def get_vanadium(run_number, npy=False):
"""
Pre-process vanadium only the first time it's used
"""
vanadiums = sorted(int(n.replace('HB2C_', '').replace('.nxs.h5', ''))
for n in os.listdir('/HFIR/HB2C/shared/Vanadium')
if 'HB2C_' in n and '.nxs.h5' in n)
van_run_number = vanadiums[np.searchsorted(vanadiums, run_number, side='right')-1]
upstream_van_file = '/HFIR/HB2C/shared/Vanadium/HB2C_{}.nxs.h5'.format(van_run_number)
if npy:
npy_van_file = '/HFIR/HB2C/shared/autoreduce/vanadium/HB2C_{}.npy'.format(van_run_number)
if os.path.exists(npy_van_file):
return np.load(npy_van_file)
else:
with h5py.File(upstream_van_file, 'r') as f:
bc = np.zeros((512*480*8))
for b in range(8):
bc += np.bincount(f['/entry/bank'+str(b+1)+'_events/event_id'].value,
minlength=512*480*8)
bc = bc.reshape((480*8, 512))
bc = (bc[::4, ::4] + bc[1::4, ::4] + bc[2::4, ::4] + bc[3::4, ::4]
+ bc[::4, 1::4] + bc[1::4, 1::4] + bc[2::4, 1::4] + bc[3::4, 1::4]
+ bc[::4, 2::4] + bc[1::4, 2::4] + bc[2::4, 2::4] + bc[3::4, 2::4]
+ bc[::4, 3::4] + bc[1::4, 3::4] + bc[2::4, 3::4] + bc[3::4, 3::4])
np.save(npy_van_file, bc)
return bc
else:
from mantid.simpleapi import LoadWAND, LoadNexus, SaveNexus
nxs_van_file = '/HFIR/HB2C/shared/autoreduce/vanadium/HB2C_{}.nxs'.format(van_run_number)
if os.path.exists(nxs_van_file):
ws = LoadNexus(nxs_van_file)
else:
ws = LoadWAND(upstream_van_file, Grouping='4x4')
SaveNexus(ws, nxs_van_file)
return ws
def test(self):
ws = LoadWAND('HB2C_7000.nxs.h5')
self.assertTrue(ws)
self.assertEquals(ws.blocksize(), 1)
self.assertEquals(ws.getNumberHistograms(), 1966080)
self.assertEquals(ws.readY(1031100), 5)
self.assertEquals(ws.run().getProtonCharge(), 907880)
self.assertAlmostEqual(ws.run().getGoniometer().getEulerAngles()[0], -142.6)
self.assertEquals(ws.run().getLogData('Wavelength').value, 1.488)
self.assertAlmostEqual(ws.run().getLogData('Ei').value, 36.94619794)
# Check masking
self.assertTrue(ws.detectorInfo().isMasked(0))
self.assertTrue(ws.detectorInfo().isMasked(1))
self.assertFalse(ws.detectorInfo().isMasked(2))
self.assertTrue(ws.detectorInfo().isMasked(512))
self.assertTrue(ws.detectorInfo().isMasked(480*512*8-256))
self.assertFalse(ws.detectorInfo().isMasked(480*512*8-256-512*32))
# Check x dimension
x=ws.getXDimension()
self.assertEquals(x.name, 'Wavelength')
self.assertEquals(x.getNBins(), 1)
self.assertEquals(x.getNBoundaries(), 2)
self.assertAlmostEqual(x.getMinimum(), 1.487)
self.assertAlmostEqual(x.getMaximum(), 1.489)
ws.delete()
def test(self):
ws = LoadWAND('HB2C_7000.nxs.h5', Grouping='2x2')
self.assertTrue(ws)
self.assertEqual(ws.blocksize(), 1)
self.assertEqual(ws.getNumberHistograms(), 1966080 // 4)
self.assertEqual(ws.readY(257775), 4)
self.assertEqual(ws.run().getProtonCharge(), 907880)
self.assertAlmostEqual(ws.run().getGoniometer().getEulerAngles()[0],
-142.6)
self.assertAlmostEqual(ws.run().getLogData('duration').value, 40.05)
# Check masking
self.assertTrue(ws.detectorInfo().isMasked(0))
