em-viewer
=========

.. code-block:: bash

    $ em-viewer $EM_TEST_DATA/relion_tutorial/micrographs/006.mrc --help
    usage: Tool for Viewer Apps

    Display the selected viewer app

    positional arguments:
      path
                            Provide a path to be visualized.
                            Path can be:
                               directory: the browser will be shown at that path.
                               image:     an ImageView will be shown with that image.
                               volume:    a VolumeView will be used to show the volume.

    optional arguments:
      -h, --help            show this help message and exit
      --display DISPLAY [DISPLAY ...]

                            Provide one or many key=value pairs with extra visualization options.
                            Bool values support on/off, 0/1, true/false, yes/no
                            Options:
                               axis:      (bool) if false, axis will not be shown (default true)
                               toolbar:   (bool) if false, toolbar will not be shown (default true)
                               histogram: (bool) if false, histogram will not shown (default true)
                               fit:       (bool) if false, the image will not be adjusted to widget size (default true)
                               view:      (string) Select the initial view. Options: gallery, columns, items, slices
                               scale:     (string) Select initial scale (use % for percentage)
      --visible [VISIBLE]    Columns to be shown (and their order).
      --render [RENDER]      Columns to be rendered.
      --sort [SORT]          Sort command.


Viewing a Micrograph
--------------------

One can visualize a single image (e.g a micrograph) by providing it as the first argument. ::

    em-viewer $EM_TEST_DATA/relion_tutorial/micrographs/006.mrc


Additionally, some extra visualization arguments can be passed via the --display option, that
accepts many flags. For example, histogram=on will display by default the histogram. ::

    em-viewer $EM_TEST_DATA/relion_tutorial/micrographs/006.mrc --display histogram=on

After this the following image should be shown:

.. image:: /images/em-viewer_mic01.png  

You can also other options available to the --display option and check the result. For example: ::

    em-viewer $EM_TEST_DATA/relion_tutorial/micrographs/006.mrc --display histogram=on axis=0 scale=0.5



Viewing a Movie
---------------
Movies can be visualizing in the same way as micrographs. The display will looks very similar, but it will also
contains a slider to select the frame that we want to visualize. Usually the movies are much more noisy than
micrographs, but it is useful to look at it sometimes.

.. image:: /images/em-viewer_mov01.png



Viewing a Volume
----------------
Volumes can be also display with the `em-viewer` application. For example: ::

    em-viewer $EM_TEST_DATA/resmap/t20s_proteasome_full.map


That will be show by default the volume with the Axis sliders view, where
slices through each axis can be inspected.

.. image:: /images/em-viewer_vol01.png
    :width: 60%
    :align: center

Many slices at once can be shown for one axis, and also switch between axis.

.. image:: /images/em-viewer_vol02.png


File Browsing
-------------