def vector_move(t_s,vecRequest): #I think t_s is a fraction of the total vector, so "1" would do the whole thing
global x_vec_end, y_vec_end, z_vec_end, x_vec, y_vec, z_vec, x_vec_start, y_vec_start, z_vec_start
# print "vec t = " + str(t_s)
t = float(t_s)
reqObj = vecRequest["request_obj"]
trans_total = reqObj["vectorParams"]["trans_total"]
trans_done = trans_total*t
percent_done = t*100.0
vec_s = "translation total = %f, translation done = %f, translation percent done = %f\n" % (trans_total,trans_done,percent_done)
print vec_s
# daq_utils.broadcast_output(vec_s)
x_vec_start=reqObj["vectorParams"]["vecStart"]["x"]
y_vec_start=reqObj["vectorParams"]["vecStart"]["y"]
z_vec_start=reqObj["vectorParams"]["vecStart"]["z"]
x_vec = reqObj["vectorParams"]["x_vec"]
y_vec = reqObj["vectorParams"]["y_vec"]
z_vec = reqObj["vectorParams"]["z_vec"]
new_x = x_vec_start + (x_vec*t)
new_y = y_vec_start + (y_vec*t)
new_z = z_vec_start + (z_vec*t)
beamline_lib.mva("X",new_x,"Y",new_y,"Z",new_z)
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 collectData(currentRequest):
global data_directory_name
logMxRequestParams(currentRequest)
reqObj = currentRequest["request_obj"]
data_directory_name = str(reqObj["directory"])
if not (os.path.isdir(data_directory_name)):
comm_s = "mkdir -p " + data_directory_name
os.system(comm_s)
print reqObj["protocol"]
prot = str(reqObj["protocol"])
if (prot == "raster"):
daq_macros.snakeRaster(currentRequest["request_id"])
# return
elif (prot == "vector"):
daq_macros.vectorScan(currentRequest)
# return
else: #standard, screening, or edna - these may require autoalign, checking first
if (reqObj["pos_x"] != 0):
beamline_lib.mva("X",reqObj["pos_x"])
beamline_lib.mva("Y",reqObj["pos_y"])
beamline_lib.mva("Z",reqObj["pos_z"])
else:
print "autoRaster"
daq_macros.autoRasterLoop(currentRequest["sample_id"])
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"])
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 = reqObj["sweep_end"]+(i*screenRange)
file_prefix = str(reqObj["file_prefix"]+"_"+str(i*screenRange))
data_directory_name = str(reqObj["directory"]) # for now
file_number_start = reqObj["file_number_start"]
beamline_lib.mva("Omega",sweep_start)
imagesAttempted = collect_detector_seq(range_degrees,img_width,exposure_period,file_prefix,data_directory_name,file_number_start)
elif (reqObj["protocol"] == "characterize"):
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["request_id"]) # because for testing I keep running the same request. Probably not in usual use.
results = resultsList[len(resultsList)-1]
strategyResults = results["result_obj"]["strategy"]
stratStart = strategyResults["start"]
stratEnd = strategyResults["end"]
stratWidth = strategyResults["width"]
stratExptime = strategyResults["exptime"]
stratDetDist = strategyResults["detDist"]
sampleID = currentRequest["sample_id"]
tempnewStratRequest = daq_utils.createDefaultRequest(sampleID)
newReqObj = tempnewStratRequest["request_obj"]
newReqObj["sweep_start"] = stratStart
newReqObj["sweep_end"] = stratEnd
newReqObj["img_width"] = stratWidth
newReqObj["exposure_time"] = stratExptime
newReqObj["detDist"] = stratDetDist
newReqObj["directory"] = data_directory_name
runNum = db_lib.incrementSampleRequestCount(sampleID)
reqObj["runNum"] = runNum
newStratRequest = db_lib.addRequesttoSample(sampleID,newReqObj["protocol"],newReqObj,priority=0)
else: #standard
sweep_start = reqObj["sweep_start"]
sweep_end = reqObj["sweep_end"]
file_prefix = str(reqObj["file_prefix"])
file_number_start = reqObj["file_number_start"]
range_degrees = abs(sweep_end-sweep_start)
beamline_lib.mva("Omega",sweep_start)
imagesAttempted = collect_detector_seq(range_degrees,img_width,exposure_period,file_prefix,data_directory_name,file_number_start)
if (reqObj["fastDP"]):
if (reqObj["fastEP"]):
fastEPFlag = 1
else:
fastEPFlag = 0
comm_s = os.environ["CBHOME"] + "/runFastDP.py " + data_directory_name + " " + file_prefix + " " + str(file_number_start) + " " + str(int(round(range_degrees/img_width))) + " " + str(currentRequest["request_id"]) + " " + str(fastEPFlag) + "&"
print comm_s
os.system(comm_s)
if (reqObj["xia2"]):
comm_s = os.environ["CBHOME"] + "/runXia2.py " + data_directory_name + " " + file_prefix + " " + str(file_number_start) + " " + str(int(round(range_degrees/img_width))) + " " + str(currentRequest["request_id"]) + "&"
os.system(comm_s)
db_lib.updatePriority(currentRequest["request_id"],-1)
refreshGuiTree()