Doxygen Source Code Documentation

AFNI_XYZcontinuous2Index.m File Reference


Functions
the default is RAI The code can be either a string or a vector of	numbers (see AFNI_CoordChange for more on that)%IndexDim(3 or 1) is an optional parameter used to specify if Indx is Mx3 or Mx1 vector%(see AfniIndex2AfniXYZ for more info)%The default is 3.If you choose to specify IndexDim
	if (nargin > 2) if(~isempty(CoordCode))
	if (nargin==4)
	if (~isempty(IndexDim))
make sure coordinate system is RAI	if (ChangeCoord)
The equations that would change the coordinate system to indices must take the indces in the same RAI permutation that the slices are entered into to3d	in (No need to worry about R versus L or A versus P)%determine the ordering map to go from any permutation of RAI to RAI%[maploc(1)
	Indx (:, 2)
	Indx (:, 3)
	Indx (:, maploc(2))
	Indx (:, maploc(3))
Feb	Indx (:, 1)
	if (~isempty(ineg))
	Indx (ineg)=0
	if (~isempty(iover))
	Indx (iover, 1)
	Indx (iover, 2)
	Indx (iover, 3)
end if change the Index dimension from Mx3 to Mx1	if (ChangeDim &IndexDim==1)
Variables
	function [err, Indx]
the default is RAI The code can be either a string or a vector of you must specify CoordCode(you could use an empty string to leave CoordCode to the default)%%Output Parameters Debug Flag	DBG = 1
	ChangeCoord = 0
end end	ChangeDim = 0
end end initailize return variables	err = 1
	Indx = []
make sure coordinate system is RAI else	XYZdic = AFNI_CoordChange (CoordCode, 'RAI', XYZmm) XYZmm
end now change dicomm to	dmm [err, XYZmm, map] = THD_dicomm_to_3dmm (Info, XYZdic)
The equations that would change the coordinate system to indices must take the indces in the same RAI permutation that the slices are entered into to3d	jnk = find(Info.Orientation == 'R')
	ineg = find(Indx < 0)
	end [iover] = find(Indx(:,1) > Info.DATASET_DIMENSIONS(1)-1)
end	Now
end if	needed
	return

Function Documentation

end if change the Index dimension from Mx3 to Mx1 if ( ChangeDim & IndexDim = = 1 )

(

isempty(iover)

)

(

isempty(ineg)

)

make sure coordinate system is RAI if

(

ChangeCoord

)

(

isempty(IndexDim)

)

if ( nargin = = 4 )

if	(	nargin	,
		2
	)

The equations that would change the coordinate system to indices must take the indces in the same RAI permutation that the slices are entered into to3d in

(

No need to worry about R versus L or A versus

)

Referenced by CalcRLEHuffLength(), cl1_fort(), DC_gray_change(), DC_gray_conbrio(), DC_gray_contrast(), init_error_limit(), main(), Make_RGB_lookup(), mp_quant_block(), mp_quant_zig_block(), mp_rle_huff_block(), mp_rle_huff_pblock(), Mpost_QuantZigBlock(), Mpost_RLEHuffIBlock(), Mpost_RLEHuffPBlock(), Mpost_UnQuantZigBlock(), Mpost_UnQuantZigBlockLaplace(), set_indent(), srface_(), SUMA_Cmap_To_SO(), SUMA_Convexity_Engine(), SUMA_CreateIcosahedron(), SUMA_FillToVoxelMask(), SUMA_isConsistent(), SUMA_isTriLinked(), SUMA_Reposition_Touchup(), SUMA_StretchToFitLeCerveau(), SUMA_Subdivide_Mesh(), SUMA_Suggest_Touchup(), SUMA_Suggest_Touchup_Grad(), THD_set_int_atr(), and UnQuantZig().

Indx	(	iover	,
		3
	)

Indx	(	iover	,
		2
	)

Indx	(	iover	,
		1
	)

Indx ( ineg ) [pure virtual]

Feb Indx	(	:	,
		1
	)

Indx	(	:	,
		maploc(3)
	)

Indx	(	:	,
		maploc(2)
	)

Indx	(	:	,
		3
	)

Indx	(	:	,
		2
	)

the default is RAI The code can be either a string or a vector of numbers

(

see AFNI_CoordChange for more on

that

)

Variable Documentation

ChangeCoord = 0

Definition at line 57 of file AFNI_XYZcontinuous2Index.m.

ChangeDim = 0

Definition at line 64 of file AFNI_XYZcontinuous2Index.m.

the default is RAI The code can be either a string or a vector of you must specify CoordCode (you could use an empty string to leave CoordCode to the default) % %Output Parameters Debug Flag DBG = 1

Definition at line 52 of file AFNI_XYZcontinuous2Index.m.

end now change dicomm to dmm[err, XYZmm, map] = THD_dicomm_to_3dmm (Info, XYZdic)

Definition at line 83 of file AFNI_XYZcontinuous2Index.m.

end[iover] = find(Indx(:,1) > Info.DATASET_DIMENSIONS(1)-1)

Definition at line 116 of file AFNI_XYZcontinuous2Index.m.

