def setSubdirectory(dirname):
try:
finder.find("GDAMetadata").setMetadataValue("subdirectory", dirname)
except:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "problem setting metadata value for 'subdirectory' to " + dirname, exceptionType, exception, traceback, False)
print "Failed to set metadata value for 'subdirectory' to:", dirname, exception
def time_command(numberOfLoops, cmd):
print "time_scan : ", `cmd`
timebase = time()
filename = strftime("%Y-%m-%d_%H-%M-%S_time_command.dat")
file = open(filename,"w")
try:
loop=0;
loop_count=0
while(True):
exec(cmd)
loop += 1
timenow = time()
t = timenow - timebase
timebase = timenow
file.write( `loop` + "," + `t`)
if numberOfLoops > 0:
loop_count += 1
if loop_count >= numberOfLoops:
break
except :
type, exception, traceback = sys.exc_info()
toRaise = not isinstance(exception, java.lang.InterruptedException)
if toRaise:
file.close
handle_messages.log(None,"time_command exception", type, exception, traceback, toRaise)
file.close
# filename = strftime("%Y-%m-%d_%H-%M-%S_time_command.dat_srs")
# if len(times)>0:
# xName="loop"
# yName="time"
# sfh = plotData.getScanFileHolderY(xName,yName,times)
# sfh.save( SRSLoader(filename))
# sfh.plot(xName, yName)
return filename
def time_command(numberOfLoops, cmd):
print "time_scan : ", ` cmd `
timebase = time()
filename = strftime("%Y-%m-%d_%H-%M-%S_time_command.dat")
file = open(filename, "w")
try:
loop = 0
loop_count = 0
while (True):
exec(cmd)
loop += 1
timenow = time()
t = timenow - timebase
timebase = timenow
file.write( ` loop ` + "," + ` t `)
if numberOfLoops > 0:
loop_count += 1
if loop_count >= numberOfLoops:
break
except:
type, exception, traceback = sys.exc_info()
toRaise = not isinstance(exception, java.lang.InterruptedException)
if toRaise:
file.close
handle_messages.log(None, "time_command exception", type, exception,
traceback, toRaise)
file.close
# filename = strftime("%Y-%m-%d_%H-%M-%S_time_command.dat_srs")
# if len(times)>0:
# xName="loop"
# yName="time"
# sfh = plotData.getScanFileHolderY(xName,yName,times)
# sfh.save( SRSLoader(filename))
# sfh.plot(xName, yName)
return filename
def getSubdirectory():
try:
return finder.find("GDAMetadata").getMetadataValue("subdirectory")
except:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "problem getting metadata value for 'subdirectory' ", exceptionType, exception, traceback, False)
print "Failed to get metadata value for 'subdirectory':", exception
return None
def update(controller,
msg,
exceptionType=None,
exception=None,
traceback=None,
Raise=False):
handle_messages.log(controller, msg, exceptionType, exception, traceback,
Raise)
def __init__(self):
self.comms_started=False
try:
self.leem_com=(Finder.find("leem2000_objects")).get("leem2000_com")
self.leem_com.setReplyTerm('\0')
self.leem_com.setCmdTerm('\0')
except:
exceptionType, exception, traceback=sys.exc_info();
handle_messages.log(None, "Error getting leem2000_com from leem2000_objects", exceptionType, exception, traceback, True)
def send(self, cmd):
if not self.comms_started:
try:
self.leem_com.send("asc")
self.comms_started=True
except:
exceptionType, exception, traceback=sys.exc_info();
handle_messages.log(None, "Error sending asc command to leem2000 at " + str(self.leem_com.address) + ":" + str(self.leem_com.port) +". Try restarting Leem2000 ", exceptionType, exception, traceback, True)
return self.leem_com.send(cmd)
def getVisit():
"""
Returns string representing current visit ID, eg cm4963-2
"""
try:
gdaMetaProvider=GDAMetadataProvider.getInstance()
except:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "problem getting GDA metadata provider", exceptionType, exception, traceback, False)
print "Failed to get GDA metadata provider:", exception
return gdaMetaProvider.getMetadataValue(GDAMetadataProvider.EXPERIMENT_IDENTIFIER)
def getVisitRootPath():
"""
Returns string representing current visit root path, eg /dls/i12/data/2014/cm4963-2
"""
try:
subDirname = finder.find("GDAMetadata").getMetadataValue("subdirectory")
except:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "problem getting metadata value for 'subdirectory' ", exceptionType, exception, traceback, False)
print "Failed to get metadata value for subdirectory:", exception
workDirpath = wd()
if (subDirname is not None) and (subDirname != ""):
visitRootpath = rreplace(workDirpath, os.sep+subDirname,"",1)
else:
visitRootpath = workDirpath
return visitRootpath
def cameraFactory(cam_name, peak2d_name, max2d_name, camdet, camdet_for_snaps):
# ----------------------------------------------------------------------
try:
print "Creating %s, %s and %s" % \
(cam_name, peak2d_name, max2d_name)
