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daq_utils.py
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daq_utils.py
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import os
from config_params import BEAM_CHECK, UNMOUNT_COLD_CHECK
from math import *
import math
import requests
import getpass
import logging
logger = logging.getLogger(__name__)
try:
import ispybLib
except Exception as e:
logger.error("daq_utils: ISPYB import error, %s" %e)
import db_lib
global beamline
beamline = os.environ["BEAMLINE_ID"]
global beamlineComm #this is the comm_ioc
beamlineComm = ""
global searchParams
global motor_dict,counter_dict,scan_list,soft_motor_list,pvLookupDict
global detector_id
detector_id = ""
pvLookupDict = {}
motor_dict = {}
counter_dict = {}
scan_list = []
soft_motor_list = []
global screenYCenterPixelsLowMagOffset
screenYCenterPixelsLowMagOffset = 58
# Constants for use with C2C
global CAMERA_ANGLE_BEAM,CAMERA_ANGLE_ABOVE, CAMERA_ANGLE_BELOW
CAMERA_ANGLE_BEAM = 0 # viewing angle is in line with beam, upstream from the sample, facing downstream, top toward ceiling
CAMERA_ANGLE_ABOVE = 1 # viewing angle is directly above sample facing downward, top of view is downstream
CAMERA_ANGLE_BELOW = 2 # viewing angle is directly below sample facing upward, top of view is downstream
global mag1ViewAngle, mag2ViewAngle, mag3VivewAngle, mag4ViewAngle
mag1ViewAngle = CAMERA_ANGLE_BEAM
mag2ViewAngle = CAMERA_ANGLE_BEAM
mag3ViewAngle = CAMERA_ANGLE_BEAM
mag4ViewAngle = CAMERA_ANGLE_BEAM
EV_ANGSTROM_CONSTANT = 12398.42 # https://www.kmlabs.com/en/wavelength-to-photon-energy-calculator
EV_ANGSTROM_CONSTANT = 12398.42 # https://www.kmlabs.com/en/wavelength-to-photon-energy-calculator
def getBlConfig(param, beamline=beamline):
return db_lib.getBeamlineConfigParam(beamline, param)
def setBlConfig(param, value, beamline=beamline):
db_lib.setBeamlineConfigParam(beamline, param, value)
def init_environment():
global beamline,detector_id,mono_mot_code,has_beamline,has_xtalview,xtal_url,xtal_url_small,unitScaling,sampleCameraCount,xtalview_user,xtalview_pass,det_type,has_dna,beamstop_x_pvname,beamstop_y_pvname,camera_offset,det_radius,lowMagFOVx,lowMagFOVy,highMagFOVx,highMagFOVy,lowMagPixX,lowMagPixY,highMagPixX,highMagPixY,screenPixX,screenPixY,screenPixCenterX,screenPixCenterY,screenProtocol,screenPhist,screenPhiend,screenWidth,screenDist,screenExptime,screenWave,screenReso,gonioPvPrefix,searchParams,screenEnergy,detectorOffline,imgsrv_host,imgsrv_port,beamlineComm,primaryDewarName,lowMagCamURL,highMagZoomCamURL,lowMagZoomCamURL,highMagCamURL,owner,dewarPlateMap,mag1ViewAngle,mag2ViewAngle,mag3ViewAngle,mag4ViewAngle
owner = getpass.getuser()
primaryDewarName = getBlConfig("primaryDewarName")
db_lib.setPrimaryDewarName(primaryDewarName)
dewarPlateMap = getBlConfig("dewarPlateMap")
lowMagCamURL = getBlConfig("lowMagCamURL")
highMagCamURL = getBlConfig("highMagCamURL")
highMagZoomCamURL = getBlConfig("highMagZoomCamURL")
lowMagZoomCamURL = getBlConfig("lowMagZoomCamURL")
lowMagFOVx = float(getBlConfig("lowMagFOVx"))
lowMagFOVy = float(getBlConfig("lowMagFOVy"))
highMagFOVx = float(getBlConfig("highMagFOVx")) #digizoom will be this/2
highMagFOVy = float(getBlConfig("highMagFOVy"))
lowMagPixX = float(getBlConfig("lowMagPixX")) #for automated images
lowMagPixY = float(getBlConfig("lowMagPixY"))
