Xmipp

xmipp_image_header (v3.0)

Usage

Operate with image files headers. By default in Xmipp, geometrical transformations comming in images files headers are ignored. Instead this information is read from the images metadata if exist. With this program geometrical transformations can be extracted to a metadata or assigned to header, also allows print or reset image file headers.

See also
transform_geometry

Parameters

-i, --input <input_file>
Input file: metadata, stack, volume or image.
--mode <mode=overwrite>
Metadata writing mode.
where <mode> can be:
  • overwrite Replace the content of the file with the Metadata
  • append Write the Metadata as a new block, removing the old one
-o, --output <output_file=>
Output file: metadata, stack, volume or image.
--print, -p <decompose=0>
Print the geometrical transformations in image file headers. if input is stack and decompose=1 print header of each individual image.
or --extract, -e ( requires -o )
The output is a selfile with geometrical transformations read from image file headers.
or --assign, -a
Write the geometrical transformations from selfile to the image file headers.
or --reset, -r
Reset the geometrical transformations in image file headers.
--round_shifts
Round shifts to integers

Examples and notes

Print the header of the images in metadata:
xmipp_header -i images.sel
Extract geometrical transformations from image file headers:
xmipp_header -i smallStack.stk --extract -o header.doc
Assign the geometrical transformations from the metadata to header:
xmipp_header -i header.doc --assign

User's comments

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