# This has no hardware triggered mode configured. This class is used to hijack its DetectorSnapper implementation.
cam = SwitchableHardwareTriggerableProcessingDetectorWrapper(
cam_name, camdet, None, camdet_for_snaps, [],
panel_name=None, panel_name_rcp='Plot 1',
toreplace=None, replacement=None, iFileLoader=TIFFImageLoader,
fileLoadTimout=15, returnPathAsImageNumberOnly=True)
peak2d = DetectorDataProcessorWithRoi(peak2d_name, cam, [TwodGaussianPeak()])
max2d = DetectorDataProcessorWithRoi(max2d_name, cam, [SumMaxPositionAndValue()])
# ----------------------------------------------------------------------
return cam, peak2d, max2d
except:
import sys
typ, exception, traceback = sys.exc_info()
handle_messages.log(None, "%s error - " % cam_name, typ, exception, traceback, False)
def time_scan(numberOfLoops, scan_constructor, scanPlotSettings, args):
print "time_scan : ", ` scan_constructor `, ` args `
times = []
timebase = time()
filename = strftime("%Y-%m-%d_%H-%M-%S_time_scan.dat")
file = open(filename, "w")
try:
loop = 0
loop_count = 0
while (True):
scan = scan_constructor(args)
if scanPlotSettings != None:
scan.setScanPlotSettings(scanPlotSettings)
scan.runScan()
loop += 1
timenow = time()
t = timenow - timebase
timebase = timenow
times.append(t)
file.write( ` loop ` + "," + ` t `)
if numberOfLoops > 0:
loop_count += 1
if loop_count >= numberOfLoops:
break
except:
type, exception, traceback = sys.exc_info()
toRaise = not isinstance(exception, java.lang.InterruptedException)
handle_messages.log(None, "time_scan exception", type, exception,
traceback, toRaise)
file.close
filename = strftime("%Y-%m-%d_%H-%M-%S_time_scan.dat_srs")
if len(times) > 0:
xName = "loop"
yName = "time"
sfh = plotData.getScanFileHolderY(xName, yName, times)
sfh.save(SRSLoader(filename))
sfh.plot(xName, yName)
return filename
def scan(*args):
"""
Moves several scannable objects simultaneously, the same number of steps.
After each movement data is collected from items in the allDetectors vector.
Expect arguments in the following format:
scannable1 start stop step scannable2 [start] [[stop] step] scannable3 [start] [[stop] step]
The number of steps is calculated from scannable1.
For subsequent scannables: if only start then they are moved only to that position. If no start value given then
the current position will be used (so this scannable will not be moved, but will be included in any output from the
scan.)
If a step value given then the scannable will be moved each time
If a stop value is also given then this is treated as a nested scan containing one scannable.
This scan will be run in full at each node of the main scan.
If there are multiple nested scans then they are nested inside each other to
create a multidimensional scan space (rasta scan).
