Eigentool Histogram
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Eigentool Plot Analysis

 

 

Histogram Window

This window is used to display and analyze histograms of image data.

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Histogram Use

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On the histogram

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Use the left mouse button to set the minimum value displayed on the X and Y axis'.

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Use the right mouse button to set the maximum value displayed on the X and Y axis'.

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Use the 's' key to enable or disable auto-scaling to Y axis.

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Use the 'c' key to select the next histogram color choice in the list.

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Use the 'L' key to enable or disable the display of the location on the histogram.

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Use the 'R' key to enable or disable the display of the reference lines.

Spectroscopy Only options

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Use the middle mouse button to select the peak for calibration or spectral shifting.  Also used to set the baselines and max when performing susceptibility processing.

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Press a number, n, for a reference peak to shift a selected peak to.

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Use the 'h' key to calibrate the parts per million scale.

Enter the value in the PPM item on the Spectroscopy dialog

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Use the 'l' key to move one spectral point to the left.

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Use the 'r' key to move one spectral point to the right.

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Use the 'u' key to move one spectral point up.

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Use the 'd' key to move one spectral point down.

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Use the 'e' key to expand the histogram.

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Use the 'f' key to display the entire histogram.

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Use the 'o' key to turn on/off the susceptibility correction for the pixel.

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Use the 'p' key to set the Parts Per Million scale from 4.1 - 0.1

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Use the left or right arrow keys to shift a spectra left or right 1 position.

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Properties (use View->Properties if the following options are not visible)

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Minimums and Maximums

bullet Enter or view the minimum and maximum values, in Y Min, Max, of the Y axis.

Note

The Y Min, Max is set automatically if View->Auto Scale has been enabled.

bullet Enter or view the minimum and maximum values, X Min, Max, of the X axis.
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Y, X Offset

bullet Enter a value for the Y offset to separate the Y axis' of a Spectroscopy stack plot.
bullet Enter a value for the X offset to separate the X axis' of a Spectroscopy stack plot.
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Browser

Select at least one of 1, 2, 3, 4 to select which browser images to use for histogram calculations.

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Butterworth Filter

bullet Enter a value for the Order of the butterworth filter.
bullet Enter a value for the Cutoff of the butterworth filter.

Note

See View->Smooth for help on selecting this filter.

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Gaussian Filter

bullet Enter a value for the Sigma of the gaussian filter.
bullet Enter for the # of times, in Iterations, to apply the gaussian filter

Note

Use 0 in Iterations to disable the filter.

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Peak Subtraction

bullet Press Sub 1 to toggle the subtraction of the first peak from the histogram.
bullet Press Sub 2 to toggle the subtraction of the second peak from the histogram.
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bullet Press Sub n to toggle the subtraction of the nth peak from the histogram.

Note

M,S must have been pressed for this list to be displayed.

 

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Options->Histogram Menu

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Plot

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Spatial to plot the number of pixels per gray level for a region, or volume, of interest.

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Horizontal to plot the average gray level for each column of a region of interest.

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Vertical to plot the average gray level for each row of a region of interest.

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Temporal to plot the average gray level, over a region of interest, for each image.

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Spectroscopy to plot the height of each spectra.  See View->Spectra for different Spectroscopy histograms and Spectroscopy Only options for operations on the histogram.

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Calculating Using

bullet Current Image to calculate the histogram using the currently selected image.
bullet All Images to calculate the histogram using all the images from the currently selected browser.
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Get Region(s) From

bullet Current Region in Current Browser to calculate the histogram using the region of interest on the currently selected image in the currently selected browser, for any image in any browser.
bullet Current Region in Each Browser to calculate the histogram using the region of interest on the currently selected image in each browser, for any image in that browser.
bullet All Regions in Current Browser to calculate the histogram using the region of interest on each image in the currently selected browser, for each image in any browser.
bullet All Regions in Each Browser to calculate the histogram using the region of interest of each image in each browser.
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Distribution

bullet Gaussian assumes a gaussian distribution in the histogram when calculating means and standard deviations.
bullet Chi-Square assumes a chi-square distribution in the histogram when calculating means and standard deviations.
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Size

