johnson-c / spe2py

Loads Princeton Instruments LightField (SPE 3.0) files into a python environment.

spe2py

spe2py is a module that imports a Princeton Instruments LightField (SPE 3.x) file into a python environment.

Basic Usage

Loading and accessing data

Use the load() function to load one or more SPE files at a time:

>>> import spe2py as spe
>>> loaded_files = spe.load()

A file selection window will open to allow browsing for source files. The result is an individual SpeFile object, or, in the case where multiple files are loaded at once, a list of SpeFile objects.

Raw data from a file is stored in NumPy arrays and can be accessed directly by

>>> frame_data = loaded_files.data[frame][regionOfInterest]  
>>> frame_data = loaded_files[n].data[frame][regionOfInterest]  # where multiple files are loaded

Alternatively one can load an individual file by passing SpeFile() the source path directly:

file_object = spe.SpeFile(path)
# is equivalent to...
file_object = spe.load()  # and selecting the same file/path

Automatic imaging and plotting

To quickly view an individual frame, region-of-interest, or spectrum, use the image() or specplot() methods. For example,

>>> loaded_file.image()  # images the first frame and region of interest
>>> loaded_file.image(f, r)  # images frame 'f' and region of interest 'r'
>>> loaded_file.specplot()  # plots the loaded spectrum

Accessing metadata

Upon loading, the metadata contained in the file's XML footer is automatically parsed and stored as an untangle object in the footer variable. Elements and attributes can be accessed by calling the different elements and subelements of footer, ending with the attribute as a string:

>>> sensor_height = loaded_file.footer.SpeFormat.Calibrations.SensorInformation['height']

One can print the full element tree by calling the xmltree() method.

Dependencies

• NumPy - data storage and file reading
• tkinter - file selection dialog
• matplotlib - imaging and plotting
• untangle - XML parsing

Version

1.0.0a - initial upload

License

MIT