This is the user manual for the PEL Visualizer (PelVis) program. The PelFile was designed to read PAPA Electronic Log (PEL) files, as designed by Lexitech in their documentation of the PAPA detector.

PelVis was written in Python 2.6 and requires the following libraries:

• NumPy for array handling
• SciPy for other numerical libraries
• wxPython for the user interface
• matplotlib for data visualization.

PelVis can load either one or PEL files at any given time. Use File -> Open to load a single file and File -> Polarized Set to load two files (for making polarization measurements).

Whenever PelVis loads a file, it first asks for the neutron data followed by the monitor data. If you do not wish to normalize a data run against monitor, simply cancel the load dialog when it asks for a monitor file. Note that PelVis normalizes against the total monitor count, not the monitor spectrum, so the intensity spectrum of the beam will still be visible after normalization.

The neutron data file can either be a PEL file for a Numpy NPZ file. The NPZ files are pre-formatted histograms which load much faster than a PEL file. NPZ files can be created through histbatch.py. The main disadvantage of NPZ files is that every NPZ files is 200MB in size, regardless of the time of data collection.

If Pelvis only loads a single file, all it can display is an intensity. With two files, there are four ways of processing the data.

• Spin up data: This is the (raw or normalized) neutron intensity in the spin up state. It can be selected from the menu with Analysis -> View Spin Up State or via Ctrl + U
• Spin down data: This is the (raw or normalized) neutron intensity in the spin down state. It can be selected from the menu with Analysis -> View Spin Down State or via Ctrl + D
• Polarization: This is the polarization of the neutron beam as a function of position. It can be selected from the menu with Analysis -> Check Polarization or via Ctrl + P
• Flipping Ratio: This is the polarization of the neutron beam as a function of position. It can be selected from the menu with Analysis -> Check Flipping Ratio or via Ctrl + F

To the right of the main image area is the color scale. Different color scales can be chosen from the Color menu. The upper and lower bounds of the color bar can be adjusted via the Minimum Intensity and Maximum Intensity text boxes on the right. If an intensity box is left empty, PelVis will default to using the largest data point for the maximum and the smallest data point for the minimum.

In addition to the main color scales of Hue, Greyscale, and Spectral, there’s also a Map Picker, which has a very large selection of color bars available. Unfortunately, the map picker is very slow the first time it is loaded, so I would recommend not using it unless you have a specific reason to chose another color bar. If you do use the map picker, simply click on your chosen color bar to change the color map for your data.

Beneath and to the left of the detector image is a one dimensional histogram of the displayed data. Note that it is a histogram of whatever is being displayed, so, when displaying the flipping ratio, it will show the sum of the flipping ratio and not the flipping ratio of the sum of the two states. Also, the histograms are automatically normalized to fill their region. Finally, the histogram only operates within the region of interest. For instance, if the region of interest was from 100 to 200 in the x direction and from 300 to 400 in the y direction, the lower histogram would contain the sum of the data between 300 and 400 in the y direction for each x position, while the left histogram would contain the sum of the data between 100 and 200 in the x direction for each y position.

There are two ways of cohsing the region of interest. The first is direct entry into the text boxes on the right (e.g. Minimum X holds the lower x bound of the region of interest). Alternately, the region of interest can be chosen directly off of the detector image. Left clicking on the detector image sets the upper left hand corner of the region of interest while right clicking selects the lower right hand corner. Changes to the region of interest do not take effect until you click on the Update button in the lower right hand corner.

In the lower left hand corner of the screen is a live set of position statistics. The X and Y values are the current pixel position of the mouse cursor. The Z value is the data under the cursor. Finally, ROI is the integratation of the region of interest. Once again, it is the integration of the processed data, not a function applied to the integrated data.

To remove background noise from the signal, first select a region of interest in the background region. Then run Noise -> Region of Disinterest. If two files are loaded, it performs the background subtraction on both files. Note that, due to memory contraints, the original, non-background subtracted data is no longer kept in memory and cannot be used for error analysis. The result of this is that the uncertainty for each spin state will be (N-n)^0.5 instead of (N+n)^0.5. There may be a way to fix this issue. If you do fix this problem, be sure to update the documentation.

File -> Spectrum loads up a spectrum dialog for viewing wavelength dependent data. There are three options for binning the data:

• Raw Binning does not perform any rebinning of the data and uses all 200 TOF channels.
• Auto Binning bins the data so that no bin has a greater relative uncertainty than that listed in the Minimum Percent Error text box. This helps pull the most visual information out of the signal, but can be difficult to use in calculations, as there’s no way to assure that two data sets will be binned the same way.
• Fixed Binning bins the data into a number of bins equal to the value in the Minimum Percent Error text box. Using a value of twenty is especially useful, as it results in one angstrom bins.

The binning options are set, click the View Spectrum button to plot the data from the current region of interest. The resulting graph will depend on the current view mode (e.g. if the main image is polarization, then the graph will be of the polarization). The Minimum Intensity and Maximum Intensity dialog boxes on the right side of the main PelVis window will set the initial y-range for the plot. As with the main image, the y-range will default to the maximum and minimum data values if the corresponding intensity value is not set.

At the top of the graph window is a set of navigation controls:

• Home: Returns the graph to its original state
• Back: Undoes the previous change to the graph
• Forward: Undoes the last undo
• Pan: Control the graph position with the mouse. Clicking and dragging with the left mouse button will move adjust the position of the graph origin. Dragging with the right mouse button will adjust the scale of the axes.
• Scale: Dragging a selected window with the left mouse button will zoom in on the selected region.

The current image can be copied to the clipboard via Edit -> Copy or Ctrl + C. It can also be saved to an image via File -> Save or Ctrl + S.

In a spectrum windows, the spectrum image can also be copied to the clipboard via Edit -> Copy. It can also be saved as an image file by clicking the save icon near the top of the window.

The Spectrum dialog can save a spectrum to a tab delimited text file. The first column is always wavelength, the second is data, and the third is uncertainty. There is currently a bug that causes the wavelength data to be saved by the number of TOF bins which it contains. I will update the documentation when this bug is fixed.