def mountSample(sampID):
global mountCounter
saveDetDist = beamline_lib.motorPosFromDescriptor("detectorDist")
warmUpNeeded = 0
if (getBlConfig("queueCollect") == 1):
mountCounter+=1
if (mountCounter > getBlConfig("robotWarmupInterval")):
warmUpNeeded = 1
mountedSampleDict = db_lib.beamlineInfo(daq_utils.beamline, 'mountedSample')
currentMountedSampleID = mountedSampleDict["sampleID"]
if (getBlConfig(TOP_VIEW_CHECK) == 1):
logger.info("setting work pos")
if (daq_utils.beamline == "amx"):
setPvDesc("robotXWorkPos",getPvDesc("robotXMountPos"))
setPvDesc("robotYWorkPos",getPvDesc("robotYMountPos"))
setPvDesc("robotZWorkPos",getPvDesc("robotZMountPos"))
setPvDesc("robotOmegaWorkPos",90.0)
logger.info("done setting work pos")
if (currentMountedSampleID != ""): #then unmount what's there
if (sampID!=currentMountedSampleID):
puckPos = mountedSampleDict["puckPos"]
pinPos = mountedSampleDict["pinPos"]
if (robot_lib.unmountRobotSample(puckPos,pinPos,currentMountedSampleID)):
db_lib.deleteCompletedRequestsforSample(currentMountedSampleID)
set_field("mounted_pin","")
db_lib.beamlineInfo(daq_utils.beamline, 'mountedSample', info_dict={'puckPos':0,'pinPos':0,'sampleID':""})
(puckPos,pinPos,puckID) = db_lib.getCoordsfromSampleID(daq_utils.beamline,sampID)
if (warmUpNeeded):
gui_message("Warming gripper. Please stand by.")
mountCounter = 0
mountStat = robot_lib.mountRobotSample(puckPos,pinPos,sampID,init=0,warmup=warmUpNeeded)
if (warmUpNeeded):
destroy_gui_message()
if (mountStat == 1):
set_field("mounted_pin",sampID)
detDist = beamline_lib.motorPosFromDescriptor("detectorDist")
if (detDist != saveDetDist):
if (getBlConfig("HePath") == 0):
beamline_lib.mvaDescriptor("detectorDist",saveDetDist)
elif(mountStat == 2):
return 2
else:
return 0
else:
return 0
else: #desired sample is mounted, nothing to do
return 1
else: #nothing mounted
(puckPos,pinPos,puckID) = db_lib.getCoordsfromSampleID(daq_utils.beamline,sampID)
mountStat = robot_lib.mountRobotSample(puckPos,pinPos,sampID,init=1)
if (mountStat == 1):
set_field("mounted_pin",sampID)
elif(mountStat == 2):
return 2
else:
return 0
db_lib.beamlineInfo(daq_utils.beamline, 'mountedSample', info_dict={'puckPos':puckPos,'pinPos':pinPos,'sampleID':sampID})
return 1
def detectorArm(angle_start,image_width,number_of_images,exposure_period,fileprefix,data_directory_name,file_number): #will need some environ info to diff eiger/pilatus
global image_started,allow_overwrite,abort_flag
detector_save_files()
detector_set_username(getpass.getuser())
detector_set_groupname(grp.getgrgid(os.getgid())[0])
detector_set_fileperms(420)
logger.info("data directory = " + data_directory_name)
file_prefix_minus_directory = str(fileprefix)
try:
file_prefix_minus_directory = file_prefix_minus_directory[file_prefix_minus_directory.rindex("/")+1:len(file_prefix_minus_directory)]
except ValueError:
pass
detector_set_exposure_time(exposure_period)
detector_set_period(exposure_period) #apparently this takes care of itself for deadtime
detector_set_numimages(number_of_images)
detector_set_filepath(data_directory_name)
detector_set_fileprefix(file_prefix_minus_directory)
detector_set_filenumber(file_number)
detector_set_fileheader(angle_start,image_width,beamline_lib.motorPosFromDescriptor("detectorDist"),beamline_lib.motorPosFromDescriptor("wavelength"),0.0,exposure_period,getPvDesc("beamCenterX"),getPvDesc("beamCenterY"),"omega",angle_start,0.0,0.0) #only a few for eiger
detector_start() #but you need wired or manual trigger
startArm = time.time()
detector_waitArmed() #don't worry about this while we're not doing hardware triggers., not quite sure what it means
endArm = time.time()
armTime = endArm-startArm
logger.info("\narm time = " + str(armTime) +"\n")
return
def gon_osc(angle_start,width,exptime):
angle_end = angle_start+width
beamline_support.setPvValFromDescriptor("oscOmegaStart",angle_start)
beamline_support.setPvValFromDescriptor("oscOmegaEnd",angle_end)
beamline_support.setPvValFromDescriptor("oscDuration",exptime)
beamline_support.setPvValFromDescriptor("oscGo",1)
oscWait()
end_osc = beamline_lib.motorPosFromDescriptor("omega")
print("end_osc in gon_osc = " + str(end_osc) + "\n")
return end_osc
def checkC2C_X(x,fovx): # this is to make sure the user doesn't make too much of an x-move in C2C
scalePixX = getPvDesc("image_X_scalePix")
centerPixX = getPvDesc("image_Y_centerPix")
xpos = beamline_lib.motorPosFromDescriptor("sampleX")
target = xpos + ((x-centerPixX) * (fovx/scalePixX))
logger.info('checkC2C_X target: %s' % target)
xlimLow = getPvDesc("robotXMountPos") + getPvDesc("robotXMountLowLim")
xlimHi = getPvDesc("robotXMountPos") + getPvDesc("robotXMountHiLim")
if (target<xlimLow or target>xlimHi):
gui_message("Click to Center out of bounds on X move. Please mount next sample.")
return 0
return 1
def center_on_click(
x,
y,
fovx,
fovy,
source="screen",
maglevel=0,
jog=0
): #maglevel=0 means lowmag, high fov, #1 = himag with digizoom option,
#source=screen = from screen click, otherwise from macro with full pixel dimensions
if (getBlConfig('robot_online')
): #so that we don't move things when robot moving?
robotGovState = (getPvDesc("robotSaActive")
or getPvDesc("humanSaActive"))
if (not robotGovState):
return
if not (checkC2C_X(x, fovx)):
return
if (source == "screen"):
waitGovNoSleep()
setPvDesc("image_X_scalePix",
daq_utils.screenPixX) #these are video dimensions in the gui
setPvDesc("image_Y_scalePix", daq_utils.screenPixY)
setPvDesc("image_X_centerPix", daq_utils.screenPixX / 2)
setPvDesc("image_Y_centerPix", daq_utils.screenPixY / 2)
setPvDesc("image_X_scaleMM", float(fovx))
setPvDesc("image_Y_scaleMM", float(fovy))
else:
if (
int(maglevel) == 0
): #I think hardcoded to not use maglevel anymore, replaced with more flexible fov
setPvDesc("image_X_scalePix", daq_utils.lowMagPixX)
setPvDesc("image_Y_scalePix", daq_utils.lowMagPixY)
setPvDesc("image_X_centerPix", daq_utils.lowMagPixX / 2)
setPvDesc("image_Y_centerPix", daq_utils.lowMagPixY / 2)
setPvDesc("image_X_scaleMM", float(fovx))
setPvDesc("image_Y_scaleMM", float(fovy))
else:
setPvDesc("image_X_scalePix", daq_utils.lowMagPixX)
setPvDesc("image_Y_scalePix", daq_utils.lowMagPixY)
setPvDesc("image_X_centerPix", daq_utils.highMagPixX / 2)
setPvDesc("image_Y_centerPix", daq_utils.highMagPixY / 2)
setPvDesc("image_X_scaleMM", float(fovx))
setPvDesc("image_Y_scaleMM", float(fovy))
omega_mod = beamline_lib.motorPosFromDescriptor("omega") % 360.0
lib_gon_center_xtal(x, y, omega_mod, 0)
if (jog):
beamline_lib.mvrDescriptor("omega", float(jog))
def checkC2C_X(x,fovx): # this is to make sure the user doesn't make too much of an x-move in C2C
scalePixX = beamline_support.getPvValFromDescriptor("image_X_scalePix")
centerPixX = beamline_support.getPvValFromDescriptor("image_Y_centerPix")
xpos = beamline_lib.motorPosFromDescriptor("sampleX")
target = xpos + ((x-centerPixX) * (fovx/scalePixX))
print(target)
# xlimLow = 11400.0
# xlimHi = 14400.0
xlimLow = beamline_support.getPvValFromDescriptor("robotXMountPos") + beamline_support.getPvValFromDescriptor("robotXMountLowLim")
xlimHi = beamline_support.getPvValFromDescriptor("robotXMountPos") + beamline_support.getPvValFromDescriptor("robotXMountHiLim")
# print(xlimHi)
if (target<xlimLow or target>xlimHi):
gui_message("Click to Center out of bounds on X move. Please mount next sample.")
