def loop_center_xrec():
global face_on
daq_lib.abort_flag = 0
for i in xrange(0, 360, 40):
if daq_lib.abort_flag == 1:
return 0
mva("Omega", i)
pic_prefix = "findloop_" + str(i)
# time.sleep(0.1)
daq_utils.take_crystal_picture(filename=pic_prefix)
comm_s = "xrec " + os.environ["CONFIGDIR"] + "/xrec_360_40.txt xrec_result.txt"
print comm_s
os.system(comm_s)
xrec_out_file = open("xrec_result.txt", "r")
target_angle = 0.0
radius = 0
x_centre = 0
y_centre = 0
reliability = 0
for result_line in xrec_out_file.readlines():
print result_line
tokens = split(result_line)
tag = tokens[0]
val = tokens[1]
if tag == "TARGET_ANGLE":
target_angle = float(val)
elif tag == "RADIUS":
radius = float(val)
elif tag == "Y_CENTRE":
y_centre_xrec = float(val)
elif tag == "X_CENTRE":
x_centre_xrec = float(val)
elif tag == "RELIABILITY":
reliability = int(val)
elif tag == "FACE":
face_on = float(tokens[3])
xrec_out_file.close()
xrec_check_file = open("Xrec_check.txt", "r")
check_result = int(xrec_check_file.read(1))
print "result = " + str(check_result)
xrec_check_file.close()
if reliability < 70 or check_result == 0: # bail if xrec couldn't align loop
return 0
mva("Omega", target_angle)
x_center = daq_utils.lowMagPixX / 2
y_center = daq_utils.lowMagPixY / 2
# set_epics_pv("image_X_center","A",x_center)
# set_epics_pv("image_Y_center","A",y_center)
print "center on click " + str(x_center) + " " + str(y_center - radius)
print "center on click " + str((x_center * 2) - y_centre_xrec) + " " + str(x_centre_xrec)
center_on_click(x_center, y_center - radius, source="macro")
center_on_click((x_center * 2) - y_centre_xrec, x_centre_xrec, source="macro")
mva("Omega", face_on)
# now try to get the loopshape starting from here
return 1
def display_images():
currentRequestID = db_lib.beamlineInfo('john', 'currentRequestID')["requestID"]
print "display images for req " + str(currentRequestID)
data_directory_name = getDetPv("data_filepath_rbv")
numimages = getDetPv("numimages")
prefix = getDetPv("data_filename_rbv")
image_period = getDetPv("image_period")
numstart = getDetPv("file_number_rbv")
numstart = numstart - 1
if (numimages>10 and image_period<10):
sample = 10
else:
sample = 1
filelist = []
for i in range (numstart,numstart+numimages,sample):
filename = "%s/%s_%05d.cbf" % (data_directory_name,prefix,i)
filelist.append(filename)
filename = "%s/%s_%05d.cbf" % (data_directory_name,prefix,numimages+numstart-1) # last image
if (len(filelist) > 0):
if (filename != filelist[len(filelist)-1]):
filelist.append(filename)
for j in range (0,len(filelist)):
filename = filelist[j]
last_dot = string.rfind(filename,".")
i = int(filename[last_dot-5:last_dot])
print "looking for " + filename
while not (os.path.exists(filename)):
os.system("ls " + data_directory_name + " >/dev/null")
time.sleep(0.03)
if (jpeg_needed == -99):
return
# time.sleep(0.1)
print "found for " + filename
time.sleep(.05) #got a corrupted file error in albula w/0 this, might not happen in real collection
## daq_utils.albulaDisp(filename) #why have the logger kicking off albula? Because that's what it does for now, don't bother with eiger, use monitor
daq_utils.diff2jpeg(filename,JPEGfilename=None,reqID=currentRequestID)
##huh? I think the filelist takes care of this if (j%10 == 0):
now = time.time()
print "take xtal picture"
daq_utils.runDials(filename)
daq_utils.take_crystal_picture(filename=None,czoom=0,reqID=currentRequestID,omega=beamline_lib.motorPosFromDescriptor("omega")) #but this is unlikely to be synchronized with diff image
def getXrecLoopShape(currentRequest):
sampleID = currentRequest["sample_id"]
# beamline_support.set_any_epics_pv("XF:17IDC-ES:FMX{Cam:07}MJPGZOOM:NDArrayPort","VAL","ROI1") #not the best, but I had timing issues doing it w/o a sleep
for i in range(4):
if (daq_lib.abort_flag == 1):
return 0
mvaDescriptor("omega",i*30)
pic_prefix = "findloopshape_" + str(i)
time.sleep(1.0) # for vid lag, sucks
daq_utils.take_crystal_picture(filename=pic_prefix,czoom=1)
comm_s = "xrec30 " + os.environ["CONFIGDIR"] + "/xrec30.txt xrec30_result.txt"
os.system(comm_s)
print ("face on = " + str(face_on))
mvaDescriptor("omega",face_on) #global, yuk.
