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values | md5 stringlengths 32 32 | text stringlengths 23 843k |
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github | rordenlab/spmScripts-master | nii_enantiomorphic.m | .m | spmScripts-master/nii_enantiomorphic.m | 5,208 | utf_8 | 8d7aa13be8f922e2dc07971afec912ad | function nii_enantiomorphic (anat,lesion)
%Enantiomorphic normalization, see Nachev et al (2008) http://www.ncbi.nlm.nih.gov/pubmed/18023365
% anat : filename(s) for anatomical scans
% lesion : filename(s) for lesion maps
%Chris Rorden 2014
% http://opensource.org/licenses/BSD-2-Clause
%Examples
% nii_enantiomorphic; %... |
github | rordenlab/spmScripts-master | nii_merge.m | .m | spmScripts-master/nii_merge.m | 2,311 | utf_8 | 6979c9a7b08fd7082aff12c7ee6a1ff1 | function nii_merge(vols, outnam)
%merge multiple images together
% vols: name of images to weld together
% outnam: optional output name, e.g. 'DTI_P195.nii'
%Examples
% nii_merge({'DTIA_P195.nii','DTIB_P195.nii'})
% nii_merge({'DTIA_P199.nii','DTIB_P199.nii'},'DTI_P199.nii')
% nii_merge %use GUI
if ~exist('vols','var')... |
github | rordenlab/spmScripts-master | nii_makeDTI.m | .m | spmScripts-master/nii_makeDTI.m | 4,875 | utf_8 | c886bfcd0d762300302a7f426c30a34a | function nii_makeDTI (RASorder)
%Generates a simple NIfTI format DTI image
% RASorder : (optional) if false then columns:rows:slices not in right:anterior:superior order
%Examples
% nii_makeDTI; %order: RAS
% nii_makeDTI(1) %order: ARS
% nii_makeDTI(2); %order: LAS
% nii_makeDTI(3); %order: SRA
fnm = 'test';
pixDim... |
github | rordenlab/spmScripts-master | nii_savehdrimg.m | .m | spmScripts-master/nii_savehdrimg.m | 5,744 | utf_8 | 5c7b7ee3eaeb07a352064431268d916d | function nii_savehdrimg(fname, hdr, img)
if ~isfield(hdr.private, 'hk')
error('Incompatible header format (must be read by nii_loadhdrimg)');
end
%next: adjust private header to etch visible protions
hdr.private.dime.datatype = hdr.dt(1); %datatype
hdr.private.dime.scl_slope = hdr.pinfo(1); %slope
hdr.private.dime.... |
github | rordenlab/spmScripts-master | bmp_sinewave_2d.m | .m | spmScripts-master/bmp_sinewave_2d.m | 4,104 | utf_8 | 66268adbe98d64db96b68d82ec397cfe | function bmp_sinewave_2d
%creates a 2D grayscale sinewave grating
%Clones Elliot Freeman code without requiring any toolboxes
% http://www.icn.ucl.ac.uk/courses/MATLAB-Tutorials/Elliot_Freeman/html/gabor_tutorial.html
%parameters
contrast = 1.0; %contrast amplitude 0..1
imSize = 200; % image... |
github | rordenlab/spmScripts-master | nii_threshreslicecluster.m | .m | spmScripts-master/nii_threshreslicecluster.m | 4,539 | utf_8 | d53963e0ffa8c25758fc90285679fb69 | function nii_threshreslicecluster(srcNam, tarNam, thresh, clusterMM3, binarize)
%Reslice image to isotropic 1mm resolution, zero dark voxels, zero small clusters
% srcNam: (optional) name of NIfTI image to reslice
% tarNam: (optional) image to match- either filename of NIfTI header or loaded NIfTI header structure
% ... |
github | rordenlab/spmScripts-master | nii_anat.m | .m | spmScripts-master/nii_anat.m | 2,810 | utf_8 | 6f2b20935b63a8b1da295a14ebb81100 | function nii_anat (Img, Outtext);
% Find normalized mm for MRIcron anat file
% Img : nifti image before normalizeation
% Outtext: name for output file [optional]
% Assumes MRIcron .anat and SPM _seg_inv_sn.mat files
% e.g. 'img.nii' with 'img.anat' and 'img_seg_inv_sn.mat
% Depends on nii_map_coords.m
%Examples
% ... |
github | rordenlab/spmScripts-master | old_setOrigin12.m | .m | spmScripts-master/old_setOrigin12.m | 4,048 | utf_8 | 1586d4d58dca1e34c1953eb1ded8919c | function coivox = setOrigin12(vols, modality)
%Align images so that origin and alignment roughly match MNI space
% vols : cell string of image name(s) - first image used for estimate, others yoked
% modality : modality of first image 1=T1, 2=T2, 3=EPI
%Example
% setOrigin('T1.nii',1); %align T1 scan
% setOrigin({'T... |
github | rordenlab/spmScripts-master | nii_render.m | .m | spmScripts-master/nii_render.m | 6,418 | utf_8 | bd385a6b915c97915ff6b15790e06893 | function nii_render (P, PreserveCSF, Normalize, Thresh, DilateVox)
%use segmentation-normalization to generate scalp stripped image for rendering
% P : input images
% Thresh: Threshold, if 0.01 then tissue >1% gray/white will be preserved
% Note: Thresh=0 modulates output (T1*(wm+gm))
% PreserveCSF : [optional... |
github | rordenlab/spmScripts-master | timeShift.m | .m | spmScripts-master/timeShift.m | 4,136 | utf_8 | af893078b06866bc4beacbce44ef4f62 | function globalSignal = timeShift (restname, t1name, TRsec)
%Compute timeshift in each voxel
% restname: base name of resting state data
% t1name: base name of T1 scan: must be warped, segmented wc1 and wc2 images
% TRsec: repeat time for MRI data
%Example
% ts = timeShift('con001_a_rest.nii', 'con001_a_T1.nii', 2.0);
... |
github | rordenlab/spmScripts-master | GPU_perm_test.m | .m | spmScripts-master/GPU_perm_test.m | 4,200 | utf_8 | 6c29a7c81c052b5f6d9dbf9e3f307a34 | function GPU_perm_test
%this code demonstrates permutation thresholding when computing millions of correlations
for ii=1:2;
if (ii==1)
vv = 70801;
else
vv = 239855;
end
for i=1:20;
%next - constants for simulations
kNumRandPerm = 5000; %number of permutations ~5000
kPc... |
github | rordenlab/spmScripts-master | nii_label.m | .m | spmScripts-master/nii_label.m | 2,263 | utf_8 | 1777f18eca7df9ddcac26b0473cd7e61 | function nii_label (fnm, threshold)
%Threshold volume, then label each cluster in the volume
% fnm : name of image
% threshold : intensity threshold, e.g. if 2.0 clusters where intensity exceeds 2.0 will survive.
