.. _segclassexam: Segclassexam ------------ Program to examine helix classes to compute their collapsed (1D) and 2D power spectrum and width profile of helices +--------------------------------------------------+--------------------------------------------------+ | |segclassexam_input.png| | |segclassexam_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Class average stack | Output: Diagnostic plot | +--------------------------------------------------+--------------------------------------------------+ .. |segclassexam_input.png| image:: ../gallery_images/segclassexam_input.png :alt: tree :width: 4 cm :target: ../_images/segclassexam_input.png .. |segclassexam_output.png| image:: ../gallery_images/segclassexam_output.png :alt: tree :width: 4 cm :target: ../_images/segclassexam_output.png .. _making_a_segclassexam_table_for_beginner: Parameters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== 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). ============================================================================== ============================================================================== ==================================================================================================== .. _segclassexam_parameter_file_for_beginner: 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) .. _making_a_segclassexam_table_for_intermediate: Additional parameters (intermediate level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== 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. ============================================================================== ============================================================================== ==================================================================================================== .. _segclassexam_parameter_file_for_intermediate: 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 .. _making_a_segclassexam_table_for_expert: Additional parameters (expert level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== 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). ============================================================================== ============================================================================== ==================================================================================================== .. _segclassexam_parameter_file_for_expert: 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 .. _using_segclassexam_on_cmdline: 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. Functions ~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 segclassexam_functions