"""
# from peloop.tfg2 import TFG2
# from uk.ac.gda.devices.mythen.epics import MythenDetector
from gda.data import NumTracker
from gda.device.scannable import SimpleScannable, ScannableBase
from types import FloatType, ListType
import threading
from time import sleep
import time
from gda.jython.commands import GeneralCommands
from threading import Thread
# mythen=MythenDetector()
# tfg2=TFG2()
scanNumTracker = NumTracker("i11")
delayTime = SimpleScannable()
delayTime.setName("delayTime")
delayTime.setCurrentPosition(0)
class DetectorThread(threading.Thread):
def __init__(self, detector, numberOfCycles, numberOfFrames, numberOfGates, scanNumber, collectionNumber):
threading.Thread.__init__(self)
self.detector = detector
self.numberOfCycles = numberOfCycles
self.numberOfFrames = numberOfFrames
self.numberOfGate = numberOfGates
self.scanNumber = scanNumber
self.collectionNumber = collectionNumber
def run(self):
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)
# make an index scannable
from gda.device.scannable import SimpleScannable
ix = SimpleScannable()
ix.name = "ix"
pos ix 0
#make scannablegroup for driving sample stage
from gda.device.scannable.scannablegroup import ScannableGroup
idd_pos_neg = ScannableGroup()
#idd_pos_neg.addGroupMember(idd_pos_neg_switchable)
idd_pos_neg.addGroupMember(idd_pos_neg_switcher)
idd_pos_neg.addGroupMember(idd_pos_neg_switchable)
idd_pos_neg.addGroupMember(ix)
idd_pos_neg.setName("idd_pos_neg")
idd_pos_neg.configure()
#make ScanPointProvider
def readfile(filepath):
"""
reads a 2 column csv file
returns a list of tuple
"""
values=[]
f = open( filepath )
lines = f.readlines()
f.close()
lineno=0
for l in lines:
lineno +=1
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)
from gda.device.scannable import SimpleScannable
from gda.device.scannable.scannablegroup import ScannableGroup
from BeamlineI06.Mainline.xmcd import XMCDScanPositionProvider
imagenum = SimpleScannable()
imagenum.name = "imagenum"
imagenum.moveTo(0)
print "Creating energy scannable groups...\n"
print " dxmcd uses iddpol & denergy"
dxmcd = ScannableGroup("dxmcd", (imagenum, iddpol, denergy))
dxmcd.configure()
print " uxmcd uses idupol & uenergy"
uxmcd = ScannableGroup("uxmcd", (imagenum, idupol, uenergy))
uxmcd.configure()
print " xxmcd uses xpol & xenergy"
xxmcd = ScannableGroup("xxmcd", (imagenum, xpol, xenergy))
xxmcd.configure()
print "\nCreating xmcd_positions...\n"
xmcd_positions = XMCDScanPositionProvider(name='xmcd_positions',
numberOfImages=10, pols=('PosCirc', 'NegCirc'), energies=(706.7, 702.3))
print " xmcd_positions.numberOfImages = %r" % xmcd_positions.numberOfImages
print " xmcd_positions.pols = %r" % (xmcd_positions.pols,)
print " xmcd_positions.energies = %r" % (xmcd_positions.energies,)
print "\nExamples\n"