%Examples
% nii_label %prompt user for files and values
% nii_label('img.nii',2.5);
%A wrapper for Jesper ... |
github | rordenlab/spmScripts-master | nii_reslice_target_thresh.m | .m | spmScripts-master/nii_reslice_target_thresh.m | 6,029 | utf_8 | 94421a8e41979ce73f7654006d5fc9eb | function [outhdr, outimg] = nii_reslice_target_thresh(inhdr, inimg, tarhdr, interp, thresh)
%Reslice input image to match dimensions of target image (either to disk or memory)
% inhdr: image to reslice- either filename of NIfTI header or loaded NIfTI header structure
% inimg: (optonal) NIfTI image data (only if inhdr... |
github | rordenlab/spmScripts-master | nii_diploe.m | .m | spmScripts-master/nii_diploe.m | 7,156 | utf_8 | eec3957aba198a0343d710034314bf4d | function nii_diploe (T1, T2)
%Wide diploic space can disrupt segmentation-normalization
%This script darkens regions around brain based on T2 scan
% T1 : T1-weighted image with wide diploic space (marrow, cancellous bone)
% T2 : T2-weighted image
%Version
% Chris Rorden 20171109
%License
% This is a simple wrapper for ... |
github | rordenlab/spmScripts-master | bmp_scramble.m | .m | spmScripts-master/bmp_scramble.m | 3,403 | utf_8 | 5db11dc00d47a127ec56959061b8d2e0 | function bmp_scramble (Filename)
%Creates phase spectrum scrambling bitmap with 's' prefix
% Filename: name of bitmap [optional]
%Example
% bmp_scramble('dog.png');
%Adds a user interface wrapper for Nicolaas Prins' code
% http://visionscience.com/pipermail/visionlist/2007/002181.html
%modified by Chris Rorden so imag... |
github | rordenlab/spmScripts-master | nii_thresh.m | .m | spmScripts-master/nii_thresh.m | 3,584 | utf_8 | 43c09b3c5cf2c509f3d62e777d186b50 | function nii_thresh (volNames, normalizeIntensity, maxThresh, maxVal, minThresh, minVal)
%Clip bright and/or dark voxels of input image(s)
% volNames : name(s) of image(s) to threshold
% normalizeIntensity : if true, brightness scaled from 0..1
% maxThresh : voxels brighter than this value are set to maxVal (if not re... |
github | rordenlab/spmScripts-master | nii_qa_moco.m | .m | spmScripts-master/nii_qa_moco.m | 7,270 | utf_8 | 3ce26719d2769875e186b0df7b4cb494 | function nii_qa_moco (imgName, rpName)
%Quality assurance: identify odd images based on 4D fMRI series and motion correction parameters
% imgName : filename(s) of images to average, either single 4D volume or a series of 3D volumes
% rpName : name of motion corection file created by SPM (e.g. rp_img.txt)
%Chris Rorden... |
github | rordenlab/spmScripts-master | bmp_yuv.m | .m | spmScripts-master/bmp_yuv.m | 8,264 | utf_8 | 1bd9fc06c9ed583aa4d116aa1be999a7 | function bmp_yuv(Filename, Sigma, ShowFigures)
%Blurs y, u, v components of an image, saving output as bitmap with prefix
% Filename: name of bitmap [optional]
% Sigma: images will be smoothed with based on this FWHM
% If Sigma is equal to zero, nearest neighbor subsampling is used
% ShowFigures: if TRUE r... |
github | rordenlab/spmScripts-master | nii_thresh_conjunction.m | .m | spmScripts-master/nii_thresh_conjunction.m | 2,201 | utf_8 | 795f4af76f4251a73c9d89200af34a96 | function nii_thresh_conjunction(fnms)
%Find voxels that survive threshold in ALL tests
% fnms : file name[s] of thresholded image[s] (optional)
%Notes
% The 'nii_thresh_conjunction' test is the valid conjunction test discussed in:
% Nichols T, Brett M, Andersson J, Wager T, Poline JB. Valid conjunction
% inferenc... |
github | rordenlab/spmScripts-master | nii_subtract_mask.m | .m | spmScripts-master/nii_subtract_mask.m | 2,257 | utf_8 | 11af9c0fb1e3905d9d8ff20cfce9a6ec | function nii_xor_mask(fnms, filt)
%Exclusive or masking, Input: multiple images, output image: voxels are unique to each input
% fnms: pair of input images
% filt: if zero all non-zero voxels, if -1 then negative voxels, if +1 then all positive voxels
% Outputs: image with name1+'not'+name2 and name2+'not'+name1
%Ex... |
github | rordenlab/spmScripts-master | stat_dprime.m | .m | spmScripts-master/stat_dprime.m | 2,214 | utf_8 | ef58f88373d18fedc74fbc773b52339d | function [d,beta] = stat_dprime(pHit,pFA)
%-- Convert to Z scores, no error checking
zHit = norminv(pHit,0,1) ;
zFA = norminv(pFA,0,1) ;
%-- Calculate d-prime
d = zHit - zFA ;
%-- If requested, calculate BETA
if (nargout > 1)
yHit = normpdf(zHit) ;
yFA = normpdf(zFA) ;
beta = yHit ./ yFA ;
end
%end dprime()
fu... |
github | rordenlab/spmScripts-master | nii_mean_stdev_roi.m | .m | spmScripts-master/nii_mean_stdev_roi.m | 1,990 | utf_8 | fb693edf32762010603f899333cb94d7 | function nii_mean_stdev_roi (fnm, roi)
%report descriptive statistics for portions of image named 'fnm' inside region of interest named 'roi'
% fnm : filename of 3D image with continuous brightness (.hdr/.img, .nii, or .nii.gz file)
% roi : filename of 3D masking image (.hdr/.img, .nii, .voi or .nii.gz file)
%Chris Ror... |
github | rordenlab/spmScripts-master | convert_ctp.m | .m | spmScripts-master/convert_ctp.m | 4,508 | utf_8 | 4af659534afc7c2d6a499b86e8dfdbc7 | function fnm = convert_ctpSub(fnm, modalityIsTime)
%Convert Siemens RGB CT-perfusion images to linear grayscale images
% V : name[s] of image[s] to convert (optional)
% modalityIsTime : Siemens uses different RGB schemes
% TRUE for MTT or TTP images (transit time, time to peak)
% FALSE for CB... |
github | rordenlab/spmScripts-master | nii_rgb_planar2packed.m | .m | spmScripts-master/nii_rgb_planar2packed.m | 2,796 | utf_8 | 488b95261161c36833e82e28ebea7473 | function nii_rgb_planar2packed(fnm)
%for 24-bit (Red/Green/Blue) images, convert between planar (Analyze) and triplet (NIfTI) image storage
%Analyze stores data as 2D planes rrrr..rggggg...gbbbb...b, NIfTI as packed triplets rgbrgbrgb...
