Segclassexam¶
Program to examine helix classes to compute their collapsed (1D) and 2D power spectrum and width profile of helices
Input: Class average stack
Output: Diagnostic plot
Parameters¶
Parameter |
Example (default) |
Description |
|---|---|---|
Class average stack |
avgerages.hdf |
Class average stack: accepted file formats (hdf). |
Diagnostic plot |
segclassexam_diag.pdf |
Output diagnostic plot: accepted file formats (pdf, .png, .bmp, .emf, .eps, .gif, .jpeg, .jpg, .ps, .raw, .rgba, .svg, .svgz, .tif, .tiff). |
Power spectrum output image |
power.hdf |
Output power spectrum image: accepted file formats (hdf). |
Pixel size in Angstrom |
1.163 |
Pixel size is an imaging parameter (accepted values min=0.001, max=100). |
Estimated helix width in Angstrom |
200 |
Generous width measure of helix required for rectangular mask (accepted values min=0, max=1500). |
Class number range to be analyzed |
(3, 5) |
Class number range to be analyzed (1st class is 0) (accepted values min=0, max=2000). |
Sample parameter file¶
You may run the program in the command line by providing the parameters via a text file:
segclassexam --f parameterfile.txt
Where the format of the parameters is:
Class average stack = avgerages.hdf
Diagnostic plot = segclassexam_diag.pdf
Power spectrum output image = power.hdf
Pixel size in Angstrom = 1.163
Estimated helix width in Angstrom = 200
Class number range to be analyzed = (3, 5)
Additional parameters (intermediate level)¶
Parameter |
Example (default) |
Description |
|---|---|---|
Class variance option |
False |
Check if variances of classes are to be analyzed. |
Class variance stack |
variances.hdf |
Stack: accepted image file formats (spi, hdf, img, hed) |
MPI option |
True |
OpenMPI installed (mpirun). |
Number of CPUs |
8 |
Number of processors to be used (accepted values min=1, max=1000). |
Temporary directory |
/tmp |
Temporary directory should have fast read and write access. |
Sample parameter file (intermediate level)¶
You may run the program in the command line by providing the parameters via a text file:
segclassexam --f parameterfile.txt
Where the format of the parameters is:
Class average stack = avgerages.hdf
Diagnostic plot = segclassexam_diag.pdf
Class variance option = False
Class variance stack = variances.hdf
Power spectrum output image = power.hdf
Pixel size in Angstrom = 1.163
Estimated helix width in Angstrom = 200
Class number range to be analyzed = (3, 5)
MPI option = True
Number of CPUs = 8
Temporary directory = /tmp
Additional parameters (expert level)¶
Parameter |
Example (default) |
Description |
|---|---|---|
Enhanced power spectrum option |
True |
Option to enhance power spectrum to compensate for decay of amplitudes. |
Enhanced power spectrum output image |
power_enhanced.hdf |
Output enhanced power spectrum image (compensated for decay of amplitudes): accepted file formats (hdf). |
Power spectrum resolution cutoff in 1/Angstrom |
0.15 |
Images are binned to obtain a suitable power spectrum (accepted values min=0, max=1). |
Sample parameter file (expert level)¶
You may run the program in the command line by providing the parameters via a text file:
segclassexam --f parameterfile.txt
Where the format of the parameters is:
Class average stack = avgerages.hdf
Diagnostic plot = segclassexam_diag.pdf
Class variance option = False
Class variance stack = variances.hdf
Power spectrum output image = power.hdf
Enhanced power spectrum option = True
Enhanced power spectrum output image = power_enhanced.hdf
Pixel size in Angstrom = 1.163
Estimated helix width in Angstrom = 200
Power spectrum resolution cutoff in 1/Angstrom = 0.15
Class number range to be analyzed = (3, 5)
MPI option = True
Number of CPUs = 8
Temporary directory = /tmp
Command line options¶
When invoking segclassexam, you may specify any of these options:
usage: segclassexam [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--class_variance_option]
[--enhanced_power_spectrum_option] [--mpi_option]
[input_output [input_output ...]]
Program to examine helix classes to compute their collapsed (1D) and 2D power spectrum and width profile of helices
positional arguments:
input_output Input and output files
optional arguments:
-h, --help show this help message and exit
--g, --GUI GUI option: read input parameters from GUI
--p, --promptuser Prompt user option: read input parameters from prompt
--f FILENAME, --parameterfile FILENAME
File option: read input parameters from FILENAME
--c, --cmd Command line parameter option: read only boolean input parameters from command line and all other parameters will be assigned
from other sources
--l LOGFILENAME, --logfile LOGFILENAME
Output logfile name as specified
--d DIRECTORY_NAME, --directory DIRECTORY_NAME
Output directory name as specified
--version show program's version number and exit
--class_variance_option, --cla
Check if variances of classes are to be analyzed. (default: False)
--enhanced_power_spectrum_option, --enh
Option to enhance power spectrum to compensate for decay of amplitudes. (default: False)
--mpi_option, --mpi OpenMPI installed (mpirun). (default: False)
Program flow¶
add_power_spectra_from_verticalized_stack: Addition of in-plane rotated power spectra
determine_width: Determine width of helix by projection along helical axis
visualize_power_avg_and_width_analysis: Visualization of width and power spectra
prepare_segclassexam: Prepare classes for analysis.
perform_class_examination: Extract classes, profiles and power spectra.
print_figures: Save diagnostic plots to file.