"""
print args
try:
ConcurrentScan(args[0]).runScan()
except:
type, exception, traceback = sys.exc_info()
handle_messages.log(None, "scan failed", type, exception, traceback,
True)
def time_scan(numberOfLoops, scan_constructor, scanPlotSettings, args):
print "time_scan : ", `scan_constructor`,`args`
times=[]
timebase = time()
filename = strftime("%Y-%m-%d_%H-%M-%S_time_scan.dat")
file = open(filename,"w")
try:
loop=0;
loop_count=0
while(True):
scan = scan_constructor(args)
if scanPlotSettings != None:
scan.setScanPlotSettings(scanPlotSettings)
scan.runScan()
loop += 1
timenow = time()
t = timenow - timebase
timebase = timenow
times.append(t)
file.write( `loop` + "," + `t`)
if numberOfLoops > 0:
loop_count += 1
if loop_count >= numberOfLoops:
break
except :
type, exception, traceback = sys.exc_info()
toRaise = not isinstance(exception, java.lang.InterruptedException)
handle_messages.log(None,"time_scan exception", type, exception, traceback, toRaise)
file.close
filename = strftime("%Y-%m-%d_%H-%M-%S_time_scan.dat_srs")
if len(times)>0:
xName="loop"
yName="time"
sfh = plotData.getScanFileHolderY(xName,yName,times)
sfh.save( SRSLoader(filename))
sfh.plot(xName, yName)
return filename
def reload_tables(logInfo=True):
"""reloads all lookup tables on the ObjectServer"""
ok = True
controller = None
prefix = "reload_tables:"
if( logInfo ):
handle_messages.log(controller, prefix + " - started")
finder = Finder.getInstance()
converters = finder.listAllObjects("IReloadableQuantitiesConverter")
for converter in converters:
try:
if( logInfo ):
handle_messages.log(controller, prefix + "..." + converter.getName() )
converter.reloadConverter()
except:
type1, exception, traceback = sys.exc_info()
handle_messages.log(controller, prefix + " - ", type1, exception, traceback, False)
ok = False
if( logInfo ):
handle_messages.log(controller, prefix + " - completed")
if( not ok):
print "reload_tables completed with error"
return ok
def reloadLookupTablesEx(logInfo):
"""version of reloadLookupTables that can be used in tests to only generate output when an error is detected"""
ok = True
controller = None
prefix = "reloadLookupTables:"
if (logInfo):
handle_messages.log(controller, prefix + " - started")
converters = Finder.listFindablesOfType(IReloadableQuantitiesConverter)
for converter in converters:
try:
if (logInfo):
handle_messages.log(controller,
prefix + "..." + converter.getName())
converter.reloadConverter()
except:
type, exception, traceback = sys.exc_info()
handle_messages.log(controller, prefix + " - ", type,
exception, traceback, False)
ok = False
if (logInfo):
handle_messages.log(controller, prefix + " - completed")
if (not ok):
print "reloadLookupTables completed with error"
return ok
#UNOmotor1 = arduinoMotor.arduinoMotor("UNOmotor1", 4096, UNOmotor1a, UNOmotor1b, UNOmotor1c, UNOmotor1d)
#===================================================
#End of Raspberry Pi Specific Objects
#===================================================
#run user editable startup script
if isLive():
run("localStationUser.py")
except:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "Error in localStation", exceptionType, exception, traceback, False)
def roboscan(sample,quality=2):
carousel.sampleCarousel(sample)
robotarm.loadSample(sample)
sleep(5)
scan turntable 0 720 14.4 picamera
robotarm.unloadSample(sample)
carousel.sampleCarousel(1)
print "*** " + picamera.datFile
def tomoScanWithFrames(description,
inBeamPosition,
outOfBeamPosition,
exposureTime=1.,
start=0.,
stop=180.,
step=0.1,
darkFieldInterval=0,
flatFieldInterval=0,
imagesPerDark=10,
imagesPerFlat=10,
optimizeBeamInterval=0,
pattern="default",
nframes=1,
tomoRotationAxis=0,
addNXEntry=True,
autoAnalyse=True,
additionalScannables=[]):
"""
Function to collect a tomography step scan with multiple projection frames per scan point
Arguments:
description - description of the scan or the sample that is being scanned. This is generally user-specific information that may be used to map to this scan later and is available in the NeXus file)
inBeamPosition - position of X drive to move sample into the beam to take a projection
outOfBeamPosition - position of X drive to move sample out of the beam to take a flat field image
exposureTime - exposure time in seconds (default=1.0)
start - first rotation angle (default=0.0)
stop - last rotation angle (default=180.0)
step - rotation step size (default=0.1)
darkFieldInterval - number of projection-frame sub-series between each dark-field sub-series.
NOTE: at least 1 dark is ALWAYS taken both at the start and end of the scan, provided imagesPerDark>0
(default=0: use this value if you DON'T want to take any darks between projections)
flatFieldInterval - number of projection-frame sub-series between each flat-field sub-series.
