def _calibration(img, calibration, calib_ref_fp=None, **kwargs):
"""Engine for performing calibration on a image with geometry
correction software. current backend is ``pyFAI``.
Parameters
----------
img : ndarray
image will be used for calibration process.
calibration : pyFAI.calibration.Calibration instance
Calibration instance with wavelength, calibrant and
detector configured.
calib_ref_fp : str
full file path to where the native pyFAI calibration information
will be saved.
kwargs:
additional keyword argument for calibration. please refer to
pyFAI documentation for all options.
"""
from pyFAI.calibration import PeakPicker
from pyFAI.gui.utils import update_fig
print("{:=^20}".format("INFO: you are able to perform calibration, "
"please refer to pictorial guide here:\n"))
print("{:^20}".format(
"http://xpdacq.github.io/usb_Running.html#calib-manual\n"))
# default params
interactive = True
# calibration
c = calibration # shorthand notation
timestr = _timestampstr(time.time())
c.gui = interactive
# annoying pyFAI logic, you need valid fn to start calibration
_is_tmp_dir = False
if calib_ref_fp is None:
_is_tmp_dir = True
td = TemporaryDirectory()
calib_ref_fp = os.path.join(td.name, "from_calib_func")
basename, ext = os.path.splitext(calib_ref_fp)
poni_fn = basename + ".npt"
c.basename = basename
c.pointfile = poni_fn
c.peakPicker = PeakPicker(img,
reconst=True,
pointfile=c.pointfile,
calibrant=c.calibrant,
wavelength=c.wavelength,
**kwargs)
c.peakPicker.gui(log=True, maximize=True, pick=True)
update_fig(c.peakPicker.fig)
c.gui_peakPicker()
# TODO: open issue at pyFAI on this crazyness
c.ai.setPyFAI(**c.geoRef.getPyFAI())
c.ai.wavelength = c.geoRef.wavelength
if _is_tmp_dir:
td.cleanup()
return c, timestr
def start(self, doc):
# Get the independent vars
self.dim_names = [
d[0][0] for d in doc.get("hints", {}).get("dimensions")
if d[0][0] != "time"
]
if "original_start_uid" not in doc:
doc["original_start_uid"] = doc["uid"]
if "original_start_time" not in doc:
doc["original_start_time"] = doc["time"]
# use the magic formatter to leave things behind
self.start_template = render2(
self._template,
start=doc,
human_timestamp=_timestampstr(doc["original_start_time"]),
**doc,
**self.kwargs,
)
return super().start(doc)
def start(self, doc):
# Get the independent vars
self.dim_names = [
d[0][0]
for d in doc.get("hints", {}).get("dimensions")
if d[0][0] != "time"
]
if "original_start_uid" not in doc:
doc["original_start_uid"] = doc["uid"]
if "original_start_time" not in doc:
doc["original_start_time"] = doc["time"]
# use the magic formatter to leave things behind
self.start_template = render2(
self._template,
start=doc,
human_timestamp=_timestampstr(doc["original_start_time"]),
**doc,
**self.kwargs,
)
return super().start(doc)
def test_timestampstr():
assert isinstance(_timestampstr(0), str)