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Removed NYX related code #421

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87ada0d
Removed NYX related code
vshekar May 23, 2025
ad9d8a9
Fixed syntax errors suggested by copilot
vshekar Jan 14, 2026
13030ce
Changed local variables to instance variables in control_main
vshekar Jan 14, 2026
7bfa0c0
Removed commented out code
vshekar Jan 14, 2026
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8 changes: 1 addition & 7 deletions beamline_support.py
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Original file line number Diff line number Diff line change
Expand Up @@ -319,14 +319,8 @@ def read_db():

def init_motors():
global motor_channel_dict
md2_motors = ["omega","sampleX","sampleY","sampleZ", "finex", "finey", "finez"]

for key in list(motor_dict.keys()):
if beamline_designation == "XF:19ID" and key in md2_motors:
from mxbluesky.devices.md2 import MD2Positioner
motor_channel_dict[motor_dict[key]] = MD2Positioner(motor_dict[key],name = key)
else:
motor_channel_dict[motor_dict[key]] = EpicsMotor(motor_dict[key],name = key)
motor_channel_dict[motor_dict[key]] = EpicsMotor(motor_dict[key],name = key)


def initControlPVs():
Expand Down
10 changes: 0 additions & 10 deletions bin/lsdcGui_nyx
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This file was deleted.

14 changes: 0 additions & 14 deletions bin/lsdcServer_nyx.cmd
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This file was deleted.

19 changes: 6 additions & 13 deletions config_params.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,40 +85,36 @@ class OnMountAvailOptions(Enum):
DETECTOR_OBJECT_TYPE_OPHYD = "ophyd" # instantiated in start_bs, using Bluesky scans
DETECTOR_OBJECT_TYPE = "detectorObjectType"

DETECTOR_SAFE_DISTANCE = {"fmx": 200.0, "amx": 180.0, "nyx": 200.0}
DETECTOR_SAFE_DISTANCE = {"fmx": 200.0, "amx": 180.0}
GOVERNOR_TIMEOUT = 120 # seconds for a governor move

DEWAR_SECTORS = {'amx':8, 'fmx':8, 'nyx':8}
PUCKS_PER_DEWAR_SECTOR = {'amx':3, 'fmx':3, 'nyx':3}
DEWAR_SECTORS = {'amx':8, 'fmx':8}
PUCKS_PER_DEWAR_SECTOR = {'amx':3, 'fmx':3}

cryostreamTempPV = {"amx": "XF:17ID1:CS700:TEMP", "fmx": "XF:17ID2:CS700:TEMP", "nyx":"XF:19ID2:CS700:TEMP"}
cryostreamTempPV = {"amx": "XF:17ID1:CS700:TEMP", "fmx": "XF:17ID2:CS700:TEMP"}

VALID_EXP_TIMES = {
"amx": {"min": 0.005, "max": 1, "digits": 3},
"fmx": {"min": 0.01, "max": 10, "digits": 3},
"nyx": {"min": 0.002, "max": 10, "digits": 4},
}
VALID_DET_DIST = {
"amx": {"min": 100, "max": 500, "digits": 3},
"fmx": {"min": 137, "max": 2000, "digits": 2},
"nyx": {"min": 100, "max": 500, "digits": 3},
}
VALID_TOTAL_EXP_TIMES = {
"amx": {"min": 0.005, "max": 300, "digits": 3},
"fmx": {"min": 0.01, "max": 300, "digits": 3},
"nyx": {"min": 0.01, "max": 1000, "digits": 3},
}
VALID_PREFIX_LENGTH = 25 # TODO centralize with spreadsheet validation?
VALID_PREFIX_NAME = "[0-9a-zA-Z-_]{0,%s}" % VALID_PREFIX_LENGTH
VALID_TRANSMISSION = {
"amx": {"min": 0.001, "max": 1.0, "digits": 3},
"fmx": {"min": 0.001, "max": 1.0, "digits": 3},
"nyx": {"min": 0.001, "max": 0.999, "digits": 3},
}

MINIMUM_RASTER_SIZE = {"amx": 6, "fmx": 6, "nyx": 2}
MINIMUM_RASTER_SIZE = {"amx": 6, "fmx": 6}

LSDC_SERVICE_USERS = ("lsdc-amx", "lsdc-fmx", "lsdc-nyx")
LSDC_SERVICE_USERS = ("lsdc-amx", "lsdc-fmx")
IS_STAFF = (
True
if os.environ.get("STAFF_GROUP") is not None and os.environ["STAFF_GROUP"] in [grp.getgrgid(g).gr_name for g in os.getgroups()]
Expand Down Expand Up @@ -154,8 +150,6 @@ def get_text(cls, enum_value):
}
return text_values.get(enum_value, "\n(Unknown State)")

