For example, when working with many sequentially-numbered, similarly-named volumes in the same directory, it can be inconvenient to create separate entries for each. E.g., this occurs when working with previously boxed-out particles or small subregions of a larger volume. Given myVol1.rec, myVol2.rec .. mvVol99.rec in directory ../dirA and m yVol001.rec .. myVol999 in ../dirB you could set flgVolNamesAreTemplates=1 and
fnVolume = {'../dirA/myVol1-99.rec', '../dirB/myVol001-999'}.
(Note the use of leading zeros in the 2nd case).
Another situation where templates can be helpful is when it is desired to apply multiple initial motive lists to copies of the same volume... e.g. during symmetrization.
Templates must end in <start number>-<stop number> followed by an optional suffix. Conversely, when flgVolNamesAreTemplates is true, filenames for which template expansion is not desired must not end in <start-number>-<stop number>.<suffix>. Templates can be used for initMOTL and tiltRange only when using external files as initial motive lists and wedge masks, respectively. Corresponding templated entries must all expand to the same number of entries. (E.g. you can not use fnVolume = ['v1-10.mrc'] in conjunction with fnModParticle = ['m1-20.mrc'], since the former expands to 10 volumes and the latter to 20 models). Non-template entries will be taken as as applying to each expanded template.
When using templated names in conjunction with a single particle reference, the volume and particle numbers used to specify the reference refer to actual (expanded) volumes rather than templates.
fnOutput_AvgVol_##P###.mrc.
where ## is the iteration number and ### is the number of particles included. The number of particles will have leading zeros so that all filenames will have the same number of digits.
If flgFairReference is 1, an integer, k, specifying that 2^k particles should be used to generate a multi-particle reference.
If flgFairReference is 0 or omitted, either:
or
0: use equal number of particles from each tomo, if possible. (Unequal numbers can still be used, if necessary to achieve the requested number of particles).
name = value
where name specifies parameter being set and value is the value to set the parameter to. value can be an integer, floating point number, complex number, string, vector or cell array. String are constructed using single quotes. Vectors are specified by white space or comma delimited values surrounded by square brackets i.e.
[1 2 3 4:7 -2:-2:-10]
the colon operator allows for the specification of uniform sequences with the first number being the start, the second number is the step and the final number is the end value of the sequence. If there are only two numbers separated by a colon, the step is assumed to be 1. Cell arrays are similar to vectors but each element can hold a value of any type including vectors and other cell arrays. Cell arrays are specified using curly brackets, for example, a cell array can be specified by
{'string', 1, 3.4, [1 2 3], variable}