.. _scansplit: Scansplit --------- Program to split large scan into individual micrographs. The location of individual micrographs is determined by a dummy micrograph reference. +--------------------------------------------------+--------------------------------------------------+ | |scansplit_input.png| | |scansplit_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrographs | Output: Output micrograph pattern | +--------------------------------------------------+--------------------------------------------------+ .. |scansplit_input.png| image:: ../gallery_images/scansplit_input.png :alt: tree :width: 4 cm :target: ../_images/scansplit_input.png .. |scansplit_output.png| image:: ../gallery_images/scansplit_output.png :alt: tree :width: 4 cm :target: ../_images/scansplit_output.png .. _making_a_scansplit_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). Output micrograph pattern cs_scan034???.mrc If single input micrograph: name of pattern. In case of multiple micrographs suffix to be attached to corresponding micrograph. Use wildcards cs_scan034\?\?\?.mrc OR cs_scan034*.mrc, accepted file formats (jpg, .tif, .mrc, .spi, .hdf, .img, .hed). Number of columns x rows (3, 2) Integer value for number of columns x rows of micrographs located on scan (accepted values min=1, max=10). Number of micrographs to be cropped 6 Integer value number of micrographs located on scan (number of rows x number of columns) (accepted values min=1, max=100). ============================================================================== ============================================================================== ==================================================================================================== .. _scansplit_parameter_file_for_beginner: Sample parameter file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You may run the program in the command line by providing the parameters via a text file:: scansplit --f parameterfile.txt Where the format of the parameters is:: Micrographs = cs_scan034.tif Output micrograph pattern = cs_scan034???.mrc Number of columns x rows = (3, 2) Number of micrographs to be cropped = 6 .. _making_a_scansplit_table_for_intermediate: Additional parameters (intermediate level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Micrograph width x height in cm (8.0, 9.0) Width x height dimension of micrograph in cm (accepted values min=0, max=50). Scanner step size in micrometer 7.0 Characteristic resolution or step size of scanner in micrometer (accepted values min=1, max=1000). Contact print option False Option to produce a contact print of the entire scan. Final print option False Option to produce a final high-contrast print of the cropped micrograph. Normscan option False Option to normalize micrograph columns to eliminate steep grey-value differences in micrograph columns that can be present in Zeiss scans. Binning option False Micrograph is reduced in size by binning. Binning factor 6 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. ============================================================================== ============================================================================== ==================================================================================================== .. _scansplit_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:: scansplit --f parameterfile.txt Where the format of the parameters is:: Micrographs = cs_scan034.tif Output micrograph pattern = cs_scan034???.mrc Number of columns x rows = (3, 2) Number of micrographs to be cropped = 6 Micrograph width x height in cm = (8.0, 9.0) Scanner step size in micrometer = 7.0 Contact print option = False Final print option = False Normscan option = False Binning option = False Binning factor = 6 MPI option = True Number of CPUs = 2 Temporary directory = /tmp .. _making_a_scansplit_table_for_expert: Additional parameters (expert level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Label width x height in cm (2.7, 1.4) Width x height dimension of black label in cm located at bottom of micrograph (accepted values min=0, max=10). Cross-correlation rejection criterion 10000.0 Use the default number to exclude empty positions with no micrograph on scan - otherwise use with caution (accepted values min=0, max=1e+08). ============================================================================== ============================================================================== ==================================================================================================== .. _scansplit_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:: scansplit --f parameterfile.txt Where the format of the parameters is:: Micrographs = cs_scan034.tif Output micrograph pattern = cs_scan034???.mrc Number of columns x rows = (3, 2) Number of micrographs to be cropped = 6 Micrograph width x height in cm = (8.0, 9.0) Label width x height in cm = (2.7, 1.4) Scanner step size in micrometer = 7.0 Cross-correlation rejection criterion = 10000.0 Contact print option = False Final print option = False Normscan option = False Binning option = False Binning factor = 6 MPI option = True Number of CPUs = 2 Temporary directory = /tmp .. _using_scansplit_on_cmdline: Command line options ~~~~~~~~~~~~~~~~~~~~~~~ When invoking scansplit, you may specify any of these options:: usage: scansplit [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--contact_print_option] [--final_print_option] [--normscan_option] [--binning_option] [--mpi_option] [input_output [input_output ...]] Program to split large scan into individual micrographs. The location of individual micrographs is determined by a dummy micrograph reference. 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 --contact_print_option, --con Option to produce a contact print of the entire scan. (default: False) --final_print_option, --fin Option to produce a final high-contrast print of the cropped micrograph. (default: False) --normscan_option, --nor Option to normalize micrograph columns to eliminate steep grey-value differences in micrograph columns that can be present in Zeiss scans. (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 #. roughsplit: Rough splitting of micrograph according to number of rows and columns #. make_refmic: Make binary reference micrograph including label #. findlabel: Find label on micrograph with respect to reference micrograph #. finesplit: Fine splitting of micrograph according to matched position #. normscan: Normalize micrograph columns using Niko Grigorieff's Normscan #. bin_micrographs: Bin micrographs by specified factor #. contactprint: Produce contact print of scan #. finalprint: Produce final prints of split micrograph Functions ~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 scansplit_functions