def extract_to_minicbf(h5master, frameno_or_path, cbfout, binning=1):
from yamtbx.dataproc import cbf
from yamtbx.dataproc.XIO.plugins import eiger_hdf5_interpreter
if type(frameno_or_path) in (tuple, list):
data = extract_data_range_sum(h5master, frameno_or_path)
nframes = len(frameno_or_path)
elif type(frameno_or_path) is int:
data = extract_data(h5master, frameno_or_path)
nframes = 1
else:
data = extract_data_path(h5master, frameno_or_path)
nframes = 1
if data is None:
raise RuntimeError("Cannot extract frame %s from %s" %
(frameno_or_path, h5master))
h = eiger_hdf5_interpreter.Interpreter().getRawHeadDict(h5master)
h5 = h5py.File(h5master, "r")
if binning > 1:
beamxy = h["BeamX"], h["BeamY"]
data, (h["BeamX"],
h["BeamY"]) = software_binning(data, binning, beamxy)
h["Detector"] = "Unknown"
if "/entry/instrument/detector/description" in h: # EIGER2 does not have this field?
h["Detector"] = h5["/entry/instrument/detector/description"].value
h["ExposurePeriod"] = h5["/entry/instrument/detector/frame_time"].value
h["PhiWidth"] *= nframes
cbf.save_numpy_data_as_cbf(data.flatten(),
size1=data.shape[1],
size2=data.shape[0],
title="",
cbfout=cbfout,
pilatus_header="""\
# Detector: %(Detector)s, S/N %(SerialNumber)s
# Pixel_size %(PixelX)e m x %(PixelY)e m
# %(SensorMaterial)s sensor, thickness %(SensorThickness).3e m
# Exposure_time %(ExposureTime).6f s
# Exposure_period %(ExposurePeriod).6f s
# Count_cutoff %(Overload)d counts
# Wavelength %(Wavelength).6f A
# Detector_distance %(Distance).3e m
# Beam_xy (%(BeamX).1f, %(BeamY).1f) pixels
# Start_angle %(PhiStart).6f deg.
# Angle_increment %(PhiWidth).6f deg.
""" % h)
def read_h5file(self):
self.cmbInfile.Clear()
for f in sorted(
glob.glob(
os.path.join(os.path.dirname(self.h5file),
"*_master.h5"))):
self.cmbInfile.Append(f)
self.cmbInfile.SetStringSelection(self.h5file)
try:
h5 = h5py.File(self.h5file, "r")
h = eiger_hdf5_interpreter.Interpreter().getRawHeadDict(
self.h5file)
self.n_images = h["Nimages"]
self.txtInfo.SetValue("""\
Filename: %s
Number of frames: %d
Date: %s
Phi start, width: %.6f, %.6f deg
Camera distance: %.2f mm
Wavelength: %.6f A
Exposure time: %.6f sec
Beam center: (%d, %d) px
""" % (os.path.basename(self.h5file), self.n_images, h["DateStr"].replace(
"T", " "), h["PhiStart"], h["PhiWidth"], h["Distance"] * 1.e3,
h["Wavelength"], h["ExposureTime"], h["BeamX"], h["BeamY"]))
except:
self.n_images = 0
self.txtInfo.SetValue(traceback.format_exc())
self.cmbFrame.Clear()
values = filter(
lambda x: x > 0,
sorted(
set([
1,
] + map(lambda x: int(self.n_images * x), (3 / 4., 1 / 4.,
1 / 2., 1)))))
for v in values:
self.cmbFrame.Append(str(v))
self.change_frameno([1])
def read_h5file(self):
self.cmbInfile.Clear()
glob_f = lambda x: glob.glob(os.path.join(os.path.dirname(self.h5file), x))
for f in sorted(glob_f("*_master.h5")+glob_f("*_onlyhits.h5")): self.cmbInfile.Append(f)
self.cmbInfile.SetStringSelection(self.h5file)
self.lstTrigger.ClearAll()
widgets = self.spnFrame, self.chkSum, self.spnSumFrame, self.spnSumDeg, self.chkKeepFrame
is_onlyhits = self.h5file.endswith("_onlyhits.h5")
try:
h5 = h5py.File(self.h5file, "r")