return 0
return 1
def center_on_click(x,y,fovx,fovy,source="screen",maglevel=0,jog=0): #maglevel=0 means lowmag, high fov, #1 = himag with digizoom option,
#source=screen = from screen click, otherwise from macro with full pixel dimensions
if (db_lib.getBeamlineConfigParam(daq_utils.beamline,'robot_online')): #so that we don't move things when robot moving?
robotGovState = (beamline_support.getPvValFromDescriptor("robotSaActive") or beamline_support.getPvValFromDescriptor("humanSaActive"))
if (not robotGovState):
return
# if (daq_utils.beamline == "amx"):
if (1):
if not (checkC2C_X(x,fovx)):
return
if (source == "screen"):
waitGovNoSleep()
beamline_support.setPvValFromDescriptor("image_X_scalePix",daq_utils.screenPixX) #these are video dimensions in the gui
beamline_support.setPvValFromDescriptor("image_Y_scalePix",daq_utils.screenPixY)
beamline_support.setPvValFromDescriptor("image_X_centerPix",daq_utils.screenPixX/2)
beamline_support.setPvValFromDescriptor("image_Y_centerPix",daq_utils.screenPixY/2)
beamline_support.setPvValFromDescriptor("image_X_scaleMM",float(fovx))
beamline_support.setPvValFromDescriptor("image_Y_scaleMM",float(fovy))
else:
if (int(maglevel)==0): #I think hardcoded to not use maglevel anymore, replaced with more flexible fov
beamline_support.setPvValFromDescriptor("image_X_scalePix",daq_utils.lowMagPixX)
beamline_support.setPvValFromDescriptor("image_Y_scalePix",daq_utils.lowMagPixY)
beamline_support.setPvValFromDescriptor("image_X_centerPix",daq_utils.lowMagPixX/2)
beamline_support.setPvValFromDescriptor("image_Y_centerPix",daq_utils.lowMagPixY/2)
beamline_support.setPvValFromDescriptor("image_X_scaleMM",float(fovx))
beamline_support.setPvValFromDescriptor("image_Y_scaleMM",float(fovy))
else:
beamline_support.setPvValFromDescriptor("image_X_scalePix",daq_utils.lowMagPixX)
beamline_support.setPvValFromDescriptor("image_Y_scalePix",daq_utils.lowMagPixY)
beamline_support.setPvValFromDescriptor("image_X_centerPix",daq_utils.highMagPixX/2)
beamline_support.setPvValFromDescriptor("image_Y_centerPix",daq_utils.highMagPixY/2)
beamline_support.setPvValFromDescriptor("image_X_scaleMM",float(fovx))
beamline_support.setPvValFromDescriptor("image_Y_scaleMM",float(fovy))
omega_mod = beamline_lib.motorPosFromDescriptor("omega")%360.0
# daq_utils.broadcast_output("\ncenter on x = %s, y = %s, omega = %f, phi = %f\n" % (x,y,omega_mod,0))
# xcheck = checkC2C_X(x,fovx)
# if (xcheck):
lib_gon_center_xtal(x,y,omega_mod,0)
if (jog):
beamline_lib.mvrDescriptor("omega",float(jog))
def detectorArm(angle_start,image_width,number_of_images,exposure_period,fileprefix,data_directory_name,file_number): #will need some environ info to diff eiger/pilatus
global image_started,allow_overwrite,abort_flag
detector_save_files()
detector_set_username(getpass.getuser())
detector_set_groupname(grp.getgrgid(os.getgid())[0])
detector_set_fileperms(420)
print("data directory = " + data_directory_name)
file_prefix_minus_directory = str(fileprefix)
try:
file_prefix_minus_directory = file_prefix_minus_directory[file_prefix_minus_directory.rindex("/")+1:len(file_prefix_minus_directory)]
except ValueError:
pass
detector_set_exposure_time(exposure_period)
detector_set_period(exposure_period) #apparently this takes care of itself for deadtime
detector_set_numimages(number_of_images)
detector_set_filepath(data_directory_name)
detector_set_fileprefix(file_prefix_minus_directory)
detector_set_filenumber(file_number)
detector_set_fileheader(angle_start,image_width,beamline_lib.motorPosFromDescriptor("detectorDist"),beamline_lib.motorPosFromDescriptor("wavelength"),0.0,exposure_period,beamline_support.getPvValFromDescriptor("beamCenterX"),beamline_support.getPvValFromDescriptor("beamCenterY"),"omega",angle_start,0.0,0.0) #only a few for eiger
# print "collect eiger %f degrees for %f seconds %d images exposure_period = %f exposure_time = %f" % (range_degrees,range_seconds,number_of_images,exposure_period,exposure_time)
detector_start() #but you need wired or manual trigger
startArm = time.time()
detector_waitArmed() #don't worry about this while we're not doing hardware triggers., not quite sure what it means
endArm = time.time()
armTime = endArm-startArm
print("\narm time = " + str(armTime) +"\n")
# image_started = range_seconds
# time.sleep(1.0) #4/15 - why so long?
# time.sleep(0.3)
# set_field("state","Expose")
# gon_osc(get_field("scan_axis"),0.0,range_degrees,range_seconds) #0.0 is the angle start that's not used
# image_started = 0
# detector_wait()
# set_field("state","Idle")
### daq_macros.fakeDC(data_directory_name,file_prefix_minus_directory,int(file_number),int(number_of_images))
# return number_of_images
return
def mountRobotSample(puckPos, pinPos, sampID, init=0, warmup=0):
global retryMountCount
global sampXadjust, sampYadjust, sampZadjust
absPos = (pinsPerPuck * (puckPos % 3)) + pinPos + 1
logger.info(f'init: {init} warmup: {warmup}')
if (getBlConfig('robot_online')):
if (not daq_lib.waitGovRobotSE()):
daq_lib.setGovRobot('SE')
if (getBlConfig(TOP_VIEW_CHECK) == 1):
try:
sample = db_lib.getSampleByID(sampID)
sampName = sample['name']
reqCount = sample['request_count']
prefix1 = sampName + "_" + str(puckPos) + "_" + str(
pinPos) + "_" + str(reqCount) + "_PA_0"
prefix90 = sampName + "_" + str(puckPos) + "_" + str(
pinPos) + "_" + str(reqCount) + "_PA_90"
daq_macros.topViewSnap(prefix1,
os.getcwd() + "/pinAlign",
1,
acquire=0)
except Exception as e:
e_s = str(e)
message = "TopView check ERROR, will continue: " + e_s
daq_lib.gui_message(message)
logger.error(message)
logger.info("mounting " + str(puckPos) + " " + str(pinPos) + " " +
str(sampID))
logger.info("absPos = " + str(absPos))
platePos = int(puckPos / 3)
rotMotTarget = daq_utils.dewarPlateMap[platePos][0]
rotCP = beamline_lib.motorPosFromDescriptor("dewarRot")
logger.info("dewar target,CP")
logger.info("%s %s" % (rotMotTarget, rotCP))
if (abs(rotMotTarget - rotCP) > 1):
logger.info("rot dewar")
try:
if (init == 0):
RobotControlLib.runCmd("park")
except Exception as e:
e_s = str(e)
message = "ROBOT Park ERROR: " + e_s
daq_lib.gui_message(message)
logger.error(message)
return 0
beamline_lib.mvaDescriptor("dewarRot", rotMotTarget)
try:
if (init):
logger.debug('main loading part')
setPvDesc("boostSelect", 0)
if (getPvDesc("sampleDetected") == 0
): #reverse logic, 0 = true
setPvDesc("boostSelect", 1)
else:
robotStatus = beamline_support.get_any_epics_pv(
"SW:RobotState", "VAL")
if (robotStatus != "Ready"):
if (daq_utils.beamline == "fmx"):
daq_macros.homePins()
time.sleep(3.0)
if (not daq_lib.setGovRobot('SE')):
return
if (getBlConfig(TOP_VIEW_CHECK) == 1):
omegaCP = beamline_lib.motorPosFromDescriptor("omega")
if (omegaCP > 89.5 and omegaCP < 90.5):
beamline_lib.mvrDescriptor("omega", 85.0)
logger.info("calling thread")
_thread.start_new_thread(wait90TopviewThread,
(prefix1, prefix90))
logger.info("called thread")
setPvDesc("boostSelect", 0)
if (getPvDesc("gripTemp") > -170):
try:
logger.debug('mounting')
RobotControlLib.mount(absPos)
except Exception as e:
e_s = str(e)
message = "ROBOT mount ERROR: " + e_s
daq_lib.gui_message(message)
logger.error(message)
return 0
else:
time.sleep(0.5)
if (getPvDesc("sampleDetected") == 0):
logger.info("full mount")
RobotControlLib.mount(absPos)
else:
logger.debug('quick mount')
RobotControlLib.initialize()
RobotControlLib._mount(absPos)
setPvDesc("boostSelect", 1)
else:
if (getBlConfig(TOP_VIEW_CHECK) == 1):
omegaCP = beamline_lib.motorPosFromDescriptor("omega")
if (omegaCP > 89.5 and omegaCP < 90.5):
beamline_lib.mvrDescriptor("omega", 85.0)
logger.info("calling thread")
_thread.start_new_thread(wait90TopviewThread,
(prefix1, prefix90))
logger.info("called thread")
if (warmup):
RobotControlLib._mount(absPos, warmup=True)
else:
RobotControlLib._mount(absPos)
logger.info(f'{getBlConfig(TOP_VIEW_CHECK)} {daq_utils.beamline}')
if (getBlConfig(TOP_VIEW_CHECK) == 1):
if (sampYadjust == 0):
logger.info("Cannot align pin - Mount next sample.")