%This script detects input images format and converts to the other style
% fnm : n... |
github | rordenlab/spmScripts-master | nii_setOrigin12x.m | .m | spmScripts-master/nii_setOrigin12x.m | 4,739 | utf_8 | d848afe510cb483387c53ef8fcb27179 | function coivox = nii_setOrigin12x(vols, modality, cropBB)
%Align images so that origin and alignment roughly match MNI space
% vols : cell string of image name(s) - first image used for estimate, others yoked
% modality : modality of first image 1=T1, 2=T2, 3=EPI
% cropBB : (optional) crop resulting image to standa... |
github | rordenlab/spmScripts-master | nii_batch12old.m | .m | spmScripts-master/nii_batch12old.m | 41,054 | utf_8 | aa439d0f5d0ec4e37e601a4135bb5470 | function nii_batch12 (p)
%preprocess and analyze fMRI data using standard settings
% p
% structure for preprocessing
% p.fmriname : name of 4D fMRI volumes
% p.fmriname, t1name, TRsec, slice_order, phase, magn
% p.t1name : name of anatomical scan, (set to -1 to skip)
% p.TRsec : TR for fMRI data, 0=auto
% ... |
github | rordenlab/spmScripts-master | nii_zoneplate3d.m | .m | spmScripts-master/nii_zoneplate3d.m | 2,598 | utf_8 | da0b8d825daa450de81ba453d536a3bf | function nii_zoneplate3d(N)
%make Fresnel zone plates - useful for checking aliasing of resampling methods
% https://en.wikipedia.org/wiki/Zone_plate
% https://www.mathworks.com/matlabcentral/mlc-downloads/downloads/submissions/35961/versions/2/previews/imzoneplate.m/index.html?access_key=
% https://www.mathworks.com/m... |
github | rordenlab/spmScripts-master | nii_make3d_new.m | .m | spmScripts-master/nii_make3d_new.m | 1,315 | utf_8 | 3cd7684beb8add1e6b772fded7f73353 | function nii_make3d_new(sz)
%Make a NIfTI image using SPM
if ~exist('sz', 'var')
sz = 128;
end
dim = [sz, sz, sz, 1]; %image resolution in columns, rows, slices, volumes
dtype = 32; %precision of data
ofile = 'test.nii';%spm_file(parfile,'path',opts.outdir,'ext',opts.ext);
scale = 1;
inter = 0;
switch dtype
... |
github | rordenlab/spmScripts-master | nii_lpi.m | .m | spmScripts-master/nii_lpi.m | 5,565 | utf_8 | cd7ac1686661b3ccb55d5715edf3b5d8 | function nii_lpi(fnms)
%Flip image to be in LPI orientation
% fnm: image to flip
%Rationale
% http://www.diedrichsenlab.org/imaging/suit_function.htm
% The algorithm works best if the T1 image is brought into LPI-orientation, and the origin of the image is set to the anterior commissure.
%Examples
% nii_lpi()
% nii_lp... |
github | rordenlab/spmScripts-master | nii_orderBval.m | .m | spmScripts-master/nii_orderBval.m | 2,172 | utf_8 | 2c18801b2af92ac8e6c216e6e1fc56fa | function nii_orderBval (bval)
%DKE requires DWI volumes sorted by bvalue
% bval: name of bval file to reorder (assumes file.bval, file.bvec,file.nii)
% Examples
% nii_orderBval('DWI_dir42_AP_27_EP.bval');
if ~exist('bval','var')
bval = spm_select(1,'^.*\.(bval)$','Select b-value file to re-order');
end;
if isempty... |
github | rordenlab/spmScripts-master | nii_setOrigin.m | .m | spmScripts-master/nii_setOrigin.m | 5,211 | utf_8 | ccd969a7597b61833b3e25be3be4f9e9 | function coivox = nii_setOrigin(vols, modality)
%Sets position and orientation of input image(s) to match SPM's templates
% SPM's normalize function uses the origin as a starting estimate
% This script provides a robust estimate for the origin.
% This is particularly important for CT, where initial origin is relativ... |
github | rordenlab/spmScripts-master | nii_makeseed.m | .m | spmScripts-master/nii_makeseed.m | 2,690 | utf_8 | 5dd869a5052b24ed39010e6d92b55084 | function nii_makeseed (V, Radius,Mask);
% Finds peak for each image V, generates image with sphere at peak
% V: Image[s] to create seed maps
% PeakRadius: Voxels radius for seed size at peak
% Mask: (optional). list of mask image[s] - constrains peak search to mask
%
%Example
% nii_makeseed('brain.nii');
% nii_makese... |
github | rordenlab/spmScripts-master | nii_merge_dti.m | .m | spmScripts-master/nii_merge_dti.m | 4,533 | utf_8 | ba8059dc4d55046568591e02ae4496db | function nii_merge_dti(fnms, minVol)
%Merge a set of DTI scans. Assumes img.nii has img.bvec/img.bval
%If no bvec/bval file is found it is assumed that this is a B0 series
% fnms: filenames to merge
% minVol: only add images with this many volumes (exclude pre-computed MD/ADC/trace)
%Examples
% nii_merge_dti; %use GUI;... |
github | rordenlab/spmScripts-master | nii_dtibatch.m | .m | spmScripts-master/nii_dtibatch.m | 6,692 | utf_8 | 1b6a86673dfac2f89bab278a3722fd5f | function nii_dtibatch (dtiBvecNames, isEddyCorrect)
%quick processing of DTI - uses faster eddy_correct rather than eddy/topup
%assumes angulations have been correctly adjusted
% dtiNii: name of bvec file(s), e.g. img.bvec
% isEddyCorrect : if true simple undistortion applied, if false than quick and dirty
%Examples
% ... |
github | rordenlab/spmScripts-master | nii_nii2objMesh.m | .m | spmScripts-master/nii_nii2objMesh.m | 10,946 | utf_8 | 2603955f5ea289abd57a4ca5519058a9 | function outnm = nii_nii2objMesh (fnm, thresh, clusterVox, isSmooth, reduce, outnm, floodfill)
%convert NIfTI image to mesh, all arguments are optional
% fnm : nifti image to meshify
% thresh : air/surface threshold, e.g. 2=voxels darker than 2 are air
% n.b. for Altases, set thresh=0: one image will be create... |
github | rordenlab/spmScripts-master | dicm_sort.m | .m | spmScripts-master/dicm_sort.m | 2,583 | utf_8 | 749020aee5a613979bf535d500a30874 | function dicm_sort(src, outFolder)
%Sort DICOMs from source folder and each series in unique folder of outFolder
% src : input folder with many DICOM images
% outFolder : output folder where images will be saved
%
%Requirements
% Xiangrui Li's dicm2nii https://github.com/xiangruili/dicm2nii
%Example
% dicm_sort() %use... |
github | rordenlab/spmScripts-master | nii_scale_dims.m | .m | spmScripts-master/nii_scale_dims.m | 6,748 | utf_8 | b6acdc0bf5b4fe7386fea0f494202668 | function nii_scale_dims(fnms, scale)
%Change image resolution: useful for faster classroom demos or artificially interpolated reconstructions
% fnms : file name[s] of image[s] (optional)
% scale : size scaling factor: 2 doubles resolution, 0.5 halves resolution, "0.5 0.5 1" halves in plane
