Sequence metafile editor (EditSequenceFile)

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This is a command-line tool for editing sequence metafiles. Operations include deleting frames from a file (TRIM command), append sequence metafiles (APPEND command), adding/deleting/changing data fields (…FIELD… commands), compress/uncompress the image data (–use-compression switch).

Examples

Generate sequence metafile that contains ImageToReference transforms

EditSequenceFile.exe --operation=ADD_TRANSFORM --add-transform=ImageToReference --config-file=PlusDeviceSet_fCal_Sim_VolumeReconstruction.xml  --source-seq-file=fCal_Test_Calibration_3NWires_fCal2.0.mha --output-seq-file=test.mha

Multiple transforms can be added, the names are separated by commas (do not add spaces):

EditSequenceFile --operation=ADD_TRANSFORM --add-transform=ImageToReference,ProbeToReference,TrackerToReference --source-seq-file=fCal_Test_Calibration_3NWires_fCal2.0.mha --output-seq-file=test.mha

Compress a sequence metafile

EditSequenceFile.exe --source-seq-file=[inputFilePath] --output-seq-file=[outputFilePath] --use-compression

Uncompress a sequence metafile

EditSequenceFile.exe --source-seq-file=[inputFilePath] --output-seq-file=[outputFilePath]

Trim a long sequence

Create a small test data file from the first 24 frames of a tracked ultrasound metafile:

EditSequenceFile --operation=TRIM --first-frame-index=0 --last-frame-index=23 --source-seq-file=e:\data\AdultScoliosis-T2.mha --output-seq-file=e:\data\AdultScoliosis-T2-24frames.mha

Use fill image rectangle for anonymization

Anonymization of sequences that contain patient information burnt into the pixels is enabled by the FILL_IMAGE_RECTANGLE operation, e.g.,

EditSequenceFile --operation=FILL_IMAGE_RECTANGLE --fill-rect-origin 52 25 --fill-rect-size 260 25 --fill-gray-level=20 --source-seq-file=SegmentationTest_BKMedical_RandomStepperMotionData2_Trimmed.mha --output-seq-file=SegmentationTest_BKMedical_RandomStepperMotionData2_Trimmed_Anonymized.mha

Input image: Non-anonymized image Image after fill rectangle operation:

Remove image data from meta file, keep only the transforms

Saves only the tracker data from a meta file that has both tracker and image data.

EditSequenceFile --operation=REMOVE_IMAGE_DATA --source-seq-file=[inputFilePath] --output-seq-file=[outputFilePath]

Add a constant transform to each frame

EditSequenceFile --operation=UPDATE_FRAME_FIELD_VALUE --source-seq-file=[inputFilePath] --output-seq-file=[outputFilePathTmp] --updated-field-name="StylusTipToStylusTransform" --updated-field-value="1  0  0  182.18    0  1  0  0.0744143    0  0  1  14.3197    0  0  0  1"
EditSequenceFile --operation=UPDATE_FRAME_FIELD_VALUE --source-seq-file=[outputFilePathTmp] --output-seq-file=[outputFilePath] --updated-field-name="StylusTipToStylusTransformStatus" --updated-field-value="OK"

Mix multiple sequence files into one

Create one sequence file that contains video of the first sequence and transforms from all others.

EditSequenceFile --operation=MIX --source-seq-files [videoInputFilePath] [transform1InputFilePath] [transform2InputFilePath] --output-seq-file=[outputFilePath]

Command-line parameters reference

\verbinclude “EditSequenceFileHelp.txt”