daq_lib.setGovRobot('SA')
return 1
except Exception as e:
logger.error(e)
e_s = str(e)
if (e_s.find("Fatal") != -1):
daq_macros.robotOff()
daq_macros.disableMount()
daq_lib.gui_message(
e_s +
". FATAL ROBOT ERROR - CALL STAFF! robotOff() executed.")
return 0
if (e_s.find("tilted") != -1
or e_s.find("Load Sample Failed") != -1):
if (getBlConfig("queueCollect") == 0):
daq_lib.gui_message(e_s + ". Try mounting again")
return 0
else:
if (retryMountCount == 0):
retryMountCount += 1
mountStat = mountRobotSample(puckPos, pinPos, sampID,
init)
if (mountStat == 1):
retryMountCount = 0
return mountStat
else:
retryMountCount = 0
daq_lib.gui_message("ROBOT: Could not recover from " +
e_s)
return 2
daq_lib.gui_message("ROBOT mount ERROR: " + e_s)
return 0
return 1
else:
return 1
def collectData(currentRequest):
global data_directory_name, currentIspybDCID, fastDPNodeCount, fastDPNodeCounter
if (daq_utils.beamline == "fmx"):
if (getPvDesc("detCoverRBV") == 0):
logger.info("opening det cover")
setPvDesc("detCoverOpen", 1)
logMe = 1
reqObj = currentRequest["request_obj"]
data_directory_name = str(reqObj["directory"])
exposure_period = reqObj["exposure_time"]
wavelength = reqObj["wavelength"]
resolution = reqObj["resolution"]
slit_height = reqObj["slit_height"]
slit_width = reqObj["slit_width"]
attenuation = reqObj["attenuation"]
img_width = reqObj["img_width"]
file_prefix = str(reqObj["file_prefix"])
logger.info(reqObj["protocol"])
prot = str(reqObj["protocol"])
sweep_start = reqObj["sweep_start"]
sweep_end = reqObj["sweep_end"]
range_degrees = abs(sweep_end - sweep_start)
sweep_start = reqObj["sweep_start"] % 360.0
file_number_start = reqObj["file_number_start"]
basePath = reqObj["basePath"]
visitName = daq_utils.getVisitName()
jpegDirectory = visitName + "/jpegs/" + data_directory_name[
data_directory_name.find(visitName) +
len(visitName):len(data_directory_name)]
colDist = reqObj["detDist"]
status = 1
if not (os.path.isdir(data_directory_name)):
logger.debug(f'creating {data_directory_name}')
comm_s = "mkdir -p " + data_directory_name
os.system(comm_s)
comm_s = "chmod 777 " + data_directory_name
os.system(comm_s)
comm_s = "mkdir -p " + jpegDirectory
os.system(comm_s)
comm_s = "chmod 777 " + jpegDirectory
os.system(comm_s)
logger.debug(
'starting initial motions - transmission and detector distance')
daq_macros.setTrans(attenuation)
if prot not in ["rasterScreen", "eScan"]:
beamline_lib.mvaDescriptor("detectorDist", colDist)
logger.debug(
'transmission and detector distance (if not fluorescence-related) done'
)
# now that the detector is in the correct position, get the beam center
currentRequest['request_obj']['xbeam'] = getPvDesc('beamCenterX')
currentRequest['request_obj']['ybeam'] = getPvDesc('beamCenterY')
db_lib.updateRequest(currentRequest)
if (prot == "raster"):
logger.info('entering raster')
status = daq_macros.snakeRaster(currentRequest["uid"])
logger.info('exiting raster')
elif (prot == "stepRaster"):
status = daq_macros.snakeStepRaster(currentRequest["uid"])
elif (prot == "specRaster"):
status = daq_macros.snakeStepRasterSpec(currentRequest["uid"])
elif (prot == "vector" or prot == "stepVector"):
imagesAttempted = collect_detector_seq_hw(sweep_start, range_degrees,
img_width, exposure_period,
file_prefix,
data_directory_name,
file_number_start,
currentRequest)
elif (prot == "multiCol"):
daq_macros.snakeRaster(currentRequest["uid"])
elif (prot == "rasterScreen"):
daq_macros.rasterScreen(currentRequest)
elif (prot == "multiColQ"):
daq_macros.multiCol(currentRequest)
elif (prot == "eScan"):
daq_macros.eScan(currentRequest)
else: #standard, screening, or edna - these may require autoalign, checking first
if (reqObj["pos_x"] != -999):
beamline_lib.mvaDescriptor("sampleX", reqObj["pos_x"])
beamline_lib.mvaDescriptor("sampleY", reqObj["pos_y"])
beamline_lib.mvaDescriptor("sampleZ", reqObj["pos_z"])
elif (reqObj["centeringOption"] == "Interactive"
): #robotic, pause and let user center
pause_data_collection()
check_pause()
else:
logger.info("autoRaster")
if not (daq_macros.autoRasterLoop(currentRequest)):
logger.info("could not center sample")
db_lib.updatePriority(currentRequest["uid"], -1)
refreshGuiTree()
return 0
else:
if (reqObj["centeringOption"] == "AutoLoop"):
reqObj[
"sweep_start"] = beamline_lib.motorPosFromDescriptor(
"omega") #%360.0?
sweep_start = reqObj["sweep_start"]
if (reqObj["centeringOption"] == "AutoRaster"):
reqObj[
"sweep_start"] = beamline_lib.motorPosFromDescriptor(
"omega") - 90.0 #%360.0?
sweep_start = reqObj["sweep_start"]
daq_macros.setTrans(attenuation)
if (reqObj["protocol"] == "screen"):
screenImages = 2
screenRange = 90
range_degrees = img_width
for i in range(0, screenImages):
sweep_start = reqObj["sweep_start"] + (i * screenRange)
sweep_end = sweep_start + screenRange
file_prefix = str(reqObj["file_prefix"] + "_" +
str(i * screenRange))
data_directory_name = str(reqObj["directory"]) # for now
file_number_start = reqObj["file_number_start"]
beamline_lib.mvaDescriptor("omega", sweep_start)
if (i == 0):
imagesAttempted = collect_detector_seq_hw(
sweep_start,
range_degrees,
img_width,
exposure_period,
file_prefix,
data_directory_name,
file_number_start,
currentRequest,
changeState=False)
else:
imagesAttempted = collect_detector_seq_hw(
sweep_start, range_degrees, img_width, exposure_period,
file_prefix, data_directory_name, file_number_start,
currentRequest)
seqNum = int(detector_get_seqnum())
node = getBlConfig("spotNode1")
comm_s = f'ssh -q {node} \"{os.environ["MXPROCESSINGSCRIPTSDIR"]}eiger2cbf.sh {currentRequest["uid"]} 1 1 sweep_start {seqNum}\"'
logger.info(comm_s)
os.system(comm_s)
elif (reqObj["protocol"] == "characterize"
or reqObj["protocol"] == "ednaCol"):
characterizationParams = reqObj["characterizationParams"]
index_success = daq_macros.dna_execute_collection3(
0.0, img_width, 2, exposure_period, data_directory_name + "/",
file_prefix, 1, -89.0, 1, currentRequest)
if (index_success):
resultsList = db_lib.getResultsforRequest(
currentRequest["uid"]
) # because for testing I keep running the same request. Probably not in usual use.
results = None
for i in range(0, len(resultsList)):
if (resultsList[i]['result_type'] ==
'characterizationStrategy'):
results = resultsList[i]
break
if (results != None):
strategyResults = results["result_obj"]["strategy"]
stratStart = strategyResults["start"]
stratEnd = strategyResults["end"]
stratWidth = strategyResults["width"]
stratExptime = strategyResults["exptime"]
stratTrans = strategyResults["transmission"]
stratDetDist = strategyResults["detDist"]
sampleID = currentRequest["sample"]
tempnewStratRequest = daq_utils.createDefaultRequest(
sampleID)
newReqObj = tempnewStratRequest["request_obj"]
newReqObj["sweep_start"] = stratStart
newReqObj["sweep_end"] = stratEnd
newReqObj["img_width"] = stratWidth
newReqObj["exposure_time"] = stratExptime
newReqObj["attenuation"] = stratTrans
newReqObj["detDist"] = stratDetDist
newReqObj["directory"] = data_directory_name
newReqObj["pos_x"] = beamline_lib.motorPosFromDescriptor(
"sampleX")
newReqObj["pos_y"] = beamline_lib.motorPosFromDescriptor(
"sampleY")
newReqObj["pos_z"] = beamline_lib.motorPosFromDescriptor(
"sampleZ")
newReqObj[
"fastDP"] = True # this is where you might want a "new from old" request to carry over stuff like this.
