subtom_bandpass
Creates and/or applies a bandpass filter to a volume.
This utility script uses one MATLAB compiled script below:
Options
Directories
- scratch_dir
Absolute path to the folder with the input to be processed. Other paths are relative to this one.
- mcr_cache_dir
Absolute path to MCR directory for the processing.
- exec_dir
Directory for executables
Variables
- bandpass_exec
Bandpass executable
File Options
- input_motl_fn
Relative path and name of the input volume to build and filter the bandpass against. If you just want to visualize an arbitrary filter you can use subtom_shape to create a template of the correct size and not ask for the filtered output.
- filter_fn
Relative path and name of the Fourier bandpass filter to write. If you do not want to output the filter volume simply leave this option blank.
- output_fn
Relative path and name of the filtered volume to write. If you do not want to output the filtered volume simply leave this option blank.
Filter Options
- high_pass_fp
High pass filter cutoff (in transform units (pixels): calculate as (box_size*pixelsize)/(resolution_real) (define as integer e.g. high_pass_fp=2)
- high_pass_sigma
High pass filter falloff sigma (in transform units (pixels): describes a Gaussian sigma for the falloff of the high-pass filter past the cutoff above.
- low_pass_fp
Low pass filter (in transform units (pixels): calculate as (box_size*pixelsize)/(resolution_real) (define as integer e.g. low_pass_fp=7).
- low_pass_sigma
Low pass filter falloff sigma (in transform units (pixels): describes a Gaussian sigma for the falloff of the low-pass filter past the cutoff above.
Example
scratch_dir="${PWD}"
mcr_cache_dir="${scratch_dir}/mcr"
exec_dir="/net/dstore2/teraraid/dmorado/software/subTOM/bin"
bandpass_exec="${exec_dir}/MOTL/subtom_unclass_motl"
input_fn="ref/ref_1.em"
filter_fn="otherinputs/bandpass_hp2s2_lp15s3.em"
output_fn="ref/ref_hp2s2_lp15s3_1.em"
high_pass_fp=2
high_pass_sigma=2
low_pass_fp=15
low_pass_sigma=3