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pycxdgui
.gitignore
README.md
buildenv.sh
setup.py

README.md

Simple GUI for xray image viewing/analysis

See buildenv.sh for a sample script on how to setup. Requires anaconda.

Running

Running is as simple as running this within python:

    from pycxdgui.startGUI import run
    run(configfile=config_filename)

where config_filename is the location to your configuration file (see below for more details).

Dependencies

  • python3.5 PyQt4 numpy h5py pip

  • pims pillow tqdm scipy scikit-image pandas cython

  • pyqtgraph. This has been copied from the pyqgraph repository from commit 4752b777921f54b3a23dfc2952697ddf11922112. To retrieve this code, run the following:

    git clone https://github.com/pyqtgraph/pyqtgraph
    cd pyqtgraph
    git checkout 4752b777921f54b3a23dfc2952697ddf11922112

Configuration

A configuration file may be used to specify initial configuration setings of the GUI. A sample configuration file is as follows (see comments for the descriptions):

# yaml file for configuration
# this is conventional yaml format:
# http://www.yaml.org/start.html
# comment out rows you don't want
setup:
    # default extension to look for
    extension: ".imm"
    # the parent directory
    DDIR: "." 
    # the storage directory
    SDIR: "."
    # beam center
    xcen: 1313.39
    ycen: 1267.81
    # wait time for file listening
    wait_time: .1
    # the initial mask name
    mask_name: "/path/to/mask.hd5"
    # the values that define masked and unmasked region >=
    mask_threshold: 1
    # sample detector distance
    rdet: 3.800 # in m
    energy: 7.44137  # in keV
    wavelength: 1.6660910558136472  # in angstroms
    dpix: 20 # pixel size in um
    # first filename to load
    filename: "/path/to/filename.tiff"
    transformation: [ [1, 0],
                      [0, 1]
                    ]
# parameters for circavg computations
circavg:
    noqs: 800 #partitioning for circular average/qphi maps
# parameters for qphi avg computations
qphiavg:
    noqs: 800 #partitioning for circular average/qphi maps
    nophis: 360 #partitioning for qphimaps in phi
deltaphicorr:
    noqs: 800 #partitioning for circular average/qphi maps
    nophis: 360 #partitioning for qphimaps in phi

Credits: Some of the icons were provided for free online by various authors. See icons/source-list.txt for the original source link for each icon

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