newReqObj["fastEP"] = reqObj["fastEP"]
newReqObj["dimple"] = reqObj["dimple"]
newReqObj["xia2"] = reqObj["xia2"]
runNum = db_lib.incrementSampleRequestCount(sampleID)
newReqObj["runNum"] = runNum
newStratRequest = db_lib.addRequesttoSample(
sampleID,
newReqObj["protocol"],
daq_utils.owner,
newReqObj,
priority=0,
proposalID=daq_utils.getProposalID())
if (reqObj["protocol"] == "ednaCol"):
logger.info("new strat req = ")
logger.info(newStratRequest)
db_lib.updatePriority(currentRequest["uid"], -1)
refreshGuiTree()
collectData(db_lib.getRequestByID(newStratRequest))
return 1
else: #standard
logger.info("moving omega to start " + str(time.time()))
beamline_lib.mvaDescriptor("omega", sweep_start)
imagesAttempted = collect_detector_seq_hw(
sweep_start, range_degrees, img_width, exposure_period,
file_prefix, data_directory_name, file_number_start,
currentRequest)
try:
if (logMe) and prot == 'raster':
logMxRequestParams(currentRequest, wait=False)
elif (logMe):
logMxRequestParams(currentRequest)
except TypeError:
logger.error("caught type error in logging")
except IndexError:
logger.error("caught index error in logging")
except KeyError as e:
logger.error('caught key error in logging: %s' % e)
# collection finished, start processing
if reqObj["protocol"] in ("standard", "vector", "raster"):
send_kafka_message(topic=f'{daq_utils.beamline}.lsdc.documents',
event='stop',
uuid=currentRequest['uid'],
protocol=reqObj["protocol"])
if (prot == "vector" or prot == "standard" or prot == "stepVector"):
seqNum = int(detector_get_seqnum())
comm_s = os.environ[
"LSDCHOME"] + "/runSpotFinder4syncW.py " + data_directory_name + " " + file_prefix + " " + str(
currentRequest["uid"]) + " " + str(seqNum) + " " + str(
currentIspybDCID) + "&"
logger.info(comm_s)
os.system(comm_s)
if img_width > 0: #no dataset processing in stills mode
if (reqObj["fastDP"]):
if (reqObj["fastEP"]):
fastEPFlag = 1
else:
fastEPFlag = 0
if (reqObj["dimple"]):
dimpleFlag = 1
else:
dimpleFlag = 0
nodeName = "fastDPNode" + str(
(fastDPNodeCounter % fastDPNodeCount) + 1)
fastDPNodeCounter += 1
node = getBlConfig(nodeName)
dimpleNode = getBlConfig("dimpleNode")
if (daq_utils.detector_id == "EIGER-16"):
seqNum = int(detector_get_seqnum())
comm_s = os.environ[
"LSDCHOME"] + "/runFastDPH5.py " + data_directory_name + " " + str(
seqNum) + " " + str(
currentRequest["uid"]
) + " " + str(fastEPFlag) + " " + node + " " + str(
dimpleFlag) + " " + dimpleNode + " " + str(
currentIspybDCID) + "&"
else:
comm_s = os.environ[
"LSDCHOME"] + "/runFastDP.py " + data_directory_name + " " + file_prefix + " " + str(
file_number_start) + " " + str(
int(round(range_degrees / img_width))
) + " " + str(currentRequest["uid"]) + " " + str(
fastEPFlag) + " " + node + " " + str(
dimpleFlag) + " " + dimpleNode + "&"
logger.info(f'Running fastdp command: {comm_s}')
visitName = daq_utils.getVisitName()
if (
not os.path.exists(visitName + "/fast_dp_dir")
) or subprocess.run(
['pgrep', '-f', 'loop-fdp-dple-populate'],
stdout=subprocess.PIPE
).returncode == 1: # for pgrep, return of 1 means string not found
os.system("killall -KILL loop-fdp-dple-populate.sh")
logger.info('starting fast dp result gathering script')
os.system("cd " + visitName +
";${LSDCHOME}/bin/loop-fdp-dple-populate.sh&")
os.system(comm_s)
if (reqObj["xia2"]):
comm_s = f"ssh -q xf17id2-srv1 \"{os.environ['MXPROCESSINGSCRIPTSDIR']}xia2.sh {currentRequest['uid']} \"&"
os.system(comm_s)
logger.info('processing should be triggered')
db_lib.updatePriority(currentRequest["uid"], -1)
refreshGuiTree()
logger.info('after refresh GUI tree')
return status
def collectData(currentRequest):
global data_directory_name, currentIspybDCID, fastDPNodeCount, fastDPNodeCounter
if (daq_utils.beamline == "fmx"):
if (getPvDesc("detCoverRBV") == 0):
logger.info("opening det cover")
setPvDesc("detCoverOpen", 1)
logMe = 1
reqObj = currentRequest["request_obj"]
data_directory_name = str(reqObj["directory"])
exposure_period = reqObj["exposure_time"]
wavelength = reqObj["wavelength"]
resolution = reqObj["resolution"]
slit_height = reqObj["slit_height"]
slit_width = reqObj["slit_width"]
attenuation = reqObj["attenuation"]
img_width = reqObj["img_width"]
file_prefix = str(reqObj["file_prefix"])
logger.info(reqObj["protocol"])
prot = str(reqObj["protocol"])
sweep_start = reqObj["sweep_start"]
sweep_end = reqObj["sweep_end"]
range_degrees = abs(sweep_end - sweep_start)
sweep_start = reqObj["sweep_start"] % 360.0
file_number_start = reqObj["file_number_start"]
basePath = reqObj["basePath"]
visitName = daq_utils.getVisitName()
jpegDirectory = visitName + "/jpegs/" + data_directory_name[
data_directory_name.find(visitName) +
len(visitName):len(data_directory_name)]
colDist = reqObj["detDist"]
status = 1
if not (os.path.isdir(data_directory_name)):
comm_s = "mkdir -p " + data_directory_name
os.system(comm_s)
comm_s = "chmod 777 " + data_directory_name
os.system(comm_s)
comm_s = "mkdir -p " + jpegDirectory
os.system(comm_s)
comm_s = "chmod 777 " + jpegDirectory
os.system(comm_s)
daq_macros.setTrans(attenuation)
beamline_lib.mvaDescriptor("detectorDist", colDist)
# now that the detector is in the correct position, get the beam center
currentRequest['request_obj']['xbeam'] = getPvDesc('beamCenterX')
currentRequest['request_obj']['ybeam'] = getPvDesc('beamCenterY')
db_lib.updateRequest(currentRequest)
if (prot == "raster"):
logger.info('entering raster')
status = daq_macros.snakeRaster(currentRequest["uid"])
logger.info('exiting raster')
elif (prot == "stepRaster"):
status = daq_macros.snakeStepRaster(currentRequest["uid"])
elif (prot == "specRaster"):
status = daq_macros.snakeStepRasterSpec(currentRequest["uid"])
elif (prot == "vector" or prot == "stepVector"):
imagesAttempted = collect_detector_seq_hw(sweep_start, range_degrees,
img_width, exposure_period,
file_prefix,
data_directory_name,
file_number_start,
currentRequest)
elif (prot == "multiCol"):
daq_macros.snakeRaster(currentRequest["uid"])
elif (prot == "rasterScreen"):
daq_macros.rasterScreen(currentRequest)
elif (prot == "multiColQ"):
daq_macros.multiCol(currentRequest)
elif (prot == "eScan"):
daq_macros.eScan(currentRequest)
else: #standard, screening, or edna - these may require autoalign, checking first
if (reqObj["pos_x"] != -999):
beamline_lib.mvaDescriptor("sampleX", reqObj["pos_x"])
beamline_lib.mvaDescriptor("sampleY", reqObj["pos_y"])
beamline_lib.mvaDescriptor("sampleZ", reqObj["pos_z"])
elif (reqObj["centeringOption"] == "Interactive"
): #robotic, pause and let user center
pause_data_collection()
check_pause()
else:
logger.info("autoRaster")
if not (daq_macros.autoRasterLoop(currentRequest)):
logger.info("could not center sample")
db_lib.updatePriority(currentRequest["uid"], -1)
refreshGuiTree()
return 0
else:
if (reqObj["centeringOption"] == "AutoLoop"):
reqObj[
"sweep_start"] = beamline_lib.motorPosFromDescriptor(
"omega") #%360.0?
sweep_start = reqObj["sweep_start"]
if (reqObj["centeringOption"] == "AutoRaster"):
reqObj[
"sweep_start"] = beamline_lib.motorPosFromDescriptor(
"omega") - 90.0 #%360.0?
