rotate_3dmarkers.py

rotate_3dmarkers.py rotates 3Dmarkers.txt file generated by ET-SPEC.

The 3Dmarkers.txt is an ascii file containing the position (x,y,z or slice) of simulated particles in the sample. These positions are generated by ET-SPEC. Rotation performed by rotate_3dmarkers.py is done on x and y keeping the z coordinate or slice the same.

Format of 3Dmarkers.txt file:

<index> <x position> <y position> <slice aka z position>

Note: All the fields above are left padded with spaces. The <index> column is left padded with 5 spaces.

Example:

     1  633.000000  638.000000   12.000000
     2  485.000000  628.000000   12.000000
     3  532.000000  582.000000   12.000000
     4  689.000000  677.000000   12.000000

Example invocation:

This command will rotate the markers by 45 degrees counter clockwise using 400x300 as the center point of rotation (0.5 x width and 0.5 x height). The output will be written to 3Dmarkers_rotated45.txt

rotate_3dmarkers.py 3Dmarkers.txt --angle 45 --outfile 3Dmarkers_rotated45.txt --width 800 --height 600