Describe Notes from day 1 here.

Display the original (full size) image

Using SPC's version of display.

Display

Image ID

n - No to single images

n - No to updating T1

Restarting with a landmark

When you finish with a landmark, then want to come back to it OR if lithos crashes.

LITHOS

i - input

AA0001 - landmark name

n - No to add images

n - No to add single image

Getting Correlation score

When you need to see how the topography is coming along, especially when you load a landmark

While running LITHOS, having already loaded the landmark (see above)

1 - Align landmarks

0 - Auto align

1 - Spacing of 1

n - No to new spacing

0 - Continue

y - yes to accept shifts

Review the output to see how well the landmarks correlate to the topography. Note, the good landmarks (the ones being used to build the template and topography) should be before the poor ones.

Getting the State of the Landmark

When you start with a landmark, or when things don't seem right, it is very good to get the "state" of the landmark. You do this with three evaluations.

Get the Correlation score (see above)

Look at which images are being used (image without a star when you go into the 0 "get template" menu

From lithos's main menu with a landmark loaded

0 - Get template

q - quit

Review the list that is displayed.

Count the number of images that are being used.

Look at the LMRK_DISPLAY1.pgm

Review the all the images that are being used.

They should all be aligned to the same location.

Review the ones not being used.

Are any of them close and worth keeping.

Look for any images that include the limb of the object.

These must be deleted.

Strongly consider removing any images that do not contain an image at position 50/50 (the center).

Eliminating images using correlation score

The typical sequence is to remove image based on geometry, then align them the best you can. Then once that is done, remove images that are not correlating at all.

Load the correlation score of the images

e - eliminate menu

o - eliminate low-correlation images (the command is the letter 'o', not the number zero)

0.1 - correlation threshold.

This will remove all images with less than 0.1 for their correlation.

Manually delete an image

Remove an image from the data set all together. Note, when you eliminate an image, it will be removed immediately. Update/save is not required.

From the main lithos menu, after you've loaded your landmark

e - eliminate menu

m - manual remove

<image number>

Can do many images, just put one per line

0 - quits the image

Manually deselect an image

When you have some images that you don't want in your template

From the main lithos menu, after you've loaded your landmark

0 - Find template menu

<image number>

0 - Quits the input

Murphy -- pre-backup landmarks

For the Tucson crew, we used an alias called 'murphy' to backup files before we started a major task. Thus, if we made changes that we didn't like, we could recover the pre-work state. Originally, we just backed up LMKFILES, but the crew wanted to backup more. This works well as long as the MAPFILES do not get too large.

To do this, you do three things

Create a backup directory.

Create this in the directory right above your working directory

mkdir back-landmarks

Create an alias, typically in the .bashrc

alias murphy='rsync --delete -hapvP LMKFILES/ ../back-landmarks/LMKFILES/; rsync --delete -hapvP MAPFILES/ ../back-landmarks/MAPFILES; rsync --delete -hapvP SUMFILES/ ../back-landmarks/SUMFILES'

When you are about ready to start some new work, just type 'murphy'.

It will just take a minute.