os.system("cp /dev/shm/masks2_hull_0.txt loopPoints.txt")
polyPoints = []
rasterPoly = None
filename = "loopPoints.txt"
xrec_out_file = open(filename,"r")
resultLine = xrec_out_file.readline()
xrec_out_file.close()
tokens = resultLine.split()
numpoints = int(tokens[0])
for i in range(1,len(tokens)-1,2):
point = [tokens[i],tokens[i+1]]
correctedPoint = [daq_utils.screenPixX-int(tokens[i]),daq_utils.screenPixY-int(tokens[i+1])]
polyPoint = QtCore.QPointF(float(correctedPoint[0]),float(correctedPoint[1]))
polyPoints.append(polyPoint)
newLoopPoint = QtGui.QGraphicsEllipseItem(correctedPoint[0],correctedPoint[1],3,3)
rasterPoly = QtGui.QGraphicsPolygonItem(QtGui.QPolygonF(polyPoints))
polyBoundingRect = rasterPoly.boundingRect()
raster_w = int(polyBoundingRect.width())
raster_h = int(polyBoundingRect.height())
center_x = int(polyBoundingRect.center().x())
center_y = int(polyBoundingRect.center().y())
if (currentRequest['request_obj']['protocol'] == "multiCol"):
stepsizeMicrons = currentRequest['request_obj']['gridStep']
else:
stepsizeMicrons = 30.0 #for now.
rasterReqID = definePolyRaster(currentRequest,raster_w,raster_h,stepsizeMicrons,center_x,center_y,rasterPoly)
return rasterReqID
def getXrecLoopShape(currentRequest):
sampleID = currentRequest["sample_id"]
beamline_support.set_any_epics_pv(
"FAMX-cam1:MJPGZOOM:NDArrayPort", "VAL", "ROI1"
) # not the best, but I had timing issues doing it w/o a sleep
for i in xrange(4):
if daq_lib.abort_flag == 1:
return 0
mvr("Omega", i * 30)
pic_prefix = "findloopshape_" + str(i)
# time.sleep(0.1)
daq_utils.take_crystal_picture(filename=pic_prefix, czoom=1)
comm_s = "xrec30 " + os.environ["CONFIGDIR"] + "/xrec30.txt xrec30_result.txt"
os.system(comm_s)
mva("Omega", face_on)
os.system("cp /dev/shm/masks2_hull_0.txt loopPoints.txt")
polyPoints = []
rasterPoly = None
filename = "loopPoints.txt"
xrec_out_file = open(filename, "r")
resultLine = xrec_out_file.readline()
xrec_out_file.close()
tokens = string.split(resultLine)
numpoints = int(tokens[0])
for i in xrange(1, len(tokens) - 1, 2):
point = [tokens[i], tokens[i + 1]]
correctedPoint = [daq_utils.screenPixX - int(tokens[i]), daq_utils.screenPixY - int(tokens[i + 1])]
polyPoint = QtCore.QPointF(float(correctedPoint[0]), float(correctedPoint[1]))
polyPoints.append(polyPoint)
newLoopPoint = QtGui.QGraphicsEllipseItem(correctedPoint[0], correctedPoint[1], 3, 3)
rasterPoly = QtGui.QGraphicsPolygonItem(QtGui.QPolygonF(polyPoints))
polyBoundingRect = rasterPoly.boundingRect()
raster_w = int(polyBoundingRect.width())
raster_h = int(polyBoundingRect.height())
center_x = int(polyBoundingRect.center().x())
center_y = int(polyBoundingRect.center().y())
stepsizeMicrons = 30.0 # for now.
