.. _view_top:

View
====

.. only:: html

   .. sidebar:: Tutorials & Sample Data

      Watch on YouTube: |br|
      `Tutorial 2: View Options <https://youtu.be/DK8OxhcT05g>`_

      :download:`Tut2data.zip (34.9MB) <https://www.firevoxel.org/im/Tut2data.zip>`

.. contents::
   :depth: 1
   :local:
   :backlinks: top

This section describes commands and options that control how the images
are displayed in FireVoxel. These commands include navigation through
slices and dynamic frames. These tools do not modify the image data,
but only change how the images are displayed. Customized views can be saved
as FireVoxel documents.

Many of these commands are available under the **View** tab on the main menu.
Selected commands are also accessible through the :ref:`Toolbar <toolbar>`.

Additional tools for adjusting the appearance of layers
(such as the layer order, visibility, ROI color, and color map options)
are available through :ref:`Layer Control <layer_control_panel>`.

.. _view_slice_film:

Slice View and Film View
------------------------

   .. _fig_slice_film:
   .. figure:: ../images/view_slice_film.png
      :alt: Slice View and Film View
      :align: center
      :figclass: align-center

      The same volume in Slice View and Film View.

Images loaded in FireVoxel can be displayed in **Slice View**, when only one
slice is shown in the document window, or **Film View**, when all slices are
shown as tiles in the same document window (:numref:`fig_slice_film`).

If the document is dynamic, Film View displays all slices at the same value
of dynamic variable (such as time, b-value, echo time, etc.).

To switch back and forth between the Slice and Film views, **double-right-click**
anywhere on the image.

To select the default initial view used when images are first loaded into FireVoxel,
use **File** > **User Interface Options** > :ref:`Initial layout <interface_initial_layout>`.

.. _view_scroll_slice_dyn_pts:

Navigating through slices and dynamic frames
--------------------------------------------

The user may navigate through the slices of a 3D volume by using the up and down
arrow keys on the keyboard or scrolling up or down the mouse wheel.
If the image is 4D, these actions enable viewing slices of a 3D volume
at a single dynamic frame.

To navigate through dynamic frames (such as time points or b-values), the user
can press the right and left arrow keys. In Slice View, the same slice will be
displayed at consecutive values of dynamic variables. In Film View, all slices
will also be displayed at each value of dynamic variable.

.. _view_interface_config:

Interface configuration (View)
------------------------------

.. _view_new_view:

New view
~~~~~~~~

Creates a copy of the active document window in a new window. The
original window is renamed [name]:1 and the new window is named
[name]:2, etc. Each view can be manipulated independently and saved
separately.

.. _view_cascade:

Cascade
~~~~~~~

Arranges all document windows as a stack (cascade), with the active
window in front.

.. _view_tile:

Tile
~~~~

Arranges all document windows as tiles (:numref:`fig_view_tile`).
Minimized windows are not tiled and remain minimized.

   .. _fig_view_tile:
   .. figure:: ../images/view_tile.png
      :alt: Tiled document windows
      :align: center
      :figclass: align-center

      Tiled document windows.


.. _view_show_toolbar:

Show Main Toolbar
~~~~~~~~~~~~~~~~~

Toggles on/off the visibility of the toolbar. Checked by default
(toolbar visible).

.. _view_select_all:

Select All
~~~~~~~~~~

Selects all vector entities (vector ROIs, polylines, and spline contours)
in the active document. With all vector entities selected, clicking anywhere
outside the vectors deselects all of them. Clicking any vector entity selects
that entity and deselects the others.

.. _view_close:

Close
~~~~~

.. _view_close_doc:

Close Document
^^^^^^^^^^^^^^

**CAUTION: No file save dialogue. Any unsaved changes may be lost.** |br|
Closes the active document.

To avoid losing unsaved work, close each document by clicking the cross
in the upper right corner. Alternatively, close FireVoxel, in which
case the file-save dialog will be shown for each document one by one.

.. _view_close_all_docs:

Close All Documents
^^^^^^^^^^^^^^^^^^^

**CAUTION: No file save dialogue.** |br|
Closes all documents.

.. _view_close_all_docs_but_this:

Close All Documents but this
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

**CAUTION: No file save dialogue.** |br|
Closes all documents except the active one.

.. _view_close_all_views_but_this:

Close All Views but this
^^^^^^^^^^^^^^^^^^^^^^^^

Closes all views of the images displayed in the active window
(usually orthogonal projections) except the active window.

.. _view_orthogonal_projections:

Orthogonal Projections
----------------------

.. _view_set_projection:

Set projection for this view (View & Toolbar)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Opens a dialog panel (Specify Volume Projection, :numref:`fig_set_projection_menu`)
to configure orthogonal projection for the current document window.
Clicking **View Projection** icon |set_project| opens the same panel.

   .. _fig_set_projection_menu:
   .. figure:: ../images/view_set_projection_menu.png
      :alt: Specify Volume Projection panel
      :figwidth: 40%
      :align: center
      :figclass: align-center

      Specify Volume Projection panel.

