Using createtrainingmrcstack with configuration to specify tiles to extract

createtrainingmrcstack.py has an option --useconfig that allows caller to dictate the location on parent images where to extract tiles. This page contains a tutorial on how to alter a configuration file and use it to select certain tiles.

Example:

createtrainingmrcstack.py ./images 2 result.mrc --useconfig tileconfig.config

Image to use:

Step 1 Download data

In this step we download an image file

mkdir images
cd images
wget https://raw.githubusercontent.com/wiki/CRBS/chmutil/images/bubbles_gray.png
cd ..

Step 2 Generate configuration file

When running createtrainingmrcstack.py in default mode, as seen below, the tool randomly picks tiles and outputs an MRC file and a tile configuration file. In the case below they will be named result.mrc and result.mrc.tile.list.config

createtrainingmrcstack.py ./images 2 result.mrc

Step 4 alter configuration file

Open the result.mrc.tile.config in an editor,

The contents will look similar to the following:

NOTE: The imagedir path will be different.

[DEFAULT]
imagedir = /home/foo/tests/customtile/images

[bubbles_gray.png]
1 = 44,435,556,947
2 = 911,339,1423,851

Lets switch the coordinates of both tiles, edit the file replacing the

1 = line with 1 = 0,0,512,512

and the

2 = line with 2 = 600,400,1112,912

like shown below:

[DEFAULT]
imagedir = /home/foo/tests/customtile/images

[bubbles_gray.png]
1 = 0,0,512,512
2 = 600,400,1112,912

Save the above file as my.tileconfig

Step 4 run createtrainingmrcstack.py with custom configuration

createtrainingmrcstack.py ./images 1 result.mrc --useconfig my.tileconfig

Step 5 check results

Run 3dmod on result.mrc with command below and the tool should show the 2 tiles as seen in screenshot below:

3dmod result.mrc