You get at the data browser by pulling down the "Tools" menu. Click
on "Data browsers" and up pops a window that lets you select a
component, a level and a box; one data browser (you can bring up more
than one) displays all the data in one box, and for one component.
(See below under "Mouse controls" for more ways to select a level and
component.)
For a 3D dataset, we display the numbers one plane at a time. The
radiobuttons opposite "normal:" are for selecting the orientation of
that plane; the default is 'z', which means you get the x-y plane.
The "format:" entry field accepts strings of the sort you would
pass to the first argument of the C printf function. Good choices
typically end in 'f', 'e', or 'g'. If your data is mostly zeros, then
'g' is an especially good choice because it brings out your non-zero
data.
The "synchronized" checkbutton enables several sorts of
synchronization. Data browsers corresponding to the same box but
different data components move their data planes together. Movements
of the slicing plane (or, in 2D reslice mode, the reslice position)
cause the databrowser to display the corresponding plane of data.
The "Picked particle" area appears if your dataset includes particles.
See below under "particle picking" for more details.
The "Go" button brings up a data browser. You can bring up as
many data browsers as you like. To see data for another component,
select that component in the "Data selection" control (under the
"Visualization" menu).
The fields labeled "hilite cell" are blank until you use the mouse
to pick a cell, whereupon they display the picked cell's coordinate
and value. See below about cell picking. If you started ChomboVis with
"slices_off=1" on the command line, i.e. no data component has been loaded yet
(a good way to begin if your dataset is huge), then picking will still display
the picked cell's box and coordinates within that box, but not value of any
field data component in that cell. To obtain such values, select, in the
databrowser launcher dialog, one of the data components.
The data browser's title bar identifies the level and box of the data
you see in there.
In the VTK rendering window, the edges of the box associated with
your data browser are colored pink. Pink turns to dark red if you
open another data browser; the box associated with the data browser
that has the mouse focus is pink, while all the others are dark red.
The data browser planes also move in response to changes in the
position of the slicing plane (3D) or reslice position (2D reslice
mode), if you have checked the "synchronized" checkbox on the data
browser launcher.
Place your mouse over the box of interest, and make sure the
level that box belongs to has been selected in the "Data selection"
control (under the "Visualization" menu). Now hold down "Ctrl" on
your keyboard, and press the left mouse button. You have just "shot"
a selector ray (a skewer as it were) through that box. In 3D mode
you can rotate (left mouse-button, move mouse) the display a little to
better see the selector ray. (In 2D mode you can't rotate.)
If you don't see the box you expected to see, double-check that you
selected the appropriate level of refinement in the "Data selection"
control, under the "Visualization" menu. It may also help to select
"Bounding boxes" in the "Grids" control (as indeed we have done to
create the picture above).
Notice that the "level" and "box" sliders of your data browser
launcher now indicate the box highlighted in green.
The box you want may not be on the outside of your domain box (3D
only), or (3D and 2D) may belong to another level than that of the
currently-highlighted box. You can get to the box you want by holding
down "Ctrl" on your keyboard and pressing the right mouse button; this
cycles through all the boxes you have skewered. The order is, first,
by increasing refinement level, and, second, by increasing distance
from your viewpoint.
To turn off the selector ray, do a "Ctrl-middle-mouse-button" or
"Ctrl-shift-left-mouse-button".
Thus, on a 2D file, open a data browser. Now place your mouse
over any cell within the box the data browser corresponds to. Do a
ctrl-left-button to turn on the selector ray. The box itself is
highlighted in pink, and within the box, you have a blue highlight
around the specific cell you skewered (you may need to zoom in to see
it).
The corresponding cell of the data browser should also be
highlighted. If it is not, make sure the data browser's box is the
one that is highlighted. The highlighted box should be pink. If it
is green, that means it is not the box the data browser is on. If you
have more than one level visible, try cycling through the levels with
ctrl-button-3. If that fails too, then look at the data browser
launcher; its level and box scales will identify the box you have
selected: compare that to the level and box numbers on the title bar
of the data browser. If they do not match, go ahead and press the
"Go" button on the launcher widget again; this will bring up a second
data browser, this one corresponding to the box you have actually
selected. If you now ctrl-left-button over the desired cell again,
you should see a blue highlight in your new data browser.
