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 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 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 logMxRequestParams(currentRequest, wait=True): global currentIspybDCID reqObj = currentRequest["request_obj"] transmissionReadback = getPvDesc("transmissionRBV") flux = getPvDesc("flux") resultObj = { "requestObj": reqObj, "transmissionReadback": transmissionReadback, "flux": flux } resultID = db_lib.addResultforRequest("mxExpParams", currentRequest["uid"], owner=daq_utils.owner, result_obj=resultObj, proposalID=daq_utils.getProposalID(), beamline=daq_utils.beamline) newResult = db_lib.getResult(resultID) newResult['result_obj']['requestObj']['xbeam'] = reqObj['xbeam'] newResult['result_obj']['requestObj']['ybeam'] = reqObj['ybeam'] db_lib.beamlineInfo(daq_utils.beamline, 'currentSampleID', info_dict={'sampleID': currentRequest["sample"]}) db_lib.beamlineInfo(daq_utils.beamline, 'currentRequestID', info_dict={'requestID': currentRequest["uid"]}) logfile = open("dataColLog.txt", "a+") try: logfile.write("\n\ntimestamp: " + time.ctime(currentRequest["time"]) + "\n") except KeyError: logger.error("caught key error in logging") logger.error(currentRequest) logfile.write("protocol: " + reqObj["protocol"] + "\n") logfile.write("data prefix: " + reqObj["file_prefix"] + "\n") logfile.write("flux: " + str(flux) + "\n") logfile.write("transimission percent: " + str(transmissionReadback) + "\n") logfile.write("total current (BCU): " + str(getPvDesc("totalCurrentBCU")) + "\n") logfile.write("omega start: " + str(reqObj["sweep_start"]) + "\n") logfile.write("omega end: " + str(reqObj["sweep_end"]) + "\n") logfile.write("image width: " + str(reqObj["img_width"]) + "\n") logfile.write("exposure time per image (s): " + str(reqObj["exposure_time"]) + "\n") logfile.write("detector distance: " + str(reqObj["detDist"]) + "\n") logfile.write("wavelength: " + str(reqObj["wavelength"]) + "\n") logfile.close() visitName = daq_utils.getVisitName() try: #I'm worried about unforseen ispyb db errors #rasters results are entered in ispyb by the GUI, no need to wait if wait: time.sleep(getBlConfig(ISPYB_RESULT_ENTRY_DELAY)) currentIspybDCID = ispybLib.insertResult(newResult, "mxExpParams", currentRequest, visitName) except Exception as e: currentIspybDCID = 999999 logger.error("logMxRequestParams - ispyb error: %s" % e)
def finish(): if (getBlConfig('robot_online')): try: RobotControlLib.runCmd("finish") return 1 except Exception as e: e_s = str(e) message = "ROBOT Finish ERROR: " + e_s daq_lib.gui_message(message) logger.error(message) return 0
def waitBeam(): waiting = 0 while (1): if (getPvDesc("beamAvailable") or getBlConfig("beamCheck") == 0): if (waiting): waiting = 0 destroy_gui_message() break else: if not (waiting): waiting = 1 gui_message("Waiting for beam. Type beamCheckOff() in lsdcServer window to continue.") time.sleep(1.0)
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 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