%License
% Created by Chris ... |
github | rordenlab/spmScripts-master | nii_mean_stdev.m | .m | spmScripts-master/nii_mean_stdev.m | 6,416 | utf_8 | 13eb5aa2c7eee4c15b2a9227d4f8594e | function nii_mean_stdev (fnms, normBrightness, outname)
%Given multiple volumes, generate mean, standard deviation, SNR maps and report unusual images. Useful for quality assurance
% fnms : filenames to average (optional)
% normBrightness : if false (0) raw intensity is used. if true (1) image intensity
% ... |
github | rordenlab/spmScripts-master | fiberQA.m | .m | spmScripts-master/fiber_QA/fiberQA.m | 2,304 | utf_8 | 852ca6d45821eda2572d5ec0687d97f0 | function fiberQA (baseDir)
if exist('baseDir','var')
cd(baseDir);
end
m = dir('*.mat');
if isempty(m), error('Unable to find mat files'); end;
fprintf('Found %d subjects in %s\n',numel(m), pwd);
label = jhuLabelSub;
isGM_R = isGMr_Sub(label);
nROI = sum(isGM_R(:));
msk = triu(ones(nROI,nROI),1);
%fieldname = 'd... |
github | fraudies/optic-flow-estimation-master | estimateOpticFlow2D.m | .m | optic-flow-estimation-master/ShizawaMase/estimateOpticFlow2D.m | 6,424 | utf_8 | 6c4a4438521fb337679f25cf87cd8cdc | function [Dx Dy C] = estimateOpticFlow2D(ImgSeq, opt)
% estimateOpticFlow2D
% ImgSeq - Image sequence as a cube with dimensions:
% height x width x frames.
% opt - Struture with options:
% * sigma - Standard deviation of Gaussian for spatial and
% tempora... |
github | fraudies/optic-flow-estimation-master | estimateOpticFlow2D.m | .m | optic-flow-estimation-master/AdelsonBergen/estimateOpticFlow2D.m | 5,182 | utf_8 | 6ee888c48f57fd3586c008bd8425eea0 | function [Dx Dy] = estimateOpticFlow2D(ImgSeq, opt)
% estimateOpticFlow2D
% ImgSeq - Image sequence as a cube with dimensions:
% height x width x frames.
% opt - Struture with options:
% * k - Parameter of temporal filter kernel.
% * htNum - Number of samples ... |
github | fraudies/optic-flow-estimation-master | estimateOpticFlow2D.m | .m | optic-flow-estimation-master/FleetJepson/estimateOpticFlow2D.m | 7,915 | utf_8 | 52ccbf2a59d7a3097c040f87eb0b9100 | function [Dx Dy] = estimateOpticFlow2D(ImgSeq, opt)
% estimateOpticFlow2D
% ImgSeq - Image sequence as a cube with dimensions:
% height x width x frames.
% opt - Struture with options:
% * f - Spatio-temporal frequency in cycles per pixel or
% cycles... |
github | fraudies/optic-flow-estimation-master | estimateOpticFlow2D.m | .m | optic-flow-estimation-master/Heeger/estimateOpticFlow2D.m | 9,105 | utf_8 | 56567bf52d22ee22343d36b35366a282 | function [Dx Dy L] = estimateOpticFlow2D(ImgSeq, opt)
% estimateOpticFlow2D
% ImgSeq - Image sequence as a cube with dimensions:
% height x width x frames.
% opt - Structure with options:
% * fxy - Spatial frequency in cycles per pixel.
% * oNum - Number of ori... |
github | tommysprague/IEM-tutorial-master | load_root.m | .m | IEM-tutorial-master/load_root.m | 300 | utf_8 | a2ddad898bd4baab8fd4a5336a968d7f | % load_root.m
% Replace "root" with the full directory in which IEM_*.m files sit (should be
% in /berlin_workshop/)
function root = load_root
root = '/Users/Tommy/Dropbox/documents/ucsd/serences/Talks/BerlinWorkshop/tutorial/';%[pwd '/'];%'/usr/local/serenceslab/tommy/berlin_workshop/';
return |
github | tommysprague/IEM-tutorial-master | plot_basis_rect.m | .m | IEM-tutorial-master/mFiles/plot_basis_rect.m | 720 | utf_8 | 6bb275b3218cde3a679877646a942b1d | % plot_basis_rect.m
% adapted from plot_basis by TCS 10/25/13
%
% plot_basis_rect(b),n_rfX,n_rfY;
function plot_basis_rect(b,n_rfX,n_rfY,resX,resY)
figure; clf;
nr = n_rfY;
nc = n_rfX;
%res = sqrt(size(b,2));
ridx = 1; cidx = 1;
for bb = 1:size(b,1);
% goes down each column first
subplot(nr,nc... |
github | tommysprague/IEM-tutorial-master | make2dcos.m | .m | IEM-tutorial-master/mFiles/make2dcos.m | 479 | utf_8 | 82e7c56a3dd6a610fe971b060c771e1a | % make2dcos.m
% TCS - 4/3/12
function z = make2dcos(x,y,x_center,y_center,r,pow)
% x, y is a meshgrid of x, y values at which to compute the 2d cos
% x_center, y_center is the center of the function
% r is the distance from center to 0 (T/2) - function will go from z = 0 to
% 0 across 2*r at widest point
% pow is powe... |
github | tommysprague/IEM-tutorial-master | IEM_hexMap_attn.m | .m | IEM-tutorial-master/stim_presentation_scripts/IEM_hexMap_attn.m | 24,959 | utf_8 | 31c693bd2faf58881a4d94133a2f02c8 | % XXX s - XXX TRs @ 2.00 sec/TR
function IEM_hexMap_attn
% mapping task - adapted from wmDrop_hexMap.m
% TCS 6/18/2015
%
% instead of grid of mapping positions, now present stimuli along a
% hexagonal grid which is offset a different amount each run
%
% on a subset of trials, mapping stimulus has contrast increment/d... |
github | tommysprague/IEM-tutorial-master | make_triangular_grid.m | .m | IEM-tutorial-master/stim_presentation_scripts/make_triangular_grid.m | 1,949 | utf_8 | dba83fe01c4f42193b2adaba2f5920cf | % make_triangular_grid.m
% takes in n_rows, n_cols
% <n_rows> is always a single number
% <n_cols> can be a single number, in which case a jittered triangular grid
% subtending a rectangle is computed
% if <n_cols> is a vector of length equal to n_rows, then each row
% contains n_cols(row_nu... |
github | tommysprague/IEM-tutorial-master | make_checkerboard.m | .m | IEM-tutorial-master/stim_presentation_scripts/make_checkerboard.m | 987 | utf_8 | 06b43db822ad19f9b789212cef794515 | %
function c = make_checkerboard(rad,sf,contrast)
% creates a circular checkerboard with parameters, in pixels (after
% conversion using deg2pix)
% returns a cell array of 2 matrices which can be turned into textures for
% use by PTB
% ex: stim = Screen('MakeTexture',w,c{1});
% GAMMA correction - this may need to be ... |
github | marcospaul/GPIS-master | barwitherr_single.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/barwitherr_single.m | 5,390 | utf_8 | a895c6ac4b7fe5703e1aaa2a2f8758fe | %**************************************************************************
%
% This is a simple extension of the bar plot to include error bars. It
% is called in exactly the same way as bar but with an extra input
% parameter "errors" passed first.
