def diff2jpeg(diffimageName,JPEGfilename=None,reqID=None):
imageJpegData = {}
imageJpegHeader = {}
imageJpegData["dataFilePath"]=diffimageName
payload = {"fileName":diffimageName,"sizeX":500,"sizeY":500,"gray":100,"percentX":0.5,"percentY":0.5,"userName":"******","sessionId":"E","zoom":1.0}
img_url = "http://"+imgsrv_host+":"+imgsrv_port+"/getImage"
r = requests.get(img_url,params=payload)
data = r.content
imageJpegData["data"] = data
img_url = "http://"+imgsrv_host+":"+imgsrv_port+"/getThumbnail"
r = requests.get(img_url,params=payload)
thumbData = r.content
imageJpegData["thumbData"] = thumbData
payload = {"fileName":diffimageName,"userName":"******","sessionId":"E"}
img_url = "http://"+imgsrv_host+":"+imgsrv_port+"/getHeader"
r = requests.get(img_url,params=payload)
imageJpegData["header"] = r
headerData = r.text
lines = headerData.split("\n")
for i in range (0,len(lines)):
line = lines[i]
print line
tokens = line.split()
if (len(tokens) > 1):
if (tokens[0] == "OSC_START"):
print "Omega start = " + tokens[1]
imageJpegHeader["oscStart"] = float(tokens[1])
elif (tokens[0] == "OSC_RANGE"):
print "Omega range = " + tokens[1]
imageJpegHeader["oscRange"] = float(tokens[1])
elif (tokens[0] == "EXPOSURE"):
print "Exposure Time = " + tokens[2]
imageJpegHeader["exptime"] = float(tokens[2])
elif (tokens[0] == "DISTANCE"):
print "Distance = " + str(float(tokens[1])/1000.0)
imageJpegHeader["detDist"] = float(tokens[1])
elif (tokens[0] == "WAVELENGTH"):
print "Wavelength = " + tokens[1]
imageJpegHeader["wave"] = float(tokens[1])
imageJpegData["header"] = imageJpegHeader
if (reqID != None): #this means I'll dump into mongo as a result
resultObj = {}
imgRef = db_lib.addFile(data)
resultObj["data"] = imgRef
imgRef = db_lib.addFile(thumbData)
resultObj["thumbData"] = imgRef
resultObj["dataFilePath"] = diffimageName
resultObj["header"] = imageJpegHeader
db_lib.addResultforRequest("diffImageJpeg",reqID,resultObj)
return imageJpegData
def diff2jpegLYNX(diffimageName,JPEGfilename=None,reqID=None):
imageJpegData = {}
imageJpegHeader = {}
imageJpegData["dataFilePath"]=diffimageName
img_url = "http://"+imgsrv_host+":"+imgsrv_port+"/getImage\?fileName="+ diffimageName+"\&sizeX=500\&sizeY=500\&gray=100\&zoom=1.0\&percentX=0.5\&percentY=0.5\&userName=me\&sessionId=E"
# comm_s = "lynx -source %s >%s" % (img_url,JPEGfilename)
comm_s = "lynx -source %s" % (img_url)
print comm_s
data = os.popen(comm_s).read()
imageJpegData["data"] = data
# os.system(comm_s)
img_url = "http://"+imgsrv_host+":"+imgsrv_port+"/getThumbnail\?fileName="+ diffimageName+"\&sizeX=500\&sizeY=500\&gray=100\&zoom=1.0\&percentX=0.5\&percentY=0.5\&userName=me\&sessionId=E"
comm_s = "lynx -source %s" % (img_url)
thumbData = os.popen(comm_s).read()
imageJpegData["thumbData"] = thumbData
# comm_s = "lynx -source %s >%s" % (img_url,"thumb_"+JPEGfilename)
print comm_s
# os.system(comm_s)
img_url = "http://"+imgsrv_host+":"+imgsrv_port+"/getHeader\?fileName="+ diffimageName+"\&userName=me\&sessionId=E"
comm_s = "lynx -source " + img_url
for outputline in os.popen(comm_s).readlines():
print outputline
tokens = string.split(outputline)
if (tokens[0] == "OSC_START"):
print "Omega start = " + tokens[1]
imageJpegHeader["oscStart"] = float(tokens[1])
elif (tokens[0] == "OSC_RANGE"):
print "Omega range = " + tokens[1]
imageJpegHeader["oscRange"] = float(tokens[1])
elif (tokens[0] == "EXPOSURE"):
print "Exposure Time = " + tokens[2]
imageJpegHeader["exptime"] = float(tokens[2])
elif (tokens[0] == "DISTANCE"):
print "Distance = " + str(float(tokens[1])/1000.0)
imageJpegHeader["detDist"] = float(tokens[1])
elif (tokens[0] == "WAVELENGTH"):
print "Wavelength = " + tokens[1]
imageJpegHeader["wave"] = float(tokens[1])
if (reqID != None):
resultObj = {}
imgRef = db_lib.addFile(data)
resultObj["data"] = imgRef
imgRef = db_lib.addFile(thumbData)
resultObj["thumbData"] = imgRef
resultObj["dataFilePath"] = diffimageName
resultObj["header"] = imageJpegHeader
db_lib.addResultforRequest("diffImageJpeg",reqID,resultObj)
return imageJpegData
def logMxRequestParams(currentRequest):
global currentIspybDCID
reqObj = currentRequest["request_obj"]
transmissionReadback = beamline_support.getPvValFromDescriptor("transmissionRBV")
flux = beamline_support.getPvValFromDescriptor("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)
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:
print("caught key error in logging")
print(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(beamline_support.getPvValFromDescriptor("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
