Support for various app and slic wrapper

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)