Commit d64e876c authored by Stephen Thompson's avatar Stephen Thompson

Issue #5 tidied data and configuration.

parent ac4b82b5
{
"camera": {
"source": 0,
"width": 640,
"height": 480,
"grab": 33,
"clock": 15,
"fullscreen": false,
"calibration" : "data/calibration.npz"
},
"pointerData": {
"pointer_tag_file": "data/pointer.txt"
},
"out path" : "pointer_positions"
}
{
"camera": {
"source": 0,
"width": 640,
"height": 480,
"grab": 33,
"clock": 15,
"fullscreen": false,
"calibration" : "data/calibration.npz"
},
"models": {
"models_dir": "data/PelvisPhantom/",
"ref_file": "data/reference.txt",
"reference_to_model" : "data/id.txt"
}
}
......@@ -8,18 +8,35 @@ Make your own pointer
BARD uses what is known as a fiducial based registration. Fiducial based
registration is the most widely used registration method in image guided
interventions, and is often used to validate new methods in research. Thus
interventions, and is often used to validate new methods in research.
However it is often misunderstood or abused, so
if you learn nothing else from this demo, please learn this.
Fiducial based registration uses a set of identifiable marker points that
can be reliably located in both the model and patient space.
Within the data directory there are the files.
Within the data directory there are files based on a CT scan of the
pelvis phantom.
::
9. Do pivot calibration of a pointer. Use the second 2 x 3 barcode pattern to make a pointer from something like a pen. See Fig 1.
ls data/PelvisPhantom
CT_Fiduicial_Markers.txt
DeciPelvis.vtk
FullPelvis.vtk
PhantomCroppedJuly08.gipl.gz
For now, have a look in the file "CT_Fiduicial_Markers.txt". This is an ordered list
of the positions of 4 fiducial markers. If we can find the corresponding points on the
physical phantom, we can register the model to the physical world. This can be done by
minimising the mean distance between the two point sets, using the "Procustes" algorithm.
Locating fiducial markers in physical space is usually done with a pointer, which
consists of some tracking markers attached to a tipped instrument. You may have seen some
examples of clinical trackers in our lab. For BARD we shall make and calibrate our own
pointer, using the "pointer" markers, a pen, some cardboard and some sort of adhesive.
Now run this:
::
bard -w ~/build/BARD/Data/ref.txt -i ~/build/BARD/Data/intrinsics.txt -x 1280 -y 720 -p ~/build/BARD/Data/pointer.txt -r -d ~/BARD
python sksurgerybard.py --config config/pointer_markers.json
This will dump tracking matrices for the pointer into the folder ~/BARD.
......
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