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scipion-em / scipion-em-relion

Plugin to use Relion SPA programs within the Scipion framework
GNU General Public License v3.0
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ewald sphere #389

Closed rmarabini closed 9 months ago

rmarabini commented 9 months ago

H @azazellochg,

I use a lot the "ewald sphere" correction in the reconstruction protocol. In practice this requires to add in the "extra parameters" line a string similar to:

--ewald --mask_diameter 1100 --sectors 2 --width_mask_edge 5 --reverse_curvature

Will it be OK if I modified the protocol "protocol_reconstruction.py" and add an extra tab with the following content?

    int ewald_section = parser.addSection("Ewald-sphere correction options");
do_ewald = parser.checkOption("--ewald", "Correct for Ewald-sphere curvature (developmental)");
mask_diameter  = textToFloat(parser.getOption("--mask_diameter", "Diameter (in A) of mask for Ewald-sphere curvature correction", "-1."));
width_mask_edge = textToInteger(parser.getOption("--width_mask_edge", "Width (in pixels) of the soft edge on the mask", "3"));
is_reverse = parser.checkOption("--reverse_curvature", "Try curvature the other way around");
newbox = textToInteger(parser.getOption("--newbox", "Box size of reconstruction after Ewald sphere correction", "-1"));
nr_sectors = textToInteger(parser.getOption("--sectors", "Number of sectors for Ewald sphere correction", "2"));
skip_mask = parser.checkOption("--skip_mask", "Do not apply real space mask during Ewald sphere correction");
skip_weighting = parser.checkOption("--skip_weighting", "Do not apply weighting during Ewald sphere correction");
azazellochg commented 9 months ago

Very good idea @rmarabini , I've made a PR for you to review