rasterReqID = definePolyRaster(currentRequest, raster_w, raster_h, stepsizeMicrons, center_x, center_y, rasterPoly)
return rasterReqID
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 insertResult(result,
resultType,
request,
visitName,
dc_id=None,
xmlFileName=None): #xmlfilename for fastDP
#keep in mind that request type can be standard and result type be fastDP - multiple results per req.
cbfComm = db_lib.getBeamlineConfigParam(beamline, "cbfComm")
try:
sessionid = core.retrieve_visit_id(visitName)
except ISPyBNoResultException as e:
logger.error(
"caught ISPyBNoResultException: %s. make sure visit name is in the format mx999999-1234"
% e)
propNum = visitName.split('-')[0]
sessionid = createVisit(propNum)
request_type = request['request_type']
if request_type in ('standard', 'vector'):
sample = request[
'sample'] # this needs to be created and linked to a DC group
if (resultType == 'fastDP'):
mx_data_reduction_dict = xml_file_to_dict(xmlFileName)
(app_id, ap_id, scaling_id,
integration_id) = mx_data_reduction_to_ispyb(
mx_data_reduction_dict, dc_id, mxprocessing)
mxprocessing.upsert_program_ex(program_id=app_id, status=1)
elif resultType == 'mxExpParams':
result_obj = result['result_obj']
request_obj = result_obj['requestObj']
directory = request_obj["directory"]
filePrefix = request_obj['file_prefix']
basePath = request_obj["basePath"]
visitName = daq_utils.getVisitName()
jpegDirectory = visitName + "/jpegs/" + directory[
directory.find(visitName) + len(visitName):len(directory)]
fullJpegDirectory = basePath + "/" + jpegDirectory
jpegImagePrefix = fullJpegDirectory + "/" + filePrefix
daq_utils.take_crystal_picture(filename=jpegImagePrefix)
jpegImageFilename = jpegImagePrefix + ".jpg"
jpegImageThumbFilename = jpegImagePrefix + "t.jpg"
node = db_lib.getBeamlineConfigParam(beamline, "adxvNode")
comm_s = "ssh -q " + node + " \"convert " + jpegImageFilename + " -resize 40% " + jpegImageThumbFilename + "\"&"
logger.info('resizing image: %s' % comm_s)
os.system(comm_s)
seqNum = int(detSeqNumPV.get())
hdfSampleDataPattern = directory + "/" + filePrefix + "_"
hdfRowFilepattern = hdfSampleDataPattern + str(int(
float(seqNum))) + "_master.h5"
# keep in mind I could do the jpeg conversion here, but maybe best to allow synchWeb on demand.
cbfDir = directory
CBF_conversion_pattern = cbfDir + "/" + filePrefix + "_"
JPEG_conversion_pattern = fullJpegDirectory + "/" + filePrefix + "_"
node = db_lib.getBeamlineConfigParam(beamline, "adxvNode")
adxvComm = os.environ["PROJDIR"] + db_lib.getBeamlineConfigParam(
daq_utils.beamline, "adxvComm")
comm_s = "ssh -q " + node + " \"sleep 6;" + cbfComm + " " + hdfRowFilepattern + " 1:1 " + CBF_conversion_pattern + ";" + adxvComm + " -sa " + CBF_conversion_pattern + "000001.cbf " + JPEG_conversion_pattern + "0001.jpeg;convert " + JPEG_conversion_pattern + "0001.jpeg -resize 10% " + JPEG_conversion_pattern + "0001.thumb.jpeg\"&"
logger.info('diffraction thumbnail image: %s' % comm_s)
os.system(comm_s)
# Create a new data collection group entry:
params = mxacquisition.get_data_collection_group_params()
params['parentid'] = sessionid
if request_type == 'standard':
params['experimenttype'] = 'OSC'
elif request_type == 'vector':
params['experimenttype'] = 'Helical'
return createDataCollection(directory, filePrefix,
jpegImageFilename, params, request_obj,
sessionid)
def insertResult(result,
resultType,
request,
visitName,
dc_id=None,
xmlFileName=None): #xmlfilename for fastDP
#keep in mind that request type can be standard and result type be fastDP - multiple results per req.
try:
sessionid = core.retrieve_visit_id(visitName)
except ISPyBNoResultException as e:
logger.error(
"insert result - caught ISPyBNoResultException: '%s'. make sure visit name is in the format mx999999-1234. NOT HAVING MX IN FRONT IS A SIGN OF PROBLEMS - try newVisit() in that case."
