Support for various app and slic wrapper

app/__init__.py

@@ -1,2 +1,4 @@
 from .adaptiveorbit import AdaptiveOrbit
 from .spectralanalysis import SpectralAnalysis
+from .hero import LaserPower,EnergyModulation
+from .dispersiontools import Dispersion

app/adaptiveorbit.py

@@ -39,7 +39,7 @@ class AdaptiveOrbit:
 
     def initBSStream(self,channels):
         print("Initializing BSstream")
-        bs = BSCache()
+        bs = BSCache(100000,10000)   # 1 second time out, capazity for 100 second.
         bs.stop()
         for cnl in channels[1:]:
             if not is_available(cnl):
@@ -63,10 +63,8 @@ class AdaptiveOrbit:
         return pvs
 
     def flush(self):
-        with self.bsAR.pt.queue.mutex:
+        self.bsAR.flush()
-            self.bsAR.pt.queue.queue.clear()       
+        self.bsAT.flush()
-        with self.bsAT.pt.queue.mutex:
-            self.bsAT.pt.queue.queue.clear()       
 
     def terminate(self):
         print('Stopping BSStream Thread...')    

app/dispersiontools.py

@@ -0,0 +1,175 @@
+import datetime
+import re
+import numpy as np
+
+from bsread import dispatcher
+import epics
+
+from slic.core.adjustable import PVAdjustable
+from slic.core.acquisition import BSAcquisition
+from slic.core.scanner import Scanner
+
+
+def getAux(pvs=None): 
+    if not pvs:
+        return
+    ret={}
+    val = epics.caget_many(pvs)
+    for i,pv in enumerate(pvs):
+        if val[i]:      # filter out None values
+            ret[pv]=float(val[i]) 
+    epics.ca.clear_cache()
+    return ret
+
+
+def getBSChannels(regexp):
+     prog = re.compile(regexp)
+     res = []
+     for bs in dispatcher.get_current_channels():
+          if prog.match(bs['name']):
+               res.append(bs['name'])
+     return res
+
+
+class Dispersion:
+     def __init__(self, branch = 'Aramis'):
+          self.scanname = 'Dispersion'
+          self.branch = 'None'
+          dirpath= datetime.datetime.now().strftime('/sf/data/measurements/%Y/%m/%d/slic_sfbd')
+          self.scandir='%s/%s' % (dirpath,self.scanname)
+
+          self.setBranch()
+          self.sc = None
+          self.Nsteps = 2
+          self.Nsamples = 1
+          
+          
+     def setBranch(self,branch = 'Aramis'):
+          if branch == 'Athos Dump':
+               self.setupAthosDump()
+          elif branch == 'Aramis':
+               self.setupAramis()
+          else:
+               self.branch = 'None'
+
+          
+     def setupAramis(self):
+          # pre-scan item
+          self.pre = {}
+          self.pre['SFB_BEAM_DUMP_AR:ONOFF1']={'Val':0,'InitVal':0}
+          self.pre['SFB_BEAM_ENERGY_ECOL_AR:ONOFF1']={'Val':0,'InitVal':0}
+          self.pre['SFB_ORBIT_S30:ONOFF1']={'Val':0,'InitVal':0}
+          self.pre['SFB_ORBIT_SAR:ONOFF1']={'Val':0,'InitVal':0}
+          for pv in self.pre.keys():
+               self.pre[pv]['adj']=PVAdjustable(pv)
+          # adjustable
+          self.adjSV = 'S30:SET-E-GAIN-OP'
+          self.adjRB = 'S30:GET-E-GAIN-OP'
+          self.adj = PVAdjustable(self.adjSV,pvname_readback = self.adjRB, accuracy = 0.1)
+          self.amp = 20    # the amplitude of the scan, which can be scaled
+          # acquisition
+          sensor1 = getBSChannels('SAR.*DBPM.*:[XY]1$')
+          sensor2 = getBSChannels('S[23].*-RLLE-DSP:.*-VS$')
+          self.sensor = sensor1+sensor2
+          self.acq = [BSAcquisition("machine","sfbd", default_channels=self.sensor)]
+          # auxiliar data to be read one
+          self.aux=[]
+          for sen in sensor2:
+               if 'PHASE-VS' in sen:
