Metadata_utilities_v31

!xmipp_metadata_utilities (v3.1)

Usage

Perform several operations on metadata files. If the -o option is not used the original metadata will be modified. Also you can use the --print option just to print out the result metadata to screen. The combination of -i and -o without other operations can serve to extract data blocks inside a medata and write to an independent one.

See also Metadata_import_v3

Parameters

$: Input metadata file $: Output metadata file, if not provided result will overwrite input file $--set, -s <set_operation> <md2_file> <labelimage> <label2=image2> where <set_operation> can be:

• • $ or``: Operations on the metadata structure where <operation> can be:
  • $ or``: File operations where <file_operation> can be:
  • $ or``: Query operations where <query_operation> can be:
  • $ or``: Fill a column values(should be of same type) where <fill_mode> can be:
  • $``: Just print medata to stdout, or if -o is specified written to disk. this option is useful for extrating data blocks inside a metadata. $--mode <modeoverwrite> where <mode> can be:

Examples and notes

Concatenate two metadatas. If label is not provided, by default is 'image'

xmipp_metadata_utilities -i mD1.doc --set union mD2.doc  -o out.doc

Intersect two metadatas using label 'order_'

xmipp_metadata_utilities -i mD1.doc --set intersection mD2.doc order_ -o out.doc

Combine columns from two metadatas. Be sure of both have same number of rows and also there aren't common columns, in that case second metadata columns will be used

xmipp_metadata_utilities -i mD1.doc --set merge mD2.doc -o out.doc

Sort the elements in metadata (using default label 'image').

xmipp_metadata_utilities -i mD1.doc -s sort -o out.doc

You can also add columns and 'filling' its values with different options By example, to add the column 'shiftX' with uniform random value between 0 and 10

xmipp_metadata_utilities -i mD1.doc --fill shiftX rand_uniform 0 10 -o out.doc

Or for initialize metadata columns 'shiftX' and 'shiftY' with a constant value of 5

xmipp_metadata_utilities -i mD1.doc -l "shiftX shiftY" constant 5 -o out.doc

If you have columns that represent the filename of a metadata with other data (ex CTFParams) you cant 'expand' the column with the values in that metadta

xmipp_metadata_utilities -i mD1.doc --fill CTFParams expand -o outExpanded.doc

For check all options availables for 'filling' mode, use:

xmipp_metadata_utilities --help fill

write metadata as table in Sqlite3 database. (use xmipp_sqlite3 to visualize results)

xmipp_metadata_utilities -i [email protected] -o [email protected]

write metadata as xml file.

xmipp_metadata_utilities -i [email protected] -o [email protected]

Copy files in metadata to a location. The metadata will be also copied to new location

xmipp_metadata_utilities -i mD1.doc --file copy /home/pepe/newLocation

Delete files in metadata.

xmipp_metadata_utilities -i mD1.doc --file delete

Select elements in metadata that satisfy a given constrain.

xmipp_metadata_utilities -i mD1.doc --query select "angleRot > 10 AND anglePsi < 0.5" -o out.doc

You can also modify your data using SQLite syntax expression

xmipp_metadata_utilities  -i a.doc --operate modify_values "angleRot=2.*angleRot" -o b.doc
xmipp_metadata_utilities  -i a.doc --operate modify_values "angleRot=radians(angleRot)" -o b.doc
xmipp_metadata_utilities  -i a.doc --operate modify_values "angleRot=sin(radians(angleRot))" -o b.doc
xmipp_metadata_utilities  -i a.doc --operate modify_values "angleRot=sqrt(angleRot)" -o b.doc
xmipp_metadata_utilities  -i a.doc --operate modify_values "image=replace(image, 'xmp','spi')" -o b.doc
xmipp_metadata_utilities  -i a.doc --operate modify_values "image='new_prefix_dir/'||image" -o b.doc

Count number of images per CTF

xmipp_metadata_utilities -i mD1.doc -q count CTFModel -o out.doc

images asigned a ctfgroup

xmipp_metadata_utilities -i mD1.doc -q sum defocusGroup count -o out.doc

Print the metadata Size

xmipp_metadata_utilities -i mD1.doc --query size

Rename Column

xmipp_metadata_utilities -i mD1.doc --operate rename_column "weight wRobust"

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