NOTE: at least 1 flat is ALWAYS taken both at the start and end the scan, provided imagesPerFlat>0
(default=0: use this value if you DON'T want to take any flats between projections)
imagesPerDark - number of images to be taken in each dark-field sub-series (default=10)
imagesPerFlat - number of images to be taken in each flat-field sub-series (default=10)
nframes - number of projection frames per angular position (default=1)
General scan sequence is: D, F, P,..., P, F, D
where D stands for dark field, F - for flat field, and P - for projection.
"""
dataFormat = LocalProperties.get("gda.data.scan.datawriter.dataFormat")
try:
darkFieldInterval = int(darkFieldInterval)
flatFieldInterval = int(flatFieldInterval)
optimizeBeamInterval = int(optimizeBeamInterval)
image_key_frame = 3
nframes = int(nframes)
if nframes < 1:
nframes = 1
jns = beamline_parameters.JythonNameSpaceMapping(
InterfaceProvider.getJythonNamespace())
tomography_theta = jns.tomography_theta
if tomography_theta is None:
raise NameError(
"tomography_theta is not defined in Jython namespace")
tomography_shutter = jns.tomography_shutter
if tomography_shutter is None:
raise NameError(
"tomography_shutter is not defined in Jython namespace")
tomography_translation = jns.tomography_translation
if tomography_translation is None:
raise NameError(
"tomography_translation is not defined in Jython namespace")
tomography_detector = jns.tomography_detector
if tomography_detector is None:
raise NameError(
"tomography_detector is not defined in Jython namespace")
tomography_optimizer = jns.tomography_optimizer
if tomography_optimizer is None:
raise NameError(
"tomography_optimizer is not defined in Jython namespace")
tomography_time = jns.tomography_time
if tomography_time is None:
raise NameError(
"tomography_time is not defined in Jython namespace")
tomography_beammonitor = jns.tomography_beammonitor
if tomography_beammonitor is None:
raise NameError(
"tomography_beammonitor is not defined in Jython namespace")
tomography_camera_stage = jns.tomography_camera_stage
if tomography_camera_stage is None:
raise NameError(
"tomography_camera_stage is not defined in Jython namespace")
tomography_sample_stage = jns.tomography_sample_stage
if tomography_sample_stage is None:
raise NameError(
"tomography_sample_stage is not defined in Jython namespace")
tomo_additional_scannables = jns.tomography_additional_scannables
if tomo_additional_scannables is None:
raise NameError(
"tomo_additional_scannables is not defined in Jython namespace"
)
index = SimpleScannable()
index.setCurrentPosition(0.0)
index.setInputNames(["imageNumber"])
index.setName("imageNumber")
index.configure()
image_key = SimpleScannable()
image_key.setCurrentPosition(0.0)
image_key.setInputNames(["image_key"])
image_key.setName("image_key")
image_key.configure()
tomoScanDevice = make_tomoScanDevice(tomography_theta,
tomography_shutter,
tomography_translation,
tomography_optimizer, image_key,
index)
# return tomoScanDevice
#generate list of positions
numberSteps = ScannableUtils.getNumberSteps(tomography_theta, start,
stop, step)
theta_points = []
theta_points.append(start)
previousPoint = start
for i in range(numberSteps):
nextPoint = ScannableUtils.calculateNextPoint(previousPoint, step)
theta_points.append(nextPoint)
previousPoint = nextPoint
#generateScanPoints
optimizeBeamNo = 0
optimizeBeamYes = 1
shutterOpen = 1
shutterClosed = 0
shutterNoChange = 2
scan_points = []
theta_pos = theta_points[0]
index = 0
#Added shutterNoChange state for the shutter. The scan points are added using the (pseudo) ternary operator,
#if index is 0 then the shutterPosition is added to the scan point, else shutterNoChange is added to scan points.