The top part (Rotation) contains boxes to enter angles (in
degrees) of rotation about X, Y, and Z axes. Orthogonal rotations can be
applied by clicking buttons +/-90 (degrees) (:numref:`fig_set_projection_z90`,
:numref:`fig_set_projection_x90`, :numref:`fig_set_projection_xyz`).

   .. _fig_set_projection_z90:
   .. figure:: ../images/view_set_projection_z90.png
      :alt: Projection at 90 deg about Z axis
      :scale: 60%
      :align: center
      :figclass: align-center

      Projection at 90 deg about Z axis.

   .. _fig_set_projection_x90:
   .. figure:: ../images/view_set_projection_x90.png
      :alt: Projection at 90 deg about X axis
      :scale: 60%
      :align: center
      :figclass: align-center

      Projection at 90 deg about X axis.

   .. _fig_set_projection_xyz:
   .. figure:: ../images/view_set_projection_xyz.png
      :alt: Projection at angles about X, Y, Z axes
      :scale: 60%
      :align: center
      :figclass: align-center

      Projection at angles about X, Y, Z axes.


Clicking **Original** restores the original orientation.
The **Type** dropdown menu offers the choice of several types of views:
Normal (regular rotation, default), Max Intensity (maximum intensity projection),
Max Intensity with Zero block, Min Intensity (minimum intensity projection),
Slab Average (each voxel contains average signal at that location over the entire slab).
:red:`ADD DETAILS`

.. _view_reset_projection:

Reset projection for this view (View)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Restore the original view for the current document window.

.. _view_max_intensity_snapshot:

Max intensity projection snapshot (View)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Opens a new document window (named **snapshot**) with the maximum
intensity projection (:numref:`fig_mip_snapshot`).

The snapshot has the same in-plane dimensions as
the original image, but contains only a single slice.

The snapshot cannot be converted back into the original image. In contrast,
maximum intensity image obtained using **Set projection** with **Type**
> **Max intensity** can be reset to the original image by selecting
**Type** > **Normal**.

   .. _fig_mip_snapshot:
   .. figure:: ../images/view_mip_snapshot.png
      :alt: MR Angiography max intensity projection snapshot
      :scale: 60%
      :align: center
      :figclass: align-center

      MR angiography axial and coronal views (left and center, respectively)
      and coronal maximum intensity projection snapshot (right).

.. _view_toolbar_3projections:

Display orthogonal projections (Toolbar)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Clicking **Display orthogonal projections**  |orthog_project|
:ref:`toolbar <toolbar_top>` icon opens document windows with orthogonal
projections complementary to the active document window.
For example, if the active document window displays an axial view,
the command opens two new document windows showing coronal and sagittal views.
By default, the new windows are :ref:`tiled <view_tile>`.

The new views are opened according to the setting in **File** >
:ref:`User Interface Options <interface_options>` > **Display** >
:ref:`View Convention <interface_view_convention>`.

If the **View Convention** is **Radiological** (left side on the right),
**Display orthogonal projections** opens *two additional windows*
(for a total of three windows, including the original).

If the **View Convention** is **Neurological** (right side on the right),
**Display orthogonal projections** opens *three additional windows*:
the orthogonal projections plus the original projection in
left-side-on-the-left orientation (for a total of four windows,
including the original).

If the user clicks **Display orthogonal projections** icon two
or more times (with the same or different windows activated),
no new windows are opened besides the original set,
although document windows may be re-tiled after each icon click.

.. _view_zoom:

Zoom
----

.. _zoom_by_window:

Zoom By Window (View & Toolbar)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Zoom in on a rectangular selection with a mouse. To launch the tool,
select **View** > **Zoom by window** or click |zoom_by_window|  icon
(cursor becomes a magnifying glass). To use, click the image,
drag the mouse to expand a white dashed rectangle and release the mouse button.
Tool quits upon mouse release. To undo and return to the original view,
use **View** > **Zoom All**.

.. _zoom_in_out:

Zoom in/out with fixed upper left corner (View & Toolbar)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Zoom whole image relative to the upper left corner. To apply, select
**View** > **Zoom in** or **Zoom out** or click
icons |zoom_in| or |zoom_out|.
Repeat until a desired zoom level is reached.

.. _zoom_all:

Zoom All and fit to View (View & Toolbar)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Restore original view (undo zoom in or out). To apply, select **View** >
**Zoom All** or clicking **Zoom All** toolbar icon |zoom_all|.

.. _zoom_1x1:

Zoom 1x1 (View)
~~~~~~~~~~~~~~~

Display each image voxel as one pixel on screen. Use **Zoom All** to
return to the original view.

.. _view_display_graphics:

Display graphics (View)
-----------------------

.. _view_display_vector:

Display\\Hide vector
~~~~~~~~~~~~~~~~~~~~

Toggles on/off (checked/unchecked) visibility of vector ROIs and
polylines in the active document window (or current view if several
orthogonal projections are open).