highMagPixX = float(getBlConfig("highMagPixX")) #for automated images
highMagPixY = float(getBlConfig("highMagPixY"))
screenPixX = float(getBlConfig("screenPixX"))
screenPixY = float(getBlConfig("screenPixY"))
try:
unitScaling = float(getBlConfig("unitScaling"))
sampleCameraCount = float(getBlConfig("sampleCameraCount"))
except KeyError as e:
unitScaling = 1
sampleCameraCount = 4
logging.info(f"Missing unitScaling or sampleCameraCount configs, switching to default values: unitScaling: {unitScaling}, sampleCameraCount: {sampleCameraCount}")
try:
mag1ViewAngle = int(getBlConfig("mag1ViewAngle"))
except KeyError as e:
mag1ViewAngle = CAMERA_ANGLE_BEAM
logging.info(f"Missing or invalid mag1ViewAngle config, using default value {mag1ViewAngle}")
try:
mag2ViewAngle = int(getBlConfig("mag2ViewAngle"))
except KeyError as e:
mag2ViewAngle = CAMERA_ANGLE_BEAM
logging.info(f"Missing or invalid mag2ViewAngle config, using default value {mag2ViewAngle}")
try:
mag3ViewAngle = int(getBlConfig("mag3ViewAngle"))
except KeyError as e:
mag3ViewAngle = CAMERA_ANGLE_BEAM
logging.info(f"Missing or invalid mag3ViewAngle config, using default value {mag3ViewAngle}")
try:
mag4ViewAngle = int(getBlConfig("mag4ViewAngle"))
except KeyError as e:
mag4ViewAngle = CAMERA_ANGLE_BEAM
logging.info(f"Missing or invalid mag4ViewAngle config, using default value {mag4ViewAngle}")
beamlineComm = getBlConfig("beamlineComm")
screenPixCenterX = screenPixX/2.0
screenPixCenterY = screenPixY/2.0
gonioPvPrefix = getBlConfig("gonioPvPrefix")
detector_id = getBlConfig("detector_id")
det_radius = getBlConfig("detRadius")
det_type = getBlConfig("detector_type")
imgsrv_port = getBlConfig("imgsrv_port")
imgsrv_host = getBlConfig("imgsrv_host")
has_dna = int(getBlConfig("has_edna"))
has_beamline = int(getBlConfig("has_beamline"))
detectorOffline = int(getBlConfig("detector_offline"))
has_xtalview = int(getBlConfig("has_xtalview"))
camera_offset = float(getBlConfig("camera_offset"))
if (has_xtalview):
xtal_url_small = getBlConfig("xtal_url_small")
xtal_url = getBlConfig("xtal_url")
mono_mot_code = getBlConfig("mono_mot_code")
screenProtocol = getBlConfig("screen_default_protocol")
screenDist, screenEnergy, screenExptime, screenPhiend, screenPhist, screenReso, screenTransmissionPercent, screenWidth, screenbeamHeight, screenbeamWidth = getScreenDefaultParams()
beamstop_x_pvname = getBlConfig("beamstop_x_pvname")
beamstop_y_pvname = getBlConfig("beamstop_y_pvname")
varname = "DETECTOR_OFFLINE"
if varname in os.environ:
detectorOffline = int(os.environ[varname])
setBlConfig(BEAM_CHECK,1)
setBlConfig(UNMOUNT_COLD_CHECK,1)
def calc_reso(det_radius,detDistance,wave,theta):
if (detDistance == 0): #in case distance reads as 0
distance = 100.0
else:
distance = detDistance
dg2rd = math.pi / 180.0
theta_radians = float(theta) * dg2rd
theta_t = (theta_radians + atan(det_radius/float(distance)))/2
dmin_t = float(wave)/(2*(sin(theta_t)))
return float("%.2f" % dmin_t)
def distance_from_reso(det_radius,reso,wave,theta):
try:
dg2rd = math.pi / 180.0
theta_radians = float(theta) * dg2rd
dx = det_radius/(tan(2*(asin(float(wave)/(2*reso)))-theta_radians))
return float("%.2f" % dx)
except ValueError:
return 501.0 #a safe value for now
def energy2wave(e, digits=2):
if (float(e)==0.0):
return 1.0
else:
return float(f"%.{digits}f" % (EV_ANGSTROM_CONSTANT/e))
def wave2energy(w, digits=2):
if (float(w)==0.0):
