Image transformations
Image translation
There are several types of image translations. The first is when the shift is by integer pixels/voxels so that no interpolation is necessary:
bimg -verb 7 -trans 15,-10,8 2omf.grd 2omf_t.map
Other options include a change in size with the -size option, and wrapping around the boundaries when the -wrap flag is specified:
bimg -verb 7 -size 80,80,80 -trans 15,-10,8 -wrap 2omf.grd 2omf_t.map
The second translation type is where the shift is not in integer units, requiring interpolation:
bint -verb 7 -trans 8.37,5.04,-11.8 2omf.grd 2omf_t.map
Image rotation
As for translation, rotation can also be done in two ways. The first requires no interpolation and is commonly refered to as reslicing. This is also useful where different image processing packages have different conventions of axis order and image orientation. The following two examples rotate an image around the y axis by 90 degrees and mirror the image along the z axis:
bimg -verbose 7 -reslice zy-x 2omf.grd test.mrc
bimg -verbose 7 -reslice xy-z 2omf.grd test.mrc
The more common rotations require interpolation. Rotations can be specified in many different ways:
- Euler angles
- Rotation around an axis by an angle
- Rotation to or from a view
Rotations occur around the origin specified in the image, or given on the command line. To rotate a volume around an axis {0.5,-0.3,0.2} by an angle 34°, using the origin {40,40,40}:
bint -verb 7 -rotate 0.5,-0.3,0.2,34 -origin 40,40,40 2omf.grd test.mrc
Image scaling
An image can be scaled:
bint -verbose 7 -scale 1.4,1.4,1.4 2omf.grd test.mrc
This will resize the image as well based on the scaling. To obtain a particular out out size, use the -size option
Image binning
Images are often binned by an integer factor to save processing time. There are three types of binning in Bsoft:
- Averaging binning
- Median binning
- Special integer binning
The most common form of binning is averaging, where the values in the kernel are averaged. For median binning, the values in the kernel are ranked and the middle value picked. Special integer binning involves a kernel with weights that decay towards its edges. To do a simple averaging binning:
bint -verbose 7 -bin 2,2,2 2omf.grd test.mrc
Combined image transformation
The operations of translation, rotation and scaling can be combined into one command line. The sampling and origin will be changed, so there are options to specify the original origin and sampling, and to specify the new origin and sampling desired in the output image:
bint -verb 7 -size 150,150,150 -trans -4,-4,-4 -rot 0.5,-0.3,0.2,34 -ori 40,40,40 -scale 0.9,0.9,0.9 -newori 44,44,44 - newsam 1.67 2omf.grd test.mrc