def reduceSANS(sampleSANS,
sampleTRANS=None,
canSANS=None,
canTRANS=None,
EBTRANS=None,
maskfile=None,
inst=inst,
cycle=cycle,
wavs=wavs,
outputdir=''):
# This is the function that runs everything using the sans instrument command interface
# by default the reduction will just reduce the sample sans with no transmission.
setupReduction(sampleSANS,
sampleTRANS=sampleTRANS,
canSANS=canSANS,
canTRANS=canTRANS,
EBTRANS=EBTRANS,
maskfile=maskfile,
inst=inst,
cycle=cycle)
wkspnames = []
# Perform the full reduction listed in the userfile
wksp1d = ici.WavRangeReduction(None, None, ici.DefaultTrans)
SaveNXcanSAS(wksp1d, os.path.join(outputdir, wksp1d + '_autoreduced.h5'))
SaveRKH(wksp1d, os.path.join(outputdir, wksp1d + '_autoreduced.dat'))
wkspnames.append(wksp1d)
# the order of 2d then everything else is importand for the multiplot to work
# perform the full 2d reduction in the user file
ici.Set2D()
#ici.WavRangeReduction(None, None, ici.DefaultTrans)
wksp2d = ici.WavRangeReduction(None, None, ici.DefaultTrans)
#SaveNexus(mtd["{}rear_2D_0.1_12.0".format(run)],join(base_dir,"{}_2D.nxs".format(run)))
SaveNXcanSAS(wksp2d, os.path.join(outputdir, wksp2d + '_autoreduced.h5'))
# Set up the figure for the 6 plots combined
fig, axes = plt.subplots(2,
3,
figsize=[12.0, 8.0],
num='Multiplot',
subplot_kw={'projection': 'mantid'})
# change the fontsize for the legends
plt.rcParams['legend.fontsize'] = 'x-small'
# plot the 2d data seperately
plot2Ddata(wksp2d, outputdir=outputdir, fig=fig, axes=axes[0, 2])
# check that the transmission workspaces exist and plot.
transwksps = []
if mtd.doesExist(wksp1d.replace("rear_1D", "trans_Sample")):
transwksps.append(wksp1d.replace("rear_1D", "trans_Sample"))
if mtd.doesExist(wksp1d.replace("rear_1D", "trans_Can")):
transwksps.append(wksp1d.replace("rear_1D", "trans_Can"))
if mtd.doesExist(wksp1d.replace("rear_1D", "trans_Sample_unfitted")):
transwksps.append(wksp1d.replace("rear_1D", "trans_Sample_unfitted"))
if mtd.doesExist(wksp1d.replace("rear_1D", "trans_Can_unfitted")):
transwksps.append(wksp1d.replace("rear_1D", "trans_Can_unfitted"))
if len(transwksps) > 0:
plotTransmissions(transwksps, fig=fig, axes=axes[0, 0])
else:
plotTransmissions(transwksps,
'No Transmission Data Found',
fig=fig,
axes=axes[0, 0])
# Now perform the overlap reduction with different wavelength ranges
ici.Set1D()
for i in range(len(wavs) - 1):
wksp1d = ici.WavRangeReduction(wavs[i], wavs[i + 1], False)
wkspnames.append(wksp1d)
#SaveNexus(mtd["{}rear_1D_0.9_12.5".format(run)],join(base_dir,"{}_1D.nxs".format(run)))
plot1Ddata(wkspnames,
fig=fig,
axes1=axes[1, 2],
axes2=axes[1, 0],
axes3=axes[0, 1])
# reset everything for the sector reduction
wkspnames = []
setupReduction(sampleSANS,
sampleTRANS=sampleTRANS,
canSANS=canSANS,
canTRANS=canTRANS,
EBTRANS=EBTRANS,
maskfile=maskfile,
inst=inst,
cycle=cycle)
# perform reduction of 4 sectors to check for anisotropy
ici.SetPhiLimit(0.0, 180.0, use_mirror=False)
wksp1d = ici.WavRangeReduction(None, None, ici.DefaultTrans)
RenameWorkspace(wksp1d, wksp1d + '_top')
wkspnames.append(wksp1d + '_top')
ici.SetPhiLimit(180.0, 360.0, use_mirror=False)
wksp1d = ici.WavRangeReduction(None, None, ici.DefaultTrans)
RenameWorkspace(wksp1d, wksp1d + '_bottom')
wkspnames.append(wksp1d + '_bottom')
ici.SetPhiLimit(90.0, 270.0, use_mirror=False)
wksp1d = ici.WavRangeReduction(None, None, ici.DefaultTrans)
RenameWorkspace(wksp1d, wksp1d + '_left')
wkspnames.append(wksp1d + '_left')
ici.SetPhiLimit(-90.0, 90.0, use_mirror=False)
wksp1d = ici.WavRangeReduction(None, None, ici.DefaultTrans)
RenameWorkspace(wksp1d, wksp1d + '_right')
wkspnames.append(wksp1d + '_right')
plot1Dsectors(wkspnames, fig=fig, axes=axes[1, 1])
fig.tight_layout() #pad=0.4, w_pad=0.5, h_pad=1.0)
if os.path.exists(outputdir):
print(outputdir)
print(os.path.join(outputdir, inst + '{:08d}.png'.format(sampleSANS)))
fig.savefig(
os.path.join(outputdir, inst + '{:08d}.png'.format(sampleSANS)))
def analyse(data_table,
masks,
output_file,
show_fits=False,
show_quality=False):
"""
Analyse a set of combined Sans and Semsans measurements.
