Interactive mode

The interactive mode is activated by using either the -i, --interact option or a non-empty --plot option. In the interactive mode the program starts an IPython interactive shell and pre-loads several functions and variables related to the PDF calculation. It also defines a %pdfgetx3 macro, which can be used with the same command-line syntax as the pdfgetx3 program from a system shell. The interactive session is also initialized with all functions from the matplotlib pylab module for convenient plotting. The functions and variables related to PDF processing are:

pdfgetter()

Instance of the PDFGetter class which serves as a low-level function that calculates the PDF. This is a callable object, which takes as an argument a pair of input arrays for (two-theta, intensity). It can be also called with a keyword argument filename=FILE, which would read the input arrays from the specified file. When called with no arguments, it calculates PDF from the last input data.

Returns:A pair of output arrays (r, G).
config

Instance of the PDFConfig class that stores the parameters and input files for the program. Use print(config) to display the current configuration values. This is the same object as pdfgetter.config. Configuration may be changed by setting a respective attribute of the config object, for example:

In [1]: config.qmax = 21

The config values may be also changed by calling the pdfgetter() or processFiles() function with a corresponding keyword argument, for example processFiles(qmax=20, force="once").

iraw
iq
sq
fq
gr

These variables are assigned the input raw intensities and the intermediate results, stored as matrix rows. The matrix rows correspond to twotheta1, intensity1, twotheta2, intensity2, etc. Because matrices are iterated row first, the raw intensities from all input files can be plotted with the matplotlib plot function as plot(*iraw).

These variables should be considered read-only and are reset with subsequent PDF calculations.

tuneconfig(plotids=None, pdfgetter=None, axeslist=None)

Show a GUI dialog for interactive tuning of configuration variables.

Parameters:
  • plotids – string or iterable that specify what interactive plots should be tuned. By default the same as config.plot. Can be also an integer index or name of a transformation in pdfgetter or a reference to a Transformation object.
  • pdfgetter – optional PDFGetter object to be tuned. This is by default the interactive pdfgetter() object.
  • axeslist – optional list of matplotlib Axes for displaying the interactive plots. When None, use subplot(N, 1, i) to create the parent axes.

Note

Changes from tuneconfig() apply only to the configuration and results in memory. Use the processFiles() function to save them to disk.

See also

Interactive tuning of parameters tutorial

processFiles(filename=None, **kwargs)

Process all input files again with the current configuration values. This is a higher-level function than pdfgetter(), as it also saves output files and produces plots as specified by the config object.

Parameters:
  • filename – One or more input files to be converted to PDFs and saved or plotted according to the config settings. Use the previous list of input files when not specified.
  • kwargs – optional keyword arguments that are applied to the config object, for example (force="once", qmax=18).

This function updates the config.inputfiles list and the iraw, iq, sq, fq and gr interactive variables.

clearSession()

Clear all elements from the config.inputfiles and also the iraw, iq, sq, fq and gr variables.

Returns:No return value.
loadData(filename, minrows=10, usecols=None, **kwargs)

Find and load data from a text file.

The data reading starts at the first matrix block of at least minrows rows and constant number of columns. This seems to work for most of the datafiles including those generated by PDFGetX2.

Parameters:
  • filename (str) – Name of the file to load the text data from.
  • minrows (int, optional) – Minimum number of rows in the first data block, by default 10. All rows must have the same number of floating point values.
  • usecols (int, str, slice, iterable, optional) – Indices or names of the columns to be loaded from the data block, the default is all columns. Data blocks that do not contain sufficient number of columns are skipped. When usecols contain string items, they are translated to column indices by looking up a header line preceding the data block. String items formatted as i:j:k are converted to slice objects. When usecols type is string it is split to a list of names at comma and whitespace characters.
  • unpack (bool, optional) – Return data as a sequence of columns that allows tuple unpacking such as x, y = loadData(FILENAME, unpack=True). Note that transposing the loaded array as loadData(FILENAME).T has the same effect. The default is False.
  • kwargs (misc, optional) – Extra keyword arguments that are passed to numpy.loadtxt.
Returns:

data (numpy.ndarray) – The data block loaded from the text file.

See also

numpy.loadtxt()

plotdata(filenames, style=None, x=None, y=None, log=None, ax=None, **kwargs)

Plot one or more text data files.

The files are searched for data blocks which have enough columns to satisfy both x and y selectors of the plotted data. This may result in an empty plot when file has none wide-enough data block (e.g., when y=100).

Parameters:
  • filenames (str or an iterable of string file names) – One or more text data files to be plotted.
  • style (str) – Optional style argument for the matplotlib plot() function.
  • x (int, str, or iterable, optional) – The column to be used for the x data. This can be a zero-based index of the desired column or a column name from data header. A special symbol “.” can be used for a sequential data index. When not specified, use the first column.
  • y (int, str, iterable, or slice, optional) – One or more columns to be used for the y data. This can be a single zero-based index of the desired column or an iterable of several indices. The y value can be also a string which is split at commas and converted to integers, column names or slice objects, e.g. “0,sine,4:7”. The slice instances are applied to the entire data block from each loaded file. Use the second column when not specified.
  • log ({‘x’, ‘y’}, optional) – Set logarithmic scaling for the specified axis and linear scaling for all others. For example, log="y" applies linear scaling to the x-axis and logarithmic to the y-axis. Keep the current axis scaling when not specified.
  • ax (matplotlib.axes.Axes, optional) – The axes to plot to. The plotting will be performed using the ax.plot method. The default is pyplot.gca().
  • kwargs (misc, optional) – Keyword arguments for the matplotlib plot() function.
Returns:

lines (list) – The matplotlib Line2D objects added to the current axis.

See also

diffpy.pdfgetx.loadData()

This function is defined in the diffpy.pdfgetx.plotdata module.

findfiles(patterns=(), path=None)

Find files in the working directory that match all specified patterns.

Pattern syntax:

  • ^start - match “start” only at the beginning of the string.
  • end$ - match “end” only at the end of string.
  • <7> - match number 7 preceded by any number of leading zeros.
  • <1-34> - match an integer range from 1 to 34 inclusive.
  • <7-> - match an integer greater or equal 7.
  • <-> - match any integer.

All integer ranges <N-M> above allow one or more leading zeros. The range syntax does not support matching of negative numbers.

Parameters:
  • patterns (iterable of strings or str, optional) – String patterns that must all match in returned filenames. Can be also a single string with patterns separated by whitespace characters. When empty match all files in the current directory or in the path.
  • path (iterable of strings or str, optional) – Directories to be searched instead of the current directory. Repeated path entries are ignored. When string take it as a single directory path.
Returns:

filenames (IPython.SList) – The list of matching filenames. Return all files when patterns were not specified.

See also

Table of special patterns