OPHYD_COLLECTIONS = {"amx": False, "fmx": False, "nyx": True}

class CollectionProtocols(str, Enum):
STANDARD = "standard"
RASTER = "raster"
Expand All @@ -176,7 +170,6 @@ def get_beamline_options(cls, beamline):
cls.STEP_RASTER, cls.STEP_VECTOR, cls.MULTI_COL, cls.CHARACTERIZE,
cls.EDNA_COL)
beamline_options = {
"nyx": (cls.STANDARD, cls.RASTER, cls.VECTOR),
"amx": all_protocols,
"fmx": all_protocols
}
Expand Down
193 changes: 58 additions & 135 deletions daq_lib.py
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Original file line number Diff line number Diff line change
Expand Up @@ -659,60 +659,9 @@ def collectData(currentRequest):
sweep_start = reqObj["sweep_start"]
daq_macros.setTrans(attenuation)

if (reqObj["protocol"] in (CollectionProtocols.CHARACTERIZE, CollectionProtocols.EDNA_COL)):
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["uid"]) # because for testing I keep running the same request. Probably not in usual use.
results = None
for i in range(0,len(resultsList)):
if (resultsList[i]['result_type'] == 'characterizationStrategy'):
results = resultsList[i]
break
if (results != None):

strategyResults = results["result_obj"]["strategy"]
stratStart = strategyResults["start"]
stratEnd = strategyResults["end"]
stratWidth = strategyResults["width"]
stratExptime = strategyResults["exptime"]
stratTrans = strategyResults["transmission"]
stratDetDist = strategyResults["detDist"]
sampleID = currentRequest["sample"]
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["attenuation"] = stratTrans
newReqObj["detDist"] = stratDetDist
newReqObj["directory"] = data_directory_name
newReqObj["pos_x"] = beamline_lib.motorPosFromDescriptor("sampleX")
newReqObj["pos_y"] = beamline_lib.motorPosFromDescriptor("sampleY")
newReqObj["pos_z"] = beamline_lib.motorPosFromDescriptor("sampleZ")
newReqObj["fastDP"] = True # this is where you might want a "new from old" request to carry over stuff like this.
newReqObj["fastEP"] = reqObj["fastEP"]
newReqObj["dimple"] = reqObj["dimple"]
newReqObj["xia2"] = reqObj["xia2"]
runNum = db_lib.incrementSampleRequestCount(sampleID)
newReqObj["runNum"] = runNum
newStratRequest = db_lib.addRequesttoSample(sampleID,newReqObj["protocol"],daq_utils.owner,newReqObj,priority=0,proposalID=daq_utils.getProposalID())
if (reqObj["protocol"] == CollectionProtocols.EDNA_COL):
logger.info("new strat req = ")
logger.info(newStratRequest)
db_lib.updatePriority(currentRequest["uid"],-1)
refreshGuiTree()
collectData(db_lib.getRequestByID(newStratRequest))
return 1
else: #standard
logger.info("moving omega to start " + str(time.time()))
if daq_utils.beamline == "nyx":
direction = (sweep_end - sweep_start) / abs(sweep_end - sweep_start)
beamline_lib.mvaDescriptor("omega",sweep_start - direction*0.05)
else:
beamline_lib.mvaDescriptor("omega",sweep_start)
collect_detector_seq_hw(sweep_start,range_degrees,img_width,exposure_period,file_prefix,data_directory_name,file_number_start,currentRequest)
logger.info("moving omega to start " + str(time.time()))
beamline_lib.mvaDescriptor("omega",sweep_start)
collect_detector_seq_hw(sweep_start,range_degrees,img_width,exposure_period,file_prefix,data_directory_name,file_number_start,currentRequest)
try:
if (logMe) and prot == CollectionProtocols.RASTER:
logMxRequestParams(currentRequest,wait=False)
Expand All @@ -729,50 +678,49 @@ def collectData(currentRequest):
if reqObj["protocol"] in (CollectionProtocols.STANDARD, CollectionProtocols.VECTOR, CollectionProtocols.RASTER):
send_kafka_message(topic=f'{daq_utils.beamline}.lsdc.documents', event='stop', uuid=currentRequest['uid'], protocol=reqObj["protocol"])
if prot in (CollectionProtocols.VECTOR, CollectionProtocols.STANDARD, CollectionProtocols.STEP_VECTOR):
if daq_utils.beamline != "nyx":
seqNum = flyer.detector.cam.sequence_id.get()
comm_s = os.environ["LSDCHOME"] + "/runSpotFinder4syncW.py " + data_directory_name + " " + file_prefix + " " + str(currentRequest["uid"]) + " " + str(seqNum) + " " + str(currentIspybDCID)+ "&"
logger.info(f"NOT running spotfinding for per-image analysis in Synchweb: {comm_s}")
#os.system(comm_s)
filename = f"{data_directory_name}/{file_prefix}_{seqNum}_master.h5"
logger.info(f"Checking integrity of {filename}")
timeout_index = 0
