Difference between revisions of "Volume list file"
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Volume list files are text files with extension {{t|.vll}}. They are used as an easy interface to describe sets of tomograms and attached models. | Volume list files are text files with extension {{t|.vll}}. They are used as an easy interface to describe sets of tomograms and attached models. | ||
| − | == | + | ==Syntax== |
A volume list file just lists tomogram files, letting the user attach under each line representing a tomogram some information about it. | A volume list file just lists tomogram files, letting the user attach under each line representing a tomogram some information about it. | ||
| + | A comment is represented by a <nowiki>#</nowiki> symbol. A text file as: | ||
<tt> | <tt> | ||
<nowiki> | <nowiki> | ||
| − | + | myTomogram1.mrc | |
| − | + | myTomogram2.mrc | |
| − | + | myTomogram3.mrc | |
| + | # tomogram 4 was awful!, we exclude it! | ||
| + | myTomogram5.mrc | ||
</nowiki> | </nowiki> | ||
</tt> | </tt> | ||
| + | |||
| + | is already a perfectly formatted volume list file that can be used for instance to create a [[#Creating catalogues| catalogue]] | ||
| + | |||
| + | === Advanced syntax=== | ||
| + | Depending on the final use of the volumen file (possibly creating a catalogue from anew or cropping particles), there are several special characters that introduce different operations: | ||
| + | # <nowiki>#</nowiki> Comment | ||
| + | # <nowiki>*</nowiki> Parameter assignation (ftype,ytilt, etc) | ||
| + | #: * label = testCatalogue_2 | ||
| + | #:* index = 2 | ||
| + | #: * ftype = 1 | ||
| + | #: * xtilt = -60 60 | ||
| + | #: * ytilt = -60 60 | ||
| + | #: * ztilt = -60 60 | ||
| + | #: * apix = 1.20 | ||
| + | #: * defocus = 2.40 | ||
| + | #<nowiki>></nowiki> Crop particles from this source | ||
| + | #<nowiki>!</nowiki> Import models from this source | ||
==Cropping particles== | ==Cropping particles== | ||
| + | |||
| + | === Manually == | ||
| + | Volume list files are useful to [[particle extraction|extract particles]] from multiple tomograms into the same [[data folder]]. This can be achieved from the command line with the order: | ||
| + | |||
| + | <tt> | ||
| + | dtcrop <vll file> reorder sidelength datafolder | ||
| + | </tt> | ||
| + | |||
| + | so, a command in real life would look like: | ||
| + | <tt> | ||
| + | dtcrop mylist.vll reorder 64 data; | ||
| + | </tt> | ||
| + | |||
| + | Here, {{t|myList.vll}} is a file text that lists tomogram files. Below each tomogram, one can insert one or several files [[model]]s or [[Cropping table|tables]] preceded with the symbol <nowiki>></nowiki> | ||
| + | |||
| + | <tt> | ||
| + | <nowiki> | ||
| + | myTomogram1.mrc | ||
| + | > myTable1.tbl | ||
| + | myTomogram2.mrc | ||
| + | > myTable2.tbl | ||
| + | > myModel_imported.omd | ||
| + | # we can mix models an tables | ||
| + | myTomogram5.mrc | ||
| + | # a volume may have no sources | ||
| + | </nowiki> | ||
| + | </tt> | ||
| + | |||
| + | |||
| + | === Through the catalogue === | ||
| + | |||
| + | |||
==Creating catalogues== | ==Creating catalogues== | ||
Revision as of 14:38, 27 April 2016
Volume list files are text files with extension .vll. They are used as an easy interface to describe sets of tomograms and attached models.
Contents
Syntax
A volume list file just lists tomogram files, letting the user attach under each line representing a tomogram some information about it. A comment is represented by a # symbol. A text file as:
myTomogram1.mrc myTomogram2.mrc myTomogram3.mrc # tomogram 4 was awful!, we exclude it! myTomogram5.mrc
is already a perfectly formatted volume list file that can be used for instance to create a catalogue
Advanced syntax
Depending on the final use of the volumen file (possibly creating a catalogue from anew or cropping particles), there are several special characters that introduce different operations:
- # Comment
- * Parameter assignation (ftype,ytilt, etc)
- * label = testCatalogue_2
- index = 2
- * ftype = 1
- * xtilt = -60 60
- * ytilt = -60 60
- * ztilt = -60 60
- * apix = 1.20
- * defocus = 2.40
- * label = testCatalogue_2
- > Crop particles from this source
- ! Import models from this source
Cropping particles
= Manually
Volume list files are useful to extract particles from multiple tomograms into the same data folder. This can be achieved from the command line with the order:
dtcrop <vll file> reorder sidelength datafolder
so, a command in real life would look like: dtcrop mylist.vll reorder 64 data;
Here, myList.vll is a file text that lists tomogram files. Below each tomogram, one can insert one or several files models or tables preceded with the symbol >
myTomogram1.mrc > myTable1.tbl myTomogram2.mrc > myTable2.tbl > myModel_imported.omd # we can mix models an tables myTomogram5.mrc # a volume may have no sources