The same sort of thing happens in 3D mode. It's trickier only
because the selector ray, on its course through three-dimensional
space, may be thought of as passing through many cells. Accordingly,
we needed to impose a few rules to define which cell to actually
highlight. The rules are as follows.
As mentioned earlier, the picked cell's coordinate and value are also
shown in the data browser launcher widget. Thus it is not necessary
to open an entire data browser at all, if all you need to do is check
a few values here or there.
Picking particles is at times a tricky business. If you do not see
the pale blue sphere around your desired particle, then try zooming
and perhaps rotating the scene so that the particle you want to pick
stands fairly isolated -- away from other particles, and away from any
grid lines. If you zoom in far enough, your particle might disappear;
in that case reduce the position of the inner clipping plane (pull
down "Tools", select "Camera parameters", and type something small
into the first box to the right of "clipping range").
Sometimes you see the pale blue sphere, but it is around the wrong
particle. At other times, the pale blue sphere does not appear at
all, but instead ChomboVis draws the green highlight around one of
your boxes: that means you hit a box boundary instead of a particle.
If you keep hitting box boundaries, try turning them off (pull down
"Visualization" and select "Grid detail").
Particle picking does not work at all -- you will get an error
message -- if particle opacity is at anything less than 1.0. (This is
because our method of calculating which particle was picked depends on
an assumption about how VTK orders elements of rendered geometry, and
setting particle opacity to less than 1.0 tends to scramble that
ordering.)
If, however, you are working from a new-style embedded boundaries
file, you will not see this special databrowser interface unless your
file provides, for each boundary, a special data component that tells
ChomboVis which cells are covered, regular and irregular.
That component needs to be named __covered-n (that's two
underscores) (where n=0,1,... indexes your boundaries), and the
component must equal 0 on covered cells, 1 on irregular cells, and 2
on regular cells. If you like, you may define these
__covered-n components at runtime, using
c.reader.defineNewComponent().
If that is too restricting, you can use any other component
(except one whose name begins with __covered-!) and any other
encoding scheme, and call c.eb.registerCoveredCellsDiscriminator(). This
function generates those __covered-n components for you.
2. Data browsers
You might want to press the "Go" button (above) before reading on.
2.1. 3D-specific features
A data browser for 3D data displays one plane of data at a time, as
mentioned above. To move among the planes, either move the slider at
the top left, or click on the tabs immediately below. You will see a
semi-transparent red plane that corresponds to the currently displayed
plane of data; move the plane-selection slider or choose another
radiobutton opposite "normal:" to see this transparent plane change
its position. You can turn the semi-transparent red plane off from a
checkbutton on the data browser.
3. Mouse controls
3.1. Box picking
As mentioned above, one data browser displays all the numbers for
one component within a single box, and you can select that box with
the sliders of the data browser launch window. The other way to
select the box is with your mouse.
3.2. Cell picking
The selector ray and the data browsers are integrated so that you can
conveniently find the numerical value corresponding to any cell in
the render window. This feature works in both 2D and 3D mode, but as
the 3D semantics are a little tricky, we will begin with 2D mode.
3.3. Particle picking
If your dataset has particles, and the particles are being
rendered as glyphs (spheres or cones, but not mere points) the
familiar ctrl-button1 motion will, subject to some limitations
discussed below, pick a particle, if one is rendered under your
current mouse position. That particle's value, along its various
components, can be seen in the data browser launcher widget. To
confirm which particle you have picked, ChomboVis draws a pale blue
sphere around the picked particle's marker (sphere or cone).
4. Embedded boundaries
The databrowser can, optionally, blank covered cells and regular
cells, as well as colorcode irregular cells. When you load an
old-style embedded boundaries file (i.e. one with components names
"fraction-0", "fraction-1", etc), databrowsers come up with buttons to
control such blanking and coloring:
ChomboVis Development Team