def main():
fly = reduceFlyData.UsaxsFlyScan(TESTFILE)
fly.reduce()
full = fly.reduced["full"]
print full.keys()
print "ar[:5]", full['ar'][:5]
for k in "R_max r_peak ar_r_peak".split():
print k, full[k]
cen, ar, R = flyscan_centroid(full, 0.4)
print "centroid:", cen
with h5py.File(OUTFILE, "w") as h5:
h5.attrs["default"] = "entry"
nxentry = h5.create_group("entry")
nxentry.attrs["NX_class"] = "NXentry"
nxentry.attrs["default"] = "data"
nxdata = nxentry.create_group("data")
nxdata.attrs["NX_class"] = "NXdata"
nxdata.attrs["signal"] = "R"
nxdata.attrs["axes"] = "ar"
ds = nxdata.create_dataset("ar", data=ar)
ds.attrs["units"] = "degrees"
ds = nxdata.create_dataset("R", data=R)
ds.attrs["units"] = "not applicable"
ds = nxdata.create_dataset("cen", data=[cen])
ds.attrs["units"] = "degrees"
def get_USAXS_FlyScan_Data(scan_obj):
scan = scan_obj.spec_scan
hdf5_file = get_Hdf5_Data_file_Name(scan)
try:
fly = reduceFlyData.UsaxsFlyScan(hdf5_file) # checks if file exists
#fly.make_archive()
fly.reduce() # open the file in this step
fly.save(hdf5_file, 'full')
if 'full' not in fly.reduced:
return None
fly.rebin(localConfig.REDUCED_FLY_SCAN_BINS)
fly.save(hdf5_file, str(localConfig.REDUCED_FLY_SCAN_BINS))
except IOError:
return None # file may not be available yet for reading if fly scan is still going
except KeyError as exc:
logger.info('HDF5 file:' + hdf5_file)
raise KeyError(exc)
except reduceFlyData.NoFlyScanData as _exc:
logger.info(str(_exc))
return None # HDF5 file exists but length of raw data is zero
fname = os.path.splitext(os.path.split(hdf5_file)[-1])[0]
title = 'S%s %s (%s)' % (str(scan.scanNum), fname, 'fly')
numbins_str = str(localConfig.REDUCED_FLY_SCAN_BINS)
if numbins_str not in fly.reduced:
return None
rebinned = fly.reduced[numbins_str]
entry = dict(qVec=rebinned['Q'], rVec=rebinned['R'], title=title)
return entry
def test_flyScan(filename):
'''test data reduction from a flyScan (in an HDF5 file)'''
if not os.path.exists(filename):
raise FileNotFound(filename)
import reduceFlyData
fs = reduceFlyData.UsaxsFlyScan(filename)
# compute the R(Q) profile
fs.reduce()
usaxs = fs.reduced
return usaxs
def main():
owd = os.getcwd()
testpath = os.path.join('testdata', '2014-04', '*_fly')
for path in sorted(glob.glob(testpath)):
os.chdir(path)
for hfile in sorted(glob.glob('S*.h5')):
print path, hfile
copy_from_archive(ARCHIVE_SUBDIR_NAME, hfile)
ufs = reduceFlyData.UsaxsFlyScan(hfile)
#ufs.make_archive()
#ufs.read_reduced()
ufs.reduce()
ufs.rebin(REDUCED_FLY_SCAN_BINS)
ufs.save(hfile, 'full')
ufs.save(hfile, REDUCED_FLY_SCAN_BINS)
os.chdir(owd)
def retrieve_flyScanData(scan):
'''retrieve reduced, rebinned data from USAXS Fly Scans'''
if hasattr(scan, "MD") and scan.MD.get("hdf5_path") is not None:
# Bluesky wrote this SPEC data file
path = scan.MD.get("hdf5_path")
hdf_file_name = scan.MD.get("hdf5_file")
else:
# SPEC wrote this data file
key_string = 'FlyScan file name = '
hdf_file_name = "" # in case key_string is not found
for comment in scan.comments:
if key_string in comment:
index = comment.find(key_string) + len(key_string)
path = os.path.dirname(scan.header.parent.fileName)
hdf_file_name = comment[index:-1]
break
abs_file = os.path.abspath(os.path.join(path, hdf_file_name))
if os.path.exists(abs_file):
s_num_bins = str(localConfig.REDUCED_FLY_SCAN_BINS)
ufs = reduceFlyData.UsaxsFlyScan(abs_file)
ufs.read_reduced()
needs_calc = dict(full=not ufs.has_reduced('full'))
needs_calc[s_num_bins] = not ufs.has_reduced(s_num_bins)
if needs_calc['full']:
#ufs.make_archive()
ufs.reduce()
ufs.save(abs_file, 'full')
needs_calc[s_num_bins] = True
if needs_calc[s_num_bins]:
ufs.rebin(localConfig.REDUCED_FLY_SCAN_BINS)
ufs.save(abs_file, s_num_bins)
Q = ufs.reduced[s_num_bins]['Q']
R = ufs.reduced[s_num_bins]['R']
plotData = (Q, R)
else:
plotData = []
return plotData
def main():
#reduction_test()
testpath = os.path.join('testdata', '2014-04', '04_14_Winans_fly', '*.h5')
#testpath = os.path.join('testdata', '*.h5')
# clear the test output files
for hfile in glob.glob(os.path.join('/tmp', 'reduced_*.h5')):
os.remove(hfile)
counter = 0
for hdf_file_name in sorted(glob.glob(testpath)):
print hdf_file_name
ufs = reduceFlyData.UsaxsFlyScan(hdf_file_name)
counter += 1
hfile = os.path.join('/tmp', 'reduced_%04d.h5' % counter)
#ufs.make_archive()
#ufs.read_reduced()
ufs.reduce()
ufs.rebin(REDUCED_FLY_SCAN_BINS)
ufs.save(hfile, 'full')
ufs.save(hfile, REDUCED_FLY_SCAN_BINS)