sweep_start = reqObj["sweep_start"]
daq_macros.setTrans(attenuation)
if (reqObj["protocol"] == "screen"):
screenImages = 2
screenRange = 90
range_degrees = img_width
for i in range(0, screenImages):
sweep_start = reqObj["sweep_start"] + (i * screenRange)
sweep_end = sweep_start + screenRange
file_prefix = str(reqObj["file_prefix"] + "_" +
str(i * screenRange))
data_directory_name = str(reqObj["directory"]) # for now
file_number_start = reqObj["file_number_start"]
beamline_lib.mvaDescriptor("omega", sweep_start)
if (i == 0):
imagesAttempted = collect_detector_seq_hw(
sweep_start,
range_degrees,
img_width,
exposure_period,
file_prefix,
data_directory_name,
file_number_start,
currentRequest,
changeState=False)
else:
imagesAttempted = collect_detector_seq_hw(
sweep_start, range_degrees, img_width, exposure_period,
file_prefix, data_directory_name, file_number_start,
currentRequest)
seqNum = int(detector_get_seqnum())
cbfComm = getBlConfig("cbfComm")
cbfDir = data_directory_name + "/cbf"
comm_s = "mkdir -p " + cbfDir
os.system(comm_s)
hdfSampleDataPattern = data_directory_name + "/" + file_prefix + "_"
hdfRowFilepattern = hdfSampleDataPattern + str(
int(float(seqNum))) + "_master.h5"
CBF_conversion_pattern = cbfDir + "/" + file_prefix + "_" + str(
int(sweep_start)) + ".cbf"
comm_s = "eiger2cbf-linux " + hdfRowFilepattern
startIndex = 1
endIndex = 1
node = getBlConfig("spotNode1")
comm_s = "ssh -q " + node + " \"sleep 6;" + cbfComm + " " + hdfRowFilepattern + " " + str(
startIndex) + ":" + str(
endIndex) + " " + CBF_conversion_pattern + "\"&"
logger.info(comm_s)
os.system(comm_s)
elif (reqObj["protocol"] == "characterize"
or reqObj["protocol"] == "ednaCol"):
characterizationParams = reqObj["characterizationParams"]
index_success = daq_macros.dna_execute_collection3(
0.0, img_width, 2, exposure_period, data_directory_name + "/",
file_prefix, 1, -89.0, 1, currentRequest)
if (index_success):
resultsList = db_lib.getResultsforRequest(
currentRequest["uid"]
) # because for testing I keep running the same request. Probably not in usual use.
results = None
for i in range(0, len(resultsList)):
if (resultsList[i]['result_type'] ==
'characterizationStrategy'):
results = resultsList[i]
break
if (results != None):
strategyResults = results["result_obj"]["strategy"]
stratStart = strategyResults["start"]
stratEnd = strategyResults["end"]
stratWidth = strategyResults["width"]
stratExptime = strategyResults["exptime"]
stratTrans = strategyResults["transmission"]
stratDetDist = strategyResults["detDist"]
sampleID = currentRequest["sample"]
tempnewStratRequest = daq_utils.createDefaultRequest(
sampleID)
newReqObj = tempnewStratRequest["request_obj"]
newReqObj["sweep_start"] = stratStart
newReqObj["sweep_end"] = stratEnd
newReqObj["img_width"] = stratWidth
newReqObj["exposure_time"] = stratExptime
newReqObj["attenuation"] = stratTrans
newReqObj["detDist"] = stratDetDist
newReqObj["directory"] = data_directory_name
newReqObj["pos_x"] = beamline_lib.motorPosFromDescriptor(
"sampleX")
newReqObj["pos_y"] = beamline_lib.motorPosFromDescriptor(
"sampleY")
newReqObj["pos_z"] = beamline_lib.motorPosFromDescriptor(
"sampleZ")
newReqObj[
"fastDP"] = True # this is where you might want a "new from old" request to carry over stuff like this.
newReqObj["fastEP"] = reqObj["fastEP"]
newReqObj["dimple"] = reqObj["dimple"]
newReqObj["xia2"] = reqObj["xia2"]
runNum = db_lib.incrementSampleRequestCount(sampleID)
newReqObj["runNum"] = runNum
newStratRequest = db_lib.addRequesttoSample(
sampleID,
newReqObj["protocol"],
daq_utils.owner,
newReqObj,
priority=0,
proposalID=daq_utils.getProposalID())
if (reqObj["protocol"] == "ednaCol"):
logger.info("new strat req = ")
logger.info(newStratRequest)
db_lib.updatePriority(currentRequest["uid"], -1)
refreshGuiTree()
collectData(db_lib.getRequestByID(newStratRequest))
return 1
else: #standard
logger.info("moving omega to start " + str(time.time()))
beamline_lib.mvaDescriptor("omega", sweep_start)
imagesAttempted = collect_detector_seq_hw(
sweep_start, range_degrees, img_width, exposure_period,
file_prefix, data_directory_name, file_number_start,
currentRequest)
try:
if (logMe):
logMxRequestParams(currentRequest)
except TypeError:
logger.error("caught type error in logging")
except IndexError:
logger.error("caught index error in logging")
except KeyError as e:
logger.error('caught key error in logging: %s' % e)
if (prot == "vector" or prot == "standard" or prot == "stepVector"):
seqNum = int(detector_get_seqnum())
comm_s = os.environ[
"LSDCHOME"] + "/runSpotFinder4syncW.py " + data_directory_name + " " + file_prefix + " " + str(
currentRequest["uid"]) + " " + str(seqNum) + " " + str(
currentIspybDCID) + "&"
logger.info(comm_s)
os.system(comm_s)
if img_width > 0: #no dataset processing in stills mode
if (reqObj["fastDP"]):
if (reqObj["fastEP"]):
fastEPFlag = 1
else:
fastEPFlag = 0
if (reqObj["dimple"]):
dimpleFlag = 1
else:
dimpleFlag = 0
nodeName = "fastDPNode" + str(
(fastDPNodeCounter % fastDPNodeCount) + 1)
fastDPNodeCounter += 1
node = getBlConfig(nodeName)
dimpleNode = getBlConfig("dimpleNode")
if (daq_utils.detector_id == "EIGER-16"):
seqNum = int(detector_get_seqnum())
comm_s = os.environ[
"LSDCHOME"] + "/runFastDPH5.py " + data_directory_name + " " + file_prefix + " " + str(
seqNum) + " " + str(
int(round(range_degrees / img_width))
) + " " + str(currentRequest["uid"]) + " " + str(
fastEPFlag) + " " + node + " " + str(
dimpleFlag) + " " + dimpleNode + " " + str(
currentIspybDCID) + "&"
else:
comm_s = os.environ[
"LSDCHOME"] + "/runFastDP.py " + data_directory_name + " " + file_prefix + " " + str(
file_number_start) + " " + str(
int(round(range_degrees / img_width))
) + " " + str(currentRequest["uid"]) + " " + str(
fastEPFlag) + " " + node + " " + str(
dimpleFlag) + " " + dimpleNode + "&"
logger.info(comm_s)
if (daq_utils.beamline == "amx"):
visitName = daq_utils.getVisitName()
if (not os.path.exists(visitName + "/fast_dp_dir")):
os.system("killall -KILL loop-fdp-dple-populate")
os.system(
"cd " + visitName +
";/GPFS/CENTRAL/xf17id2/jjakoncic/Scripts/loop-fdp-dple-populate.sh&"
)
os.system(comm_s)
if (reqObj["xia2"]):
comm_s = "ssh -q xf17id1-srv1 \"" + os.environ[
"LSDCHOME"] + "/runXia2.py " + data_directory_name + " " + file_prefix + " " + str(
file_number_start) + " " + str(
int(round(range_degrees / img_width))) + " " + str(
currentRequest["uid"]) + "\"&"
os.system(comm_s)
logger.info('processing should be triggered')
db_lib.updatePriority(currentRequest["uid"], -1)
refreshGuiTree()
logger.info('after refresh GUI tree')
return status
def mountRobotSample(puckPos,pinPos,sampID,init=0,warmup=0):
global retryMountCount
# absPos = (pinsPerPuck*puckPos)+pinPos+1
absPos = (pinsPerPuck*(puckPos%3))+pinPos+1
if (db_lib.getBeamlineConfigParam(daq_utils.beamline,'robot_online')):
if (not daq_lib.waitGovRobotSE()):
daq_lib.setGovRobotSE()
print("mounting " + str(puckPos) + " " + str(pinPos) + " " + str(sampID))
print("absPos = " + str(absPos))
platePos = int(puckPos/3)
rotMotTarget = daq_utils.dewarPlateMap[platePos][0]
rotCP = beamline_lib.motorPosFromDescriptor("dewarRot")
print("dewar target,CP")
print(rotMotTarget,rotCP)
if (abs(rotMotTarget-rotCP)>1):
print("rot dewar")
try:
if (init == 0):
RobotControlLib.runCmd("park")
except Exception as e:
e_s = str(e)
daq_lib.gui_message("ROBOT Park ERROR: " + e_s)
print(e)
return 0
beamline_lib.mvaDescriptor("dewarRot",rotMotTarget)
try:
if (init):
beamline_support.setPvValFromDescriptor("boostSelect",0)
if (beamline_support.getPvValFromDescriptor("sampleDetected") == 0): #reverse logic, 0 = true
beamline_support.setPvValFromDescriptor("boostSelect",1)
else:
# if (beamline_support.getPvValFromDescriptor("gripTemp") > 20.0): #gripper warm
robotStatus = beamline_support.get_any_epics_pv("SW:RobotState","VAL")
if (robotStatus != "Ready"):
if (daq_utils.beamline == "fmx"):
daq_macros.homePins()
time.sleep(3.0)
if (not daq_lib.setGovRobotSE()):
return
RobotControlLib.mount(absPos)
else:
if (warmup):
RobotControlLib._mount(absPos,warmup=True)
else:
RobotControlLib._mount(absPos)
daq_lib.setGovRobotSA()
return 1
except Exception as e:
print(e)
e_s = str(e)
if (e_s.find("Fatal") != -1):
daq_macros.robotOff()
daq_macros.disableMount()
daq_lib.gui_message(e_s + ". FATAL ROBOT ERROR - CALL STAFF! robotOff() executed.")