currentIspybDCID = ispybLib.insertResult(newResult,"mxExpParams",currentRequest,visitName)
except:
currentIspybDCID = 999999
print("ispyb error")
def runDials(imgPath,reqID=None):
comm_s = "dials.find_spots_client " + imgPath
print comm_s
dialsResultObj = xmltodict.parse("<data>\n"+os.popen(comm_s).read()+"</data>\n")
print "done parsing dials output"
print dialsResultObj
currentRequestID = db_lib.beamlineInfo(beamline, 'currentRequestID')["requestID"]
dialsResult = db_lib.addResultforRequest("dials",currentRequestID, dialsResultObj)
def runDialsObsolete(imgPath,reqID=None):
comm_s = "dials.find_spots_client " + imgPath
print(comm_s)
dialsResultObj = xmltodict.parse("<data>\n"+os.popen(comm_s).read()+"</data>\n")
print("done parsing dials output")
print(dialsResultObj)
currentRequestID = db_lib.getBeamlineConfigParam(beamline,'currentRequestID')
dialsResult = db_lib.addResultforRequest("dials",currentRequestID, owner=owner,result_obj=dialsResultObj)
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 take_crystal_picture(filename=None,czoom=0,reqID=None):
zoom = int(czoom)
if not (has_xtalview):
return
if (1):
if (zoom==0):
r=requests.get(xtal_url)
else:
r=requests.get(xtal_url_small)
else: #password, need to change to requests module if we need this
comm_s = "curl -u %s:%s -o %s.jpg -s %s" % (xtalview_user,xtalview_pass,filename,xtal_url)
data = r.content
if (filename != None):
fd = open(filename+".jpg","w+")
fd.write(data)
fd.close()
if (reqID != None):
xtalpicJpegDataResult = {}
imgRef = db_lib.addFile(data)
xtalpicJpegDataResult["data"] = imgRef
db_lib.addResultforRequest("xtalpicJpeg",reqID,xtalpicJpegDataResult)
def take_crystal_picture(filename=None, czoom=0, reqID=None, omega=-999):
zoom = int(czoom)
if not (has_xtalview):
return
if (zoom == 0):
r = requests.get(xtal_url)
else:
r = requests.get(xtal_url_small)
data = r.content
if (filename != None):
fd = open(filename + ".jpg", "wb+")
fd.write(data)
fd.close()
if (reqID != None):
xtalpicJpegDataResult = {}
imgRef = db_lib.addFile(data)
xtalpicJpegDataResult["data"] = imgRef
xtalpicJpegDataResult["omegaPos"] = omega
db_lib.addResultforRequest("xtalpicJpeg",
reqID,
owner=owner,
result_obj=xtalpicJpegDataResult,
beamline=beamline)
def logMxRequestParams(currentRequest):
resultObj = {"requestObj":currentRequest["request_obj"]}
db_lib.addResultforRequest("mxExpParams",currentRequest["request_id"],resultObj)
db_lib.beamlineInfo('john', 'currentSampleID', info_dict={'sampleID':currentRequest["sample_id"]})
db_lib.beamlineInfo('john', 'currentRequestID', info_dict={'requestID':currentRequest["request_id"]})
def dna_execute_collection3(
dna_start,
dna_range,
dna_number_of_images,
dna_exptime,
dna_directory,
prefix,
start_image_number,
overlap,
dna_run_num,
charRequest,
):
global collect_and_characterize_success, dna_have_strategy_results, dna_have_index_results, picture_taken
global dna_strategy_exptime, dna_strategy_start, dna_strategy_range, dna_strategy_end, dna_strat_dist
global screeningoutputid
characterizationParams = charRequest["request_obj"]["characterizationParams"]
dna_res = float(characterizationParams["aimed_resolution"])
print "dna_res = " + str(dna_res)
dna_filename_list = []
print "number of images " + str(dna_number_of_images) + " overlap = " + str(overlap) + " dna_start " + str(
dna_start
) + " dna_range " + str(dna_range) + " prefix " + prefix + " start number " + str(start_image_number) + "\n"
collect_and_characterize_success = 0
dna_have_strategy_results = 0
dna_have_index_results = 0
dg2rd = 3.14159265 / 180.0
if daq_utils.detector_id == "ADSC-Q315":
det_radius = 157.5
elif daq_utils.detector_id == "ADSC-Q210":
det_radius = 105.0
elif daq_utils.detector_id == "PILATUS-6":
det_radius = 212.0
else: # default Pilatus
det_radius = 212.0
##### theta_radians = daq_lib.get_field("theta") * dg2rd
theta_radians = 0.0
wave = 12398.5 / beamline_lib.get_mono_energy() # for now
dx = det_radius / (tan(2.0 * (asin(wave / (2.0 * dna_res))) - theta_radians))
print "distance = ", dx
# skinner - could move distance and wave and scan axis here, leave wave alone for now
print "skinner about to take reference images."
for i in range(0, int(dna_number_of_images)):
print "skinner prefix7 = " + prefix[0:7] + " " + str(start_image_number) + "\n"
if len(prefix) > 8:
if (prefix[0:7] == "postref") and (start_image_number == 1):
print "skinner postref bail\n"
time.sleep(float(dna_number_of_images * float(dna_exptime)))