% e)
propNum = visitName.split('-')[0]
sessionid = createVisit(propNum)
request_type = request['request_type']
if request_type in ('standard', 'vector'):
sample = request[
'sample'] # this needs to be created and linked to a DC group
if (resultType == 'fastDP'):
mx_data_reduction_dict = xml_file_to_dict(xmlFileName)
(app_id, ap_id, scaling_id,
integration_id) = mx_data_reduction_to_ispyb(
mx_data_reduction_dict, dc_id, mxprocessing)
mxprocessing.upsert_program_ex(program_id=app_id, status=1)
elif resultType == 'mxExpParams':
result_obj = result['result_obj']
request_obj = result_obj['requestObj']
directory = request_obj["directory"]
filePrefix = request_obj['file_prefix']
basePath = request_obj["basePath"]
visitName = daq_utils.getVisitName()
jpegDirectory = visitName + "/jpegs/" + directory[
directory.find(visitName) + len(visitName):len(directory)]
fullJpegDirectory = basePath + "/" + jpegDirectory
jpegImagePrefix = fullJpegDirectory + "/" + filePrefix
daq_utils.take_crystal_picture(filename=jpegImagePrefix)
jpegImageFilename = jpegImagePrefix + ".jpg"
jpegImageThumbFilename = jpegImagePrefix + "t.jpg"
node = db_lib.getBeamlineConfigParam(beamline, "adxvNode")
comm_s = f"ssh -q {node} \"{os.environ['MXPROCESSINGSCRIPTSDIR']}resize.sh {jpegImageFilename} {jpegImageThumbFilename} 40% \"&"
logger.info('resizing image: %s' % comm_s)
os.system(comm_s)
seqNum = int(detSeqNumPV.get())
node = db_lib.getBeamlineConfigParam(beamline, "adxvNode")
request_id = result['request']
comm_s = f"ssh -q {node} \"{os.environ['MXPROCESSINGSCRIPTSDIR']}eiger2cbf.sh {request_id} 1 1 0 {seqNum}\""
logger.info(f'diffraction thumbnail conversion to cbf: {comm_s}')
os.system(comm_s)
comm_s = f"ssh -q {node} \"{os.environ['MXPROCESSINGSCRIPTSDIR']}cbf2jpeg.sh {request_id}\""
logger.info(f'diffraction thumbnail conversion to jpeg: {comm_s}')
os.system(comm_s)
# Create a new data collection group entry:
params = mxacquisition.get_data_collection_group_params()
params['parentid'] = sessionid
if request_type == 'standard':
params['experimenttype'] = 'OSC'
elif request_type == 'vector':
params['experimenttype'] = 'Helical'
return createDataCollection(directory, filePrefix,
jpegImageFilename, params, request_obj,
sessionid)
def insertResult(result,resultType,request,visitName,dc_id=None,xmlFileName=None): #xmlfilename for fastDP
#keep in mind that request type can be standard and result type be fastDP - multiple results per req.