for i in range(imagesPerDark):
scan_points.append(
(theta_pos, [shutterClosed, shutterNoChange][i != 0],
inBeamPosition, optimizeBeamNo, image_key_dark, index)) #dark
index = index + 1
for i in range(imagesPerFlat):
scan_points.append(
(theta_pos, [shutterOpen,
shutterNoChange][i != 0], outOfBeamPosition,
optimizeBeamNo, image_key_flat, index)) #flat
index = index + 1
for frm in range(nframes):
scan_points.append(
(theta_pos, shutterOpen, inBeamPosition, optimizeBeamNo,
image_key_project if frm == 0 else image_key_frame,
index)) #first
index = index + 1
imageSinceDark = 1
imageSinceFlat = 1
optimizeBeam = 0
for i in range(numberSteps):
theta_pos = theta_points[i + 1]
for frm in range(nframes):
scan_points.append(
(theta_pos, [shutterOpen, shutterNoChange
][i != 0], inBeamPosition, optimizeBeamNo,
image_key_project if frm == 0 else image_key_frame,
index)) #main image
index = index + 1
imageSinceFlat = imageSinceFlat + 1
if imageSinceFlat == flatFieldInterval and flatFieldInterval != 0:
for i in range(imagesPerFlat):
scan_points.append(
(theta_pos, [shutterOpen, shutterNoChange
][i != 0], outOfBeamPosition,
optimizeBeamNo, image_key_flat, index))
index = index + 1
imageSinceFlat = 0
imageSinceDark = imageSinceDark + 1
if imageSinceDark == darkFieldInterval and darkFieldInterval != 0:
for i in range(imagesPerDark):
scan_points.append(
(theta_pos, [shutterClosed,
shutterNoChange][i != 0], inBeamPosition,
optimizeBeamNo, image_key_dark, index))
index = index + 1
imageSinceDark = 0
optimizeBeam = optimizeBeam + 1
if optimizeBeam == optimizeBeamInterval and optimizeBeamInterval != 0:
scan_points.append(
(theta_pos, [shutterOpen,
shutterNoChange][i != 0], inBeamPosition,
optimizeBeamYes, image_key_project, index))
index = index + 1
optimizeBeam = 0
#add dark and flat only if not done in last steps
if imageSinceFlat != 0:
for i in range(imagesPerFlat):
scan_points.append(
(theta_pos, [shutterOpen,
shutterNoChange][i != 0], outOfBeamPosition,
optimizeBeamNo, image_key_flat, index)) #flat
index = index + 1
if imageSinceDark != 0:
for i in range(imagesPerDark):
scan_points.append(
(theta_pos, [shutterClosed,
shutterNoChange][i != 0], inBeamPosition,
optimizeBeamNo, image_key_dark, index)) #dark
index = index + 1
# scan_points1 = generateScanPoints(inBeamPosition, outOfBeamPosition, theta_points, darkFieldInterval, flatFieldInterval,
# imagesPerDark, imagesPerFlat, optimizeBeamInterval, pattern=pattern)
# if pattern == 'default' or pattern == 'DFPFD':
# i = 0
# for pt1 in scan_points1:
# pt = scan_points[i]
# if pt1 != pt:
# print "Mismatch - please tell Kaz about your scan and its arguments!"
# print "i = ", i
# print "pt = ", pt
# print "pt1 = ", pt1
# i += 1
#return None
positionProvider = tomoScan_positions(start, stop, step, darkFieldInterval, imagesPerDark, flatFieldInterval, imagesPerFlat, \
inBeamPosition, outOfBeamPosition, optimizeBeamInterval, scan_points)
scan_args = [
tomoScanDevice, positionProvider, tomography_time,
tomography_beammonitor, tomography_detector, exposureTime,
tomography_camera_stage, tomography_sample_stage
]
#scan_args.append(RotationAxisScannable("approxCOR", tomoRotationAxis))
#meta_add(RotationAxisScannable("approxCOR", tomoRotationAxis))
#meta_add("RotationCoord_as_list", [tomoRotationAxis])
meta_add("approxCOR", tomoRotationAxis)
for scannable in additionalScannables:
scan_args.append(scannable)
for scannable in tomo_additional_scannables:
scan_args.append(scannable)
''' setting the description provided as the title'''
if not description == None:
setTitle(description)
else:
setTitle("undefined")
dataFormat = LocalProperties.get("gda.data.scan.datawriter.dataFormat")
if not dataFormat == "NexusDataWriter":
handle_messages.simpleLog(
"Data format inconsistent. Setting 'gda.data.scan.datawriter.dataFormat' to 'NexusDataWriter'"
)
LocalProperties.set("gda.data.scan.datawriter.dataFormat",
"NexusDataWriter")
scanObject = createConcurrentScan(scan_args)
if addNXEntry:
addNXTomoSubentry(scanObject, tomography_detector.name,
tomography_theta.name)
