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/dports/science/afni/afni-AFNI_21.3.16/src/pkundu/meica.libs/nibabel/tests/
H A Dtest_nifti1.py363 aff = img.get_affine()
365 hdr.set_qform(aff, 2)
366 hdr.set_sform(aff, 2)
880 aff = np.diag([2, 3, 4, 1])
881 simg = Nifti1Image(arr, aff)
882 pimg = Nifti1Pair(arr, aff)
927 aff = np.diag([2, 3, 4, 1])
929 img = Nifti1Image(arr, aff)
968 aff = np.eye(4)
984 aff = np.eye(4)
[all …]
H A Dtest_funcs.py78 aff = np.eye(4)
79 aff[0,1] = 0.1
81 img = Nifti1Image(arr, aff)
H A Dtest_analyze.py400 aff = np.diag((-4,5,6,1))
401 aff[:3,3] = np.array([1,2,3]) * np.array([-4,5,6]) * -1
402 assert_array_equal(hdr.get_base_affine(), aff)
405 aff[0]*=-1
406 assert_array_equal(hdr.get_base_affine(), aff)
H A Dtest_affines.py29 aff = np.diag([2, 3, 4, 1])
33 aff[:3,3] = [10, 11, 12]
36 aff[:3,:] = rng.normal(size=(3,4))
38 exp_res = np.dot(aff, exp_res)[:3,:].T
41 assert_almost_equal(validated_apply_affine(aff, pts), apply_affine(aff, pts))
47 exp_res = (np.dot(aff[:3,:3], pts.T) + aff[:3,3:4]).T
55 aff = np.eye(N)
59 res = apply_affine(aff, pts)
63 exp_pts = np.dot(aff, new_pts)
99 aff = np.array([[2,0,0],
[all …]
/dports/science/afni/afni-AFNI_21.3.16/src/pkundu/meica.libs/nibabel/nicom/
H A Ddicomreaders.py34 aff = np.dot(DPCS_TO_TAL, dcm_w.get_affine())
35 return nib.Nifti1Image(data, aff)
H A Ddicomwrappers.py291 aff = np.eye(4)
292 aff[:3,:3] = orient * np.array(vox)
293 aff[:3,3] = ipp
294 return aff
/dports/science/afni/afni-AFNI_21.3.16/src/pkundu/meica.libs/nibabel/
H A Dvolumeutils.py1347 aff = np.eye(4)
1348 aff[:3, :3] = np.diag(zooms)
1349 aff[:3, -1] = -origin * zooms
1350 return aff
H A Dtrackvis.py605 aff = trk_hdr['vox_to_ras']
606 if aff[3,3] != 0:
607 return aff
614 aff = np.eye(4)
622 aff[:3,:3] = R * vox
623 aff[:3,3] = trk_hdr['origin']
624 aff = np.dot(DPCS_TO_TAL, aff)
631 return aff
634 exp_order = ''.join(aff2axcodes(aff))
637 aff[:,2] *= -1
[all …]
H A Dspm99analyze.py161 aff = np.eye(4)
162 aff[:3, :3] = np.diag(zooms)
163 aff[:3, -1] = -origin * zooms
164 return aff
H A Dparrec.py444 aff = np.eye(4)
445 aff[:3,:3] = scaled
447 aff[:3,3] = fov_center_offset
454 aff[:3,3] += iso_offset
455 return aff
H A Dorientations.py278 def aff2axcodes(aff, labels=None, tol=None): argument
303 ornt = io_orientation(aff, tol)
H A Dminc.py95 aff = np.eye(nspatial+1)
96 aff[:nspatial, :nspatial] = rot_mat * steps
97 aff[:nspatial, nspatial] = origin
98 return aff
H A Dfuncs.py182 aff = img.get_affine()
183 ornt = io_orientation(aff)
188 if enforce_diag and not _aff_is_diag(aff):
193 out_aff = np.dot(aff, t_aff)
195 if enforce_diag and not _aff_is_diag(aff):
203 def _aff_is_diag(aff): argument
205 rzs_aff = aff[:3, :3]
H A Decat.py636 aff = np.diag(zooms)
637 aff[:3,-1] = -origin_offset * zooms[:-1] + np.array([x_off,y_off,z_off])
638 return aff
914 aff = subheaders.get_frame_affine()
915 img = klass(data, aff, header, subheaders, mlist, extra=None, file_map = file_map)
H A Daffines.py9 def apply_affine(aff, pts): argument
68 aff = np.asarray(aff)
73 rzs = aff[:-1,:-1]
74 trans = aff[:-1,-1]
172 def append_diag(aff, steps, starts=()): argument
207 aff = np.asarray(aff)
215 old_n_out, old_n_in = aff.shape[0]-1, aff.shape[1]-1
218 old_n_in + n_steps + 1), dtype=aff.dtype)
220 aff_plus[:old_n_out,:old_n_in] = aff[:old_n_out, :old_n_in]
221 aff_plus[:old_n_out,-1] = aff[:old_n_out,-1]
/dports/science/afni/afni-AFNI_21.3.16/src/pkundu/meica.libs/
