Convert from Priism's Native Format to TIFF

Overview

This application takes a Priism file and converts it into one or more TIFF files. The conversion can be direct or the data can be scaled to integers in the range of 0 to 255 first. Preservation of the original data values is the key advantage of the direct conversion. The unfortunate drawback is that the output will usually be 16-bit signed integers or 32-bit floating-point values (the exact format will depend on the format of the Priism file) and will not be readable by another application that only supports the baseline TIFF formats (1-, 4-, and 8-bit unsigned integers).

Mrc2tiff has the standard set of Priism controls for selecting a subset of the Priism file to convert. If you wish to scale the input to integers in the range of 0 to 255 before conversion, turn on the "8-bit" toggle button; you can modify the scaling parameters via the "W0 scale" through "W4 scale" fields. If you do not wish to scale the input to 8-bit, turn off the "8-bit" toggle button. The other choice you have to make is whether to turn on the "Single file" toggle button and convert each section in the input into a page in a multipage TIFF file or to turn off the "Single file" toggle button and generate a series of TIFF files which each contain a single section. If you are converting a single section, the choice does not affect the interpretation of the output file, and turning on the "Single file" toggle button is simpler: you only have to enter the output file name in the "Output file" field. When converting multiple sections into a single TIFF file, the controls that are important are the "Output file" button to browse for the output file, the field next to the "Output file" button in which the output file name can be entered directly, and the "Interleaving" menu which controls the ordering of pages in the output. For multiple TIFF files, the important controls affect the generation of the output file names: the "Name format" menu, "Directory" field, "Prefix" field, and "Template" field.

Mrc2tiff is not able to convert complex-valued data.

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8-Bit

If the "8-bit" toggle button is on, Mrc2tiff scales input data values to be integers in the range of 0 to 255 and writes the scaled result to one or more TIFF files. The "W0 scale" through "W4 scale" fields allow you to modify the scaling parameters.

If the "8-bit" toggle button is off, Mrc2tiff does not modify the input data values before writing the TIFF file or files. This direct conversion will generate TIFF files that do not conform to the baseline TIFF standard if the input data is represented as floating-point values or as 16- or 32-bit integers. Many programs that can read TIFF files do not correctly handle such files.

When you select a new input, Mrc2tiff will reset the "8-bit" toggle button. If the input is already represented by unsigned 8-bit integers, Mrc2tiff turns off the toggle button; otherwise, Mrc2tiff turns on the toggle button.

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Single File

The output of Mrc2tiff can be a single TIFF file which has multiple pages where each page has the data for one section, or can be multiple TIFF files where each TIFF file has the data for one section. If you are converting a single section, the single file is easier: all you have to enter is the output file name in the "Output file" field. If you have multiple sections, choose the format to match what your TIFF reader expects; beware that some TIFF readers may only be able to access the first page in a TIFF file with multiple pages.

To have Mrc2tiff generate a single TIFF file with multiple pages, turn on the "Single file" toggle button. Set the name of the output file with the "Output file" button or adjacent field. Use the "Interleaving" menu to control how the numbering of the pages reflects the z, wavelength, and time point indices for each section.

To have Mrc2tiff generate multiple TIFF files, turn off the "Single file" toggle. The output file names are generated automatically in a variety of formats which can incorporate a directory name, prefix, and the z, wavelength, or time point indices for the section.

When you select a new input, Mrc2tiff will reset the "Single file" toggle button. If the input contains a single section, Mrc2tiff turns off the toggle button; otherwise, Mrc2tiff turns on the toggle button.