+                    self.aux.append(sen.replace('PHASE-VS','GET-VSUM-PHASE-OFFSET').replace('RLLE-DSP','RSYS'))
+                    self.aux.append(sen.replace('PHASE-VS','GET-VSUM-AMPLT-SCALE').replace('RLLE-DSP','RSYS'))
+                    self.aux.append(sen.replace('PHASE-VS','SM-SET').replace('RLLE-DSP','RMSM'))
+          self.aux.append('S10BC02-MBND100:ENERGY-OP')
+
+          # scanner
+          self.branch='Aramis'
+          self.path = '%s-%s' % (self.scanname,self.branch)
+          self.scanner = Scanner(data_base_dir=self.path,scan_info_dir=self.path,
+                                 make_scan_sub_dir=True,
+                                 default_acquisitions=self.acq)
+
+     def setupAthosDump(self):
+          # pre-scan item
+          self.pre = {}
+          self.pre['SFB_BEAM_DUMP_AT:ONOFF1']={'Val':0,'InitVal':0}
+          self.pre['SFB_ORBIT_SAT:ONOFF1']={'Val':0,'InitVal':0}
+          for i in range(1,5):
+               self.pre['SFB_ORBIT_SAT_%2.2d:ONOFF1' % i ]={'Val':0,'InitVal':0}
+          for pv in self.pre.keys():
+               self.pre[pv]['adj']=PVAdjustable(pv)
+          # adjustable
+          self.adjSV = 'SATCB01-RSYS:SET-BEAM-PHASE'
+          self.adjRB = 'SATCB01-RSYS:GET-BEAM-PHASE'
+          self.adj = PVAdjustable(self.adjSV,pvname_readback = self.adjRB, accuracy = 0.1)
+          self.amp = 20    # the amplitude of the scan, which can be scaled
+          # acquisition
+          self.sensor = ['SATBD02-DBPM010:Y2','SATBD02-DBPM040:Y2']
+          self.acq = [BSAcquisition("machine","sfbd", default_channels=self.sensor)]
+          # auxiliar data to be read one
+          aux = ['SATCL01-MBND100:ENERGY-OP']
+          # scanner
+          self.branch='Athos_Dump'
+          self.path = '%s-%s' % (self.scanname,self.branch)
+          self.scanner = Scanner(data_base_dir=self.path,scan_info_dir=self.path,
+                                 make_scan_sub_dir=True,
+                                 default_acquisitions=self.acq)
+
+
+
+
+     def setup(self,scl = 1, Nsteps=5, Nsamples=5):
+          val = self.adj.get_current_value(readback=False)
+          dval = self.amp*scl
+          self.N = Nsteps
+          self.Ns= Nsamples
+          self.values=np.linspace(val-dval,val+dval,num=self.N)
+
+
+     def preaction(self):
+          for key in self.pre.keys():
+               self.pre[key]['InitVal'] = self.pre[key]['adj'].get_current_value(readback = False)
+               self.pre[key]['adj'].set_target_value(self.pre[key]['Val'])
+
+     def postaction(self):
+          for key in self.pre.keys():
+               self.pre[key]['adj'].set_target_value(self.pre[key]['InitVal'])
+
+
+     def scan(self):
+          self.sc=self.scanner.ascan_list(self.adj,self.values,
+                                          filename=self.scanname,start_immediately = False,
+                                          n_pulses=self.Ns,return_to_initial_values=True)
+          self.preaction()
+          self.sc.run()
+          self.auxdata = getAux(self.aux)
+          self.postaction()
+
+        
+     def stop(self):
+          if self.sc is None:
+               return
+          self.sc.stop()
+
+     def running(self):
+          return self.sc.running
+
+     def status(self):
+          si = self.sc.scan_info.to_dict()
+          steps = 0
+          if 'scan_values' in si:
+               steps=len(si['scan_values'])
+          return steps,self.N
+
+     def info(self):
+          return self.sc.scan_info.to_dict()
+
+
+
+        
+
+
+
+
+ 
+
+  

