Registering Images

12/10/2004

Image Registration

Images are registered by moving one image right, left, up, or down, relative to the other images. Registration is useful for taking jitter out of movies and adjusting stereo pairs for the best effect. Use these buttons in the Data Cube Tool to register images:

How to register a Stereo Pair

A stereo pair of images can be registered, cropped, rotated, and the brightness and contrast adjusted with the CLUT sliders. All of this is done with the Data Cube Tool. In this case, the 'cube' is only two layers thick: Here are the steps:

Load the images into a data cube using Read / as image files. (This is the Read button in the Data cube tool.) Select the images and open them.
Note that the slice slider will show one image or the other. You can see the stereo rotation effect just by wiggling the slice slider to display one image or the other.
Select the cube with the Cube! button.
Select one image with the slice slider. Click ref slc! Then select the other image and click flick slc! This seems superfluous here, as there are only two images in the cube, but it is necessary with more than two images.
Start the flickering by clicking on!
Move one of the images relative to the other by clicking and dragging on the flickering cube.
Use the jog buttons to move the flicker image one pixel at a time in any direction.
Make a new cube with the images registered as you see them now: Cube / register using offsets.
Rotate if necessary. Open the Profile Tool, select the cube, put the line along the apparent axis of rotation, then use Cube / rotate using profile tool.
Adjust the brightness or contrast, e.g. with CLUT / gamma slider on one or the other slices, then use Propigate / fix to LUT.
Open the '2 & 3 variable Tool. Select one image with the slice slider for the cube, and click 'red / x' to selec it as the red image. Select the other image as the green image and blue image. Then use RGB overlay / make rgb overlay.

How to register a data cube and make a stereo movie GIF file:

(Note - some of this is outdated because the Data Cube Tool has been changed a little. These register functions still work, but using the Offsets and Tracking buttons is much faster, and almost as tood. Registration can then be refined using some of the steps below.) Here are the steps in detail:

