def process(
*,
raw_img: np.ndarray,
ai: AzimuthalIntegrator,
dk_img: np.ndarray = None,
dk_sub_bg_img: np.ndarray = None,
integ_setting: dict = None,
mask_setting: dict = None,
pdfgetx_setting: dict = None,
) -> dict:
"""The function to process the data from event."""
data = dict()
# dark subtraction
if dk_img is None:
dk_img = np.zeros_like(raw_img)
dk_sub_img = np.subtract(raw_img, dk_img)
data.update({"dk_sub_image": dk_sub_img})
# background subtraction
if dk_sub_bg_img is None:
dk_sub_bg_img = np.zeros_like(dk_sub_img)
bg_sub_img = np.subtract(dk_sub_img, dk_sub_bg_img)
data.update({"bg_sub_image": bg_sub_img})
# auto masking
mask, _ = integ.auto_mask(bg_sub_img, ai, mask_setting=mask_setting)
data.update({"mask": mask})
# integration
x, y = ai.integrate1d(bg_sub_img, mask=mask, **integ_setting)
chi_max_ind = np.argmax(y)
data.update({
"chi_Q": x,
"chi_I": y,
"chi_max": y[chi_max_ind],
"chi_argmax": x[chi_max_ind]
})
# transformation
pdfconfig = PDFConfig(dataformat="QA", **pdfgetx_setting)
pdfgetter = PDFGetter(pdfconfig)
pdfgetter(x, y)
iq, sq, fq, gr = pdfgetter.iq, pdfgetter.sq, pdfgetter.fq, pdfgetter.gr
gr_max_ind = np.argmax(gr[1])
data.update({
"iq_Q": iq[0],
"iq_I": iq[1],
"sq_Q": sq[0],
"sq_S": sq[1],
"fq_Q": fq[0],
"fq_F": fq[1],
"gr_r": gr[0],
"gr_G": gr[1],
"gr_max": gr[1][gr_max_ind],
"gr_argmax": gr[0][gr_max_ind]
})
return data
def get_chi(
ai: AzimuthalIntegrator,
img: ndarray,
dk_img: ndarray = None,
bg_img: ndarray = None,
mask: ndarray = None,
bg_scale: float = None,
mask_setting: tp.Union[str, dict] = None,
integ_setting: dict = None,
img_setting: tp.Union[str, dict] = None,
plot_setting: tp.Union[str, dict] = None,
) -> tp.Tuple[ndarray, ndarray, ndarray, ndarray, tp.Union[None, ndarray],
dict, tp.Union[str, dict]]:
"""Process the diffraction image to get I(Q).
The image will be subtracted by the background image and then auto masked. The results will be
binned on the azimuthal direction and the average value of the intensity in the bin and their
corresponding Q will be returned. The I(Q) and background subtracted masked image will
be visualized.
Parameters
----------
ai : AzimuthalIntegrator
The AzimuthalIntegrator.
img : ndarray
The of the 2D array of the image.
dk_img : ndarray
The dark frame image. The image will be subtracted by it if provided.
bg_img : ndarray
The 2D array of the background image. If None, no background subtraction.
mask : ndarray
A mask provided by user. The auto generated mask will be multiplied by this mask.
bg_scale : float
The scale for background subtraction. If None, use 1.
mask_setting : dict
The auto final_mask setting.
If None, use _AUTOMASK_SETTING in the tools module. To turn off the auto masking, use "OFF".
integ_setting : dict
The integration setting.
If None, use _INTEG_SETTING in the tools module.
img_setting : dict
The user's modification to imshow kwargs except a special key 'z_score'. If None, use use empty dict.
To turn off the imshow, use "OFF".
plot_setting : dict
The kwargs for the plot function. If None, use empty dict.
Returns
-------
chi : ndarray
The 2D array of integrated results. The first row is the Q and the second row is the I.
bg_sub_img : ndarray
The background subtracted image. If no background subtraction, it is the dk_sub_image.
dk_sub_img : ndarray
The dark subtracted image. If no dark subtraction, it is the input img.
img : ndarray
The input image.
final_mask : ndarray or None
The final_mask array. If no auto_masking, return None.
_integ_setting: dict
The integration setting used.
_mask_setting : dict or str
The auto masking setting.
"""
if dk_img is not None:
dk_sub_img = bg_sub(img, dk_img, bg_scale=1.)
else:
dk_sub_img = img
if bg_img is not None:
bg_sub_img = bg_sub(dk_sub_img, bg_img, bg_scale=bg_scale)
else:
bg_sub_img = dk_sub_img
if mask_setting != "OFF":
final_mask, _mask_setting = auto_mask(bg_sub_img,
ai,
user_mask=mask,
mask_setting=mask_setting)
elif mask is not None:
final_mask, _mask_setting = mask, {}
else:
final_mask, _mask_setting = None, None
if img_setting != "OFF":
vis_img(bg_sub_img, final_mask, img_setting=img_setting)
chi, _integ_setting = integrate(bg_sub_img,
ai,
mask=final_mask,
integ_setting=integ_setting)
if plot_setting != "OFF":
vis_chi(chi,
plot_setting=plot_setting,
unit=_integ_setting.get('unit'))
return chi, bg_sub_img, dk_sub_img, img, final_mask, _integ_setting, _mask_setting
def process(
*,
user_config: UserConfig,
raw_img: np.ndarray,
ai: tp.Union[None, AzimuthalIntegrator],
dk_img: np.ndarray = None,
dk_sub_bg_img: np.ndarray = None,
integ_setting: dict = None,
mask_setting: dict = None,
pdfgetx_setting: dict = None,
) -> dict:
"""The function to process the data from event."""