app/hero.py

@@ -0,0 +1,111 @@
+import datetime
+import numpy as np
+
+from slic.core.acquisition import PVAcquisition
+from slic.core.acquisition import BSAcquisition
+from slic.devices.general import motor
+from slic.core.scanner import Scanner
+from sfbd.ext import CamAcquisition
+
+# some temporary wrapper
+class PollingPVAcquisition(PVAcquisition):
+     def _acquire(self, *args, polling=True, **kwargs):
+        return super()._acquire(*args, polling=polling, **kwargs)
+
+class LaserScanBase:
+    def __init__(self):
+        print('Init Base Class')
+        self.SV= 'SSL-LMOT-M1104:MOT'
+        self.pol = motor.Motor(self.SV)
+        
+    def stop(self):
+        if self.sc is None:
+            return
+        self.sc.stop()
+
+    def running(self):
+        return self.sc.running
+
+    def status(self):
+        si = self.sc.scan_info.to_dict()
+        steps = 0
+        if 'scan_values' in si:
+            steps=len(si['scan_values'])
+        return steps,self.N
+
+    def info(self):
+        return self.sc.scan_info.to_dict()
+
+    def setup(self,amax=21,Nsteps=5,Nsamples=5):
+        amin = 0
+        self.N = Nsteps
+        self.Ns= Nsamples
+        self.values=np.linspace(19,21,num=self.N)  # needs a change
+
+# measuring the pulse energy as a function of the controling PV. Note that the power should be limited to 300 uJ
+# thus limiting the value of the actuaor defining the lase rpulse energy in the EnergyModulaiton class.
+
+class LaserPower(LaserScanBase):
+    def __init__(self):
+        super(LaserPower,self).__init__()
+
+        self.scanname = 'HEROLaserEnergy'
+        dirpath= datetime.datetime.now().strftime('/sf/data/measurements/%Y/%m/%d/slic_sfbd')
+        self.scandir='%s/%s' % (dirpath,self.scanname)
+
+        self.RB = 'SSL-LENG-SLNK1:VAL_GET'
+        self.erg = PollingPVAcquisition("machine","sfbd", default_channels=[self.RB])
+     
+        self.scanner = Scanner(data_base_dir=self.scandir,scan_info_dir=self.scandir,make_scan_sub_dir=True,
+                               default_acquisitions=[self.erg])
+        
+    def scan(self):
+        self.sc=self.scanner.ascan_list(self.pol,self.values,
+                                    filename=self.scanname,start_immediately = False,
+                                    n_pulses=self.Ns,return_to_initial_values=True)
+        self.sc.run()
+        
+
+
+
+# measuring the coherent emission/space charge blow-up as a function of the hero energy modulation
+
+class EnergyModulation(LaserScanBase):
+    def __init__(self, acq = 0):
+        super(EnergyModulation,self).__init__()
+        self.scanname = 'HEROEnergyModulation'
+        dirpath= datetime.datetime.now().strftime('/sf/data/measurements/%Y/%m/%d/slic_sfbd')
+        self.scandir='%s/%s' % (dirpath,self.scanname)
+
+        self.acq = acq
+        if self.acq == 0:
+             self.RB ='SATFE10-PEPG046-EVR0:CALCI' 
+             self.erg = BSAcquisition("machine","sfbd", default_channels=[self.RB])
+        elif self.acq == 1:
+             self.RB ='SATBD02-DBPM040:Y2'
+             self.erg = BSAcquisition("machine","sfbd", default_channels=[self.RB])
+        elif self.acq == 2:
+             self.RB = 'SATBD01-DSCR210'
+             self.erg = CamAcquisition("machine","sfbd", default_channels=[self.RB])
+             self.erg.getConnection(self.RB)
+        else:
+             self.RB = 'SATBD02-DSCR050'
+             self.erg = CamAcquisition("machine","sfbd", default_channels=[self.RB])
+             self.erg.getConnection(self.RB)
+        
+        self.scanner = Scanner(data_base_dir=self.scandir,scan_info_dir=self.scandir,make_scan_sub_dir=True,
+                               default_acquisitions=[self.erg])
+        
+    def scan(self):
+        self.sc=self.scanner.ascan_list(self.pol,self.values,
+                                        filename=self.scanname,start_immediately = False,
+                                        n_pulses=self.Ns,return_to_initial_values=True)
+        self.sc.run()
+        
+
+
+
+
+ 
+
+  

app/spectralanalysis.py

@@ -11,7 +11,7 @@ class SpectralAnalysis:
     """
     def __init__(self):
 
