Copy Region

Overview

CopyRegion copies (with an optional conversion of data types) all or part of a data set to a new data set. CopyRegion's user interface uses the same set of controls for selecting and processing a region as other Priism applications. The other controls are used when the new data set is written to a window. The RGB toggle selects whether multiple wavelengths are displayed simultaneously as different color components in a single image or if images contain a single wavelength in pseudocolor. The AutoScl and Restore buttons as well as the fields for the scaling on each wave select how the data is mapped to the pixel values displayed in the image.

When used to open a complete data set in an image window, CopyRegion is very similar to ViewFile. The difference is that CopyRegion makes a copy of the data in memory (and scratch space on the local file system) while ViewFile only loads the data as needed and does not have to keep a copy (though it may do so while space is available). The effect of these differences is that ViewFile returns control to the user more quickly, but once control is returned, the initial access to the data and images is faster when CopyRegion is used. Using CopyRegion instead of ViewFile also increases the amount of memory and disk space that Priism uses.

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RGB

When the output of CopyRegion is written to an image window, select this toggle to have the data displayed with multiple wavelengths combined to form a single image. Up to three wavelengths can be displayed simultaneously with each wavelength assigned a different primary color (red, green, or blue). If the toggle is not selected, wavelengths are not superimposed and the image is shown in pseudocolor (typically shades of grey). The RGB toggle only affects how the data is displayed initially; use the controls on the image window to switch between the display mades after CopyRegion has written the data.

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AutoScl

Select this toggle when you want each section, when copied to an image window, to be displayed in such a way that the range of data values in the section maps to the full range of image values. The default scaling parameters for each wave will still be those set from the wave scaling controls, but each section will have its own scaling parameters set and those defaults won't take effect.

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Restore

Use this button to load the wave scaling values that had been used previously with the input data set and had been saved from the image window's Scale function.

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Wave scaling parameters

When CopyRegion writes its output to a window and the AutoScl toggle is not on, these values set how the data is mapped to the quantities shown in the image. For details about how this mapping is done, see the "Scaling Values" topic in the documentation for the image window's Scale application.

If CopyRegion's input is a window, the default scale values are those for that window. When the input is a file, the default scale values are drawn from the minimum and maximum values recorded in the file's header. If you have looked at a file before and saved the scale parameters used (the documentation for Scale describes how to do this), you can use the Restore button to load those scale parameters.

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Conversions

By default, the data type of the output from CopyRegion is the same as the data type of the input. If the output data type (selected with the Mode control) is not the default, then a conversion is done. There are three special cases for the conversion process:

When converting data to bytes, the wave scale values are used to map the data to values between 0 and 255. The case where the first two scaling values are zero is treated like any other for this conversion.
When converting complex data to any of the purely real formats, only the real part is converted; the imaginary part is discarded.
For the conversion of a purely real format to a complex one, the imaginary part of the result is set to zero and the real part is set to the converted value.

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Command Line

CopyRegion accepts the command-line arguments described in Region.html. In addition, it has the following options (parts in brackets are optional):

-autoscale: If this option is present and the output is an image window, each section will be scaled separately as described in the AutoScl topic.
-restore_scale: If the this option is present, CopyRegion will look up the scaling values for the input in the recently saved parameters from the image window's scale function. If scaling values for the input are found, then those are used and any -scl options (see below) are ignored.
-rgb: If this option is present and the output is an image window, the data will be displayed with multiple wavelengths superimposed as different color components in the same image.
-scl1=bound1[:bound2[:exp[:flag]]]: Sets the scaling parameters for the output drawn from the first wavelength of the input. Takes one to four parameters; parameters not specified take on their default values (see the Wave scales topic for what the default values are). The first two parameters are the intensity bounds for scaling, the third is the exponent, and the fourth sets what happens to data values outside of the intensity bounds. The documentation for the image window's Scale function describes the parameters in more detail. The scaling parameters set by this option will have no effect if you also use -autoscale; they may also be overrided when you use -restore_scale. There are similar options (-scl2, -scl3, -scl4, and -scl5) to set the scaling for the output from other input wavelengths.

As an example, the following copies the first two wavelengths from fish.dat into window 3 using a reversed scaling between 500 and 2500 for the first wavelength and a scaling between 700 and 3000 with a gamma correction factor of 0.5 for the second wavelength:

    CopyRegion fish.dat 3 -w=0:1 -scl1=2500:500 -scl2=700:3000:0.5

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Copy Region

Overview

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Related Priism Topics

RGB

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AutoScl

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Restore

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Wave scaling parameters

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Conversions

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Command Line

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