MatrixWithCoords
This class is created to define intensity maps, for which the coordinates for the pixels in the map need to be defined.
d : the actual intensity map
xc, yc : 1d arrays that define the x and y coordinates of the intensity map
xc_label, yc_label : axis lables for the intensity map
datatype : type of the data (e.g. detector raw image, \(I(q, \phi)\) map, ...), which
must be of type Enum DataType. This is useful when plotting the intensity map,
so that the correct coordinates can be displayed.
conv(self, Nx1, Ny1, xc1, yc1, mask=None, cor_factor=1, datatype=DataType.det)
convert the intensity map to new coordinates xc1, yc1. Masked pixels are omitted.
line_cut(self, x0, y0, ang, lT, lN, nT, nN, mask=None)
return a line cut from the intensity map. Masked pixels are omitted.
copy(): create a deep copy of the object
expand(): exapnd the coordinates for the intensity map, e.g. in preparation for merging
merge(): merge two or more maps with the same axis labels
plot(): plot the intensity map
roi(): return a smaller map within the specified range
val(): return the integrated intensity within the specified range
flatten(): collapse the intensity map onto the apecified axis and returns an intensity profile
average(): average multiple intensity maps together
bkg_cor(): perform background subtraction with the specified scaling factor.
fill_gap() and apply_symmetry(): attempt to exapnd the intensity map coverage
Data2d
Generic scattering data. Multiple representations can exist: data (raw detector
image), qrqz_data ( \(q_r - q_z\) map, grazing incidence), and qphi_data
( \(q - \phi\) map).
exp : the ExpPara for the scattering data.
label : by default this is set to the name of the data file. But it could be set
when the instance is initilized.
uid, timestamp : optional information. They are extracted from the data file
for Pilatus data collected at NSLS-II.
conv_Iq(self, qgrid, mask=None, cor_factor=1): convert the 2D scattering data
into a 1D scattering intensity profile.
conv_Iqphi() and conv_Iqrqz(): generate the \(I(q, \phi)\) and \(I(q_r, q_z)\)
map of the scattering data.
Axes2dPlot
This class displays 2D scattering data in a matplotlib Axes. It captures mouse
clicks to display the reciprocal coordinates at the clicked pixel, and can overlay
decorations (lines and symbols at specified reciprocal coordinates) onto the scattering data.
ax, cmap : parameters used by matplotlib to plot the sample
d2, exp : the scattering data and its ExpPara.
mark_points() , mark_coords() and mark_standard() generate the decorations
(points, lines/grids with the given coordinates, and powder rings expected from standard
samples) to be overlaid onto the scattering pattern. Refer to the Examples section.
plot(): plot the data.
Data1d
trans is the (relative) value of the transmitted intensity, which is used as a reference
for normlization during background subtraction. Two modes are allowed (defined as members of the
Enum transMode ) : external or from_waxs. For transMode.external , the trans
value must be specified explicitly. For transMode.from_waxs, the trans value is calculated
from the water scattering peak intensty near \(2.0 \unicode{x212B}^{-1}\) .
load_from_2D() populates the atrtibutes of the instance based on the input data, which can be
a Data2d object, a data file, or a numpy array, and the specified ExpPara. The azimuthally averaged
1D data is generated using Data2d.conv_Iq(), after applying the polorization and solid angle
corrections. The error bar is the standard deviation of intensity in all pixels that belong to the
same q value.
merge(): merge data with another Data1d object. Within the overlapping q-range, the
scattering intensity is averaged and the original data are saved can could be displayed later.
avg(): perform averaging with the given set of Data1d objects.
bkg_cor(): perform background subtraction, based on the trans value, optionally with a
scaling factor. For solution scattering, this scaling factor could be estiamted using py4xs.slnxs.estiamte_scaling_factor().
plot(): plot the data, in a given matplotlib Axes if specified.
save(): export the data into a text file in a 3-column format (q, intensity, error bar).
plot_Guinier(): plot \(ln[I(q)]\) vs \(q^2\) (Guinier plot) and report \(I_0\) and \(R_g\) .