def setProperty(propertyName, propertyValue):
LocalProperties.set(propertyName, propertyValue)
eventAdmin=Finder.getInstance().find("eventadmin")
if eventAdmin is None:
print "Cannot find 'eventAdmin' on the GDA server. Please create a Spring bean using 'Scriptcontroller' Java class"
else:
eventAdmin.update(propertyName, propertyValue)
def prepareEmptyGdaVarFolder():
vartest_dir = os.path.join(os.getcwd(), 'var_test')
LocalProperties.set('gda.var', vartest_dir)
if os.path.exists(vartest_dir):
print "Removing existing gda.var: ", vartest_dir
shutil.rmtree(vartest_dir)
print "Creating gda.var: ", vartest_dir
os.mkdir(vartest_dir)
def prepareEmptyGdaVarFolder():
vartest_dir = os.path.join(os.getcwd(), 'var_test')
LocalProperties.set('gda.var', vartest_dir)
if os.path.exists(vartest_dir):
print "Removing existing gda.var: ", vartest_dir
shutil.rmtree(vartest_dir)
print "Creating gda.var: ", vartest_dir
os.mkdir(vartest_dir)
def setYFieldVisibleInScanPlot(indices=[-1]):
'''set the Y fields visible in Scan Plot using indices starting from 1.
this setting will be in effect as default until next update.
@param indices - a list of indices to be visible in the plot
GAD scan default is -1, means the last index
0 index means nothing visible
'''
LocalProperties.set("gda.plot.ScanPlotSettings.YFieldIndicesVisible",
":".join(map(str, indices)))
def datadir(newpath=None):
"""
Reads or sets the data directory. May also need to configure some detectors.
"""
if newpath==None:
return LocalProperties.getPath("gda.data.scan.datawriter.datadir",None)
else:
if not os.path.exists(newpath):
raise ValueError("The directory %s does NOT exist!"%newpath)
print "Setting gda.data.scan.datawriter.datadir preference..."
LocalProperties.set("gda.data.scan.datawriter.datadir", newpath)
# Save to localShelf
return LocalProperties.getPath("gda.data.scan.datawriter.datadir",None)
def datadir(newpath=None):
"""
Reads or sets the data directory. May also need to configure some detectors.
"""
if newpath == None:
return LocalProperties.getPath("gda.data.scan.datawriter.datadir",
None)
else:
if not os.path.exists(newpath):
raise ValueError("The directory %s does NOT exist!" % newpath)
print "Setting gda.data.scan.datawriter.datadir preference..."
LocalProperties.set("gda.data.scan.datawriter.datadir", newpath)
# Save to localShelf
return LocalProperties.getPath("gda.data.scan.datawriter.datadir",
None)
def setDataWriterToSrs():
oldDW = LocalProperties.get("gda.data.scan.datawriter.dataFormat")
LocalProperties.set("gda.data.scan.datawriter.dataFormat", "SrsDataFile")
newDW = LocalProperties.get("gda.data.scan.datawriter.dataFormat")
print "Old DataWriter: ", oldDW
print "New DataWriter: ", newDW
from gda.configuration.properties import LocalProperties
from gda.factory import Finder
from gda.observable import IObserver
from uk.ac.diamond.daq.persistence.jythonshelf import LocalParameters
from gda.data.metadata import GDAMetadataProvider
BSL_CONVERSION_CONFIGURED = 'gda.scan.processing.bsl.configured'
RUNNER = Finder.getInstance().find('bslConversion')
class BslConversionUpdater(IObserver):
def update(self, source, arg):
print 'Visit changed to ' + str(arg)
restore()
if not LocalProperties.contains(BSL_CONVERSION_CONFIGURED):
LocalProperties.set(BSL_CONVERSION_CONFIGURED, 'True')
for meta in GDAMetadataProvider.getInstance().getMetadataEntries():
if meta.name == 'visit':
break
if meta:
meta.addIObserver(BslConversionUpdater())
CONFIGURATION_FILE = 'bslUsers'
DEFAULT = False
STORE = LocalParameters.getXMLConfiguration(CONFIGURATION_FILE)
def isConvertingOn():
"""Check whether new files will be converted automatically"""
return RUNNER.enabled
alias("createPVScannable")
alias("caput")
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)
def asciiformat():
LocalProperties.set(LocalProperties.GDA_DATA_SCAN_DATAWRITER_DATAFORMAT,
"SrsDataFile")
def nexusformat():
LocalProperties.set(LocalProperties.GDA_DATA_SCAN_DATAWRITER_DATAFORMAT,
"NexusDataWriter")
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)
from gda.observable import IObserver
from uk.ac.diamond.daq.persistence.jythonshelf import LocalParameters
from gda.data.metadata import GDAMetadataProvider
BSL_CONVERSION_CONFIGURED = 'gda.scan.processing.bsl.configured'
RUNNER = Finder.getInstance().find('bslConversion')
class BslConversionUpdater(IObserver):
def update(self, source, arg):
print 'Visit changed to ' + str(arg)
restore()
if not LocalProperties.contains(BSL_CONVERSION_CONFIGURED):
LocalProperties.set(BSL_CONVERSION_CONFIGURED, 'True')
for meta in GDAMetadataProvider.getInstance().getMetadataEntries():
if meta.name == 'visit':
break
if meta:
meta.addIObserver(BslConversionUpdater())
CONFIGURATION_FILE = 'bslUsers'
DEFAULT = False
STORE = LocalParameters.getXMLConfiguration(CONFIGURATION_FILE)
def isConvertingOn():
"""Check whether new files will be converted automatically"""
return RUNNER.enabled
# alias("createPVScannable")
# alias("caput")
# 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")
#===================================================
#Raspberry Pi Specific Objects
#===================================================
#RPi Communication Interface
#rpiComms.initaliseCommunicator("127.23.31.56") #enter the Pi's IP address, 127.0.0.1 (localhost) should work
#PiCamera Interface
def useSingleYAxis():
''' use the same Y axis for all Y fields in the Scan Plot
'''
LocalProperties.set("gda.plot.ScanPlotSettings.separateYAxes",
Boolean.toString(False))
def useSeparateYAxes():
'''use separate Y axes for each Y field in the Scan Plot
'''
LocalProperties.set("gda.plot.ScanPlotSettings.separateYAxes",
Boolean.toString(True))
def setXFieldInScanPlot(index):
'''set the X field to be used as X-axis in the Scan Plot.
GDA scan default to -1, the last index to be scanned
'''
LocalProperties.set("gda.plot.ScanPlotSettings.XFieldIndex", str(index))
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 asciiformat():
LocalProperties.set(LocalProperties.GDA_DATA_SCAN_DATAWRITER_DATAFORMAT,
"SixdSrsDataWriter")
