createtrainingmrcstack.py

createtrainingmrcstack.py IS AN ALPHA IMPLEMENTATION AND MAY NOT WORK

createtrainingmrcstack.py creates an MRC file with help of IMOD by extracting random tiles from a directory of images.

NOTE: createtrainingmrcstack.py requires IMOD which is used to create the MRC file.

Basic command:

createtrainingmrcstack.py <directory containing images> <# of random tiles to extract> <destination mrc file>

Example usage:

createtrainingmrcstack.py ./myimages 5 ./traindata.mrc

For help run:

createtrainingmrcstack.py --help

Examples below use the following image as input:

How to download the above image using wget:

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

Example usage with no extra options

The following command will extract 2 random tiles of default size (512x512 pixels) from the bubbles_gray.png image under the ./images directory. Those tiles will then be put into a MRC file using the IMOD command newstack

NOTE: The command below assumes the bubbles_gray.png was put in the images/ subdirectory

createtrainingmrcstack.py ./images 2 result.mrc

If above command is successful, output similar to the following will be seen:

THIS PROGRAM IS AN ALPHA IMPLEMENTATION AND MAY NOT WORK

 RO image file on unit   1 : 0000.tif     Size=        256 K

                    This is a TIFF file.

 Number of columns, rows, sections .....     512     512       1
 Map mode ..............................    0   (byte)                     
 Start cols, rows, sects, grid x,y,z ...    0     0     0     512    512      1
 Pixel spacing (Angstroms)..............   1.000      1.000      1.000    
 Cell angles ...........................   90.000   90.000   90.000
 Fast, medium, slow axes ...............    X    Y    Z
 Origin on x,y,z .......................    0.000       0.000       0.000    
 Minimum density .......................   0.0000                               
 Maximum density .......................   255.00                               
 Mean density ..........................   127.50                               
 tilt angles (original,current) ........   0.0   0.0   0.0   0.0   0.0   0.0
 Space group,# extra bytes,idtype,lens .        0        0        0        0

     0 Titles :


 NEW image file on unit   2 : /trainexample/result.mrc
 section   input min&max       output min&max  &  mean
     0      7.00    255.00      7.00    255.00     93.82

 RO image file on unit   1 : 0001.tif     Size=        256 K

                    This is a TIFF file.

 Number of columns, rows, sections .....     512     512       1
 Map mode ..............................    0   (byte)                     
 Start cols, rows, sects, grid x,y,z ...    0     0     0     512    512      1
 Pixel spacing (Angstroms)..............   1.000      1.000      1.000    
 Cell angles ...........................   90.000   90.000   90.000
 Fast, medium, slow axes ...............    X    Y    Z
 Origin on x,y,z .......................    0.000       0.000       0.000    
 Minimum density .......................   0.0000                               
 Maximum density .......................   255.00                               
 Mean density ..........................   127.50                               
 tilt angles (original,current) ........   0.0   0.0   0.0   0.0   0.0   0.0
 Space group,# extra bytes,idtype,lens .        0        0        0        0

     0 Titles :

     1     36.00    255.00     36.00    255.00     99.82

In addition, the following files should appear in the current directory:

• result.mrc -- Output IMOD MRC file with 2 tiles extracted from input image(s).

• result.mrc.tile.list.config -- ASCII text configuration file with coordinates containing locations where tiles were extracted from the input image(s).

Example contents of result.mrc.tile.list.config:

[DEFAULT]
imagedir = /foo/example/images

[bubbles_gray.png]
1 = 649,527,1161,1039
2 = 222,8,734,520

Run 3dmod to launch IMOD on result.mrc to view its contents

3dmod result.mrc

Screenshot of result.mrc