break
# skinner roi - maybe I can measure and use that for dna_start so that first image is face on.
dna_start = daq_lib.get_field("datum_omega")
colstart = float(dna_start) + (i * (abs(overlap) + float(dna_range)))
dna_prefix = "ref-" + prefix + "_" + str(dna_run_num)
image_number = start_image_number + i
dna_prefix_long = dna_directory + "/" + dna_prefix
filename = daq_utils.create_filename(dna_prefix_long, image_number)
beamline_lib.mva("Omega", float(colstart))
##### daq_lib.move_axis_absolute(daq_lib.get_field("scan_axis"),colstart)
##### daq_lib.take_image(colstart,dna_range,dna_exptime,filename,daq_lib.get_field("scan_axis"),0,1)
daq_utils.take_crystal_picture(reqID=charRequest["request_id"])
######### BECAUSE I FAKE IT imagesAttempted = collect_detector_seq(dna_range,dna_range,dna_exptime,dna_prefix,dna_directory,image_number)
if i == 0:
commFake = "ln -sf /h/pxuser/skinner/testdata/B1GGTApo_9_00001.cbf " + filename
else:
commFake = "ln -sf /h/pxuser/skinner/testdata/B1GGTApo_9_00181.cbf " + filename
os.system(commFake)
dna_filename_list.append(filename)
diffImgJpegData = daq_utils.diff2jpeg(filename, reqID=charRequest["request_id"]) # returns a dictionary
# diffImgJpegData["timestamp"] = time.time()
# imgRef = db_lib.addFile(diffImgJpegData["data"])
# diffImgJpegData["data"] = imgRef
# imgRef = db_lib.addFile(diffImgJpegData["thumbData"])
# diffImgJpegData["thumbData"] = imgRef
picture_taken = 1
# xml_from_file_list(flux,x_beamsize,y_beamsize,max_exptime_per_dc,aimed_completeness,file_list):
edna_energy_ev = (12.3985 / wave) * 1000.0
##### xbeam_size = beamline_lib.get_motor_pos("slitHum")
##### ybeam_size = beamline_lib.get_motor_pos("slitVum")
# if (xbeam_size == 0.0 or ybeam_size == 0.0): #don't know where to get these from yet
if 1:
xbeam_size = 0.1
ybeam_size = 0.16
else:
xbeam_size = xbeam_size / 1000
ybeam_size = ybeam_size / 1000
aimed_completeness = characterizationParams["aimed_completeness"]
aimed_multiplicity = characterizationParams["aimed_multiplicity"]
aimed_resolution = characterizationParams["aimed_resolution"]
aimed_ISig = characterizationParams["aimed_ISig"]
timeout_check = 0
##### while(not os.path.exists(dna_filename_list[len(dna_filename_list)-1])): #this waits for edna images
if 0:
timeout_check = timeout_check + 1
time.sleep(1.0)
if timeout_check > 10:
break
print "generating edna input\n"
# edna_input_filename = edna_input_xml.xml_from_file_list(edna_energy_ev,xbeam_size,ybeam_size,1000000,aimed_completness,aimed_ISig,aimed_multiplicity,aimed_resolution,dna_filename_list)
##### flux = 10000000000 * beamline_lib.get_epics_pv("flux","VAL")
flux = 600000000.0 # for now
edna_input_filename = dna_directory + "/adsc1_in.xml"
edna_input_xml_command = (
"/h/data/backed-up/pxsys/skinner/edna_header_code/makeAnEDNAXML-bnl.sh 1232 %s %s none %f %f 4000 0.01 0.01 0 xh1223_2_ %f %f %f > %s"
% (dna_directory, dna_prefix, 3, aimed_ISig, flux, xbeam_size, ybeam_size, edna_input_filename)
)
##### edna_input_xml_command = "ssh swill \"/h/data/backed-up/pxsys/skinner/edna_header_code/makeAnEDNAXML-bnl.sh 1232 %s %s none %f %f 4000 0.01 0.01 0 xh1223_2_ %f %f %f\" > %s" % (daq_lib.data_directory_name,dna_prefix,3,aimed_ISig,flux,xbeam_size,ybeam_size,edna_input_filename)
print edna_input_xml_command
comm_sss = "echo " + edna_input_xml_command + "> edna_comm.txt"
os.system(comm_sss)
os.system(edna_input_xml_command)
print "done generating edna input\n"
# command_string = "cd %s; /usr/local/crys/edna-mx/mxv1/bin/edna-mxv1-characterisation.py --verbose --data %s" % (dna_directory,edna_input_filename)
command_string = "/usr/local/crys/edna-mx/mxv1/bin/edna-mxv1-characterisation.py --verbose --data %s" % (
edna_input_filename
)
# command_string = "/usr/local/crys/edna-mx/mxv1/bin/edna-mxv1-characterisation.py --verbose --data /img11/data1/pxuser/staff/skinner/edna_run/adsc1_in.xml"
# old command_string = "$EDNA_HOME/mxv1/bin/edna-mxv1-characterisation --data " + edna_input_filename
print command_string
# for i in range (0,len(dna_filename_list)):
# command_string = command_string + " " + dna_filename_list[i]
broadcast_output("\nProcessing with EDNA. Please stand by.\n")
if os.path.exists("edna.log"):
os.remove("edna.log")
if os.path.exists("edna.err"):
os.remove("edna.err")
edna_execution_status = os.system("%s > edna.log 2> edna.err" % command_string)
##### fEdnaLogFile = open(daq_lib.get_misc_dir_name() + "/edna.log", "r" )
fEdnaLogFile = open("./edna.log", "r")
ednaLogLines = fEdnaLogFile.readlines()
fEdnaLogFile.close()
for outline in ednaLogLines:
# for outline in os.popen(command_string,'r',0).readlines():
####skinner6/11 seg faults? broadcast_output(outline)
if string.find(outline, "EdnaDir") != -1:
(param, dirname) = string.split(outline, "=")
strXMLFileName = (
dirname[0 : len(dirname) - 1]
+ "/ControlInterfacev1_2/Characterisation/ControlCharacterisationv1_3_dataOutput.xml"
)
##### strXMLFileName = dirname[0:len(dirname)-1]+"/ControlInterfacev1_2/Characterisation/ControlCharacterisationv1_1_dataOutput.xml"
if string.find(outline, "characterisation successful!") != -1:
collect_and_characterize_success = 1
if not collect_and_characterize_success:
