File Format Description

This file format is used to store one US acquisition operation, i.e. storing a US image stream along with tracking and probe information.

The acquisition is available from US Acquisition Widget .

All files describing one acquisition lie the same folder. The files all have the name format US-Acq_{index}_{TS}{stream}.{type}, where

{index} is a running index, for convenience.
{TS} is a timestamp
{stream} is the uid of the video stream.
{type} is the format of that specific file.

Together, the files contains information about the us images and their timestamps, the tracking positions and their timestamps, and the probe calibration.

In the following, we use {filebase} = US-Acq_{index}_{TS}{stream}.

Frame Data {filebase}_{frame}.mhd

A sequence of files in the metaheader file format containing the image data, one file for each frame. The frame index is given by the index {frame} in the file name.

The metaheader files contains orientation+position info identical to the positions in Frame Positions {filebase}.fp . The files can thus be imported directly back into CustusX and appear in the correct position.

See http://www.itk.org/Wiki/MetaIO/Documentation for more.

Replaces {filebase}.mhd.

Profile Definition {filebase}.probedata.xml

This file contains the probe definition. Replaces ProbeCalibConfigs.xml .

Frame Timestamps {filebase}.fts

This file contains the frame timestamps. This is a sequence of newline-separated floating-point numbers in milliceconds. The starting point is irrelevant. The number of timestamps must equal the number of us frames.

Frame Positions {filebase}.fp

This file contains the frame positions, one matrix for each US frame. Each matrix is the rMu, i.e. the transform from lower-left centered image space to global reference (See Coordinate Systems and US Probe Definition).

This is a newline-separated sequence of matrices, one for each position. The last line of the matrix (always containing 0 0 0 1) is omitted. The matrix numbers is whitespace-separated with newline between rows. Thus the number of lines in this file is (# tracking positions) x 3.

Tracking Timestamps {filebase}.tts

This file contains the tracking timestamps. The format equals Frame Timestamps {filebase}.fts , but the number of timestamps equals the number of tracking positions.

Tracking Positions {filebase}.tp

This file contains the tracking positions, one matrix for each tracking sample. Each matrix is the prMt, i.e. the transform from tool to patient reference (See Coordinate Systems ).

This is a newline-separated sequence of matrices, one for each position. The last line of the matrix (always containing 0 0 0 1) is omitted. The matrix numbers is whitespace-separated with newline between rows. Thus the number of lines in this file is (# tracking positions) x 3.

Image Mask {filebase}.mask.mhd

This file contains the image mask. The binary image shows what parts of the frame images contain valid US data. This file is only written, not read. It can be constructed from the probe data.

Obsolete files

{filebase}.mhd

obsolete

Used prior to version cx3.4.0.

A file in the metaheader file format containing the uncompressed image data. the z-direction is the time axis, i.e. the z dim is the number of us frames. See http://www.itk.org/Wiki/MetaIO/Documentation for more.

Two extra tags are added:

ConfigurationID = <path:inside:ProbeCalibConfigs.xml> ProbeCalibration = <not used>

The ConfigurationID refers to a specific configuration within ProbeCalibConfigs.xml, using colon separators.

ProbeCalibConfigs.xml

obsolete

This file contains the probe definition, and is copied from the config/tool/Tools folder.