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07/22/2011

Mosaic Tool

New 7/2010

Trinitite Example

This tool is for making a mosaic of  images by joining the images together where they match. 

For a series of data cubes:  you manually make a mosaic of one element by arranging the images for that element, then Lispix will make mosaics for other elements using the positions you saved.

For a folder of images - just arrange the images.

 

How To Use

Cube Mode

Select Cubes

Choose the Run folder, i.e. locate the data by selecting any file in the top level of the Run Folder.  The Run Folder contains folders for each data cube and the associated elemental images.

Choose Images Choose which image from each cube you will use, by typing in a unique name fragment such as "Ca". This assumes that each Calcium elemental image file contains "Ca" in the file name and that other image files do not.

Image Mode

Select Images

Choose the folder by selecting any image in that folder.

Choose Images

Choose the images from the list of all images in the folder.

 

Arrange

Some convenient ways to arrange the thumbnails so that they are close to where they should be, are in the Initialize Button.:

Revolve images about a central one.  This is for coarse allignment of the images - this is to help order them in the right direction:  Click on Revolve, click on central image, click and drag anywhere else in the window to move the images.

Stack the images in a slanted diagonal line.

Arrange the images in a Grid by Rows. This assumes the images are in row order, right to left.

Allign

Move the thumbnails with the mouse, so that they allign.

  1. Click and drag one thumbnail.
  2. Hold down shift key to move a group.
  3. Hold down space bar to move them all (scroll the thumbnail window).

"Fine tune" by jogging the top thumbnail (last clicked) with the arrow keys.

 

** Continue Editing Here.

  1. Drag an image or group of images (shift drag) with the mouse.  Images that touch or overlap are part of a group which is assigned automatically.  Scroll all images in the window by dragging in the white background.
  2. Jog the top image using the arrow keys.  The last clicked image is on top.
  3. Click where images overlap to start flicker. Click on background to stop flicker. During flicker, jog or drag top image.  This is the final allignment step, which is best done at full size. Lock each image in place after it is alligned.
  4. Save the allignment positions.

Make Mosaic Select the group or groups for the mosaic.  Lispix writes a TIFF file of the mosaic.

See Trinitite Example.

 

Data Organization

All cubes to be registered are in their own folder, along with any elemental images, and any other files. Let's call these folders Cube Folders. All the Cube Folders are within a single folder - the Run Folder. The Run folder can contain other folders and files which Lispix ignores.

 

 


Details


To register the cubes, you need images. These can be made from the cubes using Lispix, or some other program. The images for any cube should be in their respective Cube Folder, and have the Element Symbol, e.g. "Au", "Pt", "Ca", "S", or some other unique indicative string, e.g. "BSE" as part of their name. For registering, as well as for making a mosaic, you will type in the Element Symbol or indicative string. If this selects more than one image for the cube, Lispix will ask which image to use, or which selection scheme you wish to use, such as shortest name or longest name.

Arrange the images by moving them around manually.    Whenever you close this window, lispix saves the image positions in a file "temp-positions".txt, and will use these positions when you begin next time.  Once you have an arrangement you wish to keep, save the positions in "cube-positions" using Save.  Lispix uses the cube-positions.txt file to make the mosaic.  Lispix saves both position text files in the top level of the Run Folder.

The position of an image is changed any time you move its thumbnail.  The precision of the position thus depends on the zoom.  You save full (single precision) locations for an image only when moving it shown full size.  You can lock an image to ensure that you don't move it accidentally.  Be sure to Save the positions after adjusting at full size the ones you want to include in the mosaic.