pkarasev3 / kslice Goto Github PK

sometimes like on phil's laptop the plane is not transparent, can't see the label !?

click and hit q/w while focus is on 3D widget, image disappears in right view and must restart. Thanks to Phil for reporting.

the boundary lines right now are kind of annoying in places like physis and prevent user from seeing what they're doing. use the table of "Good Colors" and reduce opacity on the boundary colors.

need to make the multiple labels push each other, coupled level sets.

enable load & display multiple labelmap files corresponding to image, e.g. something like

KViewer_Desktop -I blah.mha -L a.mha b.mha

maybe as a separate app though... ?

@kfritshcer found this

this->ResetRotation(!this->m_RotX,!this->m_RotY,!this->m_RotZ);

in line 215 of KViewer.cpp (SaveAsSegmentation()). So the rotation is reset before saving. However, I think this line should also be added in the SaveSegmentation() method(line 212). Could you add this, please ?

This doesn't make sense if the volume is rotated! Not sure what will happen with the U terms here ....

U_integral = std::vector< cv::Mat >( num_slices );
U_t = std::vector< cv::Mat >( num_slices );
cout << "I think the # of rows is: " << mdims[0] << ", # of cols is: " << mdims[1] << endl;
for( int k = 0; k < num_slices; k++ )
{ /** per-slice user updates */
U_integral[k] = cv::Mat::zeros( mdims[1], mdims[0], CV_64F );
U_t[k] = cv::Mat::zeros( mdims[1], mdims[0], CV_64F );
}

Load image and make labels. Rotate. Now save labels. Re-load them, and they are misaligned- rotation was stored with them, or something like that.

volume measurements:

1. use the continuously changing values (non-binary), scale by max while integrating

2. look for better 3D integrator in general (numerical recipes in c++?)

info like below needs to be set from the image; otherwise, doesn't look right on opening in Slicer:

$ head -n 15 ImgCase9_R.mha
ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = True
CompressedDataSize = 4132822
TransformMatrix = -1 0 0 0 -1 0 0 0 1
Offset = 76.4062 82.9688 -64.2187
CenterOfRotation = 0 0 0
AnatomicalOrientation = LPI
ElementSpacing = 0.9375 0.9375 0.9375
DimSize = 164 178 138
ElementType = MET_SHORT
ElementDataFile = LOCAL

save uk raw input coord points nicely. concept: volume stores time of last edit, zeros to initialize. set time in seconds at the point when U generated. Should be useful for displaying {uk} vs U vs volume.

• reported from ivan kolesov, @ikolesov3
• after each "evolve, update display" set of iterations, the label along phi=0 is being set to the outside value instead of something neutral .
• bad consequence: when the force is small everywhere, zero for example, curve always marches in by 2 voxels.
• causes the *** "contours vanish really fast!" *** confusing behavior on some images, noticed by @pkarasev3 @kfritscher
• if force F is big enough, you don't see the problem happening.

add volume ratio computation:

1. things like physis / metaphysis ratio
2. relative sizes (extents)

relates to better volume computation / better integration.