REALALIGN
Function of the program :
Align focal pair images by maximizing real space corelation coefficient. Briefly determined translation and rotation matix can be input to do the refinement.
Purpose of the program:
In order to use the box information from the high defocus image, the translation and rotation matrix between the two focal pair images must be accurately determined. Searching by FFT convolution failed because of the CTF effect. Therefore, the slow searching by maximizing the real space correlation coefficient applied in the program. The program is parallelized to solve the speed problem. The magnification difference between the focal pair is also considered in the program by the scale-factor.
Usage of the program:
- Usage: realalign [option] Hi_def.pif Lw_def.pif
- Options:
- Example for REALALIGN:
| Options | explanations |
|---|---|
| -q square_size | size inpixel of the center square used in the search, better if usingvalue that is the power of 2. Default is the maximun value that issmaller than the image dimension and is the power of 2. |
| -b start_bin | starting bin factor, better if using valuse that is the power of 2. Default is making the initial bined sqare to be 512 |
| -d trans_range | Translation search range in pixel, default is 800 |
| -a phi_range | rotation search range in degree, Default is 4.0 |
| -c scale_range | scale factor searching range, default 0.01 scale search will only start when bin=2 |
| -p phi_best | initial best rotation angle in degree, default is 0.0 |
| -x trans_x_best | initial best X translation in pixel, default 0.0 |
| -y trans_y_best | initial best Y translation in pixel, default 0.0 |
| -s scale_best | initial best scale factor, default 1.0 |
| -m matrix_filename | output filename, defult is matrix |
| -l | flag to enable list intermedia CC results |
| -n list_filename_root | list filename root, default CClist |
| -h | Print the help, no calculation |
| Without Initial Value | realalign -r 5 -m matrix.1234 1234.pif 1233.pif |
| With Initial Value, eg, from FP_BRIEF | realign -r 5 -m matrix.7693 -b 2 -d 4 -a 0.08 -p 0.2288 -x 75.67 -y -133.18 -s 0.997 7693g_8.pif 7692g_8.pif |
BUG REPORT :
If you meet any bugs or problems of the programs, please email xc@purdue.edu.