return 0
if (e_s.find("tilted") != -1 or e_s.find("Load Sample Failed") != -1):
if (db_lib.getBeamlineConfigParam(daq_utils.beamline,"queueCollect") == 0):
daq_lib.gui_message(e_s + ". Try mounting again")
return 0
else:
if (retryMountCount == 0):
retryMountCount+=1
mountStat = mountRobotSample(puckPos,pinPos,sampID,init)
if (mountStat == 1):
retryMountCount = 0
return mountStat
else:
retryMountCount = 0
daq_lib.gui_message("ROBOT: Could not recover from " + e_s)
return 2
daq_lib.gui_message("ROBOT mount ERROR: " + e_s)
return 0
return 1
else:
return 1
def display_images():
currentRequestID = db_lib.beamlineInfo('john', 'currentRequestID')["requestID"]
print "display images for req " + str(currentRequestID)
data_directory_name = getDetPv("data_filepath_rbv")
numimages = getDetPv("numimages")
prefix = getDetPv("data_filename_rbv")
image_period = getDetPv("image_period")
numstart = getDetPv("file_number_rbv")
numstart = numstart - 1
if (numimages>10 and image_period<10):
sample = 10
else:
sample = 1
filelist = []
for i in range (numstart,numstart+numimages,sample):
filename = "%s/%s_%05d.cbf" % (data_directory_name,prefix,i)
filelist.append(filename)
filename = "%s/%s_%05d.cbf" % (data_directory_name,prefix,numimages+numstart-1) # last image
if (len(filelist) > 0):
if (filename != filelist[len(filelist)-1]):
filelist.append(filename)
for j in range (0,len(filelist)):
filename = filelist[j]
last_dot = string.rfind(filename,".")
i = int(filename[last_dot-5:last_dot])
print "looking for " + filename
while not (os.path.exists(filename)):
os.system("ls " + data_directory_name + " >/dev/null")
time.sleep(0.03)
if (jpeg_needed == -99):
return
# time.sleep(0.1)
print "found for " + filename
time.sleep(.05) #got a corrupted file error in albula w/0 this, might not happen in real collection
## daq_utils.albulaDisp(filename) #why have the logger kicking off albula? Because that's what it does for now, don't bother with eiger, use monitor
daq_utils.diff2jpeg(filename,JPEGfilename=None,reqID=currentRequestID)
##huh? I think the filelist takes care of this if (j%10 == 0):
now = time.time()
print "take xtal picture"
daq_utils.runDials(filename)
daq_utils.take_crystal_picture(filename=None,czoom=0,reqID=currentRequestID,omega=beamline_lib.motorPosFromDescriptor("omega")) #but this is unlikely to be synchronized with diff image
def collectData(currentRequest):
global data_directory_name,currentIspybDCID,fastDPNodeCount,fastDPNodeCounter
# print(currentRequest)
# print("pretending to collect")
# time.sleep(5)
# db_lib.updatePriority(currentRequest["uid"],-1)
# refreshGuiTree()
# return 1 #SHORT CIRCUIT
logMe = 1
reqObj = currentRequest["request_obj"]
data_directory_name = str(reqObj["directory"])
exposure_period = reqObj["exposure_time"]
wavelength = reqObj["wavelength"]
resolution = reqObj["resolution"]
slit_height = reqObj["slit_height"]
slit_width = reqObj["slit_width"]
attenuation = reqObj["attenuation"]
img_width = reqObj["img_width"]
file_prefix = str(reqObj["file_prefix"])
print(reqObj["protocol"])
prot = str(reqObj["protocol"])
sweep_start = reqObj["sweep_start"]
sweep_end = reqObj["sweep_end"]
range_degrees = abs(sweep_end-sweep_start)
sweep_start = reqObj["sweep_start"]%360.0
file_number_start = reqObj["file_number_start"]
basePath = reqObj["basePath"]
# jpegDirectory = "jpegs" + data_directory_name[data_directory_name.find(basePath)+len(basePath):len(data_directory_name)]
visitName = daq_utils.getVisitName()
jpegDirectory = visitName + "/jpegs/" + data_directory_name[data_directory_name.find(visitName)+len(visitName):len(data_directory_name)]
status = 1
if not (os.path.isdir(data_directory_name)):
comm_s = "mkdir -p " + data_directory_name
os.system(comm_s)
comm_s = "chmod 777 " + data_directory_name
os.system(comm_s)
comm_s = "mkdir -p " + jpegDirectory
os.system(comm_s)
comm_s = "chmod 777 " + jpegDirectory
os.system(comm_s)
if (prot == "raster"):
status = daq_macros.snakeRaster(currentRequest["uid"])
elif (prot == "stepRaster"):
status = daq_macros.snakeStepRaster(currentRequest["uid"])
elif (prot == "vector" or prot == "stepVector"):
if (reqObj["centeringOption"] != "Interactive"):
logMe = 0
daq_macros.autoVector(currentRequest)
else:
imagesAttempted = collect_detector_seq_hw(sweep_start,range_degrees,img_width,exposure_period,file_prefix,data_directory_name,file_number_start,currentRequest)
elif (prot == "multiCol"):
# daq_macros.multiCol(currentRequest)
daq_macros.snakeRaster(currentRequest["uid"])
elif (prot == "multiColQ"):
daq_macros.multiCol(currentRequest)
# daq_macros.snakeRaster(currentRequest["uid"])
elif (prot == "eScan"):
daq_macros.eScan(currentRequest)
else: #standard, screening, or edna - these may require autoalign, checking first
if (reqObj["pos_x"] != -999):
beamline_lib.mvaDescriptor("sampleX",reqObj["pos_x"])
beamline_lib.mvaDescriptor("sampleY",reqObj["pos_y"])
beamline_lib.mvaDescriptor("sampleZ",reqObj["pos_z"])
elif (reqObj["centeringOption"] == "Interactive"): #robotic, pause and let user center
pause_data_collection()
check_pause()
else:
print("autoRaster")
if not (daq_macros.autoRasterLoop(currentRequest)):
print("could not center sample")
db_lib.updatePriority(currentRequest["uid"],-1)
refreshGuiTree()
return 0
# if (not stateModule.gotoState("DataCollection")):
# print("State violation")
# db_lib.updatePriority(currentRequest["uid"],-1)
# refreshGuiTree()
# return 0
if (reqObj["protocol"] == "screen"):
screenImages = 2
screenRange = 90
range_degrees = img_width
for i in range (0,screenImages):
sweep_start = reqObj["sweep_start"]+(i*screenRange)
sweep_end = sweep_start+screenRange
# sweep_end = reqObj["sweep_end"]+(i*screenRange)
file_prefix = str(reqObj["file_prefix"]+"_"+str(i*screenRange))
data_directory_name = str(reqObj["directory"]) # for now
file_number_start = reqObj["file_number_start"]
beamline_lib.mvaDescriptor("omega",sweep_start)
if (1):
# if (beamline_support.getPvValFromDescriptor("gonDaqHwTrig")):
imagesAttempted = collect_detector_seq_hw(sweep_start,range_degrees,img_width,exposure_period,file_prefix,data_directory_name,file_number_start,currentRequest)
else:
imagesAttempted = collect_detector_seq(sweep_start,range_degrees,img_width,exposure_period,file_prefix,data_directory_name,file_number_start,currentRequest)
seqNum = int(detector_get_seqnum())
cbfComm = db_lib.getBeamlineConfigParam(daq_utils.beamline,"cbfComm")
cbfDir = data_directory_name+"/cbf"
comm_s = "mkdir -p " + cbfDir
os.system(comm_s)
hdfSampleDataPattern = data_directory_name+"/"+file_prefix+"_"
hdfRowFilepattern = hdfSampleDataPattern + str(int(float(seqNum))) + "_master.h5"
CBF_conversion_pattern = cbfDir + "/" + file_prefix+"_" + str(int(sweep_start))+".cbf"
comm_s = "eiger2cbf-linux " + hdfRowFilepattern
startIndex=1
endIndex = 1
node = db_lib.getBeamlineConfigParam(daq_utils.beamline,"spotNode1")
comm_s = "ssh -q " + node + " \"sleep 6;" + cbfComm + " " + hdfRowFilepattern + " " + str(startIndex) + ":" + str(endIndex) + " " + CBF_conversion_pattern + "\"&"
print(comm_s)
os.system(comm_s)
elif (reqObj["protocol"] == "characterize" or reqObj["protocol"] == "ednaCol"):
characterizationParams = reqObj["characterizationParams"]
index_success = daq_macros.dna_execute_collection3(0.0,img_width,2,exposure_period,data_directory_name+"/",file_prefix,1,-89.0,1,currentRequest)
# if (0):
if (index_success):
resultsList = db_lib.getResultsforRequest(currentRequest["uid"]) # because for testing I keep running the same request. Probably not in usual use.
