Displaying images and metadata ============================== The :command:`showinf` :doc:`command line tool ` 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:: -no-valid 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:: -no-core 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:: -format FORMAT Specifies the reader to be used for opening the specified file. The utility will look for a reader named ``loci.formats.in.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