scanObject.runScan()
if autoAnalyse:
lsdp = jns.lastScanDataPoint()
OSCommandRunner.runNoWait([
"/dls_sw/apps/tomopy/tomopy/bin/gda/tomo_at_scan_end_kz",
lsdp.currentFilename
], OSCommandRunner.LOGOPTION.ALWAYS, None)
return scanObject
except InterruptedException:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "User interrupted the scan", exceptionType,
exception, traceback, False)
raise InterruptedException("User interrupted the scan")
except:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "Error during tomography scan",
exceptionType, exception, traceback, False)
raise Exception("Error during tomography scan", exception)
finally:
handle_messages.simpleLog(
"Data Format reset to the original setting: " + dataFormat)
LocalProperties.set("gda.data.scan.datawriter.dataFormat", dataFormat)
def tomoScan(
description,
inBeamPosition,
outOfBeamPosition,
exposureTime=1.0,
start=0.0,
stop=180.0,
step=0.1,
darkFieldInterval=0,
flatFieldInterval=0,
imagesPerDark=10,
imagesPerFlat=10,
optimizeBeamInterval=0,
pattern="default",
tomoRotationAxis=0,
addNXEntry=True,
autoAnalyse=True,
additionalScannables=[],
):
"""
Function to collect a tomography step scan
Arguments:
description - description of the scan or the sample that is being scanned. This is generally user-specific information that may be used to map to this scan later and is available in the NeXus file)
inBeamPosition - position of X drive to move sample into the beam to take a projection
outOfBeamPosition - position of X drive to move sample out of the beam to take a flat field image
exposureTime - exposure time in seconds (default=1.0)
start - first rotation angle (default=0.0)
stop - last rotation angle (default=180.0)
step - rotation step size (default=0.1)
darkFieldInterval - number of projections between each dark-field sub-sequence.
NOTE: at least 1 dark is ALWAYS taken both at the start and end of the scan provided imagesPerDark>0
(default=0: use this value if you DON'T want to take any darks between projections)
flatFieldInterval - number of projections between each flat-field sub-sequence.
NOTE: at least 1 flat is ALWAYS taken both at the start and end the scan provided imagesPerFlat>0
(default=0: use this value if you DON'T want to take any flats between projections)
imagesPerDark - number of images to be taken for each dark-field sub-sequence (default=10)
imagesPerFlat - number of images to be taken for each flat-field sub-sequence (default=10)
General scan sequence is: D, F, P,..., P, F, D
where D stands for dark field, F - for flat field, and P - for projection.
"""
dataFormat = LocalProperties.get("gda.data.scan.datawriter.dataFormat")
try:
darkFieldInterval = int(darkFieldInterval)
flatFieldInterval = int(flatFieldInterval)
optimizeBeamInterval = int(optimizeBeamInterval)
jns = beamline_parameters.JythonNameSpaceMapping(InterfaceProvider.getJythonNamespace())
tomography_theta = jns.tomography_theta
if tomography_theta is None:
raise "tomography_theta is not defined in Jython namespace"
tomography_shutter = jns.tomography_shutter
if tomography_shutter is None:
raise "tomography_shutter is not defined in Jython namespace"
tomography_translation = jns.tomography_translation
if tomography_translation is None:
raise "tomography_translation is not defined in Jython namespace"
tomography_detector = jns.tomography_detector
if tomography_detector is None:
raise "tomography_detector is not defined in Jython namespace"
tomography_optimizer = jns.tomography_optimizer
if tomography_optimizer is None:
raise "tomography_optimizer is not defined in Jython namespace"
tomography_time = jns.tomography_time
if tomography_time is None:
raise "tomography_time is not defined in Jython namespace"
tomography_beammonitor = jns.tomography_beammonitor
if tomography_beammonitor is None:
raise "tomography_beammonitor is not defined in Jython namespace"
tomography_camera_stage = jns.tomography_camera_stage
if tomography_camera_stage is None:
raise "tomography_camera_stage is not defined in Jython namespace"