%
% Parameters:
% errors - the errors to be plotted (extra... |
github | marcospaul/GPIS-master | barwitherr.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/barwitherr.m | 5,273 | utf_8 | 3cbd269f80accfb7a5c07f4bd29b2103 | %**************************************************************************
%
% This is a simple extension of the bar plot to include error bars. It
% is called in exactly the same way as bar but with an extra input
% parameter "errors" passed first.
%
% Parameters:
% errors - the errors to be plotted (extra... |
github | marcospaul/GPIS-master | stlwrite.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/stlwrite.m | 9,696 | utf_8 | 61b7ad17bcc11df9fefa5301e2dfbddc | function stlwrite(filename, varargin)
%STLWRITE Write STL file from patch or surface data.
%
% STLWRITE(FILE, FV) writes a stereolithography (STL) file to FILE for a
% triangulated patch defined by FV (a structure with fields 'vertices'
% and 'faces').
%
% STLWRITE(FILE, FACES, VERTICES) takes faces an... |
github | marcospaul/GPIS-master | pdftops.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/export_figures/pdftops.m | 3,068 | utf_8 | 7a40ce10e58d68cd7eeda67992b993f3 | function varargout = pdftops(cmd)
%PDFTOPS Calls a local pdftops executable with the input command
%
% Example:
% [status result] = pdftops(cmd)
%
% Attempts to locate a pdftops executable, finally asking the user to
% specify the directory pdftops was installed into. The resulting path is
% stored for futur... |
github | marcospaul/GPIS-master | isolate_axes.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/export_figures/isolate_axes.m | 3,484 | utf_8 | 3997011940bb5b146bf10032a9cec39a | %ISOLATE_AXES Isolate the specified axes in a figure on their own
%
% Examples:
% fh = isolate_axes(ah)
% fh = isolate_axes(ah, vis)
%
% This function will create a new figure containing the axes/uipanels
% specified, and also their associated legends and colorbars. The objects
% specified must all be in th... |
github | marcospaul/GPIS-master | pdf2eps.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/export_figures/pdf2eps.m | 1,524 | utf_8 | 037f9109e96ab4385d13019a29db4639 | %PDF2EPS Convert a pdf file to eps format using pdftops
%
% Examples:
% pdf2eps source dest
%
% This function converts a pdf file to eps format.
%
% This function requires that you have pdftops, from the Xpdf suite of
% functions, installed on your system. This can be downloaded from:
% http://www.foolabs.c... |
github | marcospaul/GPIS-master | print2array.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/export_figures/print2array.m | 6,474 | utf_8 | 4ead930267fe61c9b2a87139ee559dc8 | %PRINT2ARRAY Exports a figure to an image array
%
% Examples:
% A = print2array
% A = print2array(figure_handle)
% A = print2array(figure_handle, resolution)
% A = print2array(figure_handle, resolution, renderer)
% [A bcol] = print2array(...)
%
% This function outputs a bitmap image of the given fig... |
github | marcospaul/GPIS-master | eps2pdf.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/export_figures/eps2pdf.m | 5,151 | utf_8 | b356d73460fdebe8ef6fa428d5b2c125 | %EPS2PDF Convert an eps file to pdf format using ghostscript
%
% Examples:
% eps2pdf source dest
% eps2pdf(source, dest, crop)
% eps2pdf(source, dest, crop, append)
% eps2pdf(source, dest, crop, append, gray)
% eps2pdf(source, dest, crop, append, gray, quality)
%
% This function converts an eps file... |
github | marcospaul/GPIS-master | copyfig.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/export_figures/copyfig.m | 846 | utf_8 | 289162022c603c9e11a52b6d56329188 | %COPYFIG Create a copy of a figure, without changing the figure
%
% Examples:
% fh_new = copyfig(fh_old)
%
% This function will create a copy of a figure, but not change the figure,
% as copyobj sometimes does, e.g. by changing legends.
%
% IN:
% fh_old - The handle of the figure to be copied. Default: gc... |
github | marcospaul/GPIS-master | user_string.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/export_figures/user_string.m | 2,462 | utf_8 | dd1a7fa5b4f2be6320fc2538737a2f3e | %USER_STRING Get/set a user specific string
%
% Examples:
% string = user_string(string_name)
% saved = user_string(string_name, new_string)
%
% Function to get and set a string in a system or user specific file. This
% enables, for example, system specific paths to binaries to be saved.
%
% IN:
% string_name - ... |
github | marcospaul/GPIS-master | export_fig.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/export_figures/export_fig.m | 29,829 | utf_8 | e148a5b614ce2226be691f291726feb2 | %EXPORT_FIG Exports figures suitable for publication
%
% Examples:
% im = export_fig
% [im alpha] = export_fig
% export_fig filename
% export_fig filename -format1 -format2
% export_fig ... -nocrop
% export_fig ... -transparent
% export_fig ... -native
% export_fig ... -m<val>
% export_fig... |
github | marcospaul/GPIS-master | ghostscript.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/export_figures/ghostscript.m | 4,650 | utf_8 | db7a65458702e2333638288011dc0d7e | %GHOSTSCRIPT Calls a local GhostScript executable with the input command
%
% Example:
% [status result] = ghostscript(cmd)
%
% Attempts to locate a ghostscript executable, finally asking the user to
% specify the directory ghostcript was installed into. The resulting path
% is stored for future reference.