self.assertTrue(ws.detectorInfo().isMasked(1))
self.assertFalse(ws.detectorInfo().isMasked(2))
self.assertTrue(ws.detectorInfo().isMasked(512))
self.assertTrue(ws.detectorInfo().isMasked(480 * 512 * 8 - 256))
self.assertFalse(ws.detectorInfo().isMasked(480 * 512 * 8 - 256 -
512 * 6))
ws.delete()
from mantid.simpleapi import LoadWAND, SetUB, ConvertToMD, PlusMD, mtd, DeleteWorkspace, CloneMDWorkspace
import numpy as np
import re
if 'data' in mtd:
DeleteWorkspace('data')
for run in range(95409, 98459, 1):
ws = LoadWAND(IPTS=21442, RunNumbers=run, Grouping='4x4')
ub = np.array(re.findall(
r'-?\d+\.*\d*',
ws.run().getProperty('HB2C:CS:CrystalAlign:UBMatrix').value[0]),
dtype=np.float).reshape(3, 3)
sgl = np.deg2rad(ws.run().getProperty(
'HB2C:Mot:sgl.RBV').value[0]) # 'HB2C:Mot:sgl.RBV,1,0,0,-1'
sgu = np.deg2rad(ws.run().getProperty(
'HB2C:Mot:sgu.RBV').value[0]) # 'HB2C:Mot:sgu.RBV,0,0,1,-1'
sgl_a = np.array([[1, 0, 0], [0, np.cos(sgl), np.sin(sgl)],
[0, -np.sin(sgl), np.cos(sgl)]])
sgu_a = np.array([[np.cos(sgu), np.sin(sgu), 0],
[-np.sin(sgu), np.cos(sgu), 0], [0, 0, 1]])
UB = sgl_a.dot(sgu_a).dot(
ub) # Apply the Goniometer tilts to the UB matrix
SetUB(ws, UB=UB)
md = ConvertToMD(ws,
QDimensions='Q3D',
dEAnalysisMode='Elastic',
Q3DFrames='HKL',
QConversionScales='HKL',
OtherDimensions='HB2C:SE:SampleTemp',
MinValues='-10,-10,-10,0',
normaliseBy='Monitor' # One on (None, Monitor, Time)
units = 'Theta' # One of (Theta, ElasticQ, ElasticDSpacing)
Binning = '20,140,2500' # Min,Max,Number_of_bins
use_autoreduced = True
use_autoreduced_van = True
###############################################################################
iptsdir = '/HFIR/HB2C/IPTS-{}/'.format(IPTS)
xmin, xmax, bins = Binning.split(',')
if use_autoreduced:
ws = LoadNexus(Filename=iptsdir+'shared/autoreduce/HB2C_{}.nxs'.format(run))
else:
ws = LoadWAND(Filename=iptsdir+'nexus/HB2C_{}.nxs.h5'.format(run))
if vanadium is not None:
if 'cal' in mtd:
cal = mtd['cal']
else:
if use_autoreduced_van:
cal = LoadNexus(Filename=iptsdir+'shared/autoreduce/HB2C_{}.nxs'.format(vanadium))
else:
cal = LoadWAND(Filename=iptsdir+'shared/autoreduce/HB2C_{}.nxs.h5'.format(vanadium))
else:
cal = None
reduceToPowder(ws, OutputWorkspace=name, cal=cal, target=units, XMin=xmin, XMax=xmax, NumberBins=bins, normaliseBy=normaliseBy)
###############################################################################
iptsdir = '/HFIR/HB2C/IPTS-{}/'.format(IPTS)
van_iptsdir = '/HFIR/HB2C/IPTS-{}/'.format(vanadium_IPTS)
data = name + '_data'
norm = name + '_norm'
# Get UB from file
CreateSingleValuedWorkspace(OutputWorkspace='__ub')
LoadIsawUB('__ub', ub_file)
ub = mtd['__ub'].sample().getOrientedLattice().getUB().copy()
DeleteWorkspace(Workspace='__ub')
if 'cal' not in mtd: # Only load vanadium once
LoadWAND(Filename=van_iptsdir + 'nexus/HB2C_{}.nxs.h5'.format(vanadium),
OutputWorkspace='cal')
if data in mtd:
DeleteWorkspace(data)
