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Visualize CCD data from ALS BL 4.0.2 diffractometer

Project description

ALS.Liam (version 0.8)

Overview

Liam is a Python module used to visualize CCD data that was collected on the Scattering Chamber located at Beamline 4.0.2 (a.k.a. BL402) of the Advanced Light Source (Berkeley, CA USA). This module utilizes the ALS.Milo package for processing the data.

It is distributed under the namespace package, ALS.

Installation

Install from PyPI

ALS.Liam can be installed from PyPI using pip. The following example shows how.

>> sudo python -m pip install ALS.Liam -vv

Install from local repository (download)

ALS.Liam can be installed from a local copy of the project repository using pip. The following example shows how.

>> cd ALS.Liam-0.8.0/  # Local directory of project repository
>> sudo python -m pip install . -vv

Background information

Data from the BL402 Scattering Chamber is stored in two types of files:

  • FITS files: Each image captured by the CCD (a.k.a. the camera) is stored in a separate file using the FITS format. More details below. https://fits.gsfc.nasa.gov/fits_documentation.html
  • Scan summary files: When a scan sequence is run to collect data, a text file is created to summarize the parameters of the scan and the data collected. These files typically end with the extension "*-AI.txt".

Every scan summary file contains a header that describes the scan and the types of data recorded, followed by data rows -- one row per data point. An Instrument Scan provides an image filename in each data row that can be used to access the CCD images recorded during the scan.

Using the FITS Viewer to visualize your data

To start the viewer, run the following command in your terminal or prompt:

python fitsViewer.py

Load data files

  • Click Load data file button to open a file selection dialog.
  • Select file for display. This can be a .FITS file, a *-AI.txt file, or many image file types (.png, .jpg, etc.)
  • If the file type you are looking for is not displayer or not selectable, it might be necessary to change the file filter to the appropriate file extension.
    • Mac: For OS X, the file filter might be hidden. If so, click the Options button in the file selection dialog.
    • Selecting a *-AI.txt file will allow you to browse all FITS files that were collected as part of this data scan

Viewing the data

Image data is displayed in the central region. File name and location are displayed near the top of the window. To the right of the image is a color scale bar and histogram of the data intensity values. The color scale of the image can be adjusted with these controls (see Adjusting the color scale). To the left and also to the bottom of the plot are 1D representations of the image intensity, collapsed along the orthogonal dimension. The rows and columns can be restricted for these 1D plots using control bars in the image plot (see Setting ROI horizontal and vertical limits). The cursor displays the row, column, and intensity value for the pixel under the cross-hair.

Zoom or pan 2D data

The image magnification (zoom) can be changed by using the middle mouse button (or scroll wheel). Clicking-and-dragging the mouse on the image will recenter (pan) the image by the amount that you drag it.

Adjusting the color scale

Drag the yellow bars (between the intensity labels and the color bar) to adjust the upper or lower limit of color scaling. There are options for autoscaling the intensity (covers full range) or toggling between linear and log intensity scale; these are activated by the corresponding checkboxes. The colored arrows to the right of the color bar allow the color scale to be manipulated. These arrows can be relocated, added (by double-clicking in an empty space), removed (right-click for context menu), or be changed to other colors (click on arrow).

Setting ROI horizontal and vertical limits

A Region of Interest (ROI) can be selected from the image by setting horizontal and/or vertical limits. This is done by dragging the yellow or blue bars that are initially located at the left and bottom edges of the image. The highlighted blue (yellow) regions are averaged to generate the blue (yellow) 1D plots. Initially the 1D plots average data across the entire image before the selection bars are first moved. Returning the selection bars to their initial position recovers this initial state. Intensity values for the 1D plots are displayed in the average counts per pixel.

Navigate FITS files within a scan set

Click Prev or Next buttons to display the previous or next image in the scan data set. First and Last buttons will display the first or last image in the scan data set. The image number can be typed directly into the entry field to the left of these buttons. If an out-of-range value is entered, it will automatically select the nearest available image.

Navigation is only possible for *-AI.txt files. The image number persists between data sets; i.e., it does not change when you load a new data set (unless it is out-of-bounds for the new data set).

Reloading (incomplete) data sets

Click Reload to reload the data file with the most recent information. This is most useful for datasets (*-AI.txt files) that were incomplete when initially loaded (because data was still being captured or transfered).

Export plots

Right-click on image or plot, then select Export. Select region, format, and other options. Data can be exported to file or copied to clipboard.

Notes for Developers

Additional test data

Additional CCD data files and scan sets can be downloaded from these links. Unzip and place the contents into the test_data folder.

Copyright Notice

ALS.Liam: BL402 CCD image viewer for RSXD data, Copyright (c) 2017-2019, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at IPO@lbl.gov.

NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit other to do so.

Project details


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