Difference between revisions of "Cropping unbinned particles after having worked with binned particles"

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%mbio.writeas.textlines(lines);
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% check the results
 
% check the results
ddbrowse -d targetData -t targetData/crop.tbl  
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<tt>ddbrowse -d targetData -t targetData/crop.tbl </tt>
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[[File:upScaleCroppingBinnedGallery.png|thumb|upright|250px|  1x binned particles (pixel size 2nm ) ]]
  
  
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dtcrop('mapFullTomograms.doc',tUpscale,'targetDataFull', 48);
 
dtcrop('mapFullTomograms.doc',tUpscale,'targetDataFull', 48);
  
% Now we check the results
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Now we check the results:
ddbrowse -d targetDataFull -t targetDataFull/crop.tb
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<tt>ddbrowse -d targetDataFull -t targetDataFull/crop.tbl</tt>
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[[File:upScaleCroppingUnBinnedGallery.png|thumb|upright|250px|  1x binned particles (pixel size 2nm ) ]]

Revision as of 18:49, 5 February 2020

Work in progress


Creates the catalogue in full size

dctutorial full -n 3  -cc withmodels


Let Dynamo create a bin1 version of eac tomogram

dynamo_catalogue_bin full_withmodels 1 -ss 256 

-ss 256 defines the size of the chunks that are loaded at once from disk. This parameter does not matter for small tomograms like here.


Now, create a new catalogue where the bin1 versions are the main entries (meaning that the particles will be cropped from the binned version);

dcm -c full_withmodels -l t -ws o

Creates a list with the names of the binned tomograms

binnedFiles=strrep((o.results),'.mrc','_CatBinned1.mrc');

A good policy ios to check that the chars that we generated correspond to files that actually exist:

isfile(binnedFiles);

should produce an array of 3 "trues", i.e:

% ans =
% 
%   1×3 logical array
% 
%    1   1   1 

% % create the new catalogue % We creates a text file which just a list of files

mbio.writeas.textlines(binnedFiles,'binnedFileList.vll');
which is used to create a catalogue: 
dcm -create binned1 -fromvll binnedFileList.vll

% % imports the models of the main catalogue %

scaleModels;

% checks that the new catalogue has indeed 3 models dcmodels binned1

% creates a text file that expresses which models will come from % which tomogram. The format is as follows % tomogram1 % >model file 1 in tomogram 1 % createCroppingVll();



dtcrop binned.vll reorder targetData 24; % the 'reorder' string as second argument tells dynamo to parse the % contents of the vll and to use a new set of tags on the created % particles


% check the results

ddbrowse -d targetData -t targetData/crop.tbl  
1x binned particles (pixel size 2nm )


% Ok, now the actual meat... how do we crop the particle in the unbinned
% tomogram using as input a table?

% We first upscaled the table
tUpscale = dynamo_table_rescale('targetData/crop.tbl','factor',2);

% then we create a text file that indicates which tomogram file is intended
% for which tomogram number in the table (remember that tomogram numbers
% are represented in the index entry in the column 20)
%
% The text file is formated as
% 1 tomogramFileForIndex1
% 2 tomogramFileForIndex1
% 


We run the newly created script:

createTomogramIndexMapFile();

% % Now we crop the particles with the newly created file mapFullTomograms %

dtcrop('mapFullTomograms.doc',tUpscale,'targetDataFull', 48);

Now we check the results:

ddbrowse -d targetDataFull -t targetDataFull/crop.tbl
File:UpScaleCroppingUnBinnedGallery.png
1x binned particles (pixel size 2nm )