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

Input: Micrographs

Output: Diagnostic plot pattern

Parameters¶

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).

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

Additional parameters (intermediate level)¶

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.

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

Additional parameters (expert level)¶

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

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

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¶

Documented functions with links to source