tomography_sample_stage = jns.tomography_sample_stage
if tomography_sample_stage is None:
raise "tomography_sample_stage is not defined in Jython namespace"
tomo_additional_scannables = jns.tomography_additional_scannables
if tomo_additional_scannables is None:
raise "tomo_additional_scannables is not defined in Jython namespace"
index = SimpleScannable()
index.setCurrentPosition(0.0)
index.setInputNames(["imageNumber"])
index.setName("imageNumber")
index.configure()
image_key = SimpleScannable()
image_key.setCurrentPosition(0.0)
image_key.setInputNames(["image_key"])
image_key.setName("image_key")
image_key.configure()
tomoScanDevice = make_tomoScanDevice(
tomography_theta, tomography_shutter, tomography_translation, tomography_optimizer, image_key, index
)
# return tomoScanDevice
# generate list of positions
numberSteps = ScannableUtils.getNumberSteps(tomography_theta, start, stop, step)
theta_points = []
theta_points.append(start)
previousPoint = start
for i in range(numberSteps):
nextPoint = ScannableUtils.calculateNextPoint(previousPoint, step)
theta_points.append(nextPoint)
previousPoint = nextPoint
# generateScanPoints
optimizeBeamNo = 0
optimizeBeamYes = 1
shutterOpen = 1
shutterClosed = 0
shutterNoChange = 2
scan_points = []
theta_pos = theta_points[0]
index = 0
# Added shutterNoChange state for the shutter. The scan points are added using the (pseudo) ternary operator,
# if index is 0 then the shutterPosition is added to the scan point, else shutterNoChange is added to scan points.
for i in range(imagesPerDark):
scan_points.append(
(
theta_pos,
[shutterClosed, shutterNoChange][i != 0],
inBeamPosition,
optimizeBeamNo,
image_key_dark,
index,
)
) # dark
index = index + 1
for i in range(imagesPerFlat):
scan_points.append(
(
theta_pos,
[shutterOpen, shutterNoChange][i != 0],
outOfBeamPosition,
optimizeBeamNo,
image_key_flat,
index,
)
) # flat
index = index + 1
scan_points.append((theta_pos, shutterOpen, inBeamPosition, optimizeBeamNo, image_key_project, index)) # first
index = index + 1
imageSinceDark = 1
imageSinceFlat = 1
optimizeBeam = 0
for i in range(numberSteps):
theta_pos = theta_points[i + 1]
scan_points.append(
(
theta_pos,
[shutterOpen, shutterNoChange][i != 0],
inBeamPosition,
optimizeBeamNo,
image_key_project,
index,
)
) # main image
index = index + 1
imageSinceFlat = imageSinceFlat + 1
if imageSinceFlat == flatFieldInterval and flatFieldInterval != 0:
for i in range(imagesPerFlat):
scan_points.append(
(
theta_pos,
[shutterOpen, shutterNoChange][i != 0],
outOfBeamPosition,
optimizeBeamNo,
image_key_flat,
index,
)
)
index = index + 1
imageSinceFlat = 0
imageSinceDark = imageSinceDark + 1
if imageSinceDark == darkFieldInterval and darkFieldInterval != 0:
for i in range(imagesPerDark):
scan_points.append(
(
theta_pos,
[shutterClosed, shutterNoChange][i != 0],
inBeamPosition,
optimizeBeamNo,
image_key_dark,
index,
)
)
index = index + 1
imageSinceDark = 0
optimizeBeam = optimizeBeam + 1
if optimizeBeam == optimizeBeamInterval and optimizeBeamInterval != 0:
scan_points.append(
(
theta_pos,
[shutterOpen, shutterNoChange][i != 0],
inBeamPosition,
optimizeBeamYes,
image_key_project,
index,
)
)
index = index + 1
optimizeBeam = 0
# add dark and flat only if not done in last steps
if imageSinceFlat != 0:
for i in range(imagesPerFlat):
scan_points.append(
(
theta_pos,
[shutterOpen, shutterNoChange][i != 0],
outOfBeamPosition,
optimizeBeamNo,
image_key_flat,
index,
)
) # flat
index = index + 1
if imageSinceDark != 0:
for i in range(imagesPerDark):
scan_points.append(
(
theta_pos,
[shutterClosed, shutterNoChange][i != 0],
inBeamPosition,
optimizeBeamNo,
image_key_dark,
index,
)
) # dark
index = index + 1
scan_points1 = generateScanPoints(
inBeamPosition,
outOfBeamPosition,
theta_points,
darkFieldInterval,
flatFieldInterval,
imagesPerDark,
imagesPerFlat,
optimizeBeamInterval,
pattern=pattern,
)
if pattern == "default" or pattern == "DFPFD":
i = 0
for pt1 in scan_points1:
pt = scan_points[i]
if pt1 != pt:
print "Mismatch - please tell Kaz about your scan and its arguments!"