-        self.bs = BSCache()
+        self.bs = BSCache(100000,10000)  # 100 second timeout, size for 100 second data taken 
         self.bs.stop()
         
         self.channel = ''
@@ -35,8 +35,7 @@ class SpectralAnalysis:
         self.bs.pt.running.clear() # for some reason I have to
 
     def flush(self):
-        with self.bs.pt.queue.mutex:
+        self.bs.flush()
-            self.bs.pt.queue.queue.clear()
 
     def read(self):
         data=self.bs.__next__()

ext/__init__.py

@@ -1 +1,3 @@
-from .reichebscombined import ReicheBSCombined
+from .magnet import Magnet
+from .camacquisition import CamAcquisition
+from .counteradjustable import CounterAdjustable

ext/camacquisition.py

@@ -0,0 +1,41 @@
+from time import sleep
+from tqdm import trange
+import h5py
+
+from cam_server_client import PipelineClient
+from cam_server_client.utils import get_host_port_from_stream_address
+from bsread import source, SUB
+
+
+from slic.core.acquisition.acquisition import Acquisition
+class CamAcquisition(Acquisition):
+
+    def getConnection(self,cam):
+        pipeline_client = PipelineClient()
+        cam_instance_name = str(cam) + "_sp1"
+        stream_address = pipeline_client.get_instance_stream(cam_instance_name)
+        self.host, self.port = get_host_port_from_stream_address(stream_address)
+        print(self.host,self.port)
+
+    def _acquire(self, filename, channels=None, data_base_dir=None, scan_info=None, n_pulses=100, **kwargs):
+        print("my routine")
+        print("extra kwargs:", kwargs)
+        args = (filename, n_pulses, channels)
+        args = ", ".join(repr(i) for i in args)
+        print("acquire({})".format(args))
+        print(f"dummy acquire to {filename}:")
+
+#        stream_host,stream_port = getPipeLine(channels[0])
+#        time.wait(1)
+        data= []
+        with source(host=self.host, port=self.port, mode=SUB) as input_stream:
+            input_stream.connect()
+            for i in range(n_pulses):
+                print('Camera Images', i)
+                message = input_stream.receive()
+                data.append(message.data.data)
+        hid = h5py.File(filename,'w')
+        gid = hid.create_group(channels[0])
+        for key in data[0].keys():
+            gid.create_dataset(key, data = [rec[key].value for rec in data])
+        hid.close()

ext/counteradjustable.py

@@ -0,0 +1,23 @@
+from slic.core.adjustable import Adjustable
+
+class CounterAdjustable(Adjustable):
+    def __init__(self, adjustable1, adjustable2):
+        self.adj1=adjustable1
+        self.adj2=adjustable2
+        self.ref_values()     # implementation needs reference values to convert absolute scan to relative scan
+
+    def ref_value(self):
+        self.val1 = self.adj1.get_current_value(readback = False)
+        self.val2 = self.adj2.get_current_value(readback = False)
+
+    def set_target_value(self, value):
+         t1 = self.adj1.set_target_value(self.val1 + value)
+         t2 = self.adj2.set_target_value(self.val2 - value)
+         t1.wait()
+         t2.wait()
+
+    def get_current_value(self):
+         return self.adj1.get_current_value()
+
+    def is_moving(self):
+        return any([self.adj1.is_moving(),self.adj2.is_moving()])

ext/magnet.py

@@ -0,0 +1,21 @@
+from slic.core.adjustable import PVAdjustable
+from slic.utils import typename
+
+class Magnet(PVAdjustable):
+
+     def __init__(self,name):
+          self.name=name
+          pvsv='%s:I-SET' % name
+          pvrb='%s:I-READ' % name
+          tol = 0.075
+          super().__init__(pvsv,pvname_readback=pvrb,accuracy=tol,internal=True)
+
+
+
+     @property
+     def status(self):
+          return "Cycling"   
+
+     def __repr__(self):
+        tn = typename(self)
+        return f"{tn} \"{self.name}\" is {self.status}"

ext/reichebscombined.py

@@ -1,12 +0,0 @@
-from slic.core.sensor.bsmonitor import BSMonitor
-
-class ReicheBSCombined(BSMonitor):
-
-     # Du brauchst kein extra init. BSMonitor tut schon das richtige...
-
-     def _unpack(self, data):
-         # data ist ein dict mit allen Deinen Kanälen
-         pid = data["pid"] # der effektive Channel-Name der Pulse ID
-         # hier dein Code
-         # am Ende sollte eine Zahl rauskommen:
-         return data