results = resultsList[-2]
strategyResults = results["result_obj"]["strategy"]
stratStart = strategyResults["start"]
stratEnd = strategyResults["end"]
stratWidth = strategyResults["width"]
stratExptime = strategyResults["exptime"]
stratDetDist = strategyResults["detDist"]
sampleID = currentRequest["sample"]
tempnewStratRequest = daq_utils.createDefaultRequest(sampleID)
newReqObj = tempnewStratRequest["request_obj"]
newReqObj["sweep_start"] = stratStart
newReqObj["sweep_end"] = stratEnd
newReqObj["img_width"] = stratWidth
newReqObj["exposure_time"] = stratExptime
newReqObj["detDist"] = stratDetDist
newReqObj["directory"] = data_directory_name
newReqObj["pos_x"] = beamline_lib.motorPosFromDescriptor("sampleX")
newReqObj["pos_y"] = beamline_lib.motorPosFromDescriptor("sampleY")
newReqObj["pos_z"] = beamline_lib.motorPosFromDescriptor("sampleZ")
newReqObj["fastDP"] = reqObj["fastDP"] # this is where you might want a "new from old" request to carry over stuff like this.
newReqObj["fastEP"] = reqObj["fastEP"]
newReqObj["dimple"] = reqObj["dimple"]
newReqObj["xia2"] = reqObj["xia2"]
runNum = db_lib.incrementSampleRequestCount(sampleID)
reqObj["runNum"] = runNum
newStratRequest = db_lib.addRequesttoSample(sampleID,newReqObj["protocol"],daq_utils.owner,newReqObj,priority=0,proposalID=daq_utils.getProposalID())
if (reqObj["protocol"] == "ednaCol"):
db_lib.updatePriority(currentRequest["uid"],-1)
refreshGuiTree()
collectData(newStratRequest)
return 1
else: #standard
beamline_lib.mvaDescriptor("omega",sweep_start)
if (1):
# if (beamline_support.getPvValFromDescriptor("gonDaqHwTrig")):
imagesAttempted = collect_detector_seq_hw(sweep_start,range_degrees,img_width,exposure_period,file_prefix,data_directory_name,file_number_start,currentRequest)
else:
imagesAttempted = collect_detector_seq(sweep_start,range_degrees,img_width,exposure_period,file_prefix,data_directory_name,file_number_start,currentRequest)
try:
if (logMe):
logMxRequestParams(currentRequest)
except TypeError:
print("caught type error in logging")
if (prot == "vector" or prot == "standard"):
seqNum = int(detector_get_seqnum())
comm_s = os.environ["LSDCHOME"] + "/runSpotFinder4syncW.py " + data_directory_name + " " + file_prefix + " " + str(currentRequest["uid"]) + " " + str(seqNum) + " " + str(currentIspybDCID)+ "&"
print(comm_s)
os.system(comm_s)
if (reqObj["fastDP"]):
if (reqObj["fastEP"]):
fastEPFlag = 1
else:
fastEPFlag = 0
if (reqObj["dimple"]):
dimpleFlag = 1
else:
dimpleFlag = 0
# node = db_lib.getBeamlineConfigParam(daq_utils.beamline,"fastDPNode")
nodeName = "fastDPNode" + str((fastDPNodeCounter%fastDPNodeCount)+1)
fastDPNodeCounter+=1
node = db_lib.getBeamlineConfigParam(daq_utils.beamline,nodeName)
dimpleNode = db_lib.getBeamlineConfigParam(daq_utils.beamline,"dimpleNode")
if (daq_utils.detector_id == "EIGER-16"):
seqNum = int(detector_get_seqnum())
# seqNum = beamline_support.get_any_epics_pv("XF:17IDC-ES:FMX{Det:Eig16M}cam1:SequenceId","VAL")
comm_s = os.environ["LSDCHOME"] + "/runFastDPH5.py " + data_directory_name + " " + file_prefix + " " + str(seqNum) + " " + str(int(round(range_degrees/img_width))) + " " + str(currentRequest["uid"]) + " " + str(fastEPFlag) + " " + node + " " + str(dimpleFlag) + " " + dimpleNode + " " + str(currentIspybDCID)+ "&"
else:
comm_s = os.environ["LSDCHOME"] + "/runFastDP.py " + data_directory_name + " " + file_prefix + " " + str(file_number_start) + " " + str(int(round(range_degrees/img_width))) + " " + str(currentRequest["uid"]) + " " + str(fastEPFlag) + " " + node + " " + str(dimpleFlag) + " " + dimpleNode + "&"
print(comm_s)
os.system(comm_s)
if (reqObj["xia2"]):
comm_s = "ssh -q xf17id1-srv1 \"" + os.environ["LSDCHOME"] + "/runXia2.py " + data_directory_name + " " + file_prefix + " " + str(file_number_start) + " " + str(int(round(range_degrees/img_width))) + " " + str(currentRequest["uid"]) + "\"&"
# comm_s = os.environ["CBHOME"] + "/runXia2.py " + data_directory_name + " " + file_prefix + " " + str(file_number_start) + " " + str(int(round(range_degrees/img_width))) + " " + str(currentRequest["request_id"]) + "&"
os.system(comm_s)
db_lib.updatePriority(currentRequest["uid"],-1)
refreshGuiTree()
return status
def unmountRobotSample(puckPos, pinPos,
sampID): #will somehow know where it came from
absPos = (pinsPerPuck * (puckPos % 3)) + pinPos + 1
robotOnline = getBlConfig('robot_online')
logger.info("robot online = " + str(robotOnline))
if (robotOnline):
detDist = beamline_lib.motorPosFromDescriptor("detectorDist")
if (detDist < ROBOT_MIN_DISTANCE):
setPvDesc("govRobotDetDistOut", ROBOT_MIN_DISTANCE)
setPvDesc("govHumanDetDistOut", ROBOT_MIN_DISTANCE)
daq_lib.setRobotGovState("SE")
logger.info("unmounting " + str(puckPos) + " " + str(pinPos) + " " +
str(sampID))
logger.info("absPos = " + str(absPos))
platePos = int(puckPos / 3)
rotMotTarget = daq_utils.dewarPlateMap[platePos][0]
rotCP = beamline_lib.motorPosFromDescriptor("dewarRot")
logger.info("dewar target,CP")
logger.info("%s %s" % (rotMotTarget, rotCP))
if (abs(rotMotTarget - rotCP) > 1):
logger.info("rot dewar")
try:
RobotControlLib.runCmd("park")
except Exception as e:
e_s = str(e)
message = "ROBOT park ERROR: " + e_s
daq_lib.gui_message(message)
logger.error(message)
return 0
beamline_lib.mvaDescriptor("dewarRot", rotMotTarget)
try:
par_init = (beamline_support.get_any_epics_pv(
"SW:RobotState", "VAL") != "Ready")
par_cool = (getPvDesc("gripTemp") > -170)
RobotControlLib.unmount1(init=par_init, cooldown=par_cool)
except Exception as e:
e_s = str(e)
message = "ROBOT unmount ERROR: " + e_s
daq_lib.gui_message(message)
logger.error(message)
return 0
if daq_utils.beamline == "fmx":
det_z_pv = 'XF:17IDC-ES:FMX{Det-Ax:Z}Mtr'
detDist = caget(f'{det_z_pv}.RBV')
if detDist < ROBOT_MIN_DISTANCE:
caput(
f'{det_z_pv}.VAL', ROBOT_MIN_DISTANCE, wait=True
) # TODO shouldn't this wait for SE transition or something??
detDist = caget(f'{det_z_pv}.RBV')
else:
detDist = beamline_lib.motorPosFromDescriptor("detectorDist")
if detDist < ROBOT_MIN_DISTANCE and abs(
detDist - ROBOT_MIN_DISTANCE) > ROBOT_DISTANCE_TOLERANCE:
logger.error(
f"ERROR - Detector closer than {ROBOT_MIN_DISTANCE} and move than {ROBOT_DISTANCE_TOLERANCE} from {ROBOT_MIN_DISTANCE}! actual distance: {detDist}. Stopping."