% ... |
github | marcospaul/GPIS-master | pclviewer.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlab_pcl/pclviewer.m | 1,291 | utf_8 | f58f1e96b93686f38351e26b2c2db93f | %PCLVIEWER View a point cloud using PCL
%
% PCLVIEWER(P) writes the point cloud P (MxN) to a temporary file and invokes
% the PCL point cloud viewer for fast display and visualization. The columns of P
% represent the 3D points.
%
% If M=3 then the rows are x, y, z.
% If M=6 then the rows are x, y, z, R, G, B where R,... |
github | marcospaul/GPIS-master | loadpcd.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlab_pcl/loadpcd.m | 8,446 | utf_8 | bd81dc4be8f32e981c4b579ee6b6f52f | %LOADPCD Load a point cloud from a PCD format file
%
% P = LOADPCD(FNAME) is a set of points loaded from the PCD format
% file FNAME.
%
% For an unorganized point cloud the columns of P represent the 3D points,
% and the rows are: x, y, z, r, g, b, a depending on the FIELDS in the file.
%
% For an organized point clo... |
github | marcospaul/GPIS-master | lzfd.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlab_pcl/lzfd.m | 1,904 | utf_8 | 480802ce84bcdc10b27d3cd49fb744cd | %LZFD LZF decompression
%
% OUT = LZFD(IN) is the decompressed version of the uint8 array IN.
%
% OUT = LZFD(IN, LEN) as above but sets the internal working buffer to length
% LEN which should exceed the expected uncompressed data size.
%
% Notes::
% - LZF is an algorithm that is efficient and gives reasonable compres... |
github | marcospaul/GPIS-master | lspcd.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlab_pcl/lspcd.m | 2,071 | utf_8 | e67de9778584a673b9569720ea4c72f9 | %LSPCD List attributes of PCD format files
%
% LSPCD() list the attributes of all .PCD files in the current folder.
%
% LSPCD(FILESPEC) as above but list only files that match FILESPEC which
% might contain a directory name and/or a wildcard.
%
%
% See also pclviewer, loadpcd.
%
% Copyright (C) 2013, by Peter I. Corke... |
github | marcospaul/GPIS-master | savepcd.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlab_pcl/savepcd.m | 4,205 | utf_8 | 55bba13facc867f4b8d662b57581d351 | %SAVEPCD Write a point cloud to file in PCD format
%
% SAVEPCD(FNAME, P) writes the point cloud P to the file FNAME as an
% as a PCD format file.
%
% If P is a 2-dimensional matrix (MxN) then the columns of P represent the
% 3D points and an unorganized point cloud is generated.
%
% If M=3 then the rows of P are x... |
github | marcospaul/GPIS-master | vertexArea.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/mesh/vertexArea.m | 2,763 | utf_8 | e49cc9be087c71fc2d7b5c1992869166 | function [ A ] = vertexArea( mesh, vertices, mode )
%[ A ] = vertexArea( mesh, vertices, mode )
% estimate area of mesh vertices
% Valid modes are:
% 'uniform' - area = 1
% 'onering' - sum of areas of one-ring triangles
% 'voronoi' - voronoi areas from [Meyer02] (invalid for obtuse triangles)
... |
github | marcospaul/GPIS-master | laplacian.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/mesh/laplacian.m | 1,120 | utf_8 | bdc751c7e39cd018b47b41003b19036b | function [ L ] = laplacian( mesh, vertices, mode )
%MEANCURV estimate vertex laplacians
% [Ryan Schmidt rms@dgp.toronto.edu 09/2008]
% - If vertices empty or undefined compute laplacians for entire mesh
% - Valid modes are:
% 'uniform' - uniform weights
% 'cotan' - cotangent weights
if ~ exist('mode',... |
github | marcospaul/GPIS-master | estimateNormal.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/mesh/estimateNormal.m | 2,542 | utf_8 | 5028c727d25c8e32ff08ae24f4c7f272 | function [ N ] = estimateNormal( surface, vertices, mode )
%[ N ] = estimateNormal( mesh, vertices, mode )
% [Ryan Schmidt rms@dgp.toronto.edu 09/2008]
% - if vertices is undefined/empty, compute for entire mesh
% - valides modes are:
% 'faceavg' - straight average of one-ring face normals
% 'faceav... |
github | marcospaul/GPIS-master | meanCurv.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/mesh/meanCurv.m | 5,409 | utf_8 | f8eed7ca7fdb6ddf93da3a22a5787e39 | function [ H, data ] = meanCurv( mesh, vertices, mode )
%MEANCURV estimate mean curvature at vertices
% [Ryan Schmidt rms@dgp.toronto.edu 09/2008]
% - if vertices is undefined/empty, compute for entire mesh
% - returned data is mode specific
% - valid modes are:
% 'normal' - Schneider & Kobbelt 01 version... |
github | marcospaul/GPIS-master | findBoundaries.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/mesh/findBoundaries.m | 4,223 | utf_8 | 81b139d65721a685014825c69ba7f672 | function [ loops ] = findBoundaries( pointset, iboundary, mode, Vu, Vv, parameter )
%FINDBOUNDARIES Summary of this function goes here
% Detailed explanation goes here
if strcmp(mode,'uv')
found_loops = findBoundaries_uv(pointset, iboundary, Vu, Vv);
elseif strcmp(mode,'3D')
if ~ exist('parameter','var')
... |
github | marcospaul/GPIS-master | meshDeform_Lipman04.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/deformation/meshDeform_Lipman04.m | 4,458 | utf_8 | 32122caa0958dee4f46ef39d5a0ea19c | function [ deformed_mesh ] = meshDeform_Lipman04( mesh, constraints, rotation_iters, smooth_radius )
%MESHDEFORM_LIPMAN04 Laplacian mesh deformation using estimated rotations
% implementation of Lipman et al SMI04 paper
% "Differential Coordinates for Interactive Mesh Editing"
%
% constraints: rows of [vt... |
github | marcospaul/GPIS-master | deformRotInvCoords.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/deformation/deformRotInvCoords.m | 5,243 | utf_8 | f14fbc8edd519271e11ee4251525cd9c | function [ deformed_mesh, rotations ] = deformRotInvCoords( mesh, consF, consP )
%[ deformed_mesh ] = deformRotInvCoords( mesh, consF, consP )
%
% consF: rows of [vtx_i, m11, m12,... m33, weight_i] (m = 3x3 transformation matrix)
% consP: rows of [vtx_i, x, y, z, weight_i]
pcount = numel(mesh.vidx);
[... |
github | marcospaul/GPIS-master | poissonMesh_Yu04.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/deformation/poissonMesh_Yu04.m | 5,264 | utf_8 | 9f58d120c73e6771a9b03c0390ad1e40 | function [ output_mesh ] = poissonMesh_Yu04( mesh, boundary_cons, target_tris )
%POISSONMESH_YU04 Summary of this function goes here
% Detailed explanation goes here
% boundary_cons: rows of [vtx_i, x, y, z]
%
% [RMS TODO] replace target_tris with a list of transformation
% matrices for original tris. Move ... |
github | marcospaul/GPIS-master | pdf2eps.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/util/external/export_fig/pdf2eps.m | 1,262 | utf_8 | 0251762cd3a15c3b79c2d61e51d15b99 | %PDF2EPS Convert a pdf file to eps format using pdftops
%
% Examples:
% pdf2eps source dest
%
% This function converts a pdf file to eps format.
