Script command to Align Slice Horizontally by Calibration - dm-script

Question

Is there a script command that I can specify a particular slice in a LinePlotImageDisplay and do the Align Slice Horizontally by Calibration (or Uncalibrated (channels)) action?

Answer 1

The following scipt is a complete implantation based on example codes provided by BmyGuest. It will align all slices in a LinePlotImageDisplay horizontally either by calibration or by channel (i.e. un-calibrated).
class SliceAlignment : object {
number true, false; // boolean
image imgLPID;
imageDisplay LPID; // line plot image display
number CalculateImageToGroupTransformFactors( object self, image slice_src, image slice_ref, number &relOff, number &relScale ) {
number origin_ref, scale_ref, origin_src, scale_src;
string unit_ref, unit_src;
number calFMT = 0; // origin is expressed in calibrated unit
//
slice_src.ImageGetDimensionCalibration( 0, origin_src, scale_src, unit_src, calFMT );
slice_ref.ImageGetDimensionCalibration( 0, origin_ref, scale_ref, unit_ref, calFMT );
//
relScale = scale_src / scale_ref;
relOff = (origin_src - origin_ref) / scale_ref ;
// check if both images are calibrated in same unit
if( unit_src != unit_ref ) return false
return true;
};
void AlignNthSliceHorizontallyByChannel( object self, number slice_idx ) {
// get current reference slice index
number refSlice_idx = LPID.LinePlotImageDisplayGetSlice();
// get slice ID's (as objects)
object slice_ref = LPID.ImageDisplayGetSliceIDByIndex(refSlice_idx);
object slice_src = LPID.ImageDisplayGetSliceIDByIndex(slice_idx);
number int_offset = 0, int_scale = 1.0; // vertical (intensity) offset and scaling factors
number pos_offset = 0, pos_scale = 1.0; // horizontal (position) offset and scaling factors
LPID.LinePlotImageDisplaySetImageToGroupTransform( slice_src, slice_ref, int_offset, int_scale, pos_offset, pos_scale );
};
void AlignNthSliceHorizontallyByCalibration( object self, number slice_idx ) {
// get current reference slice index
number refSlice_idx = LPID.LinePlotImageDisplayGetSlice();
// get slice ID's (as objects)
object slice_ref = LPID.ImageDisplayGetSliceIDByIndex(refSlice_idx);
object slice_src = LPID.ImageDisplayGetSliceIDByIndex(slice_idx);
number int_offset = 0, int_scale = 1.0; // vertical (intensity) offset and scaling factors
number pos_offset, pos_scale; // horizontal (position) offset and scaling factors
number unit_check = self.CalculateImageToGroupTransformFactors( imgLPID{slice_idx}, imgLPID{refSlice_idx}, pos_offset, pos_scale );
if( unit_check == false ) {
string prompt = "slice #" + slice_idx + " [" + LPID.ImageDisplayGetSliceLabelById( LPID.ImageDisplayGetSliceIDByIndex(slice_idx) ) + "] is calibrated in different unit!";
if( !ContinueCancelDialog( prompt ) ) return
};
LPID.LinePlotImageDisplaySetImageToGroupTransform( slice_src, slice_ref, int_offset, int_scale, pos_offset, pos_scale );
return;
};
void AlignAllSlicesHorizontallyByChannel( object self ) {
number nSlices = LPID.LinePlotImageDisplayCountSlices();
for( number idx = 0; idx < nSlices; idx++ ) self.AlignNthSliceHorizontallyByChannel( idx );
return;
};
void AlignAllSlicesHorizontallyByCalibration( object self ) {
number nSlices = LPID.LinePlotImageDisplayCountSlices();
for( number idx = 0; idx < nSlices; idx++ ) self.AlignNthSliceHorizontallyByCalibration( idx );
return;
};
object init( object self, image img ) {
// check if the image display is correct type
imgLPID := img;
LPID = imgLPID.ImageGetImageDisplay(0);
if( LPID.ImageDisplayGetDisplayType() != 3 ) throw( "Please choose a valid line plot display" );
return self;
};
SliceAlignment( object self ) {
true = 1; false = 0;
result( "SliceAlignment [obj ID:" + self.ScriptObjectGetID().hex() + "] constructured\n" );
};
~SliceAlignment( object self ) {
result( "SliceAlignment [obj ID:" + self.ScriptObjectGetID().hex() + "] destructured\n\n" );
}; };
{; object objAlign = alloc(SliceAlignment);
objAlign.init( GetFrontImage() );
if( OptionDown() ) objAlign.AlignAllSlicesHorizontallyByChannel();
else objAlign.AlignAllSlicesHorizontallyByCalibration(); };

Answer 2

No, there is no single 'convenience' command to achieve this alignment. You will have to create the according function yourself from reading a slices calibration and setting its display-coordinate system. You might find the following (old) tutorial PDF on the FELMI homepage might be useful:
SlicesInLinePlotDisplay.pdf
The following example script might also be useful. It shows how one slice is aligned relative to another slice. (Just on the X-axis)
// All Slices in a LinePlot are grouped into a single 'group'
// Slices can be moved relative to each other by specifying their image-to-group transform,
// and the whole image (i.e. the group) can be moved with respect to the display using the group-to-display transform.
// To set the image-to-group transform of the slice specified by 'slice_id', with respect to the slice specified by 'ref_id'
// use the command:
// LinePlotImageDisplaySetImageToGroupTransform( LinePlotImageDisplay lpid, ScriptObject slice_id, ScriptObject ref_id, double off_val, double scale_val, double off_dim_0, double scale_dim_0 )
/*********************************************************/
// Create 2 LinePlots and add them into one display
// (Initially they are aligned by their calibrations)
number sc1 = 1
number of1 = -50
number sc2 = 2
number of2 = -20
image sl1 := realImage("S1",4,300)
image sl2 := realImage("S2",4,300)
sl1 = (iwidth-icol)/iwidth
sl2 = (iwidth-icol)/iwidth
sl1[0,50,1,60] = 1
sl1[0,250,1,260] = 1
sl2[0,10,1,15] = 1
sl2[0,110,1,115] = 1
// Adding Calibrations
sl1.ImageSetDimensionCalibration(0,of1,sc1,"CH",0)
sl2.ImageSetDimensionCalibration(0,of2,sc2,"CH",0)
sl1.DisplayAt(20,30)
sl2.DisplayAt(750,30)
OKDialog( "Put into one Display" )
imageDisplay disp = sl1.ImageGetImageDisplay(0)
disp.ImageDisplayAddImage( sl2, "S2") // When added like this, the slices are automatically aligned by their respective calibration!
disp.LinePlotImageDisplaySetDoAutoSurvey( 0, 0 )
object ref_id = disp.ImageDisplayGetSliceIDByIndex(0) // Slice 0
object slice_id = disp.ImageDisplayGetSliceIDByIndex(1) // Slice 1
OKDialog("Now align by channels (i.e. undo any relative sclice alignment)")
// Simply set the relative "shifts" and "scales" to 0 and 1.
disp.LinePlotImageDisplaySetImageToGroupTransform( slice_id, ref_id, 0, 1, 0, 1 )
OKDialog("Now align by chalibration ")
number relScale = sc2/sc1
number relOff = of2-of1
disp.LinePlotImageDisplaySetImageToGroupTransform( slice_id, ref_id, 0, 1, relOff, relScale )