return 12600.0
else:
return float(f"%.{digits}f" % (EV_ANGSTROM_CONSTANT/w))
def gonio2lab(x_gonio, y_gonio, z_gonio, omega_deg):
"""Utility function to convert gonio co-ordinates to lab co-ordinates
"""
#YL = cO*YP + sO*ZP
#ZL = -sO*YP + cO*ZP
cosO = math.cos(math.radians(omega_deg))
sinO = math.sin(math.radians(omega_deg))
y_lab = (cosO * y_gonio) + (sinO * z_gonio)
z_lab = -(sinO * y_gonio) + (cosO * z_gonio)
return x_gonio, y_lab, z_lab, omega_deg
def lab2gonio(x_lab, y_lab, z_lab, omega_deg):
"""Utility function to convert lab co-ordinates to gonio co-ordinates
"""
#YP = cO*YL - sO*ZL
#ZP = sO*YL + cO*ZL
cosO = math.cos(math.radians(omega_deg))
sinO = math.sin(math.radians(omega_deg))
y_gonio = (cosO * y_lab) - (sinO * z_lab)
z_gonio = (sinO * y_lab) + (cosO * z_lab)
return x_lab, y_gonio, z_gonio, omega_deg
def createDefaultRequest(sample_id,createVisit=True):
"""
Doesn't really create a request, just returns a dictionary
with the default parameters that can be passed to addRequesttoSample().
But note that these then get overwritten anyway, and I no longer expose them in screen params dialog
"""
sample = db_lib.getSampleByID(sample_id)
try:
propNum = sample["proposalID"]
except KeyError:
propNum = 999999
if (propNum == None):
propNum = 999999
if (propNum != getProposalID()):
setProposalID(propNum,createVisit)
screenDist, screenEnergy, screenExptime, screenPhiend, screenPhist, screenReso, screenTransmissionPercent, screenWidth, screenbeamHeight, screenbeamWidth = getScreenDefaultParams()
sampleName = str(db_lib.getSampleNamebyID(sample_id))
basePath = getBlConfig("visitDirectory")
runNum = db_lib.getSampleRequestCount(sample_id)
(puckPosition,samplePositionInContainer,containerID) = db_lib.getCoordsfromSampleID(beamline,sample_id)
request = {"sample": sample_id}
request["beamline"] = beamline
requestObj = {
"sample": sample_id,
"sweep_start": screenPhist, "sweep_end": screenPhiend,
"img_width": screenWidth,
"exposure_time": screenExptime,
"protocol": "standard",
"detDist": screenDist,
"parentReqID": -1,
"basePath": basePath,
"dataPath": getBlConfig("data_path"),
"file_prefix": sampleName,
"directory": basePath+"/" + str(getVisitName()) + "/"+sampleName+"/" + str(runNum) + "/" +db_lib.getContainerNameByID(containerID)+"_"+str(samplePositionInContainer+1)+"/",
"file_number_start": 1,
"energy":screenEnergy,
"wavelength": energy2wave(screenEnergy),
"resolution": screenReso,
"slit_height": screenbeamHeight, "slit_width": screenbeamWidth,
"attenuation": screenTransmissionPercent,
"visit_name": getVisitName(),
"detector": os.environ["DETECTOR_NAME"],
"beamline": os.environ["BEAMLINE_ID"],
"pos_x": -999, "pos_y": 0, "pos_z": 0, "pos_type": 'A', "gridStep": 20}
request["request_obj"] = requestObj
return request
def getScreenDefaultParams():
screenPhist = float(getBlConfig( "screen_default_phist"))
screenPhiend = float(getBlConfig( "screen_default_phi_end"))
screenWidth = float(getBlConfig( "screen_default_width"))
screenDist = float(getBlConfig( "screen_default_dist"))
screenExptime = float(getBlConfig( "screen_default_time"))
screenReso = float(getBlConfig( "screen_default_reso"))
screenWave = float(getBlConfig( "screen_default_wave"))
screenEnergy = float(getBlConfig( "screen_default_energy"))
screenbeamWidth = float(getBlConfig( "screen_default_beamWidth"))
screenbeamHeight = float(getBlConfig( "screen_default_beamHeight"))