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Interleaving

Interleaving specifies how the z, wavelength, and time point indices map to the page number for multiple page output and how output section numbers are computed for custom filename templates. If the output has nz z-sections, nw wavelengths, and nt time points, and a given section has a z-section index in the output of iz (0 <= iz < nz), wavelength index in the output of iw (0 <= iw < nw), and time point index in the output of it (0 <= it < nt) then the page number (or output section number), p, with the different interleaving options is:

twz: it+nt*(iw+nw*iz)
tzw: it+nt*(iz+nz*iw)
wtz: iw+nw*(it+nt*iz)
wzt: iw+nw*(iz+nz*it)
ztw: iz+nz*(it+nt*iw)
zwt: iz+nz*(iw+nw*it)

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Name Format

When multiple TIFF files are generated, the file names are generated by filling in a template. From the "Name format" menu you may select a standard template or choose the "custom template" option to use the template entered in the "Template" field. For the standard templates, the generated file names will all start with the contents of the "Directory" field, followed by a slash, and followed by the contents of the "Prefix" field. The remainder of the file name depends on which template was chosen: it will be the template name ("prefix_w#_z#_t#.tif", for instance) without the leading "prefix" and with "w#" replaced with a w followed by the output wave index for the section in the file, "t#" replaced with a t followed by the output time index for the section in the file, and "z#" replaced with a z followed by the output z index for the section in the file. The numbers of digits used for an index is the digits needed to represent the largest index in that dimension. As an example, with the "prefix_w#_z#_t#.tif" template, /var/tmp as the output directory, exp12_2002 as the output prefix, and an input region that has 3 wavelengths, 500 time points, and 30 z sections, the file name for the section whose output z, wavelength, and time indices are 1, 2, and 3 respectively would be /var/tmp/exp12_2002_w2_z01_t003.tif.

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Prefix

When multiple TIFF files are written and one of the standard file name formats is used, the generated file names will include the contents of the "Prefix" field. The section on name formats has an example of this. For a custom template, the contents of the "Prefix" field are substituted for any %p conversion codes.

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Template

The file name generation mechanism for multiple TIFF files may use a custom file name template. To do so select "custom template" from the "Name format" menu and enter the template in the "Template" field. When generating file names, special conversion codes are expanded in the template. The conversion codes have the following general form: %[width][modifier]code.

The recognized codes are:

%: Causes a percent sign to be inserted in the file name.
d: This conversion code is replaced with the contents of the "Directory" field.
p: This conversion code is replaced with the contents of the "Prefix" field.
z: This conversion code is replaced with the z index for the section stored in the file.
w: This conversion code is replaced with the wavelength index for the section stored in the file.
t: This conversion code is replaced with the time point index for the section stored in the file.
s: This conversion code is replaced with the section number for the section stored in the file.

width is optional and may be used with the z, w, t, and s codes to specify the minimum number of digits which are used to display the index value. width may be a positive integer indicating the minimum number of digits to use or the letter a to indicate that the minimum number of digits should be the number of digits in the maximum corresponding index. If an index would have less than the minimum number of digits, leading zeros are added to fill in the missing portion.

modifier is optional and may be used with the z, w, t, and s codes. If modifier is not present, the index generated by those codes is computed for the output file. If modifier is the letter i, then the index is computed relative to the input file.

As an example, the standard name format, "prefix_w#_z#_t#.tif", is equivalent to the custom template, %d/%p_w%aw_z%az_t%at.tif. The custom template, /var/tmp/%2iz_%2iw_%2it.tif, would generate file names which included the input z, wavelength, and time indices of the section in the file. Each index would be displayed with at least two digits.

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Scaling

If the "8-bit" toggle button is on, the values in the "W0 scale" field control how the data from the first wavelength in the input is scaled to fit in the range of 0 to 255. The "W1 scale" through "W4 scale" fields are similar, but affect the second through fifth wavelengths in the input. For more information about the meaning of the scaling values, see the "Scaling Values" topic in the documentation for the image window's Scale application (the special case mentioned in that documentation does not apply in this situation and is handled like all other combinations of scaling values).

If the input to be converted is an image window, the default scaling parameters are the scaling values in effect when Mrc2tiff opens the image window. If the input is a file, the default scaling values are set to reflect a linear scaling between the minimum and maximum values recorded in the file's header.

