SICS-458: Add dsc command to run a DSC acquisition on Quokka.

Also added dsc.py utility which finds the start of a DSC profile in hdf files.

site_ansto/instrument/sans/config/commands/growfile.tcl

@@ -0,0 +1,96 @@
+# \file Implements 'dsc actime interval' command.
+set GROWFILE_STATE "DISABLED"
+set growfileSaveIndex 0
+
+
+proc doGrowFile {} {
+  global GROWFILE_STATE
+  global growfileSaveIndex
+
+# Reset the GROWFILE_STATE variable in case some naughty user sets it directly
+  set GROWFILE_STATE "ENABLED"
+  set HMSTATE [SplitReply [hmm configure daq]]
+  set FSTATE  [SplitReply [file_status]]
+# broadcast CALLED: [info level 0], HMSTATE = $HMSTATE, FSTATE = $FSTATE
+  if { $FSTATE != "UNKNOWN" && $FSTATE != "OPEN" && $HMSTATE == "Started"} {
+#   broadcast growfile $growfileSaveIndex
+    save $growfileSaveIndex "growfile"
+    incr growfileSaveIndex
+  } else {
+    if {$growfileSaveIndex == 0} {
+      broadcast ERROR: GROWFILE HMSTATE = $HMSTATE, FSTATE = $FSTATE. The histmem must be running and you must create a newfile before calling "growfile"
+    } else {
+      broadcast STOP GROWFILE Acquisition finished. HMSTATE = $HMSTATE, FSTATE = $FSTATE.
+      save $growfileSaveIndex "growfile"
+      newfile clear
+      broadcast Saved [hval /experiment/file_name]
+    }
+    set growfileSaveIndex 0
+    sicspoll del doGrowFile
+    set GROWFILE_STATE "DISABLED"
+    hsetprop /instrument/detector/hmm mutable true
+  }
+}
+publish doGrowFile user
+
+
+proc growfile { {interval 300} } {
+  global GROWFILE_STATE
+  global growfileSaveIndex
+
+  set GROWFILE_STATE "DISABLED"
+  set growfileSaveIndex 0
+
+  set as_error 0
+
+  set myrights [set_rights manager]
+  if {$myrights == -1} {
+    return -code error "ERROR: You are not authorized for this operation"
+  }
+  set interval [string tolower $interval]
+  if {$interval == "check" || $interval == "status"} {
+    if { $GROWFILE_STATE == "ENABLED" } {
+      return "GROWFILE $GROWFILE_STATE [sicspoll intervall doGrowFile]"
+    } else {
+      return "GROWFILE $GROWFILE_STATE"
+    }
+  } elseif {[string is integer $interval]} {
+    if {$interval <= 0} {
+      if { $GROWFILE_STATE == "ENABLED" } {
+        sicspoll del doGrowFile
+        set GROWFILE_STATE "DISABLED"
+      }
+    } else {
+      if {$GROWFILE_STATE == "DISABLED"} {
+        sicspoll add doGrowFile script $interval doGrowFile
+#       sicspoll listen # WARNING:When the listening client exits it leaves SICSPOLL task with a corrupt connection object.  
+        set GROWFILE_STATE "ENABLED"
+      } else {
+        sicspoll intervall doGrowFile $interval
+      }
+    }
+  } else {
+    set as_error 1
+  }
+  
+  set_rights $myrights
+
+  if {$as_error} {
+    return -code error "ERROR: Invalid argument in '[info level 0]', should be an integer or 'check'"
+  }
+}
+publish growfile user
+
+# \brief Run histogram for the specified time and save XY binned data at the given interval.
+# \param actime Acquisition time in seconds.
+# \param saveint Save interval in seconds.
+proc dsc {actime saveint} {
+  hsetprop /instrument/detector/hmm mutable false
+  newfile HISTOGRAM_XY
+  histmem mode time
+  histmem preset $actime
+  histmem start
+  growfile $saveint
+}
+
+publish dsc user

