Analyzing Cubes

This page describes how to use the components of the Analysis Layout, specifically, the Histogram, Colormap, and Animator, specifically as applied. In the standard Analysis Layout, these Views appear on the right side of the analysis panel. Each of these Views can be configured by clicking on the appropriate Settings box in the Menu Bar or by right-clicking on the Settings option in the context menu that appears.


By default, the 'histogram' tool shows the distribution of data values in a given plane (channel) of a three dimensional image. The frequency with which a data value appears is shown as a histogram. The Histogram Settings have three different tabs.

Display: This tab controls how many histogram bins there are or, alternatively, the number of bins shown for the data. The display components draw the histogram with different styles, including checkboxes for whether to show the log of the counts and whether to color the histogram by the same color map as is used in the data. The image below shows editing the number of bins in the image to be 1000.

Histogram tool

Range: This tab has two main parts. The Zoom component controls which part of the histogram is shown on the histogram view. To zoom to part of the histogram, click and drag left-to-right in the histogram view. Alternatively, enter text values for either the image values or the quantiles ("Percent") in the image.

The Linked Image clip controls which part of the color map are displayed in the Image view. By holding down the shift button and dragging over a section or entering text values, the minimum and maximum values of the color map can be determined. Clicking Apply to Image will reset the color map. The image below shows the result of clipping the image to the selected range of the histogram.

Selecting colormap parameters using histogram

Selection: This tab controls what data are displayed in the histogram. For large data sets, seeing the whole histogram will require unchecking the "if size is <= 1000000 pixels" box. The 2D controls what part of the 2D image (spatial coordinates) are being displayed in the histogram.


The 'colormap' tool controls the color transform applied to the data in the image.  The colormap is displayed and the tool is controlled through the components at the bottom of the tool.

From left to right, the Miniumum Value sets the bottom of the color table, the Color Map determines what color transform to use on the screen, the Transform menu controls the mathematical transform between the data values and the color values show.  The Units button allows the units of the color bar to be set.  Finally, the Maximum Value sets the maximum bound for the data set.


In the Colormap Settings, the color map can be controlled in more detail.  

Color map Settings

The four tabs control details of the transform. The first tab, Color Map, controls the details of the color map.  The Red / Green / Blue (RGB) transfer functions are shown as graphs of the appropraite color showing the data value on the x-axis and the saturation of that color on the y-axis.  By unchecking the Synchronize Color box, the individual color saturations can be controlled individually.  Similarly, checking Reverse or Invert will modify the Color table.  

The NaN tab controls the default value of NaN or missing data in the cube.  These default to the value at the bottom of the color table.  To change the color, uncheck the Default box.

The Tranform tab allows the Gamma correction for the image to be controlled.  This can be entered as a number (Default = 1) or controlled using the 2D slider.  The 2D slider is constructed to allow for both coarse control and fine control.

The Border Background tab is a color picker to select the color of the background of the image. To change the color, uncheck the Default box.


The Animator View controls what sets of data the Image Viewer will show. The Animator is used to display two dimensional image subsets of three-dimensional spectral line data sets, continuum polarization data sets, or to change between multiple images.

The Animator uses "tape deck" style controls and many of the controls have linked behavior.


To select a specific channel (or polarization, or image), the number can be directly entered in the Channel Number box. Dragging the Slider will also update which image is displayed. Images can also be played in an animation by pressing the Play Forward or Play Backward buttons. The animation is halted by pressing the Stop button. The animation can be incremented by a single image at a time by clicking on the Step Forward or Step Backward buttons. Pressing the First Image or Last Image buttons jumps to the first or last image in the animation. The range of the animation is controlled by setting the Lower and Upper Bounds of the animation.

Clicking on the Settings checkbox opens more options for the animation. The Step value indicates how many images to increment by in the animation. The Boundary Behavior buttons indicates what the animation should do at a boundary. Wrap jumps from the last image to the first image and continues the animation. Reverse changes the direction of animation upon reaching the boundary and Jump will alternate between the first and last image in the animation range (which is good for "blinking" images).