dna_comment = "Indexing Failure"
##### pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_comment)
return 0
xsDataCharacterisation = XSDataResultCharacterisation.parseFile(strXMLFileName)
xsDataIndexingResult = xsDataCharacterisation.getIndexingResult()
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution()
xsDataStatisticsIndexing = xsDataIndexingSolutionSelected.getStatistics()
numSpotsFound = xsDataStatisticsIndexing.getSpotsTotal().getValue()
numSpotsUsed = xsDataStatisticsIndexing.getSpotsUsed().getValue()
numSpotsRejected = numSpotsFound - numSpotsUsed
beamShiftX = xsDataStatisticsIndexing.getBeamPositionShiftX().getValue()
beamShiftY = xsDataStatisticsIndexing.getBeamPositionShiftY().getValue()
spotDeviationR = xsDataStatisticsIndexing.getSpotDeviationPositional().getValue()
try:
spotDeviationTheta = xsDataStatisticsIndexing.getSpotDeviationAngular().getValue()
except AttributeError:
spotDeviationTheta = 0.0
diffractionRings = 0 # for now, don't see this in xml except message string
reflections_used = 0 # for now
reflections_used_in_indexing = 0 # for now
rejectedReflections = 0 # for now
xsDataOrientation = xsDataIndexingSolutionSelected.getOrientation()
xsDataMatrixA = xsDataOrientation.getMatrixA()
rawOrientationMatrix_a_x = xsDataMatrixA.getM11()
rawOrientationMatrix_a_y = xsDataMatrixA.getM12()
rawOrientationMatrix_a_z = xsDataMatrixA.getM13()
rawOrientationMatrix_b_x = xsDataMatrixA.getM21()
rawOrientationMatrix_b_y = xsDataMatrixA.getM22()
rawOrientationMatrix_b_z = xsDataMatrixA.getM23()
rawOrientationMatrix_c_x = xsDataMatrixA.getM31()
rawOrientationMatrix_c_y = xsDataMatrixA.getM32()
rawOrientationMatrix_c_z = xsDataMatrixA.getM33()
xsDataCrystal = xsDataIndexingSolutionSelected.getCrystal()
xsDataCell = xsDataCrystal.getCell()
unitCell_alpha = xsDataCell.getAngle_alpha().getValue()
unitCell_beta = xsDataCell.getAngle_beta().getValue()
unitCell_gamma = xsDataCell.getAngle_gamma().getValue()
unitCell_a = xsDataCell.getLength_a().getValue()
unitCell_b = xsDataCell.getLength_b().getValue()
unitCell_c = xsDataCell.getLength_c().getValue()
mosaicity = xsDataCrystal.getMosaicity().getValue()
xsSpaceGroup = xsDataCrystal.getSpaceGroup()
spacegroup_name = xsSpaceGroup.getName().getValue()
pointGroup = spacegroup_name # for now
bravaisLattice = pointGroup # for now
statusDescription = "ok" # for now
try:
spacegroup_number = xsSpaceGroup.getITNumber().getValue()
except AttributeError:
spacegroup_number = 0
xsStrategyResult = xsDataCharacterisation.getStrategyResult()
resolutionObtained = -999
if xsStrategyResult != None:
dna_have_strategy_results = 1
xsCollectionPlan = xsStrategyResult.getCollectionPlan()
xsStrategySummary = xsCollectionPlan[0].getStrategySummary()
resolutionObtained = xsStrategySummary.getRankingResolution().getValue()
xsCollectionStrategy = xsCollectionPlan[0].getCollectionStrategy()
xsSubWedge = xsCollectionStrategy.getSubWedge()
for i in range(0, len(xsSubWedge)):
xsExperimentalCondition = xsSubWedge[i].getExperimentalCondition()
xsGoniostat = xsExperimentalCondition.getGoniostat()
xsDetector = xsExperimentalCondition.getDetector()
xsBeam = xsExperimentalCondition.getBeam()
dna_strategy_start = xsGoniostat.getRotationAxisStart().getValue()
dna_strategy_start = dna_strategy_start - (dna_strategy_start % 0.1)
dna_strategy_range = xsGoniostat.getOscillationWidth().getValue()
dna_strategy_range = dna_strategy_range - (dna_strategy_range % 0.1)
dna_strategy_end = xsGoniostat.getRotationAxisEnd().getValue()
dna_strategy_end = (dna_strategy_end - (dna_strategy_end % 0.1)) + dna_strategy_range
dna_strat_dist = xsDetector.getDistance().getValue()
dna_strat_dist = dna_strat_dist - (dna_strat_dist % 1)
dna_strategy_exptime = xsBeam.getExposureTime().getValue()
# wtf? dna_strategy_exptime = dna_strategy_exptime-(dna_strategy_exptime%.2)
program = "edna-1.0" # for now
##### screeningoutputid = pxdb_lib.insert_dna_index_results(daq_lib.sweep_seq_id,daq_lib.get_field("xtal_id"),program,statusDescription,rejectedReflections,resolutionObtained,spotDeviationR,spotDeviationTheta,beamShiftX,beamShiftY,numSpotsFound,numSpotsUsed,numSpotsRejected,mosaicity,diffractionRings,spacegroup_name,pointGroup,bravaisLattice,rawOrientationMatrix_a_x,rawOrientationMatrix_a_y,rawOrientationMatrix_a_z,rawOrientationMatrix_b_x,rawOrientationMatrix_b_y,rawOrientationMatrix_b_z,rawOrientationMatrix_c_x,rawOrientationMatrix_c_y,rawOrientationMatrix_c_z,unitCell_a,unitCell_b,unitCell_c,unitCell_alpha,unitCell_beta,unitCell_gamma)
dna_comment = (
"spacegroup = "
+ str(spacegroup_name)
+ " mosaicity = "
+ str(mosaicity)
+ " resolutionHigh = "
+ str(resolutionObtained)
+ " cell_a = "
+ str(unitCell_a)
+ " cell_b = "
+ str(unitCell_b)
+ " cell_c = "
+ str(unitCell_c)
+ " cell_alpha = "
+ str(unitCell_alpha)
+ " cell_beta = "
+ str(unitCell_beta)
+ " cell_gamma = "
+ str(unitCell_gamma)
+ " status = "
+ str(statusDescription)
)
##### print "\n\n skinner " + dna_comment + "\n" +str(daq_lib.sweep_seq_id) + "\n"
print "\n\n skinner " + dna_comment + "\n"
##### pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_comment)
if dna_have_strategy_results:
