Support for various app and slic wrapper

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+    # this part is obsolete - dimension should be given from the individual datasets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)