.. _micexam: Micexam ------- Program to examine micrograph quality by computing a localized power spectrum using EMAN2's e2scaneval.py and an averaged power spectrum from overlapping tiles using SPARX' sx_welch_pw2.py +--------------------------------------------------+--------------------------------------------------+ | |micexam_input.png| | |micexam_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrographs | Output: Diagnostic plot pattern | +--------------------------------------------------+--------------------------------------------------+ .. |micexam_input.png| image:: ../gallery_images/micexam_input.png :alt: tree :width: 4 cm :target: ../_images/micexam_input.png .. |micexam_output.png| image:: ../gallery_images/micexam_output.png :alt: tree :width: 4 cm :target: ../_images/micexam_output.png .. _making_a_micexam_table_for_beginner: Parameters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Micrographs cs_scan034.tif Input micrographs: accepted file formats (tif, .mrc, .mrcs, .spi, .hdf, .img, .hed). Diagnostic plot pattern micexam_diag.pdf If single input micrograph: name of diagnostic plot file. In case of multiple input micrographs suffix to be attached to corresponding input micrograph. Output: 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). ============================================================================== ============================================================================== ==================================================================================================== .. _micexam_parameter_file_for_beginner: Sample parameter file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You may run the program in the command line by providing the parameters via a text file:: micexam --f parameterfile.txt Where the format of the parameters is:: Micrographs = cs_scan034.tif Diagnostic plot pattern = micexam_diag.pdf Pixel size in Angstrom = 1.163 .. _making_a_micexam_table_for_intermediate: Additional parameters (intermediate level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Binning option True Micrograph is reduced in size by binning. Binning factor 3 Micrograph is reduced in size by binning factor (accepted values min=1, max=20). MPI option True OpenMPI installed (mpirun). Number of CPUs 2 Number of processors to be used. Maximum number corresponds directly to number of input scans, i.e. no gain in performance if single input micrograph chosen (accepted values min=1, max=300). Temporary directory /tmp Temporary directory should have fast read and write access. ============================================================================== ============================================================================== ==================================================================================================== .. _micexam_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:: micexam --f parameterfile.txt Where the format of the parameters is:: Micrographs = cs_scan034.tif Diagnostic plot pattern = micexam_diag.pdf Pixel size in Angstrom = 1.163 Binning option = True Binning factor = 3 MPI option = True Number of CPUs = 2 Temporary directory = /tmp .. _making_a_micexam_table_for_expert: Additional parameters (expert level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Tile size power spectrum in Angstrom 1800 Tile size to be used for analysis (accepted values min=1, max=10000). Tile overlap in percent 50 Overlap influences degree of averaging (accepted values min=0, max=90). Complete tile array option False A complete array of tiles with no gaps will be generated across the micrograph ============================================================================== ============================================================================== ==================================================================================================== .. _micexam_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:: micexam --f parameterfile.txt Where the format of the parameters is:: Micrographs = cs_scan034.tif Diagnostic plot pattern = micexam_diag.pdf Pixel size in Angstrom = 1.163 Tile size power spectrum in Angstrom = 1800 Tile overlap in percent = 50 Complete tile array option = False Binning option = True Binning factor = 3 MPI option = True Number of CPUs = 2 Temporary directory = /tmp .. _using_micexam_on_cmdline: Command line options ~~~~~~~~~~~~~~~~~~~~~~~ When invoking micexam, you may specify any of these options:: usage: micexam [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--complete_tile_array_option] [--binning_option] [--mpi_option] [input_output [input_output ...]] Program to examine micrograph quality by computing a localized power spectrum using EMAN2's e2scaneval.py and an averaged power spectrum from overlapping tiles using SPARX' sx_welch_pw2.py 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 --complete_tile_array_option, --com A complete array of tiles with no gaps will be generated across the micrograph (default: False) --binning_option, --bin Micrograph is reduced in size by binning. (default: False) --mpi_option, --mpi OpenMPI installed (mpirun). (default: False) Program flow ~~~~~~~~~~~~~~~~~~~~ #. readmic: Read input micrograph #. e2scaneval: e2scaneval.py computes local powerspectra across micrograph #. computepower: Compute powerspectrum of overlapping tiles #. visualize_power: Visualize powerspectrum Functions ~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 micexam_functions