##### pxdb_lib.insert_to_screening_strategy_table(screeningoutputid,dna_strategy_start,dna_strategy_end,dna_strategy_range,dna_strategy_exptime,resolutionObtained,program)
dna_strat_comment = (
"\ndna Strategy results: Start="
+ str(dna_strategy_start)
+ " End="
+ str(dna_strategy_end)
+ " Width="
+ str(dna_strategy_range)
+ " Time="
+ str(dna_strategy_exptime)
+ " Dist="
+ str(dna_strat_dist)
)
# characterizationResult = {}
characterizationResultObj = {}
# characterizationResult["type"] = "characterizationStrategy"
# characterizationResult["timestamp"] = time.time()
characterizationResultObj = {
"strategy": {
"start": dna_strategy_start,
"end": dna_strategy_end,
"width": dna_strategy_range,
"exptime": dna_strategy_exptime,
"detDist": dna_strat_dist,
}
}
# characterizationResult["resultObj"] = characterizationResultObj
db_lib.addResultforRequest("characterizationStrategy", charRequest["request_id"], characterizationResultObj)
##### pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_strat_comment)
xsStrategyStatistics = xsCollectionPlan[0].getStatistics()
xsStrategyResolutionBins = xsStrategyStatistics.getResolutionBin()
now = time.time()
# edna_isig_plot_filename = dirname[0:len(dirname)-1] + "/edna_isig_res_" + str(now) + ".txt"
edna_isig_plot_filename = dirname[0 : len(dirname) - 1] + "/edna_isig_res.txt"
isig_plot_file = open(edna_isig_plot_filename, "w")
for i in range(0, len(xsStrategyResolutionBins) - 1):
i_over_sigma_bin = xsStrategyResolutionBins[i].getIOverSigma().getValue()
maxResolution_bin = xsStrategyResolutionBins[i].getMaxResolution().getValue()
print str(maxResolution_bin) + " " + str(i_over_sigma_bin)
isig_plot_file.write(str(maxResolution_bin) + " " + str(i_over_sigma_bin) + "\n")
isig_plot_file.close()
if dna_have_strategy_results:
broadcast_output(dna_strat_comment)
return 1
def generateGridMap(rasterRequest):
reqObj = rasterRequest["request_obj"]
rasterDef = reqObj["rasterDef"]
stepsize = float(rasterDef["stepsize"])
omega = float(rasterDef["omega"])
rasterStartX = float(rasterDef["x"])
rasterStartY = float(rasterDef["y"])
rasterStartZ = float(rasterDef["z"])
omegaRad = math.radians(omega)
filePrefix = reqObj["directory"] + "/" + reqObj["file_prefix"]
# testImgFileList = glob.glob("/home/pxuser/Test-JJ/DataSets/Eiger1M-Tryps-cbf/*.cbf")
testImgFileList = glob.glob("/h/pxuser/skinner/Eiger1M/*.cbf")
testImgCount = 0
rasterCellMap = {}
for i in xrange(len(rasterDef["rowDefs"])):
numsteps = float(rasterDef["rowDefs"][i]["numsteps"])
if i % 2 == 0: # left to right if even, else right to left - a snake attempt
startX = rasterDef["rowDefs"][i]["start"]["x"] + (
stepsize / 2.0
) # this is relative to center, so signs are reversed from motor movements.
else:
startX = (numsteps * stepsize) + rasterDef["rowDefs"][i]["start"]["x"] - (stepsize / 2.0)
startY = rasterDef["rowDefs"][i]["start"]["y"] + (stepsize / 2.0)
xRelativeMove = startX
yyRelativeMove = startY * sin(omegaRad)
yxRelativeMove = startY * cos(omegaRad)
# old yxRelativeMove = startY*sin(omegaRad)
zMotAbsoluteMove = rasterStartZ - xRelativeMove
# old yMotAbsoluteMove = rasterStartY-yyRelativeMove
# xMotAbsoluteMove = yxRelativeMove+rasterStartX
yMotAbsoluteMove = rasterStartY + yyRelativeMove
xMotAbsoluteMove = rasterStartX - yxRelativeMove
numsteps = int(rasterDef["rowDefs"][i]["numsteps"])
for j in xrange(numsteps):
if i % 2 == 0: # left to right if even, else right to left - a snake attempt
zMotCellAbsoluteMove = zMotAbsoluteMove - (j * stepsize)
else:
zMotCellAbsoluteMove = zMotAbsoluteMove + (j * stepsize)
# zMotAbsoluteMove = zMotAbsoluteMove-(j*stepsize)
dataFileName = daq_utils.create_filename(filePrefix + "_" + str(i), j + 1)
os.system("mkdir -p " + reqObj["directory"])
comm_s = "ln -sf " + testImgFileList[testImgCount] + " " + dataFileName
os.system(comm_s)
testImgCount += 1
rasterCellCoords = {"x": xMotAbsoluteMove, "y": yMotAbsoluteMove, "z": zMotCellAbsoluteMove}
rasterCellMap[dataFileName[:-4]] = rasterCellCoords
comm_s = "ls -rt " + reqObj["directory"] + "/" + reqObj["file_prefix"] + "*.cbf|dials.find_spots_client"
print comm_s
dialsResultObj = xmltodict.parse("<data>\n" + os.popen(comm_s).read() + "</data>\n")
print "done parsing dials output"
print dialsResultObj
if rasterRequest["request_obj"].has_key("parentReqID"):
parentReqID = rasterRequest["request_obj"]["parentReqID"]
else:
parentReqID = -1
rasterResultObj = {
"parentReqID": parentReqID,
"rasterCellMap": rasterCellMap,
"rasterCellResults": {"type": "dialsRasterResult", "resultObj": dialsResultObj},
}
# rasterResult = daq_utils.createResult("rasterResult",rasterResultObj)
rasterResult = db_lib.addResultforRequest("rasterResult", rasterRequest["request_id"], rasterResultObj)
return rasterResult
os.system(comm_s)
os.chdir(runningDir)
filePrefix = sys.argv[2]
numstart = int(sys.argv[3])
numimages = int(sys.argv[4])
request_id = int(sys.argv[5])
expectedFilenameList = []
timeoutLimit = 60 #for now
prefix_long = directory + "/" + filePrefix
for i in range(numstart, numstart + numimages):
filename = daq_utils.create_filename(prefix_long, i)
expectedFilenameList.append(filename)
timeout_check = 0
while (not os.path.exists(expectedFilenameList[len(expectedFilenameList) -
