def dryGripper():
try:
saveThreshold = getPvDesc("warmupThresholdRBV")
setPvDesc("warmupThreshold",50)
_thread.start_new_thread(warmupGripperRecoverThread,(saveThreshold,0))
warmupGripperForDry()
except Exception as e:
e_s = str(e)
daq_lib.gui_message("Dry gripper failed! " + e_s)
setPvDesc("warmupThreshold",saveThreshold)
def toggleLowMagCameraSettings(stateCode):
if (stateCode == "DA"):
lowMagExpTime = getBlConfig("lowMagExptimeDA")
if daq_utils.beamline == 'amx':
setPvDesc("lowMagGain",32)
else:
setPvDesc("lowMagGain",25)
setPvDesc("lowMagAcquireTime",lowMagExpTime)
else:
lowMagExpTime = getBlConfig("lowMagExptime")
setPvDesc("lowMagGain",1)
setPvDesc("lowMagAcquireTime",lowMagExpTime)
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 toggleLowMagCameraSettings(stateCode):
if (stateCode == "DA"):
setPvDesc("lowMagGain", getBlConfig(LOW_MAG_GAIN_DA))
setPvDesc("lowMagAcquireTime", getBlConfig(LOW_MAG_EXP_TIME_DA))
else:
setPvDesc("lowMagGain", getBlConfig(LOW_MAG_GAIN))
setPvDesc("lowMagAcquireTime", getBlConfig(LOW_MAG_EXP_TIME))
def unlatchGov(): # Command needed for FloCos to recover robot
print(
f"OLD: unlatchGov called, gov active state = {getPvDesc('robotGovActive')}"
)
logger.info(
f"OLD: unlatchGov called, gov active state = {getPvDesc('robotGovActive')}"
)
setPvDesc("robotGovActive", 1)
time.sleep(0.2)
print(
f"NEW: unlatchGov called, gov active state = {getPvDesc('robotGovActive')}"
)
logger.info(
f"NEW: unlatchGov called, gov active state = {getPvDesc('robotGovActive')}"
)
def unmountCold():
mountedSampleDict = db_lib.beamlineInfo(daq_utils.beamline, 'mountedSample')
currentMountedSampleID = mountedSampleDict["sampleID"]
if (currentMountedSampleID != ""):
puckPos = mountedSampleDict["puckPos"]
pinPos = mountedSampleDict["pinPos"]
if (robot_lib.unmountRobotSample(puckPos,pinPos,currentMountedSampleID)):
db_lib.deleteCompletedRequestsforSample(currentMountedSampleID)
robot_lib.parkGripper()
set_field("mounted_pin","")
db_lib.beamlineInfo(daq_utils.beamline, 'mountedSample', info_dict={'puckPos':0,'pinPos':0,'sampleID':""})
setPvDesc("robotGovActive",1)
return 1
else:
return 0
def abort_data_collection(flag):
global datafile_name, abort_flag, image_started
if (flag == 2): #stop queue after current collection
abort_flag = 2
return
gui_message("Aborting. This may take a minute or more.")
while not (getPvDesc("VectorActive")): #only stop if actually collecting
time.sleep(0.1)
destroy_gui_message()
abort_flag = 1
time.sleep(1.0)
gon_stop() #this calls osc abort
setPvDesc("zebraDisarm", 1)
time.sleep(2)
detector_stop()
def runDCQueue(): #maybe don't run rasters from here???
global abort_flag
autoMounted = 0 #this means the mount was performed from a runQueue, as opposed to a manual mount button push
logger.info("running queue in daq server")
while (1):
if (getBlConfig("queueCollect") == 1
and getBlConfig("beamCheck") == 1):
waitBeam()
if (abort_flag):
abort_flag = 0 #careful about when to reset this
return
currentRequest = db_lib.popNextRequest(daq_utils.beamline)
if (currentRequest == {}):
break
logger.info("processing request " + str(time.time()))
reqObj = currentRequest["request_obj"]
setPvDesc("govRobotDetDist", reqObj["detDist"])
setPvDesc("govHumanDetDist", reqObj["detDist"])
if (reqObj["detDist"] >= ROBOT_MIN_DISTANCE
and getBlConfig("HePath") == 0):
setPvDesc("govRobotDetDistOut", reqObj["detDist"])
setPvDesc("govHumanDetDistOut", reqObj["detDist"])
sampleID = currentRequest["sample"]
mountedSampleDict = db_lib.beamlineInfo(daq_utils.beamline,
'mountedSample')
currentMountedSampleID = mountedSampleDict["sampleID"]
if (currentMountedSampleID != sampleID):
if (getBlConfig("queueCollect") == 0):
gui_message(
"You can only run requests on the currently mounted sample. Remove offending request and continue."
)
return
mountStat = mountSample(sampleID)
logger.info("automounting mp= " + currentMountedSampleID +
" samp= " + str(sampleID))
if (mountStat == 1):
autoMounted = 1
elif (mountStat == 2):
db_lib.updatePriority(currentRequest["uid"], -1)
refreshGuiTree()
continue
else:
return 0
db_lib.updatePriority(currentRequest["uid"], 99999)
currentRequest[
'priority'] = 99999 #TODO have updatePriority return an updated request?
refreshGuiTree(
) #just tells the GUI to repopulate the tree from the DB
logger.info("calling collect data " + str(time.time()))
colStatus = collectData(currentRequest)
logger.info("done collecting data")
if (autoMounted and db_lib.queueDone(daq_utils.beamline)):
unmountSample()
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 setRobotGovState(stateString):
if (getRobotConfig() == "Robot"):
setPvDesc("robotGovGo", stateString)
else:
setPvDesc("humanGovGo", stateString)
def setWorkposThread(init, junk):
logger.info("setting work pos in thread")
setPvDesc("robotGovActive", 1)
setPvDesc("robotXWorkPos", getPvDesc("robotXMountPos"))
setPvDesc("robotYWorkPos", getPvDesc("robotYMountPos"))
setPvDesc("robotZWorkPos", getPvDesc("robotZMountPos"))
setPvDesc("robotOmegaWorkPos", 90.0)
if (init):
time.sleep(20)
setPvDesc("robotGovActive", 0)
def warmupGripperRecoverThread(savedThreshold, junk):
time.sleep(120.0)
setPvDesc("warmupThreshold", savedThreshold)
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 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 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
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 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 set_xbeam(xbeam): #detector center for image header, in pixels
setPvDesc("beamCenterX", float(xbeam))
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 set_ybeam(ybeam):
setPvDesc("beamCenterY", float(ybeam))
