Introduction

This program is able to read and display binary SPE files, generated by WinSpec software (Princeton Instruments). It works in a very similar to a photo-viewing application fashion, i.e. the spectrum is displayed after the file is clicked in a filemanager. Arrows keys are used to show next/previous file in the folder. Press the space bar to hold the current line.

The program is able to subtract a dark file and perform a wavenumber calibration.

Details

Data storage model

The basic idea is that all your SPE files, which are relevant to each other (e.g. data, calibration, dark), should be placed into a single folder. speview reads the relevant files that are necessary to display the data, as well as creates some new files in the same folder. Ideally, all the spectra should be taken with the same settings (accumulations, gain, exposure time, slit width, readout rate and so on).

So remember, speview can work only with those files, which are located in the same directory.

How it works, or short manual

To display an SPE file correctly, speview requires a simple configuration file, called ".speview.conf". The file is created if it is not present. If this is the case, speview would ask user the following questions:

• Do you want to perform wavenumber calibration?
  • If yes, then select an SPE file with the spectrum of a standard substance, then select the corresponding dark file.
• Do you want to subtract dark from your actual data to be displayed?
  • If yes, then select the corresponding dark file.

speview accepts only a single argument, which is a filename of the SPE file to be displayed. The directory of this file becomes the working directory. The spectrum is obtained from the binary SPE file using module "winspec". If the wavenumber calibration is required, it is performed with a module called "xcalraman". The calibration report and calibration coefficients are stored in files "calibration_report-<substance>.pdf" and "xcal_coeffs.csv", respectively.

After the data are processed, speview calls matplotlib to create a plot and displays it with the default backend, e.g. qt4agg. A window with a plot will pop up.

Installation

You should be able to install the package with just one command:

pip install speview --allow-unverified pyzenity

PyZenity is not stored on PyPi and therefore is considered by pip as potentially dangerous package. For this reason you have to allow it explicitly.

Troubleshooting

Please note, that you may encounter two troubles:

1. The matplotlib uses a non-interactive backend (no window appears)
2. Pylab has some problems with shared libraries of PySide:

ImportError: libpyside-python2.7.so.1.2: cannot open shared object file: No such file or directory

Selecting default backend for matplotlib

You can select your default backend, e.g. qt4agg, in matplotlibrc file. The location of this file can be determined from python:

import matplotlib as m
m.get_configdir()

Usually it is something like ".config/matplotlib/", and placing a file named "matplotlibrc" there should work just fine. More info could be found at http://matplotlib.org/users/customizing.html

You may wish to use a qt4agg backend, which requires PySide. If you install PySide with pip, make sure that you have tools cmake and qmake. The last one is typically found in something like libqt4-dev. Command for installation of PySide:

pip install pyside

Fixing Pylab

Problem happens because for some reason the post-installation script "pyside_postinstall.py" did not run. I faced this problem only when working with virtual environment. Fix it by executing the following command in your virtual environment (e.g. python ~/.virtualenvs/<env>):

bin/pyside_postinstall.py -install

Description of requirements

I tested the package using virtual environment and generated a list of dependencies with the "pip freeze" command. Basically, you should have on your computer the following packages:

• pylab for plotting (note: you need support for an interactive backend, e.g. qt4agg, wxagg, gtkagg, tkagg, etc.). You can test whether you have a suitable backend by running the following line of code in your python interpeter: import pylab as p; p.gca(); p.show(). If a window with empty axes will pop up, then everything is correct!
• xcal_raman for x-axis calibration and reading of SPE files (available on https://pypi.python.org/pypi/xcal_raman)
• pyZenity for graphical interaction with user

Use

You can select this programm to be the default application to open SPE files. Then if you click an SPE file, the programm gets its filename as a first argument.

First run

If you start it for the first time in some specific folder, it will ask you a couple of questions and create a config file .speview.conf based on your answers.

User interaction

Then a standard matplotlib window with a plotted spectrum will popup. You can use all features the matplotlib offers you:

• Adjust figure size and line parameters
• Pan and scale the plot with mouse and icons on top
• Save figure (s key)
• Turn grid on/off (g key)
• Turn axis scale (log or linear) with l key for y-axis and L key for x-axis

Use the following keystrokes for additional functions, not offered by matplotlib:

• Right and left arrows: go to next/previous SPE file
• Space bar: save current spectrum to buffer or remove it from buffer
• d key to subtract a saved spectrum from the current one (the result is displayed in another scale)
• D to remove the result of subtraction (opposite of d)
• v or V to toggle the visibility of current spectrum (useful if you, for example, would like to see only the result of the subtraction)
• i or I to display the file info (acquisition parameters and comments)
• F5 to select the default figure format
• h or H to display the help message and the program version

Future plans

What I would like to implement in the future:

• Reading of SPE files with multiple spectra
• Reading of CSV files generated by WinSpec

For more details, see https://github.com/ximeg/speview/issues