H A Dtedana.py110 niwrite(unmask(data,mask),aff,'__clin.nii.gz',header)
519 niwrite(cbetas[:,:,:,:],aff,'_'.join(['betas',suffix])+'.nii')
530 niwrite(zfac,aff,'zfac.nii')
555 niwrite(unmask(feats,mask),aff,'_'.join(['feats',suffix])+'.nii')
589 niwrite(ts,aff,'ts_OC.nii')
594 niwrite(ts_B[:,:,:,:],aff,'_'.join(['betas','OC'])+'.nii')
652 aff = catim.get_affine() variable
659 if options.fout: options.fout = aff
681 niwrite(s0,aff,'s0v.nii')
682 niwrite(t2s,aff,'t2sv.nii')
[all …]
H A Dt2smap.py250 aff = catim.get_affine() variable
286 niwrite(tsoc,aff,'ocv%s.nii' % suf)
287 niwrite(s0,aff,'s0v%s.nii' % suf)
288 niwrite(t2s,aff,'t2sv%s.nii' % suf )
289 niwrite(t2sm,aff,'t2svm%s.nii' % suf )
H A Dselect_model.py69 if debugout: fout=aff
169 sel = spatclust(None,mask,csize,1.95,head,aff,infile=ccname,dindex=3,tindex=3)
175 …s_R2[:,i] = spatclust(rankvec(tsoc_Babs[:,i]),mask,csize,max(tsoc_Babs.shape)-countsigFR2,head,aff)
176 …s_S0[:,i] = spatclust(rankvec(tsoc_Babs[:,i]),mask,csize,max(tsoc_Babs.shape)-countsigFS0,head,aff)
/dports/science/afni/afni-AFNI_21.3.16/src/python_scripts/scripts/
H A Dauto_warp.py761 def qwarp_applying(self, a, aff, wrp, prefix=None, dxyz=0.0, master=None): argument
770 if (aff != "ID"):
772 nwarp = '"%s %s"' % (wrp.input(), aff) # 7 Nov, 2014 [rickr]
803 def align_epi_anat(self, e, a, aff): argument
810 if (aff != "ID"):
811 waff = "-post_matrix %s" % aff
867 aw = ps.qwarp_applying(a=ps.input, aff=ps.affine_input_xmat,
877 …ps.affine_followers_xmat[k] = ps.align_epi_anat(e=fol, a = ps.anat_no_skull, aff=ps.affine_input_x…
878 … ps.qwarp_applying(a=fol, aff=ps.affine_followers_xmat[k], wrp=ps.warp_input_xform, dxyz=2.5)
/dports/science/afni/afni-AFNI_21.3.16/src/scripts_install/
H A D@animal_warper2984 aff = affine
2990 shft = 'full' shift (includes aff align) to base
/dports/x11/pixman/
H A D.PLIST.readelf4738 000000003aff 005100000002 R_X86_64_PC32 0000000000000020 .LC5 - 4
/dports/math/gap/gap-4.11.0/lib/
H A Dclashom.gi1655 aff, # <N> as affine space
1723 aff := ExtendedVectors( field ^ r );
1758 imgs{[radidx+1..Length(gens)]},cl[4],hom,gpsz,OnRight,aff);
2551 aff, # <N> as affine space
2638 aff := ExtendedVectors( field ^ r );
2698 aff:orbitseed:=reps[p].vector);
H A Dclaspcgs.gi312 aff, # <N> as affine space
313 xset, # affine operation of <C> on <aff>
366 aff:=ExtendedVectors( field ^ r );
410 xset:=ExternalSet(SubgroupByPcgs(H,Cgens),aff,gens,imgs,OnPoints);
465 #xset:=ExternalSet( C, aff, gens, imgs );
472 dict:=NewDictionary(aff[1],true,aff:blistlimit:=Size(aff));
475 blist:=BlistList([1..Length(aff)],[]);
483 S:=Pcs_OrbitStabilizer(gens,aff,aff[next],imgs,OnRight,dict);
486 S:=Pcs_OrbitStabilizer(gens,aff,aff[next],imgs,OnRight);
488 blist[PositionCanonical(aff,i)]:=true;
/dports/math/gap/gap-4.11.0/pkg/polycyclic-2.15.1/gap/pcpgrp/
H A Dnormcon.gi14 local aff, l, i, lin, trl, j;
15 aff := OperationOnH1( CR, cc );
17 for i in [1..Length(aff)] do
18 if aff[i] = 1 then
19 aff[i] := IdentityMat( l+1 );
28 if not IsBool(cc.fld) then aff := aff * One(cc.fld); fi;
29 return aff;
119 aff := AffineActionOnH1( CR, cc );
142 aff := InducedByPcp( CR.super, act, aff );
149 oper := function( pt, aff )
[all …]
/dports/math/gap/gap-4.11.0/pkg/polycyclic-2.15.1/gap/action/
H A Dorbstab.gi109 OnAffMod := function( pt, aff )
111 im := pt * aff[1] + aff[2];
207 OnAffMod := function( pt, aff )
209 im := pt * aff[1] + aff[2];

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