cbfComm = db_lib.getBeamlineConfigParam(daq_utils.beamline,"cbfComm")
try:
sessionid = core.retrieve_visit_id(visitName)
except ISPyBNoResultException:
print("caught ISPyBNoResultException")
sessionid = createVisit(visitName)
request_type = request['request_type']
if request_type in('standard', 'vector') :
sample = request['sample'] # this needs to be created and linked to a DC group
if (resultType == 'fastDP'):
mx_data_reduction_dict = xml_file_to_dict(xmlFileName)
(app_id, ap_id, scaling_id, integration_id) = mx_data_reduction_to_ispyb(mx_data_reduction_dict, dc_id, mxprocessing)
elif resultType == 'mxExpParams':
result_obj = result['result_obj']
request_obj = result_obj['requestObj']
directory = request_obj["directory"]
filePrefix = request_obj['file_prefix']
basePath = request_obj["basePath"]
visitName = daq_utils.getVisitName()
jpegDirectory = visitName + "/jpegs/" + directory[directory.find(visitName)+len(visitName):len(directory)]
# jpegDirectory = "jpegs" + directory[directory.find(basePath)+len(basePath):len(directory)]
fullJpegDirectory = basePath + "/" + jpegDirectory
jpegImagePrefix = fullJpegDirectory+"/"+filePrefix
daq_utils.take_crystal_picture(filename=jpegImagePrefix)
jpegImageFilename = jpegImagePrefix+".jpg"
jpegImageThumbFilename = jpegImagePrefix+"t.jpg"
node = db_lib.getBeamlineConfigParam(daq_utils.beamline,"adxvNode")
# node = db_lib.getBeamlineConfigParam(daq_utils.beamline,"spotNode1")
comm_s = "ssh -q " + node + " \"convert " + jpegImageFilename + " -resize 40% " + jpegImageThumbFilename + "\"&"
print(comm_s)
os.system(comm_s)
# seqNum = int(det_lib.detector_get_seqnum())
seqNum = int(detSeqNumPV.get())
hdfSampleDataPattern = directory+"/"+filePrefix+"_"
hdfRowFilepattern = hdfSampleDataPattern + str(int(float(seqNum))) + "_master.h5"
#jpeg folder cbfDir = os.getcwd()+"/jpegs/"+directory[len(os.getcwd()):len(directory)] #good luck with that working
# keep in mind I could do the jpeg conversion here, but maybe best to allow synchWeb on demand.
cbfDir = directory
CBF_conversion_pattern = cbfDir + "/" + filePrefix+"_"
JPEG_conversion_pattern = fullJpegDirectory + "/" + filePrefix+"_"
node = db_lib.getBeamlineConfigParam(daq_utils.beamline,"adxvNode")
# node = db_lib.getBeamlineConfigParam(daq_utils.beamline,"spotNode1")
adxvComm = os.environ["PROJDIR"] + db_lib.getBeamlineConfigParam(daq_utils.beamline,"adxvComm")
comm_s = "ssh -q " + node + " \"sleep 6;" + cbfComm + " " + hdfRowFilepattern + " 1 " + CBF_conversion_pattern + "0001.cbf;" + adxvComm + " -sa " + CBF_conversion_pattern + "0001.cbf " + JPEG_conversion_pattern + "0001.jpeg;convert " + JPEG_conversion_pattern + "0001.jpeg -resize 10% " + JPEG_conversion_pattern + "0001.thumb.jpeg\"&"
# comm_s = "ssh -q " + node + " \"sleep 6;" + cbfComm + " " + hdfRowFilepattern + " 1 " + CBF_conversion_pattern + "0001.cbf;" + adxvComm + " -sa " + CBF_conversion_pattern + "0001.cbf " + JPEG_conversion_pattern + "0001.jpeg;cp " + JPEG_conversion_pattern + "0001.jpeg " + JPEG_conversion_pattern + "0001.thumb.jpeg\"&"
print(comm_s)
os.system(comm_s)
# Create a new data collection group entry:
params = mxacquisition.get_data_collection_group_params()
params['parentid'] = sessionid
# params['sampleid'] = ?
if request_type == 'standard':
params['experimenttype'] = 'OSC'
elif request_type == 'vector':
params['experimenttype'] = 'Helical'
params['starttime'] = datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d %H:%M:%S')
params['endtime'] = datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d %H:%M:%S')
# params['starttime'] = datetime.fromtimestamp(request['time']).strftime('%Y-%m-%d %H:%M:%S')
# params['endtime'] = datetime.fromtimestamp(request['time']).strftime('%Y-%m-%d %H:%M:%S')
dcg_id = mxacquisition.insert_data_collection_group(list(params.values()))
print("dcg_id: %i" % dcg_id)
params = mxacquisition.get_data_collection_params()
params['parentid'] = dcg_id
params['visitid'] = sessionid
params['imgdir'] = directory
params['imgprefix'] = filePrefix
params['imgsuffix'] = 'cbf' # assume CBF ...?
