def defaultScriptFolder():
'''Return the default location for Jython scripts.'''
from gdascripts.parameters import beamline_parameters
jythonNameMap = beamline_parameters.JythonNameSpaceMapping()
command_server = jythonNameMap.command_server
return command_server.getDefaultScriptProjectFolder() + "/"
def reportJythonNamespaceMapping():
jns = beamline_parameters.JythonNameSpaceMapping()
objectOfInterestSTEP = {}
objectOfInterestSTEP['tomography_theta'] = jns.tomography_theta
objectOfInterestSTEP['tomography_shutter'] = jns.tomography_shutter
objectOfInterestSTEP['tomography_translation'] = jns.tomography_translation
objectOfInterestSTEP['tomography_detector'] = jns.tomography_detector
objectOfInterestSTEP_INFO = {}
objectOfInterestSTEP_INFO[
'tomography_camera_stage'] = jns.tomography_camera_stage
objectOfInterestSTEP_INFO[
'tomography_sample_stage'] = jns.tomography_sample_stage
objectOfInterestFLY = {}
objectOfInterestFLY['tomography_shutter'] = jns.tomography_shutter
objectOfInterestFLY['tomography_translation'] = jns.tomography_translation
objectOfInterestFLY[
'tomography_flyscan_theta'] = jns.tomography_flyscan_theta
objectOfInterestFLY['tomography_flyscan_det'] = jns.tomography_flyscan_det
objectOfInterestFLY[
'tomography_flyscan_flat_dark_det'] = jns.tomography_flyscan_flat_dark_det
msg = "\n These mappings can be changed by editing a file named jythonNamespaceMapping_live, "
msg += "\n located in GDA Client under Scripts: Config (this can be done by beamline staff)."
msg += "\n Note that PRIMARY SETTINGS for the desired type of tomography scan should normally"
msg += "\n not include any dummy objects because they are typically used only for testing."
print "\n ****** STEP-SCAN PRIMARY SETTINGS (essential for running a tomography step-scan) ******"
idx = 1
for key, val in objectOfInterestSTEP.iteritems():
name = "object undefined!"
if val is not None:
name = str(val.getName())
print ` idx ` + "." + key + ' = ' + name
idx += 1
#print msg
print "\n ****** STEP-SCAN SECONDARY SETTINGS (for additional, per-scan-point data, ie NOT essential for running a tomography step-scan) ******"
idx = 1
for key, val in objectOfInterestSTEP_INFO.iteritems():
name = "object undefined!"
if val is not None:
name = str(val.getName())
print ` idx ` + "." + key + ' = ' + name
idx += 1
#print msg
print "\n ****** FLY-SCAN PRIMARY SETTINGS (essential for running a tomography fly-scan) ******"
idx = 1
for key, val in objectOfInterestFLY.iteritems():
name = "object undefined!"
if val is not None:
name = str(val.getName())
print ` idx ` + "." + key + ' = ' + name
idx += 1
print msg
def __test2_tomoScan():
jns = beamline_parameters.JythonNameSpaceMapping()
sc = tomoScan(step=5,
darkFieldInterval=5,
flatFieldInterval=0,
inBeamPosition=0.,
outOfBeamPosition=10.,
exposureTime=1.)
lsdp = jns.lastScanDataPoint()
positions = lsdp.getPositionsAsDoubles()
if positions[0] != 180. or positions[4] != 47.:
print "Error - points are not correct :" + ` positions `
return sc
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)