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07/08/2010

Mosaic Tool Example

Trinitite Data Set

(The data set is large, 19 Gb, and not available for download.)

This data set supplied by Dale Newbury, NIST, 4/ 2010.

This is the Run Folder.

Each cube folder contains a spectral image and associated elemental images or electron micrographs (see below).  Lispix ignores other folders.

User saves image locations in the cube-positions.txt file by clicking on the Save button.  Lispix makes temp-positions.txt automatically, to recover from where you quit.  The "Mosaic..." files are mosaics made from the data set, with the elemental symbol and color of the group as the file name.  Lispix ignores other files.

Sample Cube folder:

 

Processing Steps

Open the Mosaic Tool.

Click Select Data, and then select any individual file in the top level of the Run Folder.  I just selected Thumbs.db.  (Lispix does nothing with this file, except to locate the Run Folder.

The tool then lets you know how many cubes there are, and the length of the data collection.

Click Choose Images and select which of the elemental images to view.  I chose Ca.  Lispix shows that sometimes there is more than one image in a Cube folder with "Ca" in the name:

Choosing Shortest does the right thing with this data set - selecting the orignal extracted images.

The twenty two images are shown cascaded in the thumbnail registration window:

The image positions are arbitrary, of course.  Assuming that the images should be more or less in a line, you can get the images quickly into positions that may be approximately correct by revolving the images about a central one.  First, I centered the window on the A5 image (by dragging on the white background in the Thumbnail window) and zoomed (using the Zoom button in the Mosaic Tool) to 1/3 size.  From previous inspection, it seemed like A5 and A6 could be registered easily.

Click on Revolve, then click on the A5 image, which will then be locked temporarily (red title, with 'x'es on the ends). Click and drag the A6 image around to be on top of the A5 image and allign.  Other images will follow.  Letting up on the mouse halts the rotation.

The images can be alligned further at this zoom by dragging with the mouse.  First, click on A5 and Lock to lock it in position.  Locked images have XX's on both sides of their names.  The images need not be locked, but if not, it is easy to move them by accident, spoiling the registration. (Lispix beeps when you try to move or jog a locked image.)  Then move A6 with the mouse to about the right position.  Then, Zoom to full size, click where the images overlap to start the flicker, and jog A6 with the arrow keys so that it matches A5 exactly.  Click on the background to stop the flicker.  You can adjust the flicker speed.

 

After A6 is positioned, lock it, if you want.  Note that locking does not fix the window layer - clicking an image always puts it in front.  Continue positioning images until you are satisfied.   Here, I've registered the images going downward, finishing with A1.

Lispix assigns groups automatically -- images in a group touch each other, and, presumably when you are done, are registered with each other.  Here, the blue group is registered, the green are not.

At this point, it is a good idea to save the image positions (in cube-positions.txt) using Save in the Mosaic Tool.  When you close the Thumbnail window, Lispix will save the positions automatically in another file (temp-positions.txt) so that you can start again where you left off.  Since the temp file is over-written automatically, you might wish to use Save.

To make a mosaic of the blue group, click Make Mosaic and select the blue group.  Lispix draws a rectangle around the group so you will know what the mosaic will look like.

White is the default for the mosaic background.

After you input the file name (the default is "Mosaic" <element name> <group color>), lispix writes a mosaic TIFF file to the top level of the Run Folder.  Here it is, in Photoshop*.  Photoshop automatically zooms the image down to fit in the window.  The TIFF file has the mosaic at full resolution.

To make a mosaic for another element, close the Thumbnail window, click Choose Images and type in another element name. The images will appear in a new Thumbnail window with positions, groups and locked state corresponding to the old Thumbnail window which you just closed.  You can make mosaics from the new window in a similar way.