Particle File List

The Particle File List is a generic data container that can be used an alternative for Data folder. This object contains a list of tags and a list of particle files, both lists having equal length.Thus, the tag of. a file is defined by the value of tag property inside the object, not by the name of particle file (unlike in a classic Dynamo folder). The ParticleListFile object is just a wrapper on a list of files: the particle files still need to be stored somewhere. They can be stored in any Dynamo storage folder (as classical Dynamo folders or 'dBoxes folders ), but this restriction is not necessary. Any

The particle list star file

An object is something that lives in memory and can thus be operated upon. In most Dynamo commands you can use the object "alive" in memory or its representation in disk. An object of type ParticleListFile can be saved into memory through an star file. For instance, if you have in memory an object plf of this class, the command:

plf.writeFile('test.star')

will create a star file with this structure:

data_
loop_
_tag
_particleFile
1  <absolute path>/particle_00008.em
2  <absolute path>particle_00009.em

Conversely, if you have a star file in your disk, you can create a ParticleListFile object out of it first initializing the object:

plfNew = dpkdata.containers.ParticleListFile();

where the name plfNew is arbirary. You can check what is inside by just typing the name of object variable that you choose, in this case plfNew without a semicolon at the end, i.e.:

>> plfNew

plfNew = 

  ParticleListFile with properties:

                   tag: []
          particleFile: []
                 facts: []
                source: []
                  type: []
              metadata: [1×1 dpkdata.aux.metadata.StarTable]
    why_data_not_valid: 'not initialized'

Then filling it with a file

 plfNew.fillFromStarFile('test.star');

Converting old data folders

Converting one single data folder

You can get a file representing a ParticleFileList object simply with the command:

dpkdata.containers.ParticleListFile.data2starFile(,<star file>);

This file can be used as input for average or an alignment project. You can use a table flag in order to pass a table. With this format, the tags of the particles are not changed.

Merging several data folders

The command for this functionality is:

dpkdata.containers.ParticleListFile.mergeDataFolders
which is be fed with a cell array of names of data folders. Here, you can pass along a cell array of tables (one per data folder) using the flag table

Example of use

The script below is In your Dynamo distribution under

dpkdata.examples.setOfDataFoldersIntoParticleListFile.

It creates three classical data folders, each with its own 8 particles, and a table to refer them. This table contains the actual alignment parameters of the particles in the respective data folder. All particles of all files are indexed into a single new object that keeps track of data folders and tables, renaming the tags coherently. Note that initial particle files are not moved or copied; the new object just references them. In this example, it is fed into average, but if can be input into a project (after saving the object into a star file).

<nowiki>% create three different data folders

N = 3; testNameRoot = 'testFolder'; for i=1:N

  testName{i} = sprintf('%s%03d',testNameRoot,i)
  
  % each folder has the same particle tags (1 to 8), but the same 
  % tag on each folder is a different particle
  dynamo_tutorial(testName{i},'real_random',1,'linear_tags',1); 

end

%% % keeps the positions of data and tables for i=1:N

  dataname{i}  = mbparse.files.absolutePath.getAbsolutePath([testName{i},filesep,'/data']);
  tableName{i} = mbparse.files.absolutePath.getAbsolutePath([testName{i},filesep,'/real.tbl']);

end

% % merges all data folders into one single ParticleListFile object %

% we can pass a table attached to each data folder plf = dpkdata.containers.ParticleListFile.mergeDataFolders(dataname,'tables',tablename);

% The storage object keeps track of the accumulated metadata

% gets a table of the old Dynamo style (just a matrix of numbers) tMerged = plf.metadata.table.getClassicalTable();

% computes the average in the classical way ws = daverage(plf,'t',tMerged); </nowki>