def fakeDC(directory, filePrefix, numstart, numimages):
# testImgFileList = glob.glob("/home/pxuser/Test-JJ/johnPil6/data/B1GGTApo_9_*.cbf")
testImgFileList = glob.glob("/h/pxuser/skinner/testdata/B1GGTApo_9_*.cbf")
testImgFileList.sort()
prefix_long = directory + "/" + filePrefix
expectedFilenameList = []
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)):
comm_s = "ln -sf " + testImgFileList[i] + " " + expectedFilenameList[i]
print comm_s
os.system(comm_s)
def fakeDC(directory,filePrefix,numstart,numimages):
if (numimages > 900):
return
testImgFileList = glob.glob("/GPFS/CENTRAL/XF17ID1/skinner/eiger16M/cbf/*.cbf")
# testImgFileList = glob.glob("/GPFS/CENTRAL/XF17ID1/skinner/testdata/johnPil6/data/B1GGTApo_9_0*.cbf")
testImgFileList.sort()
prefix_long = directory+"/"+filePrefix
expectedFilenameList = []
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)):
comm_s = "ln -sf " + testImgFileList[i] + " " + expectedFilenameList[i]
print(comm_s)
os.system(comm_s)
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
directory = sys.argv[1]
runningDir = directory + "/xia2Output"
comm_s = "mkdir -p " + runningDir
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)
directory = sys.argv[1]
runningDir = directory+"/fastDPOutput"
comm_s = "mkdir -p " + runningDir
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])
runFastEP = int(sys.argv[6])
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)
#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")
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
#12/15 not sure why dna_run_num in prefix 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.mvaDescriptor("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 /nfs/skinner/testdata/johnPil6/data/B1GGTApo_9_00001.cbf " + filename
else:
commFake = "ln -sf /nfs/skinner/testdata/johnPil6/data/B1GGTApo_9_00181.cbf " + filename
os.system(commFake)
print(commFake)
dna_filename_list.append(filename)
###4/16, don't bother with image server for now 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 = .1
ybeam_size = .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
##### flux = 10000000000 * beamline_lib.get_epics_pv("flux","VAL")
flux = 600000000.0 #for now
edna_input_filename = dna_directory + "/adsc1_in.xml"
comm_s = "ssh -q xf17id1-srv1 \"" + os.environ["LSDCHOME"] + "/runEdna.py " + dna_directory + " " + dna_prefix + " " + str(aimed_ISig) + " " + str(flux) + " " + str(xbeam_size) + " " + str(ybeam_size) + " " + edna_input_filename + " " + str(charRequest["request_id"]) + "\""
print(comm_s)
os.system(comm_s)
return 1
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
