmval)
-        self.message = 'Snapshot saved to '+files
-        return True
-
-    def restore(self,filename,refilter='',force=True):
-        filepath=self.savepath+filename
-        prog=re.compile(refilter)
-        save_pvs=parse_from_save_file(filepath)
-        res={}
-        for ele in save_pvs:
-            if isinstance(ele,dict):
-                for key in ele.keys():
-                    if prog.match(key):
-                        res[key]=ele[key]['value']
-
-        for pv in self.pvs:
-            if pv.pvname in res.keys():
-                val=pv.get()
-                if val is None or np.abs(val-res[pv.pvname]) > self.tolerance:
-                    pv.put(res[pv.pvname])
-        self.message ='Snap restored'
-