.. _seglayer2lattice: Seglayer2lattice ---------------- Program to simulate helical diffraction pattern and plot helical lattice from a series of indexed layer lines or rise/rotation parameters +--------------------------------------------------+--------------------------------------------------+ | |seglayer2lattice_input.png| | |seglayer2lattice_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Analyze power spectrum | Output: Power spectrum input image | +--------------------------------------------------+--------------------------------------------------+ .. |seglayer2lattice_input.png| image:: ../gallery_images/seglayer2lattice_input.png :alt: tree :width: 4 cm :target: ../_images/seglayer2lattice_input.png .. |seglayer2lattice_output.png| image:: ../gallery_images/seglayer2lattice_output.png :alt: tree :width: 4 cm :target: ../_images/seglayer2lattice_output.png .. _making_a_seglayer2lattice_table_for_beginner: Parameters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Analyze power spectrum True Option to analyze experimental power spectrum. Power spectrum input image power.hdf Input power spectrum image: accepted file formats (hdf). Batch mode False Batch mode for plot. Otherwise interactive. Diagnostic plot seglayer2lattice_diag.pdf Output diagnostic plot: accepted file formats (pdf, .png, .bmp, .emf, .eps, .gif, .jpeg, .jpg, .ps, .raw, .rgba, .svg, .svgz, .tif, .tiff). Pixel size in Angstrom 1.163 Pixel size is an imaging parameter (accepted values min=0.001, max=100). Layer line/Bessel order or helical rise/rotation choice rise/rotation Choose whether 'layer/bessel', 'rise/rotation' or 'pitch/unit_number ' pairs are given for generating the helical lattice. Layer line/Bessel or rise/rotation pair(s) (0.03, 2); (0.06, -4); (0.09, 6) List of comma-separated pairs in brackets. Pairs are separated by semicolon. (Layer line position [1/Angstrom], Bessel order [integer]) or (Helical rise [Angstrom], rotation [degrees]) Precise helix width in Angstrom 180 Precise width of helix for layer line interpretation (accepted values min=20, max=1500). ============================================================================== ============================================================================== ==================================================================================================== .. _seglayer2lattice_parameter_file_for_beginner: Sample parameter file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You may run the program in the command line by providing the parameters via a text file:: seglayer2lattice --f parameterfile.txt Where the format of the parameters is:: Analyze power spectrum = True Power spectrum input image = power.hdf Batch mode = False Diagnostic plot = seglayer2lattice_diag.pdf Pixel size in Angstrom = 1.163 Layer line/Bessel order or helical rise/rotation choice = rise/rotation Layer line/Bessel or rise/rotation pair(s) = (0.03, 2); (0.06, -4); (0.09, 6) Precise helix width in Angstrom = 180 .. _making_a_seglayer2lattice_table_for_intermediate: Additional parameters (intermediate level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== High-pass filter option False Option to high-pass filter images before alignment or band-pass filter in combination with low-pass filter. Low-pass filter option True Option to low-pass filter images before alignment or band-pass filter in combination with high-pass filter. High and low-pass filter cutoffs in 1/Angstrom (0.001, 0.09) Filter design for high- and low-pass filter with cutoffs in 1/Angstrom. Maximum spatial frequency is 1/(2*pixelsize) (accepted values min=0, max=1). Rotational symmetry 1 Additional x-fold rotational symmetry or x-number of helix start (accepted values min=1, max=100). ============================================================================== ============================================================================== ==================================================================================================== .. _seglayer2lattice_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:: seglayer2lattice --f parameterfile.txt Where the format of the parameters is:: Analyze power spectrum = True Power spectrum input image = power.hdf Batch mode = False Diagnostic plot = seglayer2lattice_diag.pdf Pixel size in Angstrom = 1.163 High-pass filter option = False Low-pass filter option = True High and low-pass filter cutoffs in 1/Angstrom = (0.001, 0.09) Layer line/Bessel order or helical rise/rotation choice = rise/rotation Layer line/Bessel or rise/rotation pair(s) = (0.03, 2); (0.06, -4); (0.09, 6) Rotational symmetry = 1 Precise helix width in Angstrom = 180 .. _making_a_seglayer2lattice_table_for_expert: Additional parameters (expert level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== ============================================================================== ============================================================================== ==================================================================================================== .. _seglayer2lattice_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:: seglayer2lattice --f parameterfile.txt Where the format of the parameters is:: Analyze power spectrum = True Power spectrum input image = power.hdf Batch mode = False Diagnostic plot = seglayer2lattice_diag.pdf Pixel size in Angstrom = 1.163 High-pass filter option = False Low-pass filter option = True High and low-pass filter cutoffs in 1/Angstrom = (0.001, 0.09) Layer line/Bessel order or helical rise/rotation choice = rise/rotation Layer line/Bessel or rise/rotation pair(s) = (0.03, 2); (0.06, -4); (0.09, 6) Rotational symmetry = 1 Precise helix width in Angstrom = 180 .. _using_seglayer2lattice_on_cmdline: Command line options ~~~~~~~~~~~~~~~~~~~~~~~ When invoking seglayer2lattice, you may specify any of these options:: usage: seglayer2lattice [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--analyze_power_spectrum] [--batch_mode] [--high-pass_filter_option] [--low-pass_filter_option] [input_output [input_output ...]] Program to simulate helical diffraction pattern and plot helical lattice from a series of indexed layer lines or rise/rotation parameters 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 --analyze_power_spectrum, --ana Option to analyze experimental power spectrum. (default: False) --batch_mode, --bat Batch mode for plot. Otherwise interactive. (default: False) --high-pass_filter_option, --hig Option to high-pass filter images before alignment or band-pass filter in combination with low-pass filter. (default: False) --low-pass_filter_option, --low Option to low-pass filter images before alignment or band-pass filter in combination with high-pass filter. (default: False) Program flow ~~~~~~~~~~~~~~~~~~~~ #. plot_layer_lines_to_power_and_lattice: Plots assigned layer lines to helical lattice Functions ~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 seglayer2lattice_functions