1])): #this waits for images
timeout_check = timeout_check + 1
time.sleep(1.0)
if (timeout_check > timeoutLimit):
break
comm_s = "xia2 " + directory
print(comm_s)
os.system(comm_s)
fd = open("xia2.json")
resultObj = json.loads(fd.read())
fd.close()
print(resultObj)
db_lib.addResultforRequest("xia2", request_id, resultObj)
print("finished xia2")
program = "edna-1.0" # for now
##### screeningoutputid = pxdb_lib.insert_dna_index_results(daq_lib.sweep_seq_id,daq_lib.get_field("xtal_id"),program,statusDescription,rejectedReflections,resolutionObtained,spotDeviationR,spotDeviationTheta,beamShiftX,beamShiftY,numSpotsFound,numSpotsUsed,numSpotsRejected,mosaicity,diffractionRings,spacegroup_name,pointGroup,bravaisLattice,rawOrientationMatrix_a_x,rawOrientationMatrix_a_y,rawOrientationMatrix_a_z,rawOrientationMatrix_b_x,rawOrientationMatrix_b_y,rawOrientationMatrix_b_z,rawOrientationMatrix_c_x,rawOrientationMatrix_c_y,rawOrientationMatrix_c_z,unitCell_a,unitCell_b,unitCell_c,unitCell_alpha,unitCell_beta,unitCell_gamma)
dna_comment = "spacegroup = " + str(spacegroup_name) + " mosaicity = " + str(mosaicity) + " resolutionHigh = " + str(resolutionObtained) + " cell_a = " + str(unitCell_a) + " cell_b = " + str(unitCell_b) + " cell_c = " + str(unitCell_c) + " cell_alpha = " + str(unitCell_alpha) + " cell_beta = " + str(unitCell_beta) + " cell_gamma = " + str(unitCell_gamma) + " status = " + str(statusDescription)
##### print "\n\n skinner " + dna_comment + "\n" +str(daq_lib.sweep_seq_id) + "\n"
print("\n\n skinner " + dna_comment + "\n")
##### pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_comment)
if (dna_have_strategy_results):
##### pxdb_lib.insert_to_screening_strategy_table(screeningoutputid,dna_strategy_start,dna_strategy_end,dna_strategy_range,dna_strategy_exptime,resolutionObtained,program)
dna_strat_comment = "\ndna Strategy results: Start=" + str(dna_strategy_start) + " End=" + str(dna_strategy_end) + " Width=" + str(dna_strategy_range) + " Time=" + str(dna_strategy_exptime) + " Dist=" + str(dna_strat_dist)
# characterizationResult = {}
characterizationResultObj = {}
# characterizationResult["type"] = "characterizationStrategy"
# characterizationResult["timestamp"] = time.time()
characterizationResultObj = {"strategy":{"start":dna_strategy_start,"end":dna_strategy_end,"width":dna_strategy_range,"exptime":dna_strategy_exptime,"detDist":dna_strat_dist}}
# characterizationResult["resultObj"] = characterizationResultObj
db_lib.addResultforRequest("characterizationStrategy",request_id, characterizationResultObj)
##### pxdb_lib.update_sweep(2,daq_lib.sweep_seq_id,dna_strat_comment)
xsStrategyStatistics = xsCollectionPlan[0].getStatistics()
xsStrategyResolutionBins = xsStrategyStatistics.getResolutionBin()
now = time.time()
# edna_isig_plot_filename = dirname[0:len(dirname)-1] + "/edna_isig_res_" + str(now) + ".txt"
edna_isig_plot_filename = dirname[0:len(dirname)-1] + "/edna_isig_res.txt"
isig_plot_file = open(edna_isig_plot_filename,"w")
for i in range (0,len(xsStrategyResolutionBins)-1):
i_over_sigma_bin = xsStrategyResolutionBins[i].getIOverSigma().getValue()
maxResolution_bin = xsStrategyResolutionBins[i].getMaxResolution().getValue()
print(str(maxResolution_bin) + " " + str(i_over_sigma_bin))
isig_plot_file.write(str(maxResolution_bin) + " " + str(i_over_sigma_bin)+"\n")
isig_plot_file.close()
if (dna_have_strategy_results):
# broadcast_output(dna_strat_comment)
def eScan(energyScanRequest):
sampleID = energyScanRequest["sample_id"]
reqObj = energyScanRequest["request_obj"]
exptime = reqObj['exposure_time']
print("energy scan for " + str(reqObj['scanEnergy']))
scan_element = "Se"
scanID = RE(dscan(omega,-20,20,10,exptime))
scanData = db[scanID]
for ev in get_events(scanData):
if ('mercury_mca_spectrum' in ev['data']):
print(ev['seq_num'], ev['data']['mercury_mca_spectrum'].sum())
scanDataTable = get_table(scanData)
#these next lines only make sense for the mca
specFile = open("spectrumData.txt","w+")
for i in range (0,len(scanDataTable.mercury_mca_spectrum.values)):
for j in range (0,len(scanDataTable.mercury_mca_spectrum.values[i])):
specFile.write(str(scanDataTable.mercury_mca_spectrum.values[i][j]) + ",")
specFile.write("\n")
specFile.close()
# scanDataTable = get_table(scanData,["omega","cam_7_stats1_total"])
eScanResultObj = {}
eScanResultObj["databrokerID"] = scanID
eScanResultObj["sample_id"] = sampleID
eScanResult = db_lib.addResultforRequest("eScanResult",energyScanRequest["request_id"], eScanResultObj)
print(scanDataTable)
if (reqObj["runChooch"]):
chooch_prefix = "choochData1"
choochOutfileName = chooch_prefix+".efs"
choochInputFileName = "/nfs/skinner/temp/choochData1.raw"
comm_s = "chooch -e %s -o %s %s" % (scan_element, choochOutfileName,choochInputFileName)
# comm_s = "chooch -e %s -o %s -p %s %s" % (scan_element,chooch_prefix+".efs",chooch_prefix+".ps",chooch_prefix+".raw")
print(comm_s)
choochInputData_x = []
choochInputData_y = []
choochInputFile = open(choochInputFileName,"r")
for outputLine in choochInputFile.readlines():
tokens = outputLine.split()
if (len(tokens) == 2): #not a very elegant way to get past the first two lines that I don't need.