request = db_lib.getRequestByID( request_id ) #add another argument false to allow finished requests to be retrieved for testing owner = request["owner"] runFastEP = int(sys.argv[6]) node = sys.argv[7] runDimple = int(sys.argv[8]) dimpleNode = sys.argv[9] ispybDCID = int(sys.argv[10]) expectedFilenameList = [] timeoutLimit = 600 #for now prefix_long = directory + "/" + filePrefix + "_" + str(numstart) hdfFilepattern = prefix_long + "_master.h5" CBF_conversion_pattern = cbfDir + "/" + filePrefix + "_" fastdpComm = ";source " + os.environ[ "PROJDIR"] + "wrappers/fastDPWrap2;" + getBlConfig("fastdpComm") dimpleComm = getBlConfig("dimpleComm") comm_s = "ssh -q " + node + " \"cd " + runningDir + fastdpComm + hdfFilepattern + "\"" logger.info(comm_s) os.system(comm_s) fastDPResultFile = runningDir + "/fast_dp.xml" fd = open(fastDPResultFile) resultObj = xmltodict.parse(fd.read()) logger.info("finished fast_dp") logger.info(resultObj) resultID = db_lib.addResultforRequest("fastDP", request_id, owner, resultObj, beamline=os.environ["BEAMLINE_ID"]) newResult = db_lib.getResult(resultID)
dimpleNode = sys.argv[7] ispybDCID = int(sys.argv[8]) comm_s = f"ssh -q {node} \"{os.environ['MXPROCESSINGSCRIPTSDIR']}fast_dp.sh {request_id} {numstart}\"" logger.info(comm_s) os.system(comm_s) fastDPResultFile = runningDir + "/fast_dp.xml" fd = open(fastDPResultFile) resultObj = xmltodict.parse(fd.read()) logger.info("finished fast_dp") resultID = db_lib.addResultforRequest("fastDP", request_id, owner, resultObj, beamline=os.environ["BEAMLINE_ID"]) newResult = db_lib.getResult(resultID) visitName = getBlConfig("visitName") try: ispybLib.insertResult(newResult, "fastDP", request, visitName, ispybDCID, fastDPResultFile) except Exception as e: logger.error("runfastdph5 insert result ispyb error: %s" % e) if (runFastEP): os.system("fast_ep") #looks very bad! running on ca1! if (runDimple): dimpleComm = getBlConfig("dimpleComm") comm_s = f"ssh -q {dimpleNode} \"{os.environ['MXPROCESSINGSCRIPTSDIR']}dimple.sh {request_id} {numstart}\"" logger.info(f"running dimple: {comm_s}") os.system(comm_s)
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
import db_lib from daq_utils import getBlConfig import xmltodict import ispybLib from config_params import * baseDirectory = os.environ["PWD"] directory = sys.argv[1] cbfDir = directory+"/cbf" comm_s = "mkdir -p " + cbfDir os.system(comm_s) filePrefix = sys.argv[2] request_id = sys.argv[3] seqNum = int(sys.argv[4]) beamline = os.environ["BEAMLINE_ID"] node = getBlConfig("SynchWebSpotNode") ispybDCID = int(sys.argv[5]) request=db_lib.getRequestByID(request_id) reqObj = request["request_obj"] img_width = reqObj["img_width"] sweep_start = reqObj["sweep_start"] sweep_end = reqObj["sweep_end"] range_degrees = abs(sweep_end-sweep_start) numimages = round(range_degrees/img_width) numstart = reqObj["file_number_start"] cbfComm = getBlConfig("cbfComm") dialsComm = getBlConfig("dialsComm") dialsTuneLowRes = getBlConfig(RASTER_TUNE_LOW_RES) dialsTuneHighRes = getBlConfig(RASTER_TUNE_HIGH_RES)
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
import sys import db_lib from daq_utils import getBlConfig import xmltodict import ispybLib baseDirectory = os.environ["PWD"] directory = sys.argv[1] cbfDir = directory + "/cbf" comm_s = "mkdir -p " + cbfDir os.system(comm_s) filePrefix = sys.argv[2] request_id = sys.argv[3] seqNum = int(sys.argv[4]) beamline = os.environ["BEAMLINE_ID"] node = getBlConfig("SynchWebSpotNode") ispybDCID = int(sys.argv[5]) request = db_lib.getRequestByID(request_id) reqObj = request["request_obj"] img_width = reqObj["img_width"] sweep_start = reqObj["sweep_start"] sweep_end = reqObj["sweep_end"] range_degrees = abs(sweep_end - sweep_start) numimages = round(range_degrees / img_width) numstart = reqObj["file_number_start"] cbfComm = getBlConfig("cbfComm") dialsComm = getBlConfig("dialsComm") dialsTuneLowRes = getBlConfig("rasterTuneLowRes") dialsTuneHighRes = getBlConfig("rasterTuneHighRes")