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Command Line

mrc2tiff accepts the command-line arguments described in Region.html. In addition, it has the following options (parts in brackets are optional):

-8bit

Causes the input to be scaled to unsigned 8-bit integers. You can modify the scaling parameters with the -scl options. If you mix -8bit or the -scl options with -preserve_type, the one that appears last on the command line takes precedence. By default, mrc2tiff will scale to unsigned 8-bit integers unless the input pixel format is unsigned 8-bit integer.

-dir=dir

Sets the name of the directory to use in the file name template when mrc2tiff generates multiple output files from the input file. If you use the -single option to force mrc2tiff to generate one output file, the -dir option has no effect. By default, the directory name is an empty string.

-interleave=arrangement

Sets the interleaving to use when writing multiple sections to a single TIFF file or for calculating output section indices for custom file name templates. Allowed values for arrangement are twz, tzw, wtz, wzt, ztw, or zwt; ztw is the default.

-out=name or -out=name_format

If you use the -single option, use -out to set the name of the file to generate. If you do not use the -single option, you can use -out to select one of the predefined output file name templates. The allowed values for name_format when you do not use the -single option are:

prefix+wzt: Causes mrc2tiff to generate output file names as if "prefix_w#_z#_t#.tif" had been selected from the user interface. This is the default.
prefix+wz: Causes mrc2tiff to generate output file names as if "prefix_w#_z#.tif" had been selected from the user interface.
prefix+wt: Causes mrc2tiff to generate output file names as if "prefix_w#_t#.tif" had been selected from the user interface.
prefix+zt: Causes mrc2tiff to generate output file names as if "prefix_z#_t#.tif" had been selected from the user interface.
prefix+w: Causes mrc2tiff to generate output file names as if "prefix_w#.tif" had been selected from the user interface.
prefix+z: Causes mrc2tiff to generate output file names as if "prefix_z#.tif" had been selected from the user interface.
prefix+t: Causes mrc2tiff to generate output file names as if "prefix_t#.tif" had been selected from the user interface.

When you do not use the -single option, the -template option will override the -out option.

-prefix=pref

Sets the prefix to use in the file name template when mrc2tiff generates multiple output files from the input file. If you use the -single option to force mrc2tiff to generate one output file, the -prefix option has no effect. By default, the prefix is an empty string.

-preserve_type

Forces the TIFF output to have the same pixel format (i.e. 16-bit signed integer, 32-bit floating-point, etc ...) as the input MRC file and prevents mrc2tiff from trying to scale the input data. If you mix this option with -8bit or the -scl options, the one that appears last on the command-line takes precedence. By default, mrc2tiff will scale the input data and not preserve the pixel format except in the case where the input pixel format is unsigned 8-bit integer.

-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 scaling 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. Using this option implicitly sets the -8bit option. There are similar options (-scl2, -scl3, -scl4, and -scl5) to set the scaling for the output from other input wavelengths. If you mix -8bit or the -scl options with -preserve_type, the one that appears last on the command-line takes precedence.

-single

If you use this option, mrc2tiff will generate a single output file (whose name is controlled by the -out option) and each section drawn from the input file will become a page in the TIFF file. If you do not use this option, mrc2tiff will generate one TIFF file for each section drawn from the input file.

-template=custom_template

Sets the file name template mrc2tiff will use when generating one TIFF file per section in the MRC file. This option has no effect if you use the -single option and overrides the -out option when you do not use the -single option. By default, the template is an empty string.

The following example writes out the sections in fish.dat as a sequence of TIFF files in the directory /var/tmp; the names of the TIFF files will start with "fish" and (because it is the default) include the wavelength, z, and time point indices.

    mrc2tiff fish.dat -dir=/var/tmp -prefix=fish

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Overview

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Related Priism Topics

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