choochInputData_x.append(float(tokens[0]))
choochInputData_y.append(float(tokens[1]))
choochInputFile.close()
for outputline in os.popen(comm_s).readlines():
print(outputline)
tokens = outputline.split()
if (len(tokens)>4):
if (tokens[1] == "peak"):
peak = float(tokens[3])
fprime_peak = float(tokens[7])
f2prime_peak = float(tokens[5])
elif (tokens[1] == "infl"):
infl = float(tokens[3])
fprime_infl = float(tokens[7])
f2prime_infl = float(tokens[5])
else:
pass
# os.system("xmgrace spectrum.spec&")
# os.system("gv.sh "+chooch_prefix+".ps") #kludged with a shell call to get around gv bug
# os.system("ln -sf "+chooch_prefix+".ps latest_chooch_plot.ps")
choochResultObj = {}
choochResultObj["infl"] = infl
choochResultObj["peak"] = peak
choochResultObj["f2prime_infl"] = f2prime_infl
choochResultObj["fprime_infl"] = fprime_infl
choochResultObj["f2prime_peak"] = f2prime_peak
choochResultObj["fprime_peak"] = fprime_peak
choochResultObj["sample_id"] = sampleID
choochOutFile = open("/nfs/skinner/temp/choochData1.efs","r")
chooch_graph_x = []
chooch_graph_y1 = []
chooch_graph_y2 = []
for outLine in choochOutFile.readlines():
tokens = outLine.split()
chooch_graph_x.append(float(tokens[0]))
chooch_graph_y1.append(float(tokens[1]))
chooch_graph_y2.append(float(tokens[2]))
choochOutFile.close()
choochResultObj["choochOutXAxis"] = chooch_graph_x
choochResultObj["choochOutY1Axis"] = chooch_graph_y1
choochResultObj["choochOutY2Axis"] = chooch_graph_y2
choochResultObj["choochInXAxis"] = choochInputData_x
choochResultObj["choochInYAxis"] = choochInputData_y
# plt.plot(chooch_graph_x,chooch_graph_y1)
# plt.plot(chooch_graph_x,chooch_graph_y2)
# plt.show()
# print(choochResultObj)
choochResult = db_lib.addResultforRequest("choochResult",energyScanRequest["request_id"], choochResultObj)
choochResultID = choochResult["result_id"]
set_field("choochResultFlag",choochResultID)
#fastdpComm = db_lib.getBeamlineConfigParam(os.environ["BEAMLINE_ID"],"fastdpComm")
dimpleComm = db_lib.getBeamlineConfigParam(os.environ["BEAMLINE_ID"],"dimpleComm")
comm_s = "ssh -q " + node + " \"cd " + runningDir + fastdpComm + hdfFilepattern + "\""
#comm_s = "ssh -q " + node + " \"cd " + runningDir +";source /nfs/skinner/wrappers/fastDPWrap2;fast_dp -j 12 -J 12 -k 60 " + hdfFilepattern + "\""
#comm_s = "ssh -q " + node + " \"cd " + runningDir +";source /nfs/skinner/wrappers/fastDPWrap;/usr/local/crys-local/fast_dp/bin/fast_dp -J 16 -j 16 -k 70 " + hdfFilepattern + "\""
print(comm_s)
os.system(comm_s)
fastDPResultFile = runningDir+"/fast_dp.xml"
#fastDPResultFile = "/GPFS/CENTRAL/xf17id2/skinner/ispyb/fast_dp.xml"
#fd = open("fast_dp.xml")
fd = open(fastDPResultFile)
resultObj = xmltodict.parse(fd.read())
print("finished fast_dp")
print(resultObj)
resultID = db_lib.addResultforRequest("fastDP",request_id,owner,resultObj,beamline=os.environ["BEAMLINE_ID"])
newResult = db_lib.getResult(resultID)
visitName = db_lib.getBeamlineConfigParam(os.environ["BEAMLINE_ID"],"visitName")
try:
ispybLib.insertResult(newResult,"fastDP",request,visitName,ispybDCID,fastDPResultFile)
except:
print("ispyb error")
if (runFastEP):
os.system("fast_ep") #looks very bad! running on ca1!