h = eiger_hdf5_interpreter.Interpreter().getRawHeadDict(self.h5file)
self.n_images = h["Nimages"]
self.n_images_each = h["Nimages_each"]
except:
self.n_images = self.n_images_each = 0
self.txtInfo.SetValue(traceback.format_exc())
return
try:
safe_val = lambda x, k, a: x[k].value if k in x else a
yes_or_no = lambda x, k: ("no", "yes", "?")[safe_val(x, k, 2)]
self.txtInfo.SetValue("""\
Filename: %s
Detector: %s (%s)
Number of frames: %d (%d * %d trigger)
Date: %s
Omega step: %.4f deg
Camera distance: %.2f mm
Wavelength: %.5f A
Frame time: %.6f sec
Beam center: (%d, %d) px
Corrections: countrate=%s
flatfield=%s
efficiency=%s
ROI mode: %s
Sensor: %s %.1f um
Eiger fw ver: %s
""" % (os.path.basename(self.h5file),
safe_val(h5["/entry/instrument/detector"], "description", "?"), safe_val(h5["/entry/instrument/detector"], "detector_number", "?"),
self.n_images, self.n_images_each, h["Ntrigger"],
h["DateStr"].replace("T", " "),
h["PhiWidth"],
h["Distance"]*1.e3,
h["Wavelength"],
safe_val(h5["/entry/instrument/detector"], "frame_time", float("nan")),
h["BeamX"], h["BeamY"],
yes_or_no(h5["/entry/instrument/detector"], "countrate_correction_applied"),
yes_or_no(h5["/entry/instrument/detector"], "flatfield_correction_applied"),
yes_or_no(h5["/entry/instrument/detector"], "efficiency_correction_applied"),
safe_val(h5["/entry/instrument/detector/detectorSpecific"], "roi_mode", "?"),
h.get("SensorMaterial", "?"), h.get("SensorThickness", float("nan"))*1.e6,
safe_val(h5["/entry/instrument/detector/detectorSpecific"], "eiger_fw_version", "?")
))
except:
self.txtInfo.SetValue(traceback.format_exc())
if is_onlyhits:
for w in widgets: w.Disable()
self.stFrameRange.SetLabel("")
self.lstTrigger.InsertColumn(0, "Frame", width=55)
self.lstTrigger.InsertColumn(1, "Spots", width=55)
self.onlyhits_keys = sorted(h5["/entry/data"].keys())
if not self.onlyhits_keys: return
for i, v in enumerate(self.onlyhits_keys):
nspots = h5["/entry/data"][v]["data"].attrs.get("n_spots")
nspots = "%3d" % nspots if nspots is not None else ""
frame = int(v[v.rindex("_")+1:])
self.lstTrigger.InsertStringItem(i, str(frame))
self.lstTrigger.SetStringItem(i, 1, nspots)
self.lstTrigger.Select(0) # this calls an event to load image
else:
for w in widgets: w.Enable()
self.onlyhits_keys = []
self.stFrameRange.SetLabel(" (from 1 to %d)"%self.n_images_each)
self.spnFrame.SetRange(1, self.n_images_each)
self.spnFrame.SetIncrement(1)
self.spnSumFrame.SetRange(1, self.n_images_each)
self.spnSumDeg.SetIncrement(h["PhiWidth"])
self.spnSumDeg.SetRange(h["PhiWidth"], h["PhiWidth"]*self.n_images_each)
if h["PhiWidth"] > 1e-5:
self.spnSumDeg.Enable()
self.spnSumFrame.SetValue(int(1./h["PhiWidth"]+.5))
self.onSpnSumFrame(None)
else:
self.spnSumFrame.SetValue(1)
self.spnSumDeg.Disable()
self.lstTrigger.InsertColumn(0, "Trigger")
self.lstTrigger.InsertColumn(1, "Omega")
omega = h5["/entry/sample/goniometer/omega"]
for i in xrange(h["Ntrigger"]):
self.lstTrigger.InsertStringItem(i, "%d"%(i+1))
try:
oms = omega[i*self.n_images_each]
self.lstTrigger.SetStringItem(i, 1, "%.3f"%oms)
except: pass
self.lstTrigger.Select(0) # this calls an event to load image