Referenced by cmp_chars(), cmp_doubles(), cmp_floats(), cmp_ints(), cmp_longs(), cmp_schars(), cmp_shorts(), convert1(), CTF_count(), decode_mpeg2(), demux(), dup_NC_attrarrayV(), dup_NC_dimarrayV(), dup_NC_vararrayV(), elvis_CB(), es_loop(), fill_NC_var(), free_NC_attrarrayV0(), free_NC_dimarrayV0(), free_NC_vararrayV0(), JMovie2JPEG(), memplot_to_RGB_sef(), memplot_to_X11_sef(), modify_ex(), mpeg2_buffer(), mpeg2_slice_region(), NC_computeshapes(), NC_fill_char(), NC_fill_double(), NC_fill_float(), NC_fill_int(), NC_fill_schar(), NC_fill_short(), NC_varoffset(), NCedgeck(), ncx_getn_float_float(), ncx_getn_int_int(), ncx_getn_int_long(), ncx_len_NC_attrarray(), ncx_len_NC_dimarray(), ncx_len_NC_vararray(), ncx_putn_float_float(), ncx_putn_int_int(), ncx_putn_int_long(), ps_loop(), pva_demux(), pva_loop(), queryTabletPos(), ReadInputFileNames(), set_upper(), SUMA_BinarySuck(), SUMA_binSearch(), t_pad_getn_schar_double(), t_pad_getn_schar_float(), t_pad_getn_schar_int(), t_pad_getn_schar_long(), t_pad_getn_schar_schar(), t_pad_getn_schar_short(), t_pad_getn_schar_uchar(), t_pad_getn_short_double(), t_pad_getn_short_float(), t_pad_getn_short_int(), t_pad_getn_short_long(), t_pad_getn_short_schar(), t_pad_getn_short_short(), t_pad_getn_short_uchar(), t_pad_putn_schar_double(), t_pad_putn_schar_float(), t_pad_putn_schar_int(), t_pad_putn_schar_long(), t_pad_putn_schar_schar(), t_pad_putn_schar_short(), t_pad_putn_schar_uchar(), t_pad_putn_short_double(), t_pad_putn_short_float(), t_pad_putn_short_int(), t_pad_putn_short_long(), t_pad_putn_short_schar(), t_pad_putn_short_short(), t_pad_putn_short_uchar(), ts_loop(), v1h_get_NC_attrarray(), v1h_get_NC_dimarray(), v1h_get_NC_vararray(), v1h_put_NC_attrarray(), v1h_put_NC_dimarray(), v1h_put_NC_vararray(), write_indent(), and writeblanks().

end if change the Index dimension from Mx3 to Mx1 end err = 1

Definition at line 125 of file AFNI_XYZcontinuous2Index.m.

function[err, Indx]

Initial value:

 AFNI_XYZcontinuous2Index (XYZmm, Info, CoordCode, IndexDim)
%
%   [err,Indx] = AFNI_XYZcontinuous2Index (XYZmm, Info, [CoordCode], [IndexDim])
%
%Purpose:
%   Change from voxel XYZ in mm to XYZindex (called Voxel Coords in AFNI) 
%   The mm and voxel coordinates refer to the values displayed 
%   on the top left corner of AFNI controller.
%   CoordCode is the one you'd set from the Coord Order plugin
%   
%   
%Input Parameters:
%   XYZmm : The continuous coordinates corresponding to Indx
%       The coordnate system is assumed to be RAI (DICOM) 
%       unless otherwise specified by CoordCode
%   Info is the output of BrikInfo
%   CoordCode is an optional parameter used to specify the coordinates system of XYZmm
%      if empty or not specified

Definition at line 1 of file AFNI_XYZcontinuous2Index.m.

end Indx = []

Definition at line 29 of file AfniIndex2AfniXYZ.m.

ineg = find(Indx < 0)

Definition at line 107 of file AFNI_XYZcontinuous2Index.m.

The equations that would change the coordinate system to indices must take the indces in the same RAI permutation that the slices are entered into to3d jnk = find(Info.Orientation == 'R')

Definition at line 88 of file AFNI_XYZcontinuous2Index.m.

end if needed

Definition at line 120 of file AFNI_XYZcontinuous2Index.m.

Referenced by THD_reconcile_parents().

end Now

Definition at line 120 of file AFNI_XYZcontinuous2Index.m.

return

Definition at line 126 of file AFNI_XYZcontinuous2Index.m.

make sure coordinate system is RAI else XYZdic = AFNI_CoordChange (CoordCode, 'RAI', XYZmm) XYZmm

Definition at line 79 of file AFNI_XYZcontinuous2Index.m.