.. _view_display_raster:

Display\\Hide raster
~~~~~~~~~~~~~~~~~~~~

Toggles on/off visibility of image layers and raster ROI layers in the
active document window (or current view if several orthogonal
projections are open).

.. _view_display_grid:

Display\\Hide grid
~~~~~~~~~~~~~~~~~~

Toggles on/off visibility of a rectangular grid.
Opens dialog (**Specify Grid Step**) with a box for entering
the Grid Step in millimeters.
Displays a square grid of green lines spaced by grid step in row and
column dimensions. The grid is shown for all slices, but only for the
current view (if orthogonal projections are displayed). To change the
grid step, use this command twice and enter a new grid step.

   .. _fig_curve_length:
   .. figure:: ../images/view_curve_length.png
      :alt: Display curve length
      :scale: 70%
      :align: center
      :figclass: align-center

      Display curve length.

.. _view_display_curve_length:

Display\\Hide Curve Length
~~~~~~~~~~~~~~~~~~~~~~~~~~

For a vector (a two-point polyline), toggles on/off the visibility
of the length of the segment between two points. The length
(in millimeters) is displayed next to the polyline as a red number
(:numref:`fig_curve_length`).

For a sector (a three-point polyline), toggles on/off the angle
measure, displayed as a green number.

.. _view_enumerate_polylines:

Enumerate polylines
~~~~~~~~~~~~~~~~~~~

Toggles on/off the visibility of the numbers labeling control points
in polylines and MagTrace splines (:numref:`fig_enumerate_polylines`).

The numbers are shown as red numbers next to each control point.
The numbers remain visible for both active and inactive polylines.

   .. _fig_enumerate_polylines:
   .. figure:: ../images/view_enumerate_polylines.png
      :alt: Enumerate polylines
      :scale: 70%
      :align: center
      :figclass: align-center

      Enumerate polylines option ON.

.. _view_contour_properties:

Contour and Fill Properties
~~~~~~~~~~~~~~~~~~~~~~~~~~~

Opens a panel (**Polyline and Spline properties**) for adjusting
parameters of vector polylines and splines. This panel can also be open
by double-clicking a polyline or spline. This panel is described in detail
in :ref:`Trace <trace_top>` section on Magnetic Trace tool.

.. _toolbar_dyn_exp:

Dynamic experiment (Toolbar)
----------------------------

.. _toolbar_play_4D:

Play 4D experiment (Toolbar)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Clicking **Play 4D experiment** icon |play_4d_exp_icon| to display
the dynamic frames of the current slice consecutively
for a user-specified time interval.
Opens dialog (**Specify Interframe time delay** (.001 sec precision))
with a box for entering the time during which each frame is shown.
Clicking OK starts the sequence of views. The cursor turns into a blue wheel.

.. _toolbar_voxel_tac:

Display voxel TAC (Toolbar)
~~~~~~~~~~~~~~~~~~~~~~~~~~~

Clicking **Display voxel TAC** icon |voxel_tac_icon|
opens a panel to view the time-activity curve (TAC) at the current voxel
(**Dynamic Activity Curve: Signal values**, :numref:`fig_display_voxel_tac`).

   .. _fig_display_voxel_tac:
   .. figure:: ../images/view_display_voxel_tac.png
      :alt: Display voxel time-activity curve panel
      :scale: 60%
      :align: center
      :figclass: align-center

      Display voxel TAC panel.

The panel shows the TAC plot, with the origin and maximum values
of the horizontal and vertical axes.

Options:

**Attributes** – Opens dialog to enter T1 value for conversion to
concentration.

**Concentration** – Opens panel (Concentration Conversion) for converting
MRI signal intensity to gadolinium concentration.

**Radius** (voxels) – Up and down arrow buttons for adjusting the size of
the sampled area. Default size, 0 (1 voxel).

**2D** (checkbox) – Checked by default, toggles between 2D and 3D sampling
mode.

**Save** – Opens browse for file dialog for saving the current TAC as a text
file with two columns: dynamic dimension and signal.
|top|

.. |window_level_icon| image:: ../images/toolbar_window_level_icon.png
.. |zoom_by_window| image:: ../images/toolbar_zoom_by_window_icon.png
.. |zoom_all| image:: ../images/toolbar_zoom_all_icon.png
.. |zoom_in| image:: ../images/toolbar_zoom_in_corner_icon.png
.. |zoom_out| image:: ../images/toolbar_zoom_out_corner_icon.png
.. |orthog_project| image:: ../images/toolbar_orthog_projections_icon.png
.. |set_project| image:: ../images/toolbar_set_projection_icon.png
.. |play_4d_exp_icon| image:: ../images/toolbar_play_4d_exp_icon.png
.. |voxel_tac_icon| image:: ../images/toolbar_voxel_tac_icon.png