bullet 480 x 640 to set the histogram viewing area to 480 rows by 640 columns.
bullet 256 x 256 to set the histogram viewing area to 256 rows by 256 columns.
bullet 256 x 512 to set the histogram viewing area to 256 rows by 512 columns.
bullet 256 x 1024 to set the histogram viewing area to 256 rows by 1024 columns.
bullet 380 x 760 to set the histogram viewing area to 380 rows by 760 columns.
bullet 512 x 512 to set the histogram viewing area to 512 rows by 512 columns.
bullet 512 x 1024 to set the histogram viewing area to 512 rows by 1024 columns.
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Style

bullet Bar to display the data points as vertical bars rising from the x axis.
bullet Connect to connect the data points with a single-width line.
bullet Points to display the data points as dots.
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Spectra

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Single to display a single spectra with a reference spectra, if it exists.

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Grid to display multiple spectra, each in its own grid.

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Stack to display multiple spectra, stacked in the same plot.  See Y,X offset on how to separate each spectra on its own axis'.

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Y Axis

bullet Linear to use a linear scale for the Y axis.
bullet Log to use a log scale for the Y axis.
bullet Exponential to use an exponential scale for the Y axis.
bullet Squared to use a squared scale for the Y axis.
bullet Square Root to use a square root scale for the Y axis.
bullet Cubed to use a cubed scale for the Y axis.
bullet Cube Root to use a cube root scale for the Y axis.
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X Axis

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Non Spectroscopy Histograms

bullet Linear to use a linear scale for the X axis.
bullet Log to use a log scale for the X axis.
bullet Exponential to use an exponential scale for the X axis.
bullet Squared to use a squared scale for the X axis.
bullet Square Root to use a square root scale for the X axis.
bullet Cubed to use a cubed scale for the X axis.
bullet Cube Root to use a cube root scale for the X axis.
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Spectroscopy Histograms

bullet Hertz to use a frequency scale for the X axis.
bullet Parts Per Million to use a parts per million scale for the X axis.
bullet Height to use a height scale for the X axis.
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Horizontal/Vertical

bullet Gray Level to calculate and display the average gray level versus the row/column position.
bullet # of Pixels to calculate and display the the number of pixels versus the row/column position.
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Annotate

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Label to toggle on/off the display of a label on the histogram.

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Raw File to toggle on/off the display of the raw file name on the histogram.

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Name to toggle on/off the display of the patient name on the histogram.

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MRN to toggle on/off the display of the patient medical record number on the histogram.

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Coordinates to toggle on/off the display of the region of interest coordinates on the histogram.

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Date to toggle on/off the display of the date on the histogram.

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Study Date to toggle on/off the display of the study date on the histogram.

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Location to toggle on/off the display of the location on the histogram. (See key shortcuts 'L')

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Zero Line to toggle on/off the display of a zero line on the histogram.

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Box to toggle on/off the display of a box around the histogram.

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2 Cursors to toggle on/off the display of 2 cursors on the histogram.

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Reference Lines to toggle on/off the display of the lines indicating the reference peaks. (See key shortcuts 'R')

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X-Axis to enable or disable the display of the x-axis.

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Cursor Set Range to enable or disable using the cursors to set the Y Min and Max and X Min and MaxAuto Scale overrides this option for the Y Min and Max.

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On Image to enable or disable the display of a Horizontal Histogram or Vertical Histogram on the Display Image.

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Color to select the colors to use to display the histogram.   (See key shortcuts 'c')

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Color to display a histogram in color using black, white, Roi Draw Color, and Roi Erase Color, black is used for the axis and light grey is used for the background.

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Monochrome to display a histogram in black, white and 2 gray levels, with black for the axis and light gray for the background.

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Black and White to display a histogram with a white background and black for the axis and histogram.

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Auto Scale to toggle between manual scaling or automatic scaling of the histogram data.  Automatic scaling will set the Y Min and Max to the minimum and maximum of the histogram data between the X Min and Max. (See key shortcuts 's')

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Smooth to enable or disable the smoothing of histogram data using a butterworth filter (See Butterworth Filter to set the values for the butterworth filter).

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Dialog Items

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Plot

Press Plot to plot the histogram, using the options you have selected.

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Reset

Press Reset to return to delete the current histogram calculation.

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Cancel

Press Cancel to remove the histogram window

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Last modified: 01/17/05