This page holds stubs for functions that will be included in the api documentation

load_file

pyspecdata.load_files.find_file(searchstring, exp_type=None, postproc=None, print_result=True, verbose=False, prefilter=None, expno=None, dimname='', return_acq=False, add_sizes=[], add_dims=[], use_sweep=None, indirect_dimlabels=None, lookup={}, **kwargs)

Find the file given by the regular expression searchstring inside the directory identified by exp_type, load the nddata object, and postprocess with the function postproc.

It looks at the top level of the directory first, and if that fails, starts to look recursively. Whenever it finds a file in the current directory, it will not return data from files in the directories underneath. (For information on how to set up the file searching mechanism, see register_directory()).

Note that all loaded files will be logged in the data_files.log file in the directory that you run your python scripts from (so that you can make sure they are properly synced to the cloud, etc.).

It calls load_indiv_file(), which finds the specific routine from inside one of the modules (sub-packages) associated with a particular file-type.

If it can’t find any files matching the criterion, it logs the missing file and throws an exception.

Parameters:

• searchstring (str) – Most commonly, this is just a fragment of the file name, with any literal *, ., or ? characters preceded by a backslash. More generally, it is a regular expression, where .*searchstring.* matches a filename inside the directory appropriate for exp_type.
• expno (int) – For Bruker NMR and Prospa files, where the files are stored in numbered subdirectories, give the number of the subdirectory that you want. Currently, this parameter is needed to load Bruker and Kea files. If it finds multiple files that match the regular expression, it will try to load this experiment number from all the directories.
• exp_type (str) – Since the function assumes that you have different types of experiments sorted into different directories, this argument specifies the type of experiment see getDATADIR() for more info.
• postproc (function, str, or None) –

  This function is fed the nddata data and the remaining keyword arguments (kwargs) as arguments. It’s assumed that each module for each different file type provides a dictionary called postproc_lookup (some are already available in pySpecData, but also, see the lookup argument, below).

  If postproc is a string, it looks up the string inside the postproc_lookup dictionary that’s appropriate for the file type.

  If postproc is None, it checks to see if the any of the loading functions that were called set the postproc_type property – i.e. it checks the value of data.get_prop('postproc_type') – if this is set, it uses this as a key to pull the corresponding value from postproc_lookup. For example, if this is a bruker file, it sets postproc to the name of the pulse sequence.

  For instance, when the acert module loads an ACERT HDF5 file, it sets postproc_type to the value of (h5 root).experiment.description['class']. This, in turn, is used to choose the type of post-processing.

  dimname:passed to load_indiv_file() return_acq:passed to load_indiv_file() add_sizes:passed to load_indiv_file() add_dims:passed to load_indiv_file() use_sweep:passed to load_indiv_file() indirect_dimlabels:  passed to load_indiv_file()
• lookup (dictionary with str:function pairs) – types of postprocessing to add to the postproc_lookup dictionary

pyspecdata.load_files.load_indiv_file(filename, dimname='', return_acq=False, add_sizes=[], add_dims=[], use_sweep=None, indirect_dimlabels=None, expno=None)

Open the file given by filename, use file signature magic and/or filename extension(s) to identify the file type, and call the appropriate function to open it.

Parameters:

• dimname (str) – When there is a single indirect dimension composed of several scans, call the indirect dimension dimname.
• return_acq (DEPRECATED) –
• add_sizes (list) – the sizes associated with the dimensions in add_dims
• add_dims (list) – Can only be used with dimname. Break the dimension dimname into several dimensions, with the names given by the list add_dims and sizes given by add_sizes. If the product of the sizes is not the same as the original dimension given by dimname, retain it as the “outermost” (leftmost) dimension. pyspecdata.core.chunkoff() is used to do this, like so: data.chunkoff(dimname,add_dims,add_sizes)
• indirect_dimlabels (str or None) – passed through to acert.load_pulse (names an indirect dimension when dimlabels isn’t provided)

Returns:

the nddata containing the data, or else, None, indicating that this is part of a pair of files that should be skipped

Return type:

nddata or None

safe modules

Here, include modules that are safe – that is, modules that don’t import a lot of junk, and for which we can just call autosummary.

datadir	Allows the user to run the same code on different machines, even though the location of the raw spectral data might change.
latexscripts	Provides the pdflatex_notebook_wrapper shell/dos command, which you run instead of your normal Latex command to build a lab notebook.