%
% This function requires that you have pdftops, from the Xpdf suite of
% functions, installed on your system. This can be downloaded from:
% http://www.foolabs.c... |
github | marcospaul/GPIS-master | print2array.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/util/external/export_fig/print2array.m | 1,507 | utf_8 | c14317ca983a2360d06b099b88b08b93 | %PRINT2ARRAY Exports a figure to an image array
%
% Examples:
% A = print2array
% A = print2array(figure_handle)
% A = print2array(figure_handle, resolution)
% A = print2array(figure_handle, resolution, renderer)
%
% This function outputs a bitmap image of the given figure, at the desired
% resolution... |
github | marcospaul/GPIS-master | eps2pdf.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/util/external/export_fig/eps2pdf.m | 2,082 | utf_8 | 3823a6407d2d68f1710e61a32b8b7d35 | %EPS2PDF Convert an eps file to pdf format using ghostscript
%
% Examples:
% eps2pdf source dest
% eps2pdf(source, dest, crop)
%
% This function converts an eps file to pdf format. If the output pdf file
% already exists, the eps file is appended as a new page on the end of the
% eps file.
%
% This funct... |
github | marcospaul/GPIS-master | export_fig.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/util/external/export_fig/export_fig.m | 15,855 | utf_8 | 411d4c84de8017f964da98cfaee14f92 | %EXPORT_FIG Exports figures suitable for publication
%
% Examples:
% im = export_fig
% [im alpha] = export_fig
% export_fig filename
% export_fig filename -format1 -format2
% export_fig ... -nocrop
% export_fig ... -a2
% export_fig ... -zbuffer
% export_fig(..., handle)
%
% This function sa... |
github | marcospaul/GPIS-master | print2eps.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/util/external/export_fig/print2eps.m | 1,539 | utf_8 | 6b958a5ba6927d1f2864a556fb4d87e9 | %PRINT2EPS Prints figures to eps with improved line styles
%
% Examples:
% print2eps filename
% print2eps(filename, fig_handle)
%
% This function saves a figure as an eps file, and improves the line style,
% making dashed lines more like those on screen and giving grid lines their
% own dotted style.
%
%... |
github | marcospaul/GPIS-master | pdftops.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/util/external/export_fig/private/pdftops.m | 3,225 | utf_8 | c35c498fe21718d73f8ce5d91da63bab | function varargout = pdftops(cmd)
%PDFTOPS Calls a local pdftops executable with the input command
%
% Example:
% [status result] = pdftops(cmd)
%
% Attempts to locate a pdftops executable, finally asking the user to
% specify the directory pdftops was installed into. The resulting path is
% stored for futur... |
github | marcospaul/GPIS-master | ghostscript.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/util/external/export_fig/private/ghostscript.m | 3,569 | utf_8 | ee026c7d71a033563e758f0ce19845b2 | function varargout = ghostscript(cmd)
%GHOSTSCRIPT Calls a local GhostScript executable with the input command
%
% Example:
% [status result] = ghostscript(cmd)
%
% Attempts to locate a ghostscript executable, finally asking the user to
% specify the directory ghostcript was installed into. The resulting path... |
github | marcospaul/GPIS-master | myaa.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/util/external/myaa/myaa.m | 11,141 | utf_8 | a66dd7fc188c3f6a1a0a0c07623cf831 | function [varargout] = myaa(varargin)
%MYAA Render figure with anti-aliasing.
% MYAA
% Anti-aliased rendering of the current figure. This makes graphics look
% a lot better than in a standard matlab figure, which is useful for
% publishing results on the web or to better see the fine details in a
% complex... |
github | marcospaul/GPIS-master | expmap.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/expmap.m | 7,228 | utf_8 | d236dbc59067064400a579222a0cdddc | function [ uv, geo_dists, options_cache ] = expmap( points, normals, vtx, options )
% [ uv, geo_dists, options_cache ] = expmap( points, normals, vtx, options)
% compute discrete exponential
% points, normals are lists of points and normals
% vtx is vertex you want expmap around (arbitrary points not supported)
% optio... |
github | marcospaul/GPIS-master | embedMIPS.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/embedMIPS.m | 5,408 | utf_8 | 577faf068d0aabad357ecbd680c1076b | function [ uvmesh ] = embedMIPS( mesh, max_iter )
%EMBEDMIPS computes free-boundary MIPS parameterization of mesh
% [Ryan Schmidt rms@dgp.toronto.edu 09/2008]
% Described in 'MIPS: An Efficient Global Parameterization Method'
% by Hormann & Griener)
% embed mesh inside circle as initialization
mymesh = mesh;
... |
github | marcospaul/GPIS-master | embedSCP.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/embedSCP.m | 6,547 | utf_8 | 9aef8b48d1675f6b16c950a2410fcb74 | function [ uv ] = embedSCP( mesh, mode, W, faceAreaWeighted )
% uv = embedSCP(mesh, mode, W)
% Spectral Conformal Parameterization [Mullen08]
% mode: computation mode
% 'fiedler' - Fielder vector (sec 3.2)
% 'generalized' - generalized (default) (sec 3.3)
% 'robust' - generaliz... |
github | marcospaul/GPIS-master | mani.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/external/mani.m | 67,520 | utf_8 | 843d997d322a019aa31825135c9f3d3e | function varargout = mani(varargin)
% mani: MANIfold learning demonstration GUI
% by Todd Wittman, Department of Mathematics, University of Minnesota
% E-mail wittman@math.umn.edu with comments & questions.
% MANI Website: http://www.math.umn.edu/~wittman/mani/index.html
% Last Modified by GUIDE v2.5 10-Ap... |
github | marcospaul/GPIS-master | LEigenmaps.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/external/LEigenmaps.m | 751 | utf_8 | dc48ade294e07f695b32bdc70c2776b8 | % --- leigs function for Laplacian eigenmap.