screenTransmissionPercent = float(getBlConfig( "stdTrans"))
return screenDist, screenEnergy, screenExptime, screenPhiend, screenPhist, screenReso, screenTransmissionPercent, screenWidth, screenbeamHeight, screenbeamWidth
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 create_filename(prefix,number):
if (detector_id == "EIGER-16"):
tmp_filename = findOneH5Master(prefix)
else:
tmp_filename = "%s_%05d.cbf" % (prefix,int(number))
if (prefix[0] != "/"):
cwd = getBlConfig("visitDirectory")
filename = "%s/%s" % (cwd,tmp_filename)
else:
filename = tmp_filename
return filename
def findOneH5Master(prefix):
comm_s = "ls " + prefix + "*_master.h5 | head -1"
masterFilename = os.popen(comm_s).read()[0:-1]
return masterFilename
def readPVDesc():
global beamline_designation,motor_dict,soft_motor_list,scan_list,counter_dict
envname = "EPICS_BEAMLINE_INFO"
try:
dbfilename = os.environ[envname]
except KeyError:
logger.info(envname + " not defined. Defaulting to epx.db.")
dbfilename = "epx.db"
if (os.path.exists(dbfilename) == 0):
error_msg = "EPICS BEAMLINE INFO %s does not exist.\n Program exiting." % dbfilename
logger.info(error_msg)
sys.exit()
else:
dbfile = open(dbfilename,'r')
line = dbfile.readline()
line = dbfile.readline()
beamline_designation = line[:-1]
line = dbfile.readline()
i = 0
while(1):
line = dbfile.readline()
if (line == ""):
break
else:
line = line[:-1]
if (line == "#virtual motors"):
break
else:
motor_inf = line.split()
motor_dict[motor_inf[1]] = beamline_designation + motor_inf[0]
while(1):
line = dbfile.readline()
if (line == ""):
break
else:
line = line[:-1]
if (line == "#control PVs"):
break
else:
motor_inf = line.split()
soft_motor_list.append(beamline_designation + motor_inf[0])
motor_dict[motor_inf[1]] = beamline_designation + motor_inf[0]
while(1):
line = dbfile.readline()
if (line == ""):
break
else:
line = line[:-1]
if (line == "#scanned motors"):
break
else:
inf = line.split()
pvLookupDict[inf[1]] = beamline_designation + inf[0]
while(1):
line = dbfile.readline()
if (line == ""):
break
else:
line = line[:-1]
if (line == "#counters"):
break
else:
scan_list.append(beamline_designation + line + "scanParms")
line = dbfile.readline()
counter_inf = line.split()
counter_dict[counter_inf[1]] = beamline_designation + counter_inf[0]
def createVisitNameRaw(proposalName, maxNumber=None):
if maxNumber:
number = maxNumber + 1
else:
number = 1
return f'mx{proposalName}-{number}', number
def createVisitName(proposalName, maxNumber=None):
return createVisitNameRaw(proposalName, maxNumber)
def setProposalID(proposalID,createVisit=True): # TODO JA proposalID implies a database ID, which it is not (just proposal number). Misleading
if (getProposalID() != proposalID): #proposalID changed - create a new visit.
logger.info("you changed proposals! " + str(proposalID))
logger.info('ignoring createVisit for now - ISPyB required to properly account for visit numbers')
try:
visitName, visitNum = createVisitName(proposalID)
db_lib.setBeamlineConfigParam(beamline,"proposal",proposalID)
except Exception as e:
visitName = "999999-1234"
logger.error("error in set proposal. Error: %s" % e)
setVisitName(visitName)
def getProposalID():
return getBlConfig("proposal")
def getVisitName():
return getBlConfig("visitName")
def setVisitName(visitName):
return db_lib.setBeamlineConfigParam(beamline,"visitName",visitName)