h5xs

This is the base class that enables interaction with the h5 file that stores the experimental data, by associating the raw information in the h5 file into meaningful py4xs objects (e.g. Data1d instances), on which data analysis can be carried out. It is assumed that the file structure follow the convention:

• the data are organized by samples
• under each sample, the raw data are stored under the primary group. Two datasets are expected: data and timestamps
• the processed data are saved under the processed group. In this base class, processing is limited to azimuthal average. The datasets include those from the individual detectors, merged (from all detectors), averaged (from multiple frames/exposures), and possibly subtracted (for background).

The file structure associated with specific types of experiments supported at LiX are defined under lixtools.

Each h5xs object must be initialized with detector configurations and a \(q\)-grid.

fh5: the file handle to the associated h5 file. py4xs now closes the file any time it is not actively reading or writing data. Call explicit_open() to get the file handle. And close it afterward using explicit_close().

d1s : dictionaries of Data1d objects derived from the scattering patterns.

load_data(): generate the initial d1s objects for each detector

merge_d1s(): merge the processed data from individual detectors

average_d1s(): average together multiple scattering patterns for the same sample, based on a similarity analysis. Selection of the frames to be averaged together can be specified.

save_d1s(): save the d1s dictionaries into the h5 file. load_d1s(): load the d1s dictionaries back from the h5 file.

plot_d1s(): plot the 1D data from single sample, useful for showing how the frames are selected

compare_d1s(): plot the 1D data from multiple samples, useful for visualizing the difference between samples

export_d1s(): export the 1D data to a specified path

get_d2(): return the Data2d object(s) corresponding to a specified sample name and frame number

get_d1(): return the Data1d object corresponding to a specified sample name and frame number. By default returns the merged data.

get_mon(): get the beam intensity monitor data corresponding to the individual scattering patterns. The source of the intensity data is defined in py4xs.local.

show_data(), show_data_qphi(), and show_data_qxy(): display the scattering pattern in the h5 file in various coordinates (see examples).

check_bm_center(): take horizontal and vertical line cuts near the beam center and compare the intensity on either side of the beam center, as a simplified means to verify whether the beam center specified in the detector configuration is correct.

md_dict(): return the meta data to be recorded in the exported ascii file, derived from the info defined in py4xs.local.

header(): return the header of the Bluesky scan that produced the data

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h5exp

h5exp is derived from h5xs and is used to store the detector configuration and \(q\)-grid so that this information can be propagated easily to other h5xs objects.

save_detectors() and read_detectors() are provided to exchange information between a h5 file and the corresponding h5exp object.

recalibrate() : recalibrate the detector exp_para based on the scattering data collected from a standard sample (silver behenate).