% Written by Belkin & Niyogi, 2002.
function [Y] = LEigenmaps(DATA, K, d)
n = size(DATA,1);
A = sparse(n,n);
step = 100;
for i1=1:step:n
i2 = i1+step-1;
if (i2> n)
i2=n;
end;
XX= DATA(i1:i2,:);
dt = L2_distance(XX',DATA',0);
[Z,I] = so... |
github | marcospaul/GPIS-master | ltsa.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/external/ltsa.m | 1,890 | utf_8 | 8ab4aeb72c91791f3d802e912874dd77 | % --- LTSA function
% Written by Zhenyue Zhang & Hongyuan Zha, 2004.
% Reference: http://epubs.siam.org/sam-bin/dbq/article/41915
function [T,NI] = LTSA(data,d,K,NI)
[m,N] = size(data); % m is the dimensionality of the input sample points.
% Step 0: Neighborhood Index
if nargin<4
if length(K)==1
K = repm... |
github | marcospaul/GPIS-master | lle.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/external/lle.m | 2,220 | utf_8 | 532a6ccfbb08e8f2bce865c7bea4eb7b | % LLE ALGORITHM (using K nearest neighbors)
%
% [Y] = lle(X,K,dmax)
%
% X = data as D x N matrix (D = dimensionality, N = #points)
% K = number of neighbors
% dmax = max embedding dimensionality
% Y = embedding as dmax x N matrix
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [Y] = lle(X,K,d)
... |
github | marcospaul/GPIS-master | HessianLLE.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/external/HessianLLE.m | 2,459 | utf_8 | c6a8434b7d519808cda409da7cacda46 | % --- HLLE function
% Written by David Donoho & Carrie Grimes, 2003.
function [Y, mse] = HessianLLE(X,k,d)
N = size(X,2);
if max(size(k)) ==1
kvec = repmat(k,N,1);
elseif max(size(k)) == N
kvec=k;
end;
%Compute Nearest neighbors
if ~exist('W','var')
D1 = L2_distance(X,X,1);
dim = size(X,1);
nind = r... |
github | marcospaul/GPIS-master | mvu_readsol.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/external/mvu/mvu_readsol.m | 3,687 | utf_8 | 42ece43173eafaae0e27119974b0b845 | %
% [x,y,z]=readsol(fname,K,m)
%
% fname File name to read solution from.
% K structure of the matrices.
% m size of y vector.
%
% Modified 7/15/04, for greater MATLAB acceleration.
%
function [x,y,z]=readsol(fname,K,m)
%
% First, eliminate special cases that we don't handle.
%
%
% Check fo... |
github | marcospaul/GPIS-master | mvu_csdp.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/external/mvu/mvu_csdp.m | 4,482 | utf_8 | f91c54dc230ed4594eb343bfe65769a8 | %
% [x,y,z,info]=csdp(At,b,c,K,pars)
%
% Uses CSDP to solve a problem in SeDuMi format.
%
% Input:
% At, b, c, K SDP problem in SeDuMi format.
% pars CSDP parameters (optional parameter.)
%
% Output:
%
% x, y, z solution.
% info CSDP return code.
% ... |
github | marcospaul/GPIS-master | mvu.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/external/mvu/mvu.m | 12,901 | utf_8 | 1fc62abd772455399d82853b2a192a27 | function [Y,details]=mvu(DD,K,varargin)
% [Y,details]=mvu(DD,K,pars)
%
%
% DD SQUARED distance matrix of the input vectors (e.g. euclidean distances)
%
% Optional:
%
% K number of neighbors
%
% pars Parameters
%
% pars.solver chooses the MVU solver:
% pars.solver=0 CSDP (default)
% pars... |
github | marcospaul/GPIS-master | mvu_writesdpa.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlabmesh/parameterization/external/mvu/mvu_writesdpa.m | 7,470 | utf_8 | 3fc52dd04326a97ae0a6c3355634a6ff | % This function takes a problem in SeDuMi MATLAB format and writes it out
% in SDPA sparse format.
%
% Usage:
%
% ret=writesdpa(fname,A,b,c,K,pars)
%
% fname Name of SDPpack file, in quotes
% A,b,c,K Problem in SeDuMi form
% pars Optional parameters.
% ... |
github | marcospaul/GPIS-master | testSample.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlab_xunit_3_1_1/architecture/testSample.m | 190 | utf_8 | 3abbb98a6fbff1370b0549687f95fd1c | function test_suite = testSample
% Copyright 2013 The MathWorks, Inc.
initTestSuite;
function testMyCode
assertEqual(1, 1);
assertElementsAlmostEqual(1, 1.1);
assertTrue(10 == 10);
|
github | marcospaul/GPIS-master | testFliplr.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlab_xunit_3_1_1/doc/example_subfunction_tests/testFliplr.m | 250 | utf_8 | 0c3ac3ed3014a5815a7cac9f9614cf0e | function test_suite = testFliplr
% Copyright 2013 The MathWorks, Inc.
initTestSuite;
function testFliplrMatrix
in = magic(3);
assertEqual(fliplr(in), in(:, [3 2 1]));
function testFliplrVector
assertEqual(fliplr([1 4 10]), [10 4 1]);
|
github | marcospaul/GPIS-master | test_that.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlab_xunit_3_1_1/doc/+abc/+tests/test_that.m | 161 | utf_8 | 97300fd8d3adec69102d836a63110ca5 | % Do-nothing test used in the examples for organizing tests inside packages.
%
% Steven L. Eddins
% Copyright 2010 The MathWorks, Inc.
function test_that
|
github | marcospaul/GPIS-master | test_this.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlab_xunit_3_1_1/doc/+abc/+tests/test_this.m | 161 | utf_8 | fa26021122fc1ebe7ff54a143d85c458 | % Do-nothing test used in the examples for organizing tests inside packages.
%
% Steven L. Eddins
% Copyright 2010 The MathWorks, Inc.
function test_this
|
github | marcospaul/GPIS-master | testWithSetupError.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlab_xunit_3_1_1/doc/examples_general/testWithSetupError.m | 338 | utf_8 | 83622123b00ba5d08689e111e5fb651f | function test_suite = testWithSetupError
% Copyright 2013 The MathWorks, Inc.
%
%Example of a test with an error. The setup function calls cos with
%too many input arguments.
initTestSuite;
function testData = setup
testData = cos(1, 2);
function testMyFeature(testData)
assertEqual(1, 1);
function te... |
github | marcospaul/GPIS-master | testSetupExample.m | .m | GPIS-master/dependencies/matlab_visualization_scripts/matlab_xunit_3_1_1/doc/examples_general/testSetupExample.m | 325 | utf_8 | 79f5a41617af82cc45d3ba4118a7555b | function test_suite = testSetupExample
% Copyright 2013 The MathWorks, Inc.
initTestSuite;
function fh = setup
fh = figure;
function teardown(fh)
delete(fh);
function testColormapColumns(fh)
assertEqual(size(get(fh, 'Colormap'), 2), 3);
function testPointer(fh)
assertEqual(get(fh, 'Pointer'), 'arrow... |
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