if (runDimple):
sampleID = request["sample"]
sample = db_lib.getSampleByID(sampleID)
try:
modelFilename = sample["model"]
if (modelFilename == 'nan'):
modelPDBname = "model.pdb"
node = sys.argv[5]
runDimple = int(sys.argv[6])
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}")
def generateGridMap(rasterRequest):
global dialsResultDict,rasterRowResultsList
reqObj = rasterRequest["request_obj"]
rasterDef = reqObj["rasterDef"]
stepsize = float(rasterDef["stepsize"])
omega = float(rasterDef["omega"])
rasterStartX = float(rasterDef["x"])
rasterStartY = float(rasterDef["y"])
rasterStartZ = float(rasterDef["z"])
omegaRad = math.radians(omega)
filePrefix = reqObj["directory"]+"/"+reqObj["file_prefix"]
testImgFileList = glob.glob("/GPFS/CENTRAL/XF17ID1/skinner/eiger16M/cbf/*.cbf")
# testImgFileList = glob.glob("/GPFS/CENTRAL/XF17ID1/skinner/testdata/Eiger1M/*.cbf")
testImgCount = 0
rasterCellMap = {}
os.system("mkdir -p " + reqObj["directory"])
for i in range(len(rasterDef["rowDefs"])):
numsteps = float(rasterDef["rowDefs"][i]["numsteps"])
if (i%2 == 0): #left to right if even, else right to left - a snake attempt
startX = rasterDef["rowDefs"][i]["start"]["x"]+(stepsize/2.0) #this is relative to center, so signs are reversed from motor movements.
else:
startX = (numsteps*stepsize) + rasterDef["rowDefs"][i]["start"]["x"]-(stepsize/2.0)
startY = rasterDef["rowDefs"][i]["start"]["y"]+(stepsize/2.0)
xRelativeMove = startX
yzRelativeMove = startY*sin(omegaRad)
yyRelativeMove = startY*cos(omegaRad)
xMotAbsoluteMove = rasterStartX+xRelativeMove
yMotAbsoluteMove = rasterStartY-yyRelativeMove
zMotAbsoluteMove = rasterStartZ-yzRelativeMove
numsteps = int(rasterDef["rowDefs"][i]["numsteps"])
for j in range(numsteps):
if (i%2 == 0): #left to right if even, else right to left - a snake attempt
xMotCellAbsoluteMove = xMotAbsoluteMove+(j*stepsize)
else:
xMotCellAbsoluteMove = xMotAbsoluteMove-(j*stepsize)
dataFileName = daq_utils.create_filename(filePrefix+"_Raster_"+str(i),j+1)
## comm_s = "ln -sf " + testImgFileList[testImgCount] + " " + dataFileName
## os.system(comm_s)
testImgCount+=1
rasterCellCoords = {"x":xMotCellAbsoluteMove,"y":yMotAbsoluteMove,"z":zMotAbsoluteMove}
rasterCellMap[dataFileName[:-4]] = rasterCellCoords
#commented out all of the processing, as this should have been done by the thread
if ("parentReqID" in rasterRequest["request_obj"]):
parentReqID = rasterRequest["request_obj"]["parentReqID"]
else:
parentReqID = -1
print("RASTER CELL RESULTS")
dialsResultLocalList = []
for i in range (0,len(rasterRowResultsList)):
for j in range (0,len(rasterRowResultsList[i])):
try:
dialsResultLocalList.append(rasterRowResultsList[i][j])
except KeyError: #this is to deal with single cell row. Instead of getting back a list of one row, I get back just the row from Dials.
dialsResultLocalList.append(rasterRowResultsList[i])
break
###############
print(dialsResultLocalList)
rasterResultObj = {"sample_id": rasterRequest["sample_id"],"parentReqID":parentReqID,"rasterCellMap":rasterCellMap,"rasterCellResults":{"type":"dialsRasterResult","resultObj":dialsResultLocalList}}
rasterResult = db_lib.addResultforRequest("rasterResult",rasterRequest["request_id"], rasterResultObj)
return rasterResult
for i in range (numstart,numstart+numimages):
filename = daq_utils.create_filename(prefix_long,i)
expectedFilenameList.append(filename)
#for i in range (0,len(expectedFilenameList)):
# print expectedFilenameList[i]
timeout_check = 0
while(not os.path.exists(expectedFilenameList[len(expectedFilenameList)-1])): #this waits for images
timeout_check = timeout_check + 1
time.sleep(1.0)
if (timeout_check > timeoutLimit):
break
node = "cpu-004"
comm_s = "ssh -q " + node + " \"cd " + runningDir +";fast_dp " + expectedFilenameList[0] + "\""
#comm_s = "fast_dp " + expectedFilenameList[0] #note this the first image
print(comm_s)
os.system(comm_s)
fd = open("fast_dp.xml")
#nresult = {}
#result["timestamp"] = time.time()
#result["type"] = "fastDP"
resultObj = xmltodict.parse(fd.read())
#result["resultObj"] = resultObj
db_lib.addResultforRequest("fastDP",request_id,resultObj)
print("finished fast_dp")
if (runFastEP):
os.system("fast_ep")
prefix_long = directory+"/"+filePrefix
for i in range (numstart,numstart+numimages):
filename = daq_utils.create_filename(prefix_long,i)
expectedFilenameList.append(filename)
#for i in range (0,len(expectedFilenameList)):
# print expectedFilenameList[i]
timeout_check = 0
while(not os.path.exists(expectedFilenameList[len(expectedFilenameList)-1])): #this waits for images
timeout_check = timeout_check + 1
time.sleep(1.0)
if (timeout_check > timeoutLimit):
break
comm_s = "xia2 " + directory
print comm_s
os.system(comm_s)
#result = {}
#result["timestamp"] = time.time()
#result["type"] = "xia2"
fd = open("xia2.json")
resultObj = json.loads(fd.read())
fd.close()
print resultObj
#result["resultObj"] = resultObj
db_lib.addResultforRequest("xia2",request_id,resultObj)
print "finished xia2"