print "i = ", i
print "pt = ", pt
print "pt1 = ", pt1
i += 1
# return None
positionProvider = tomoScan_positions(
start,
stop,
step,
darkFieldInterval,
imagesPerDark,
flatFieldInterval,
imagesPerFlat,
inBeamPosition,
outOfBeamPosition,
optimizeBeamInterval,
scan_points,
)
scan_args = [
tomoScanDevice,
positionProvider,
tomography_time,
tomography_beammonitor,
tomography_detector,
exposureTime,
tomography_camera_stage,
tomography_sample_stage,
]
# scan_args.append(RotationAxisScannable("approxCOR", tomoRotationAxis))
# meta_add(RotationAxisScannable("approxCOR", tomoRotationAxis))
# meta_add("RotationCoord_as_list", [tomoRotationAxis])
meta_add("approxCOR", tomoRotationAxis)
for scannable in additionalScannables:
scan_args.append(scannable)
for scannable in tomo_additional_scannables:
scan_args.append(scannable)
""" setting the description provided as the title"""
if not description == None:
setTitle(description)
else:
setTitle("undefined")
dataFormat = LocalProperties.get("gda.data.scan.datawriter.dataFormat")
if not dataFormat == "NexusDataWriter":
handle_messages.simpleLog(
"Data format inconsistent. Setting 'gda.data.scan.datawriter.dataFormat' to 'NexusDataWriter'"
)
LocalProperties.set("gda.data.scan.datawriter.dataFormat", "NexusDataWriter")
scanObject = createConcurrentScan(scan_args)
if addNXEntry:
addNXTomoSubentry(scanObject, tomography_detector.name, tomography_theta.name)
scanObject.runScan()
if autoAnalyse:
lsdp = jns.lastScanDataPoint()
OSCommandRunner.runNoWait(
["/dls_sw/apps/tomopy/tomopy/bin/gda/tomo_at_scan_end", lsdp.currentFilename],
OSCommandRunner.LOGOPTION.ALWAYS,
None,
)
return scanObject
except InterruptedException:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "User interrupted the scan", exceptionType, exception, traceback, False)
raise InterruptedException("User interrupted the scan")
except:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "Error during tomography scan", exceptionType, exception, traceback, False)
raise Exception("Error during tomography scan", exception)
finally:
handle_messages.simpleLog("Data Format reset to the original setting: " + dataFormat)
LocalProperties.set("gda.data.scan.datawriter.dataFormat", dataFormat)
def localStation_exception(exc_info, msg):
typ, exception, traceback = exc_info
simpleLog("! Failure %s !" % msg)
localStation_exceptions.append(" %s" % msg)
handle_messages.log(None, "Error %s - " % msg , typ, exception, traceback, False)
alias("caget")
from gda.scan.RepeatScan import create_repscan, repscan
vararg_alias("repscan")
#setup tools to create metadata in Nexus files
from gdascripts.metadata.metadata_commands import setTitle, meta_add, meta_ll, meta_ls, meta_rm
alias("setTitle")
alias("meta_add")
alias("meta_ll")
alias("meta_ls")
alias("meta_rm")
from gda.data.scan.datawriter import NexusDataWriter
LocalProperties.set(NexusDataWriter.GDA_NEXUS_METADATAPROVIDER_NAME,"metashop")
#create time scannables
from gdascripts.pd.time_pds import waittimeClass2, showtimeClass, showincrementaltimeClass, actualTimeClass
waittime=waittimeClass2('waittime')
showtime=showtimeClass('showtime')
inctime=showincrementaltimeClass('inctime')
actualTime=actualTimeClass("actualTime")
#run user editable startup script
if isLive():
run("localStationUser.py")
except:
exceptionType, exception, traceback = sys.exc_info()
handle_messages.log(None, "Error in localStation", exceptionType, exception, traceback, False)