if norm in mtd:
DeleteWorkspace(norm)
for run in range(first_run, last_run + 1, load_every):
filename = iptsdir + 'nexus/HB2C_{}.nxs.h5'.format(run)
LoadWAND(filename, OutputWorkspace='__ws')
CopyInstrumentParameters('__ws', 'cal')
mtd['cal'].run().getGoniometer().setR(
mtd['__ws'].run().getGoniometer().getR())
convertToHKL('__ws',
OutputWorkspace=data,
name_MDE = name + '_MDE'
if not append and name_MDE in mtd:
DeleteWorkspace(name_MDE)
for run in range(first_run, last_run + 1, load_every):
if use_autoreduced:
filename = iptsdir + 'shared/autoreduce/HB2C_{}_MDE.nxs'.format(run)
try:
LoadMD(Filename=filename,
LoadHistory=False,
OutputWorkspace='__md')
except ValueError:
filename = iptsdir + 'nexus/HB2C_{}.nxs.h5'.format(run)
LoadWAND(filename, OutputWorkspace='__ws')
ConvertToMD('__ws',
QDimensions='Q3D',
dEAnalysisMode='Elastic',
Q3DFrames='Q_sample',
OutputWorkspace='__md',
MinValues='-10,-1,-10',
MaxValues='10,1,10')
accumulateMD('__md', OutputWorkspace=name_MDE)
SaveMD(
name_MDE, iptsdir + 'shared/' + name +
'_MDE_{}_to_{}_every_{}.nxs'.format(first_run, last_run, load_every))
# Convert MD Event workspace to MD Histo workspace
return bc
else:
from mantid.simpleapi import LoadWAND, LoadNexus, SaveNexus
nxs_van_file = '/HFIR/HB2C/shared/autoreduce/vanadium/HB2C_{}.nxs'.format(van_run_number)
if os.path.exists(nxs_van_file):
ws = LoadNexus(nxs_van_file)
else:
ws = LoadWAND(upstream_van_file, Grouping='4x4')
SaveNexus(ws, nxs_van_file)
return ws
if powder:
from mantid.simpleapi import LoadWAND, WANDPowderReduction, SavePlot1D, SaveFocusedXYE, Scale
data = LoadWAND(filename, Grouping='4x4')
runNumber = data.getRunNumber()
cal = get_vanadium(runNumber)
WANDPowderReduction(InputWorkspace=data,
CalibrationWorkspace=cal,
Target='Theta',
NumberBins=1200,
OutputWorkspace='reduced')
Scale(InputWorkspace='reduced',OutputWorkspace='reduced',Factor=100)
SaveFocusedXYE('reduced', Filename=os.path.join(outdir, output_file+'.xye'), SplitFiles=False, IncludeHeader=False)
div = SavePlot1D('reduced', OutputType='plotly')
request = publish_plot('HB2C', runNumber, files={'file': div})
else: # Single Crystal
with h5py.File(filename, 'r') as f:
outdir = sys.argv[2]
powder = False
with h5py.File(filename, 'r') as f:
if '/entry/DASlogs/HB2C:CS:ITEMS:Nature' in f:
nature = f['/entry/DASlogs/HB2C:CS:ITEMS:Nature/value'].value[0][0]
if nature == 'Powder':
powder = True
if powder:
sys.path.append("/opt/mantidnightly/bin")
from mantid.simpleapi import LoadWAND, WANDPowderReduction, SavePlot1D
data = LoadWAND(filename)
runNumber = data.getRunNumber()
cal = LoadWAND(IPTS=7776, RunNumbers=101567)
WANDPowderReduction(InputWorkspace=data,
CalibrationWorkspace=cal,
Target='Theta',
NumberBins=1000,
OutputWorkspace='reduced')
div = SavePlot1D('reduced', OutputType='plotly')
request = publish_plot('HB2C', runNumber, files={'file': div})
else: # Single Crystal
import matplotlib as mpl
mpl.use("agg")
import matplotlib.pyplot as plt