while not validation.validate_master_HDF5_file(filename):
timeout_index += 1
time.sleep(3)
if timeout_index > 15:
logger.error(f"Unable to verify master file after {timeout_index} tries, not proceeding with processing")
return
if img_width > 0: #no dataset processing in stills mode
if (reqObj["fastDP"]):
if (reqObj["fastEP"]):
fastEPFlag = 1
else:
fastEPFlag = 0
if (reqObj["dimple"]):
dimpleFlag = 1
else:
dimpleFlag = 0
nodeName = "fastDPNode" + str((fastDPNodeCounter%fastDPNodeCount)+1)
fastDPNodeCounter+=1
node = getBlConfig(nodeName)
dimpleNode = getBlConfig("dimpleNode")
if (daq_utils.detector_id == "EIGER-16"):
seqNum = flyer.detector.cam.sequence_id.get()
comm_s = os.environ["LSDCHOME"] + "/runFastDPH5.py " + data_directory_name + " " + str(seqNum) + " " + str(currentRequest["uid"]) + " " + str(fastEPFlag) + " " + node + " " + str(dimpleFlag) + " " + dimpleNode + " " + str(currentIspybDCID)+ "&"
else:
comm_s = os.environ["LSDCHOME"] + "/runFastDP.py " + data_directory_name + " " + file_prefix + " " + str(file_number_start) + " " + str(int(round(range_degrees/img_width))) + " " + str(currentRequest["uid"]) + " " + str(fastEPFlag) + " " + node + " " + str(dimpleFlag) + " " + dimpleNode + "&"
logger.info(f'Running fastdp command: {comm_s}')
if daq_utils.beamline in ("amx", "fmx"):
visitName = daq_utils.getVisitName()
if (not os.path.exists(visitName + "/fast_dp_dir")) or subprocess.run(['pgrep', '-f', 'loop-fdp-dple-populate'], stdout=subprocess.PIPE).returncode == 1: # for pgrep, return of 1 means string not found
os.system("killall -KILL loop-fdp-dple-populate")
logger.info('starting fast dp result gathering script')
os.system("cd " + visitName + ";${LSDCHOME}/bin/loop-fdp-dple-populate.sh&")
os.system(comm_s)
if (reqObj["xia2"]):
comm_s = f"ssh -q xf17id2-srv1 \"{os.environ['MXPROCESSINGSCRIPTSDIR']}xia2.sh {currentRequest['uid']} \"&"
os.system(comm_s)
seqNum = flyer.detector.cam.sequence_id.get()
comm_s = os.environ["LSDCHOME"] + "/runSpotFinder4syncW.py " + data_directory_name + " " + file_prefix + " " + str(currentRequest["uid"]) + " " + str(seqNum) + " " + str(currentIspybDCID)+ "&"
logger.info(f"NOT running spotfinding for per-image analysis in Synchweb: {comm_s}")
#os.system(comm_s)
filename = f"{data_directory_name}/{file_prefix}_{seqNum}_master.h5"
logger.info(f"Checking integrity of {filename}")
timeout_index = 0
while not validation.validate_master_HDF5_file(filename):
timeout_index += 1
time.sleep(3)
if timeout_index > 15:
logger.error(f"Unable to verify master file after {timeout_index} tries, not proceeding with processing")
return
if img_width > 0: #no dataset processing in stills mode
if (reqObj["fastDP"]):
if (reqObj["fastEP"]):
fastEPFlag = 1
else:
fastEPFlag = 0
if (reqObj["dimple"]):
dimpleFlag = 1
else:
dimpleFlag = 0
nodeName = "fastDPNode" + str((fastDPNodeCounter%fastDPNodeCount)+1)
fastDPNodeCounter+=1
node = getBlConfig(nodeName)
dimpleNode = getBlConfig("dimpleNode")
if (daq_utils.detector_id == "EIGER-16"):
seqNum = flyer.detector.cam.sequence_id.get()
comm_s = os.environ["LSDCHOME"] + "/runFastDPH5.py " + data_directory_name + " " + str(seqNum) + " " + str(currentRequest["uid"]) + " " + str(fastEPFlag) + " " + node + " " + str(dimpleFlag) + " " + dimpleNode + " " + str(currentIspybDCID)+ "&"
else:
comm_s = os.environ["LSDCHOME"] + "/runFastDP.py " + data_directory_name + " " + file_prefix + " " + str(file_number_start) + " " + str(int(round(range_degrees/img_width))) + " " + str(currentRequest["uid"]) + " " + str(fastEPFlag) + " " + node + " " + str(dimpleFlag) + " " + dimpleNode + "&"
logger.info(f'Running fastdp command: {comm_s}')
if daq_utils.beamline in ("amx", "fmx"):
visitName = daq_utils.getVisitName()
if (not os.path.exists(visitName + "/fast_dp_dir")) or subprocess.run(['pgrep', '-f', 'loop-fdp-dple-populate'], stdout=subprocess.PIPE).returncode == 1: # for pgrep, return of 1 means string not found
os.system("killall -KILL loop-fdp-dple-populate")
logger.info('starting fast dp result gathering script')
os.system("cd " + visitName + ";${LSDCHOME}/bin/loop-fdp-dple-populate.sh&")
os.system(comm_s)
if (reqObj["xia2"]):
comm_s = f"ssh -q xf17id2-srv1 \"{os.environ['MXPROCESSINGSCRIPTSDIR']}xia2.sh {currentRequest['uid']} \"&"
os.system(comm_s)