1) Load the original data into a cube.
a) The files probably should be sorted by their write date/time. See 'Sort Method' in the File Utilities Tool.
b) Set the READ directory
2) Examine with single slice slider by clicking and dragging the vertical line with the
circle in the middle.
3) Pick registration point.
a) Note - the point should be seen easily in most or all of the images.
b) The reference slice can be any slice, and the flicker slice can be any slice,
so it is possible to hop through the stack pairwise. This is prone to
accumulation of errors, however, and I wouldn't recommend it. The '+!' button bumps up
the flicker slice, but the reference slice stays put.
4) Select the cube by clicking on the 'Cube !' button.
5) Initialize the offsets by using the tracking function.
a) 'Tracking -> Click to track'.
b) Click on the reference point in each slice. The next slice is automatically displayed.
The slider displays the current slice.
c) 'Offsets -> Set from tracking'.
6) Examine the offsets by showing the stack as an oscillating movie and look for jitter.
7) IF there is jitter, refine the offsets using steps 8-14:
8) Select registration and flicker slices. For example:
a) Slide to select slice 0.
b) Click on 'Ref slc' button (the Reference Slice button).
c) Slide to select slice 1.
d) Click on 'Flick slc' button (the Flicker slice button). It is this slice that
moves when you drag the mouse.
9) Start flicker by clicking 'On'.
10) Change flicker rate by clicking 'VFast', 'Fast', 'Med', 'Slow', or '??!'.
a) The '??!' button is for setting an arbitrary flicker speed. The number
you input is the delay in seconds, or fractions thereof, between switching
slice views.
11) Tweak the offset by either:
a) Jogging the slice Up, Down, Left or Right with the U,D,L and R buttons.
b) Put mouse on the registration point you have chosen, for the flicker slice,
and drag it to the corresponding point in the reference image.
12) Register subsequent slices using these steps - you can do these with
the flicker remaining 'On'.
a) Bump up to the next flicker slice: use the '+!' button.
... or ...
a) Slide to select slice 2. {corresponds to step 2}
b) Click on 'Flick Slc!'. {corresponds to step 8c,d}
c) Drag with mouse. {corresponds to step 11b}
Registration note: Sometimes this is easier with the cube zoomed x2 or x3.
Use '***Buttons*** -> Zoom'.
13) At any time, examine, store, recall or reset the offsets with the 'Offset' button.
14) At any time, check the offsets by playing the movie. On the PC, click the '->size<-!'
button to avoid filcker. This is the size of the registered cube.
15) Once the offsets are satisfactory, make a new registered cube: 'Cube -> Register using offsets'.
This cube plays movies and flickers just like the parent cube, but the offsets are all zero,
the slider will show the slices in their registered position.
16) Crop the cube with the rectangle tool: '*** Buttons *** -> Rectangle -> Draw' sets the
coordinates for the rectangle (also available via '*** Buttons *** -> Help -> Parameters',
where specific numeric values can be set.) Make a new cropped cube:
'Cube -> Crop using rectangle'.
17) Rotate (or reorient) the cube to make the cube rotation axis (of the animated objects) vertical:
a) Select a point that is visually near to the viewer (when viewing the movie), and track it
with the 'Tracking -> Click to track' button.
b) Display the track with 'Tracking -> Show coordinates'. If the line is hard to see, change the color
using the '***Buttons*** -> Pick Color' button. Hopefully this line is more or less straight.
c) Make the profile window: '*** Buttons *** -> Profiles !'.
d) Select the cube in the profile window. With the cube being the front image (click on it),
click the '**Profiles** ->Image !' button.
e) Turn the line on. '**Profiles** -> Line On'. Note that the line has a direction shown by
the little arrow. Select from the list of compass points,
the aproximate direction of the rotation axis, which will be perpendicular to the tracking line.
f) Set the width of the line to something about as wide as the tracking line is long.
g) Turn the cursor of the profile line on, if necessary, and position near the tracking line.
h) Adjust the angle of the profile line by dragging its end points, so that the cursor line, or
one of the end lines lines up with the tracking line (or is parallel to it). This makes the
profile line along the rotation axis.
i) Make a new cube
using the '**Data Cube** -> Cube -> Rotate using profile tool'. Select the desired direction
of the (new) rotation axis, which should be UP for stereo pairs, from the list of compass points
(N is up). This will generate
a new cube, with a vertical rotation axis. Since the axis is vertical, then
various slices can be used to make stereo pairs.
18) Save the rotated cube as a folder of TIFF or JPEG files, mirror to make an oscillating movie.
a) '**Buttons ** -> File -> Set default write directory'.
1) If this does not show the desired area, use 'File -> Clear Defaults', then
'File -> Set default write directory'.
2) The dialog to choose the default write directory should be one level up from
the default read directory. Clearing the defaults has you start from the top level
on your machine.
3) Select TIFF or JPEG for the output file type. 'Write -> Set file type'
a) If you selected JPEG, select the compression amount. (0 is default, but considerable space
saving is to be had at settings of 2 or 3, without too much of a quality decrease in
in the final movie. '***Buttons*** -> File -> Set JPEG compression'.
JPEG Quality note: If an RGB stack is loaded as a normal cube rather than as an RGB cube, the
images appear as gray level images. (The Value image is extracted from the HSV equivalent of
the RGB image.) I've found a JPEG compression level of 2 is particularly
noticable here.
b) '**Data Cube** -> Write ->
1)Mirror w/ numerical names' This is good for oscillating movies. Doubles
the number of files.
2) Original slice names' Retains original file names. Make sure you are writing
to a different folder. You will get an overwrite notice if you don't. This option is
ok if the files are named such that they load in the right order.
3)Numerical slice names' Good for files loaded by file write date. Keeps proper
slice order when reloading or exporting to other software.
4) as Raw cube file.' Brings up raw file format buttons.
For Lispix internal use, or for Vox Blast import. Writes cube
all in one file with no header information - only pixel information.
Fastest way to read / write cubes, but does not preserve slice names.
19) Convert the TIFF or JPEG files to GIF files with Photoshop so that they can all be
dragged and dropped into GifMation.
(This is a specialization of ***Buttons*** / Help / Photoshop /
Processing a folder full of images with Photoshops * ...)
a) Record an action by going through the motions with one of the images:
1) Window -> Show Actions
2) .. New Action .., name it 't2g', and click 'Record'
3) File -> Open (open the image file)
4) File -> Save As (save as Compuserve GIF).
5) .. Stop recording the Action ...
b) Use the action in the automated mode for the entire folder.
1) Have only the TIFF files for the cube in the input folder.
2) Make an empty folder for the output files.
3) File -> Automate -> Batch. Settings for the dialog window:
a) Set: Default Actions
b) Action: t2g (or whatever you named the action)
c) Source: folder (select the input folder)
d) check the Override Action Open Commands. (It is not clear from their docs that
you should do this, but it won't work if you don't.)
e) Destination: None (If you specify the output folder, then TIFF files will
be recorded, not GIF files. This IS according to their documentation.)
f) Errors: Stop for errors. (This is the default.)
This should run through all of the files - takes a matter of minutes.
20) Make an animated GIF with GifMation.
a) Open GifMation.
b) File -> New.
c) Select and drag the GIF files to the gray border of the movie window,
OUTSIDE of the black square. (Dragging into the black square does nothing.)
d) Files should load quickly. Run the movie to check.
e) Gifmation seems to swap a pair of random slices. If slices need reordering, use
'Window -> Show frame info', right click on a frame to set to small icons, drag
the frames to the right places. Lispix inserts the image number in tiny letters
into the upper left corner of files written in mirror mode.
f) Files -> Save As. Save the movie file as a GIF file.
21) View with Netscape
a) Open netscape browser.
b) File -> Open Page, file type = * All files, select the GIF movie.
c) See animated cube by itself in the browser window.