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add code to call spotfinder script #239

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add code to call spotfinder script #239

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889e966
add code to call spotfinder script
JunAishima Oct 6, 2022
3ad43dd
remove unnecessary extra snapshot saving
JunAishima Oct 11, 2022
9202e20
handle raster separately for number of images for ISPyB
JunAishima Oct 12, 2022
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5 changes: 5 additions & 0 deletions ispybLib.py
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Original file line number Diff line number Diff line change
Expand Up @@ -347,6 +347,11 @@ def createDataCollection(directory, filePrefix, jpegImageFilename, params, reque
params['datacollection_number'] = request_obj['runNum']
if request_obj['img_width'] > 0:
params['n_images'] = int(round((request_obj['sweep_end'] - request_obj['sweep_start']) / request_obj['img_width']))
if request_obj['protocol'] == "raster":
row_defs = request_obj['rasterDef']['rowDefs']
num_rows = len(row_defs)
num_images_per_row = row_defs[0]['numsteps']
params['n_images'] = int(num_images_per_row * num_rows)
else:
params['n_images'] = 1 # stills mode
params['exp_time'] = request_obj['exposure_time']
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1 change: 0 additions & 1 deletion lsdcGui.py
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Expand Up @@ -3969,7 +3969,6 @@ def takeRasterSnapshot(self,rasterReq):
jpegImageThumbFilename = jpegImagePrefix+"t.jpg"
logger.info("saving raster snapshot")
self.saveVidSnapshotCB("Raster Result from sample " + str(rasterReq["request_obj"]["file_prefix"]),useOlog=False,reqID=rasterReq["uid"],rasterHeatJpeg=jpegImageFilename)
self.saveVidSnapshotCB("Raster Result from sample " + str(rasterReq["request_obj"]["file_prefix"]),useOlog=False,reqID=rasterReq["uid"],rasterHeatJpeg=jpegImageFilename)
try:
ispybLib.insertRasterResult(rasterReq,visitName)
except Exception as e:
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20 changes: 4 additions & 16 deletions runSpotFinder4syncW.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,25 +29,13 @@
numimages = round(range_degrees/img_width)
numstart = reqObj["file_number_start"]

dialsComm = getBlConfig("dialsComm")
dialsTuneLowRes = getBlConfig(RASTER_TUNE_LOW_RES)
dialsTuneHighRes = getBlConfig(RASTER_TUNE_HIGH_RES)
dialsTuneIceRingFlag = getBlConfig(RASTER_TUNE_ICE_RING_FLAG)
dialsTuneResoFlag = getBlConfig(RASTER_TUNE_RESO_FLAG)
dialsTuneIceRingWidth = getBlConfig(RASTER_TUNE_ICE_RING_WIDTH)
if (dialsTuneIceRingFlag):
iceRingParams = " ice_rings.filter=true ice_rings.width=" + str(dialsTuneIceRingWidth)
else:
iceRingParams = ""
if (dialsTuneResoFlag):
resoParams = " d_min=" + str(dialsTuneLowRes) + " d_max=" + str(dialsTuneHighRes)
else:
resoParams = ""
dialsCommWithParams = dialsComm + resoParams + iceRingParams
print(dialsCommWithParams)
for i in range (numstart,numimages,10):
comm_s = f"ssh -q {node} \"{os.environ['MXPROCESSINGSCRIPTSDIR']}eiger2cbf.sh {request_id} {i} {i} 0 {seqNum}\""
os.system(comm_s)
# now handle the cbfs with dials
# prerequisite: dials.spot_server running on the host where the processing is to occur, owned by the user who runs LSDC server
comm_s = f"ssh -q {node} \"{os.environ['MXPROCESSINGSCRIPTSDIR']}dials_spotfind.sh {request_id} 0 {seqNum} per_image\""
print(comm_s)

retry = 3
localDialsResultDict = {}
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