logger.info('processing should be triggered')
db_lib.updatePriority(currentRequest["uid"],-1)
Expand Down Expand Up @@ -810,28 +758,18 @@ def collect_detector_seq_hw(sweep_start,range_degrees,image_width,exposure_perio

logger.info("collect %f degrees for %f seconds %d images exposure_period = %f exposure_time = %f" % (range_degrees,range_seconds,number_of_images,exposure_period,exposure_time))

if OPHYD_COLLECTIONS[daq_utils.beamline]:
logger.info("ophyd collections enabled")
if (protocol == CollectionProtocols.STANDARD):
RE(daq_macros.standard_plan_wrapped(currentRequest))
elif (protocol == CollectionProtocols.VECTOR):
RE(daq_macros.vector_plan_wrapped(currentRequest))
else:
if (protocol in (CollectionProtocols.STANDARD, CollectionProtocols.CHARACTERIZE,
CollectionProtocols.EDNA_COL, CollectionProtocols.BURN)):
logger.info("vectorSync " + str(time.time()))
daq_macros.vectorSync()
logger.info("zebraDaq " + str(time.time()))

vector_params = daq_macros.gatherStandardVectorParams()
logger.debug(f"vector_params: {vector_params}")
RE(daq_macros.standard_zebra_plan(flyer,angleStart,number_of_images,range_degrees,image_width,exposure_period,file_prefix_minus_directory,data_directory_name,file_number, vector_params, file_prefix_minus_directory))
elif (protocol == CollectionProtocols.VECTOR):
RE(daq_macros.vectorZebraScan(currentRequest))
elif (protocol == CollectionProtocols.STEP_VECTOR):
daq_macros.vectorZebraStepScan(currentRequest)
else:
pass
if (protocol in (CollectionProtocols.STANDARD, CollectionProtocols.BURN)):
logger.info("vectorSync " + str(time.time()))
daq_macros.vectorSync()
logger.info("zebraDaq " + str(time.time()))

vector_params = daq_macros.gatherStandardVectorParams()
logger.debug(f"vector_params: {vector_params}")
RE(daq_macros.standard_zebra_plan(flyer,angleStart,number_of_images,range_degrees,image_width,exposure_period,file_prefix_minus_directory,data_directory_name,file_number, vector_params, file_prefix_minus_directory))
elif (protocol == CollectionProtocols.VECTOR):
RE(daq_macros.vectorZebraScan(currentRequest))
elif (protocol == CollectionProtocols.STEP_VECTOR):
daq_macros.vectorZebraStepScan(currentRequest)
return


Expand Down Expand Up @@ -884,21 +822,6 @@ def center_on_click(x,y,fovx,fovy,source="screen",maglevel=0,jog=0,viewangle=daq
#source=screen = from screen click, otherwise from macro with full pixel dimensions
#viewangle=daq_utils.CAMERA_ANGLE_BEAM, default camera angle is in-line with the beam

if daq_utils.beamline == "nyx":
logger.info("center_on_click: %s" % str((x,y)))
lsdc_x = daq_utils.screenPixX
lsdc_y = daq_utils.screenPixY
md2_x = getPvDesc("md2CenterPixelX") * 2
md2_y = getPvDesc("md2CenterPixelY") * 2
scale_x = md2_x / lsdc_x
scale_y = md2_y / lsdc_y
x = x * scale_x
y = y * scale_y
str_coords = f'{x} {y}'
logger.info(f'center_on_click: {str_coords}')
setPvDesc("MD2C2C", str_coords)
return

if (getBlConfig('robot_online')): #so that we don't move things when robot moving?
robotGovState = (getPvDesc("robotSaActive") or getPvDesc("humanSaActive"))
if (not robotGovState):
Expand Down
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