The :command:`showinf` :doc:`command line tool <index>` can be used to show the images and metadata contained in a file.
If no options are specified, :program:`showinf` displays a summary of available options.
.. program:: showinf
To simply display images:
showinf /path/to/file
All of the images in the first 'series' (or 5 dimensional stack) will be opened and displayed in a simple image viewer. The number of series, image dimensions, and other basic metadata will be printed to the console.
.. option:: -noflat
Do not flatten resolutions into individual series::
showinf -noflat /path/to/file
.. option:: -series SERIES
Displays a different series, for example the second one:
::
showinf -series 1 /path/to/file
Note that series numbers begin with 0.
.. option:: -omexml
Displays the OME-XML metadata for a file on the console:
::
showinf -omexml /path/to/file
.. option:: -nopix
Image reading can be suppressed if only the metadata is needed:
::
showinf -nopix /path/to/file
.. option:: -option KEY VALUE
Passes options expressed as key/value pairs::
showinf -option key value /path/to/file
e.g. additional reader options, see :doc:`/formats/options`::
showinf -option leicalif.old_physical_size true /path/to/file
.. versionadded:: 5.3.0
.. option:: -range START END
A subset of images can also be opened instead of the entire stack, by
specifying the start and end plane indices (inclusive):
::
showinf -range 0 0 /path/to/file
That opens only the first image in first series in the file.
.. option:: -crop X,Y,WIDTH,HEIGHT
For very large images, it may also be useful to open a small tile from the
image instead of reading everything into memory. To open the
upper-left-most 512×512 tile from the images:
::
showinf -crop 0,0,512,512 /path/to/file
The parameter to :option:`-crop` is of the format ``x,y,width,height``.
The (x, y) coordinate (0, 0) is the upper-left corner of the image;
``x + width`` must be less than or equal to the image width and
``y + height`` must be less than or equal to the image height.
.. option:: -no-upgrade
By default, :program:`showinf` will check for a new version of
Bio-Formats. This can take several seconds (especially on a slow internet
connection); to save time, the update check can be disabled:
::
showinf -no-upgrade /path/to/file
.. option:: -novalid
Similarly, if OME-XML is displayed then it will automatically be validated.
On slow or missing internet connections, this can take some time, and so
can be disabled:
::
showinf -novalid /path/to/file
.. option:: -nocore
Most output can be suppressed:
::
showinf -nocore /path/to/file
.. option:: -omexml-only
Displays the OME-XML alone:
::
showinf -omexml-only /path/to/file
This is particularly helpful when there are hundreds or thousands of
series.
.. option:: -debug
Enables debugging output if more information is needed:
::
showinf -debug /path/to/file
.. option:: -fast
Displays an image as quickly as possible. This is achieved by converting
the raw data into a 8 bit RGB image::
showinf -fast /path/to/file
.. note::
Due to the data conversion to a RGB image, using this option results in
a loss of precision.
.. option:: -autoscale
Adjusts the display range to the minimum and maximum pixel values::
showinf -autoscale /path/to/file
.. note::
This option automatically sets the :option:`-fast` option and suffers
from the same limitations.
.. option:: -cache
Caches the reader under the same directory as the input file after
initialization::
showinf -cache /path/to/file
.. option:: -cache-dir DIR
Specifies the base directory under which the reader should be cached::
showinf -cache-dir /tmp/cachedir /path/to/file
.. option:: -swap DIMENSIONORDER
Overrides the default input dimension order::
showinf -swap XYZTC /path/to/file
.. option:: -format FORMAT
Specifies the reader to be used for opening the specified file. The utility
will look for a reader named ``loci.formats.in.<FORMAT>Reader``. If the
reader does not exist or no :option:`-format` option is passed, the file
will be opened with ``loci.formats.in.ImageReader``::
showinf -format APNG test.png
.. option:: -fill UNSIGNED_BYTE
Sets the fill value to use for undefined pixels.
Valid values are 0-255, with 0 representing a black pixel and 255 representing a white pixel.
The value set here will be applied to all bytes in an undefined pixel, e.g. setting to 128 (0x80)
on a uint16 image will result in a pixel value of 32896 (0x8080).
The default fill value is typically 0, but some readers may have different defaults.
.. versionadded:: 6.13.0