# initialize the data dictionary
data = {
"dk_sub_image": raw_img.copy(),
"bg_sub_image": raw_img.copy(),
"mask": np.zeros_like(raw_img),
"chi_Q": np.array([0.]),
"chi_I": np.array([0.]),
"chi_max": 0.,
"chi_argmax": 0.,
"iq_Q": np.array([0.]),
"iq_I": np.array([0.]),
"sq_Q": np.array([0.]),
"sq_S": np.array([0.]),
"fq_Q": np.array([0.]),
"fq_F": np.array([0.]),
"gr_r": np.array([0.]),
"gr_G": np.array([0.]),
"gr_max": 0.,
"gr_argmax": 0.
}
# dark subtraction
if dk_img is not None:
data["dk_sub_image"] = np.subtract(raw_img, dk_img)
# background subtraction
if dk_sub_bg_img is not None:
data["bg_sub_image"] = np.subtract(data["dk_sub_image"], dk_sub_bg_img)
# if no calibration, output data now
if ai is None:
return data
# do auto masking if specified
if user_config.do_auto_masking:
data["mask"], _ = integ.auto_mask(data["bg_sub_image"],
ai,
mask_setting=mask_setting,
user_mask=user_config.user_mask)
# if user gives a mask, use it
elif user_config.user_mask is not None:
data["mask"] = user_config.user_mask.copy()
# integration
x, y = ai.integrate1d(data["bg_sub_image"],
mask=data["mask"],
**integ_setting)
chi_max_ind = np.argmax(y)
data.update({
"chi_Q": x,
"chi_I": y,
"chi_max": y[chi_max_ind],
"chi_argmax": x[chi_max_ind]
})
# transformation
pdfconfig = PDFConfig(dataformat="QA", **pdfgetx_setting)
pdfgetter = PDFGetter(pdfconfig)
pdfgetter(x, y)
iq, sq, fq, gr = pdfgetter.iq, pdfgetter.sq, pdfgetter.fq, pdfgetter.gr
gr_max_ind = np.argmax(gr[1])
data.update({
"iq_Q": iq[0],
"iq_I": iq[1],
"sq_Q": sq[0],
"sq_S": sq[1],
"fq_Q": fq[0],
"fq_F": fq[1],
"gr_r": gr[0],
"gr_G": gr[1],
"gr_max": gr[1][gr_max_ind],
"gr_argmax": gr[0][gr_max_ind]
})
return data
def process(
*,
raw_img: np.ndarray,
ai: tp.Union[None, AzimuthalIntegrator],
user_mask: np.ndarray = None,
auto_mask: bool = True,
dk_img: np.ndarray = None,
integ_setting: dict = None,
mask_setting: dict = None,
pdfgetx_setting: dict = None,
) -> dict:
"""The function to process the data from event."""
# initialize the data dictionary
data = {
"dk_sub_image": raw_img,
"mask": np.zeros_like(raw_img),
"chi_Q": np.array([0.]),
"chi_I": np.array([0.]),
"chi_max": np.float(0.),
"chi_argmax": np.float(0.),
"iq_Q": np.array([0.]),
"iq_I": np.array([0.]),
"sq_Q": np.array([0.]),
"sq_S": np.array([0.]),
"fq_Q": np.array([0.]),
"fq_F": np.array([0.]),
"gr_r": np.array([0.]),
"gr_G": np.array([0.]),
"gr_max": np.float(0.),
"gr_argmax": np.float(0.)
}
# dark subtraction
if dk_img is not None:
data["dk_sub_image"] = np.subtract(raw_img, dk_img)
# if no calibration, output data now
if ai is None:
return data
# do auto masking if specified
if auto_mask:
data["mask"], _ = integ.auto_mask(data["dk_sub_image"],
ai,
mask_setting=mask_setting,
user_mask=user_mask)
elif user_mask is not None:
data["mask"] = user_mask
# integration
x, y = ai.integrate1d(data["dk_sub_image"],
mask=data["mask"],
**integ_setting)
chi_max_ind = np.argmax(y)
data.update({
"chi_Q": x,
"chi_I": y,
"chi_max": y[chi_max_ind],
"chi_argmax": x[chi_max_ind]
})
# transformation
if not _PDFGETX_AVAILABLE:
io.server_message(
"diffpy.pdfgetx is not installed. No use [0.] for all the relevant data."
)
return data
pdfconfig = PDFConfig(**pdfgetx_setting)
pdfgetter = PDFGetter(pdfconfig)
pdfgetter(x, y)
iq, sq, fq, gr = pdfgetter.iq, pdfgetter.sq, pdfgetter.fq, pdfgetter.gr
gr_max_ind = np.argmax(gr[1])
data.update({
"iq_Q": iq[0],
"iq_I": iq[1],
"sq_Q": sq[0],
"sq_S": sq[1],
"fq_Q": fq[0],
"fq_F": fq[1],
"gr_r": gr[0],
"gr_G": gr[1],
"gr_max": gr[1][gr_max_ind],
"gr_argmax": gr[0][gr_max_ind]
})
return data
def test_auto_mask(db):
mask, _ = auto_mask(db["Ni_img"], db["ai"])
assert np.array_equal(mask[0], np.ones_like(mask[0]))