params['wavelength'] = request_obj['wavelength']
params['starttime'] = datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d %H:%M:%S')
# params['starttime'] = datetime.fromtimestamp(request['time']).strftime('%Y-%m-%d %H:%M:%S')
params['run_status'] = 'DataCollection Successful' # assume success / not aborted
params['datacollection_number'] = request_obj['runNum']
params['n_images'] = int(round((request_obj['sweep_end'] - request_obj['sweep_start']) / request_obj['img_width']))
params['exp_time'] = request_obj['exposure_time']
params['start_image_number'] = request_obj['file_number_start']
params['axis_start'] = request_obj['sweep_start']
params['axis_end'] = request_obj['sweep_end']
params['axis_range'] = request_obj['img_width']
params['resolution'] = request_obj['resolution']
params['detector_distance'] = request_obj['detDist']
params['slitgap_horizontal'] = request_obj['slit_width']
params['slitgap_vertical'] = request_obj['slit_height']
params['transmission'] = request_obj['attenuation']
params['file_template'] = '%s_####.cbf' % (request_obj['file_prefix']) # assume cbf ...
# params['file_template'] = '%s_%s_####.cbf' % (request_obj['file_prefix'], request_obj['runNum']) # assume cbf ...
# params['flux'] = ?
params['overlap'] = 0.0
params['rotation_axis'] = 'Omega' # assume Omega unless we know otherwise
print("jpegimfilename = " + jpegImageFilename)
params['xtal_snapshot1'] = jpegImageFilename
# params['xtal_snapshot1'] = '/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_1_0.0.png'
params['xtal_snapshot2'] = '/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_1_90.0.png'
params['xtal_snapshot3'] = '/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_1_183.0.png'
params['xtal_snapshot4'] = '/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_1_93.0.png'
dc_id = mxacquisition.insert_data_collection(list(params.values()))
print("dc_id: %i" % dc_id)
return dc_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
#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 loop_center_xrec():
global face_on
daq_lib.abort_flag = 0
for i in range(0,360,40):
if (daq_lib.abort_flag == 1):
print("caught abort in loop center")
return 0
mvaDescriptor("omega",i)
pic_prefix = "findloop_" + str(i)
time.sleep(1.0) #for video lag. This sucks
daq_utils.take_crystal_picture(filename=pic_prefix)
comm_s = "xrec " + os.environ["CONFIGDIR"] + "/xrec_360_40.txt xrec_result.txt"
print(comm_s)
os.system(comm_s)
xrec_out_file = open("xrec_result.txt","r")
target_angle = 0.0
radius = 0
x_centre = 0
y_centre = 0
reliability = 0
for result_line in xrec_out_file.readlines():
print(result_line)
tokens = result_line.split()
tag = tokens[0]
val = tokens[1]
if (tag == "TARGET_ANGLE"):
target_angle = float(val )
elif (tag == "RADIUS"):
radius = float(val )
elif (tag == "Y_CENTRE"):
y_centre_xrec = float(val )
elif (tag == "X_CENTRE"):
x_centre_xrec = float(val )
elif (tag == "RELIABILITY"):
reliability = int(val )
elif (tag == "FACE"):
face_on = float(tokens[3])
xrec_out_file.close()
xrec_check_file = open("Xrec_check.txt","r")
check_result = int(xrec_check_file.read(1))
print("result = " + str(check_result))
xrec_check_file.close()
if (reliability < 70 or check_result == 0): #bail if xrec couldn't align loop
return 0
mvaDescriptor("omega",target_angle)
x_center = daq_utils.lowMagPixX/2
y_center = daq_utils.lowMagPixY/2
# set_epics_pv("image_X_center","A",x_center)
# set_epics_pv("image_Y_center","A",y_center)
print("center on click " + str(x_center) + " " + str(y_center-radius))
print("center on click " + str((x_center*2) - y_centre_xrec) + " " + str(x_centre_xrec))
fovx = daq_utils.lowMagFOVx
fovy = daq_utils.lowMagFOVy
center_on_click(x_center,y_center-radius,fovx,fovy,source="macro")
center_on_click((x_center*2) - y_centre_xrec,x_centre_xrec,fovx,fovy,source="macro")
# center_on_click(y_centre_xrec,x_centre_xrec,source="macro")
mvaDescriptor("omega",face_on)
#now try to get the loopshape starting from here
return 1