interface/__init__.py

@@ -2,3 +2,4 @@ from .snap import getSnap
 from .save import saveDataset
 from .load import loadDataset
 from .elog import writeElog
+from .slic import SlicScan

interface/save.py

@@ -50,7 +50,8 @@ def saveDataset(program,data,actuator=None,snap=None,analysis=None,figures=None)
     writeSnap(hid,snap)
     hid.close()
     
-    writeFigure(filename,figures)
+    if figures:
+        writeFigure(filename,figures)
     return filename
 
 
@@ -83,6 +84,16 @@ def openDataset(program):
 
 
 def writeData(hid, data, scanrun=1):
+    # 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'
+    # this part is obsolete - dimension should be given from the individual datasets
     if not 'pid' in data.keys():
         return
     shape = data['pid'].shape
@@ -95,15 +106,7 @@ def writeData(hid, data, scanrun=1):
     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:

interface/slic.py

@@ -0,0 +1,93 @@
+import h5py
+import numpy as np
+import time
+from threading import Thread
+from PyQt5.QtCore import QObject, pyqtSignal
+
+# to do:
+# 1 - check if scan thread is running
+# 2 - import of BSread data
+
+from sfbd.interface import getSnap
+
+class SlicScan(QObject):
+
+    siginc  = pyqtSignal(int, int)  # signal for increment
+    sigterm = pyqtSignal(int)       # signal for termination
+    sigsnap = pyqtSignal(bool)
+
+    def __init__(self):
+        QObject.__init__(self)
+        self.clear()
+
+    def clear(self):
+        self.daq = None
+        self.data = None
+        self.act = None
+        self.snap = None
+
+    def start(self,daq,snap=False):
+        self.clear()
+        Thread(target=self.Tmonitor).start()
+        self.startSnap(snap)
+
+    def startSnap(self,snap=False):
+        if not snap:
+            Thread(target=self.Tsnap).start()
+
+    def Tsnap(self):
+        self.snap = getSnap()
+        self.sigsnap.emit(True)
+
+    def Tmonitor(self):
+        mythread =  Thread(target=self.Tscanner).start()
+        time.sleep(1)
+        ostep = -1
+        while(self.daq.running()):
+            istep,nstep=self.daq.status()
+            if istep>ostep:
+                ostep=istep
+                self.siginc.emit(istep,nstep)
+            time.sleep(1)
+        if not mythread == None:  # wait till scanning thread is done
+            mythread.join()
+        istep,nstep=self.daq.status()
+        self.siginc.emit(istep,nstep)
+        self.data,self.act = importSlicScan(self.daq.info())
+        if hasattr(self.daq,'auxdata'):
+            self.data.update(self.daq.auxdata)
+        self.sigterm.emit(istep==nstep)
+
+    def Tscanner(self):
+        self.daq.scan()
+
+    def stop(self):
+        self.daq.stop()
+
+
+def importSlicScan(scan_info):
+    if not isinstance(scan_info,dict):
+        return None,None
+    if not 'scan_files' in scan_info.keys():
+        return None,None
+    sfiles = scan_info['scan_files']
+    data = {}
+    for istep, sfile in enumerate(sfiles):
+        hid = h5py.File(sfile[0],'r')
+        for name, h5obj in hid.items():        
+            if isinstance(h5obj,h5py.Dataset):   # pv channels
+                data[name] = addDatasetToData(data,name,h5obj)
+            elif isinstance(h5obj,h5py.Group):  # bs read channels
+                if 'data' in h5obj:
+                    data[name] = addDatasetToData(data,name,h5obj['data'])
+    actuator = {}
+    name = scan_info['scan_parameters']['name'][0]
+    actuator[name]=np.array(scan_info['scan_values'])
+    data[name]=np.array(scan_info['scan_readbacks'])
+    return data,actuator
+
+def addDatasetToData(data,name,h5obj):
+    if not name in data:
+        return np.array([h5obj[()]])
+    else:
+        return np.append(data[name],np.array([h5obj[()]]),axis=0)