site_ansto/instrument/sans/quokka_configuration.tcl

@@ -73,6 +73,7 @@ fileeval $cfPath(environment)/sct_antonparr_MCR500.tcl
 fileeval $cfPath(beamline)/spin_flipper.tcl
 fileeval $cfPath(commands)/pulser.tcl
 fileeval $cfPath(commands)/hvcommands.tcl
+fileeval $cfPath(commands)/growfile.tcl
 
 source gumxml.tcl
 

site_ansto/instrument/sans/util/dsc.py

@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+# vim: ft=python ts=8 sts=4 sw=4 expandtab autoindent smartindent
+""" Find the trigger time for Differenctial Scanning Calorimetry data in nx.hdf files. """
+
+import sys
+import os
+import h5py
+import argparse
+import time
+from collections import defaultdict
+
+class SkipFile(BaseException):
+    """This exception should be raised to skip processing a file"""
+    pass
+
+PARSER = argparse.ArgumentParser(
+    description = """Report the time offset for the start of the DSC profile relative to the start time of the histogram data.
+    This program can process multiple hdf files by specifying the path to the first file and the number of files to process.
+    You can also speficy a list of 'file_path numfile' pairs.""",
+    usage='dsc file_path numfile {file_path numfile}'
+)
+PARSER.add_argument('files', nargs='+', help = 'List of "file_path numfile" pairs')
+ARGS = PARSER.parse_args()
+
+FAILS = defaultdict(list)
+for startfile, num in zip(ARGS.files[0::2], ARGS.files[1::2]):
+    numfiles = int(num)
+    hfdir = os.path.dirname(startfile)
+    hfbase = os.path.basename(startfile)
+    idx = hfbase.find('.')
+    startFID = hfbase[:idx]
+    ext = hfbase[idx:]
+    idnum = int(startFID[3:])
+    inst_abname = hfbase[:3]
+
+    hfval = {}
+    print
+    for i in range(numfiles):
+        try:
+            currid = idnum + i
+            fileID = inst_abname + '%07d' % currid
+            if (hfdir == ''):
+                nxfile = fileID + ext
+            else:
+                nxfile = hfdir + '/' + fileID + ext
+
+            try:
+                hf = h5py.File(nxfile, 'r')
+            except:
+                FAILS['badfile'].append(nxfile)
+                continue
+
+            if (hfbase.startswith('QKK')):
+                rootpath = fileID + '/'
+            else:
+                rootpath = 'entry1/'
+
+            for dpath in ['time_stamp', 'instrument/detector/start_time', 'sample/dsc_val']:
+                dscpath = rootpath + dpath
+                if dscpath in hf:
+                    hfval[dpath] = hf[dscpath][:]
+                else:
+                    FAILS['badpath:{0}'.format(dpath)].append(nxfile)
+                    hf.close()
+                    raise SkipFile
+
+            print fileID
+            datiter = {}
+            dat_hasnext = 0
+            time_tuple = time.strptime(hf[rootpath + 'start_time'][0], '%Y-%m-%d %H:%M:%S')
+            hfval['time_stamp'] += time.mktime(time_tuple)
+            hfval['time_stamp'] -= hfval['instrument/detector/start_time']
+            dsc0 = hfval['sample/dsc_val'][0]
+            no_transition = True
+            for i in range(1, len(hfval['sample/dsc_val'][1:])):
+                dsc1 = hfval['sample/dsc_val'][i]
+                if abs(dsc1 - dsc0) > 1.9:
+                    no_transition = False
+                    msg = 'dsc_val transition from {dsc0} to {dsc1} volts at {time} seconds from detector start time, array index = {index}'
+                    print msg.format(dsc0=dsc0, dsc1=dsc1, time=hfval['time_stamp'][i], index=i)
+                dsc0 = dsc1
+
+            if no_transition:
+                print 'dsc_val no transition'
+
+            print
+            hf.close()
+        except SkipFile:
+            continue
+
+for k in FAILS.keys():
+    if (len(FAILS[k])):
+        print >> sys.stderr, 'Skipped following files. Reason = ', k
+        print >> sys.stderr, FAILS[k]