)
return 0
try:
RobotControlLib.unmount2(absPos)
except Exception as e:
e_s = str(e)
if (e_s.find("Fatal") != -1):
daq_macros.robotOff()
daq_macros.disableMount()
daq_lib.gui_message(
e_s +
". FATAL ROBOT ERROR - CALL STAFF! robotOff() executed.")
return 0
message = "ROBOT unmount2 ERROR: " + e_s
daq_lib.gui_message(message)
logger.error(message)
return 0
if (not daq_lib.waitGovRobotSE()):
daq_lib.clearMountedSample()
logger.info("could not go to SE")
return 0
return 1
def unmountRobotSample(puckPos,pinPos,sampID): #will somehow know where it came from
# absPos = (pinsPerPuck*puckPos)+pinPos+1
absPos = (pinsPerPuck*(puckPos%3))+pinPos+1
robotOnline = db_lib.getBeamlineConfigParam(daq_utils.beamline,'robot_online')
print("robot online = " + str(robotOnline))
if (robotOnline):
detDist = beamline_lib.motorPosFromDescriptor("detectorDist")
if (detDist<199.0):
beamline_support.setPvValFromDescriptor("govRobotDetDistOut",200.0)
beamline_support.setPvValFromDescriptor("govHumanDetDistOut",200.0)
daq_lib.setRobotGovState("SE")
print("unmounting " + str(puckPos) + " " + str(pinPos) + " " + str(sampID))
print("absPos = " + str(absPos))
platePos = int(puckPos/3)
rotMotTarget = daq_utils.dewarPlateMap[platePos][0]
rotCP = beamline_lib.motorPosFromDescriptor("dewarRot")
print("dewar target,CP")
print(rotMotTarget,rotCP)
if (abs(rotMotTarget-rotCP)>1):
print("rot dewar")
try:
RobotControlLib.runCmd("park")
except Exception as e:
e_s = str(e)
daq_lib.gui_message("ROBOT park ERROR: " + e_s)
print(e)
return 0
beamline_lib.mvaDescriptor("dewarRot",rotMotTarget)
try:
par_init=(beamline_support.get_any_epics_pv("SW:RobotState","VAL")!="Ready")
par_cool=(beamline_support.getPvValFromDescriptor("gripTemp")>-170)
if par_cool == False and daq_utils.beamline == "fmx":
time.sleep(3)
RobotControlLib.unmount1(init=par_init,cooldown=par_cool)
except Exception as e:
e_s = str(e)
daq_lib.gui_message("ROBOT unmount ERROR: " + e_s)
print(e)
return 0
detDist = beamline_lib.motorPosFromDescriptor("detectorDist")
if (detDist<200.0):
beamline_lib.mvaDescriptor("detectorDist",200.0)
if (beamline_lib.motorPosFromDescriptor("detectorDist") < 199.0):
print("ERROR - Detector < 200.0!")
return 0
try:
RobotControlLib.unmount2(absPos)
except Exception as e:
e_s = str(e)
if (e_s.find("Fatal") != -1):
daq_macros.robotOff()
daq_macros.disableMount()
daq_lib.gui_message(e_s + ". FATAL ROBOT ERROR - CALL STAFF! robotOff() executed.")
return 0
daq_lib.gui_message("ROBOT unmount2 ERROR: " + e_s)
print(e)
return 0
if (not daq_lib.waitGovRobotSE()):
daq_lib.clearMountedSample()
print("could not go to SE")
return 0
return 1
def wait90TopviewThread(prefix1, prefix90):
global sampXadjust, sampYadjust, sampZadjust
sampXadjust = 0
sampYadjust = 0
sampZadjust = 0
startTime = time.time()
if (getPvDesc("gripTemp") > -170):
threadTimeout = 130.0
else:
threadTimeout = 30.0
while (1):
omegaCP = beamline_lib.motorPosFromDescriptor("omega")
if (omegaCP > 89.5 and omegaCP < 90.5):
logger.info("leaving topview thread for 90")
break
if (time.time() - startTime > threadTimeout):
logger.info("leaving topview thread for " + str(threadTimeout))
setPvDesc("topViewTrigMode", 0)
setPvDesc("topViewImMode", 2)
setPvDesc("topViewDataType", 1)
setPvDesc("topViewAcquire", 1, wait=False)
return
time.sleep(0.10)
try:
daq_macros.topViewWrite()
daq_macros.topViewSnap(prefix90, os.getcwd() + "/pinAlign", 1)
snapshot1Name = prefix1 + "_001.jpg"
snapshot2Name = prefix90 + "_001.jpg"
if (
not filecmp.cmp(os.getcwd() + "/pinAlign/" + snapshot1Name,
os.getcwd() + "/pinAlign/" + snapshot2Name)
): #this would mean something is wrong if true because the pictures are identical
comm_s = os.environ[
"LSDCHOME"] + "/runPinAlign.py " + snapshot1Name + " " + snapshot2Name
logger.info(comm_s)
lines = os.popen(comm_s).readlines()
logger.info("printing lines right after popen ")
logger.info(lines)
logger.info(" done")
if (lines[0].find("CANNOT CENTER") == -1):
offsetTokens = lines[0].split()
logger.info(offsetTokens[0] + " " + offsetTokens[1] + " " +
offsetTokens[2])
xlimLow = getPvDesc("robotXMountPos") + getPvDesc(
"robotXMountLowLim")
xlimHi = getPvDesc("robotXMountPos") + getPvDesc(
"robotXMountHiLim")
xpos = beamline_lib.motorPosFromDescriptor("sampleX")
target = xpos + float(offsetTokens[0]) * 1000.0
if (target < xlimLow or target > xlimHi):
logger.info("Pin X move beyond limit - Mount next sample.")
##else it thinks it worked return 0
else:
sampXadjust = 1000.0 * float(offsetTokens[0])
sampYadjust = 1000.0 * float(offsetTokens[1])
sampZadjust = 1000.0 * float(offsetTokens[2])
sampXCP = beamline_lib.motorPosFromDescriptor("sampleX")
sampYCP = beamline_lib.motorPosFromDescriptor("sampleY")
sampZCP = beamline_lib.motorPosFromDescriptor("sampleZ")
sampXAbsolute = sampXCP + sampXadjust
sampYAbsolute = sampYCP + sampYadjust
sampZAbsolute = sampZCP + sampZadjust
setPvDesc("robotXWorkPos", sampXAbsolute)
setPvDesc("robotYWorkPos", sampYAbsolute)
setPvDesc("robotZWorkPos", sampZAbsolute)
else:
logger.info("Cannot align pin - Mount next sample.")
#else it thinks it worked return 0
for outputline in lines:
logger.info(outputline)
except Exception as e:
e_s = str(e)
message = "TopView check ERROR, will continue: " + e_s
daq_lib.gui_message(message)
logger.error(message)
def unmountRobotSample(puckPos, pinPos,
sampID): #will somehow know where it came from
absPos = (pinsPerPuck * (puckPos % 3)) + pinPos + 1
robotOnline = getBlConfig('robot_online')
logger.info("robot online = " + str(robotOnline))
if (robotOnline):
detDist = beamline_lib.motorPosFromDescriptor("detectorDist")
if (detDist < 200.0):
setPvDesc("govRobotDetDistOut", 200.0)
setPvDesc("govHumanDetDistOut", 200.0)
daq_lib.setRobotGovState("SE")
logger.info("unmounting " + str(puckPos) + " " + str(pinPos) + " " +
str(sampID))
logger.info("absPos = " + str(absPos))
platePos = int(puckPos / 3)
rotMotTarget = daq_utils.dewarPlateMap[platePos][0]
rotCP = beamline_lib.motorPosFromDescriptor("dewarRot")
logger.info("dewar target,CP")
logger.info("%s %s" % (rotMotTarget, rotCP))
if (abs(rotMotTarget - rotCP) > 1):
logger.info("rot dewar")
try:
RobotControlLib.runCmd("park")
except Exception as e:
e_s = str(e)
message = "ROBOT park ERROR: " + e_s
daq_lib.gui_message(message)
logger.error(message)
return 0
beamline_lib.mvaDescriptor("dewarRot", rotMotTarget)
try:
par_init = (beamline_support.get_any_epics_pv(
"SW:RobotState", "VAL") != "Ready")
par_cool = (getPvDesc("gripTemp") > -170)
RobotControlLib.unmount1(init=par_init, cooldown=par_cool)
except Exception as e:
e_s = str(e)
message = "ROBOT unmount ERROR: " + e_s
daq_lib.gui_message(message)
logger.error(message)
return 0
detDist = beamline_lib.motorPosFromDescriptor("detectorDist")
if (detDist < 200.0):
beamline_lib.mvaDescriptor("detectorDist", 200.0)
if (beamline_lib.motorPosFromDescriptor("detectorDist") < 199.0):
logger.error("ERROR - Detector < 200.0!")
return 0
try:
RobotControlLib.unmount2(absPos)
except Exception as e:
e_s = str(e)
if (e_s.find("Fatal") != -1):
daq_macros.robotOff()
daq_macros.disableMount()
daq_lib.gui_message(
e_s +
". FATAL ROBOT ERROR - CALL STAFF! robotOff() executed.")
return 0
message = "ROBOT unmount2 ERROR: " + e_s
daq_lib.gui_message(message)
logger.error(message)
return 0
if (not daq_lib.waitGovRobotSE()):
daq_lib.clearMountedSample()
logger.info("could not go to SE")
return 0
return 1