The result will be a set of workspaces with the Semsans data
and a csv file that can be loaded into the batch sans interface
to load the sans data.
Parameters
----------
data_table
The name of WorkspaceTable with the runs that need to be analysed. This
table should be generated by the get_log function.
masks
A list of strings containing the filenames of the masks for the
individual tubes used in the semsans polarisation calculation
output_file
Where to save the CSV file that will generate the SANS runs
show_fits
Whether to show the individual tube fits used to calculate the spin echo
length. Defaults to False
show_quality
Whether to show the quality of the linear fit of the precession
frequencies used to calculate the spin echo length. Defaults to False
"""
if "Full_Blank" not in mtd.getObjectNames():
int3samples(table_to_run(mtd["metadata_Full_Blank_runs"]),
"Full_Blank", masks)
const = sel_const(
[mtd["Full_Blank_{}".format(tube)] for tube, _ in enumerate(masks)],
show_fits=show_fits,
show_quality=show_quality)
k = data_table[9:-5]
runs = table_to_run(mtd[data_table])
for run in runs:
get_shimed(run.number, dirname(output_file))
get_shimed(run.trans, dirname(output_file))
get_shimed(run.csans, dirname(output_file))
get_shimed(run.ctrans, dirname(output_file))
get_shimed(run.direct, dirname(output_file))
semsans_ws = "{}_hours_{:0.02f}".format(
k, (run.start - runs[0].start).seconds / 3600.0)
int3samples([run], semsans_ws, masks)
# DeleteWorkspace("{}_sans_nxs".format(run.number))
norm(semsans_ws, "Full_Blank", masks)
sel(semsans_ws + "_norm", const)
DeleteWorkspaces([semsans_ws, semsans_ws + "_Norm"])
with open(output_file, "w") as outfile:
framework = "sample_sans,{}-add," \
"sample_trans,{}-add," \
"sample_direct_beam,{}-add,"\
"can_sans,{}-add,"\
"can_trans,{}-add,"\
"can_direct_beam,{}-add,"\
"output_as,{}_hours_{:0.2f}\n"
for idx, run in enumerate(runs):
outfile.write(
framework.format(run.number, run.trans, run.direct, run.csans,
run.ctrans, run.direct, k,
(run.start - runs[0].start).seconds / 3600.0))
import sans.command_interface.ISISCommandInterface as ici
ici.Clean()
ici.LARMOR()
ici.MaskFile(
r"\\isis\inst$\NDXLARMOR\User\Users\Masks\USER_Edler_171B_a2_8mm_SEMSANS_r20287.txt"
)
ici.BatchReduce(output_file, format=".nxs", verbose=True)
def setupReduction(sampleSANS,
sampleTRANS=None,
canSANS=None,
canTRANS=None,
EBTRANS=None,
maskfile=None,
inst=inst,
cycle=cycle):
# Helper to setup the reduction so that it can be reset for the sector plots easily.
# set the search path folders needed.
setDataSearchPath()
# initial 1d reduction
ici.Clean()
ici.UseCompatibilityMode()
if inst == "LARMOR":
ici.LARMOR()
else:
ici.LARMOR()
ici.Set1D()
if platform == "linux" or platform == "linux2":
prefix = "/archive"
else:
prefix = "//isis/inst$"
if len(maskfile) > 0:
#ici.MaskFile("/mnt/ceph/auxiliary/sans/Larmor/Masks/"+maskfile)
ici.MaskFile(prefix + "/NDX" + inst + "/User/Users/Masks/" + maskfile)
else:
print('No Mask File Defined')
return
# assign the sample SANS run
ici.AssignSample(prefix + "/NDX" + inst + "/Instrument/data/cycle_" +
cycle + "/" + inst + "{:08d}.nxs".format(sampleSANS))
titleoption = 0
# if a can has been specified assign it
if canSANS is not None:
ici.AssignCan(prefix + "/NDX" + inst + "/Instrument/data/cycle_" +
cycle + "/" + inst + "{:08d}.nxs".format(canSANS))
titleoption += 1
# if a sample TRANS has been specified check that the empty beam has too and assign
if sampleTRANS is not None and EBTRANS is not None:
TRsam = prefix + "/NDX" + inst + "/Instrument/data/cycle_" + cycle + "/" + inst + "{:08d}.nxs".format(
sampleTRANS)
TREB = prefix + "/NDX" + inst + "/Instrument/data/cycle_" + cycle + "/" + inst + "{:08d}.nxs".format(
EBTRANS)
print(TRsam)
print(TREB)
ici.TransmissionSample(TRsam, TREB)
titleoption += 1
# if a can TRANS has been specified check that the empty beam has too and assign
if canTRANS is not None and EBTRANS is not None:
TRcan = prefix + "/NDX" + inst + "/Instrument/data/cycle_" + cycle + "/" + inst + "{:08d}.nxs".format(
canTRANS)
TREB = prefix + "/NDX" + inst + "/Instrument/data/cycle_" + cycle + "/" + inst + "{:08d}.nxs".format(
EBTRANS)
print(TRcan)
print(TREB)
ici.TransmissionCan(TRcan, TREB)
titleoption += 1
if titleoption == 0:
titlewarning = ''
elif titleoption == 1:
titlewarning = ''
elif titleoption == 2:
titlewarning = ''
elif titleoption == 3:
titlewarning = ''
return titlewarning