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value | repo_name stringlengths 13 113 | name stringlengths 3 74 | ext stringclasses 1
value | path stringlengths 12 229 | size int64 23 843k | source_encoding stringclasses 9
values | md5 stringlengths 32 32 | text stringlengths 23 843k |
|---|---|---|---|---|---|---|---|---|
github | diazlab/scell-master | choose_file_type.m | .m | scell-master/mfiles/choose_file_type.m | 9,366 | utf_8 | 23013a2801b981342f44b275858cf2b4 | function varargout = choose_file_type(varargin)
% CHOOSE_FILE_TYPE MATLAB code for choose_file_type.fig
% CHOOSE_FILE_TYPE by itself, creates a new CHOOSE_FILE_TYPE or raises the
% existing singleton*.
%
% H = CHOOSE_FILE_TYPE returns the handle to a new CHOOSE_FILE_TYPE or the handle to
% the exist... |
github | diazlab/scell-master | skipped_correlation.m | .m | scell-master/mfiles/skipped_correlation.m | 17,779 | utf_8 | e21c4b632fdf62ab6e0373e085bed595 | function [r,t,h,outid,hboot,CI]=skipped_correlation(x,y,fig_flag)
% performs a robust correlation using pearson/spearman correlation on
% data cleaned up for bivariate outliers - that is after finding the
% central point in the distribution using the mid covariance determinant,
% orthogonal distances are computed... |
github | diazlab/scell-master | choose_dbscan_params.m | .m | scell-master/mfiles/choose_dbscan_params.m | 7,272 | utf_8 | d639ae9c4175061818b1fcad2254c372 | function varargout = choose_dbscan_params(varargin)
% CHOOSE_kmeans_params MATLAB code for choose_kmeans_params.fig
% CHOOSE_kmeans_params by itself, creates a new CHOOSE_kmeans_params or raises the
% existing singleton*.
%
% H = CHOOSE_kmeans_params returns the handle to a new CHOOSE_kmeans_params or th... |
github | diazlab/scell-master | bendcorr.m | .m | scell-master/mfiles/bendcorr.m | 5,885 | utf_8 | c59189f68712fd303dcc05029995da86 | function [r,t,p,hboot,CI,H,pH] = bendcorr(X,Y,fig_flag,beta)
% Computes the percentage bend correlation along with the bootstrap CI
%
% FORMAT: [r,t,p] = bendcorr(X,Y)
% [r,t,p,hboot,CI,H,pH] = bendcorr(X,Y,fig_flag,beta)
%
% INPUTS: X and Y are 2 vectors or matrices. In the latter case,
% ... |
github | diazlab/scell-master | choose_gauss_params.m | .m | scell-master/mfiles/choose_gauss_params.m | 8,366 | utf_8 | ef8a99dd4b1b370da2c427cb5f193233 | function varargout = choose_gauss_params(varargin)
% CHOOSE_kmeans_params MATLAB code for choose_kmeans_params.fig
% CHOOSE_kmeans_params by itself, creates a new CHOOSE_kmeans_params or raises the
% existing singleton*.
%
% H = CHOOSE_kmeans_params returns the handle to a new CHOOSE_kmeans_params or the... |
github | diazlab/scell-master | distinguishable_colors.m | .m | scell-master/mfiles/distinguishable_colors.m | 5,840 | utf_8 | c6a720e9f0a2e0a5d3f4cb9e28c1add1 | function colors = distinguishable_colors(n_colors,bg,func)
% DISTINGUISHABLE_COLORS: pick colors that are maximally perceptually distinct
%
% When plotting a set of lines, you may want to distinguish them by color.
% By default, Matlab chooses a small set of colors and cycles among them,
% and so if you have more than ... |
github | diazlab/scell-master | pca_tool2.m | .m | scell-master/pca_tool/pca_tool2.m | 13,563 | utf_8 | 53c8f2f95005ef7a9d16317764d3d428 | function varargout = pca_tool2(varargin)
%PCA_TOOL2 M-file for pca_tool2.fig
% PCA_TOOL2, by itself, creates a new PCA_TOOL2 or raises the existing
% singleton*.
%
% H = PCA_TOOL2 returns the handle to a new PCA_TOOL2 or the handle to
% the existing singleton*.
%
% PCA_TOOL2('Property','Value',... |
github | greefeet/TrussOptimization-master | displayAllTruss.m | .m | TrussOptimization-master/displayAllTruss.m | 4,077 | utf_8 | 1ead1667c1f6c48074b1df3e8cf59a02 | function displayAllTruss(dirName)
%displayAllTruss Display All Results
%Get File List %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dirData = dir(fullfile(dirName,'*.mat'));
dirIndex = [dirData.isdir];
fileList = {dirData(~dirIndex).name};
%Initialization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
github | greefeet/TrussOptimization-master | TopologyTest.m | .m | TrussOptimization-master/TopologyTest.m | 3,357 | utf_8 | f7315baebea731f69b793e021f12133a | function TopologyTest
%TopologyTest Bruce Force Display All Topology
prob = 'BKI';
feval(strcat(prob)); % Load Problem
global PRB;
% %BKI
% PRB.bc.FreeNode=[
% 360 360
% 720 360
% ];
PRB.bc.FreeNode=[
60 60
180 60
300 60
420 60
540 60
660 60
60 180
180 180
... |
github | greefeet/TrussOptimization-master | TrussSymmetry2D.m | .m | TrussOptimization-master/TrussSymmetry2D.m | 4,921 | utf_8 | 2e83493d1814569b66a137e3dad99301 | function [fitness, penalty, weight] = TrussSymmetry2D(indi)
%Truss2D fitness [in] mp,bc,dv [out] fitness,penalty,weight
[node, member]=TrussSymmetry2Ddecode(indi); %Decode individual
[fitness, penalty, weight]=getFitness(node,member); %Calculate Fitness
end
function [fitness, penalty, weight] = getFitness(n... |
github | greefeet/TrussOptimization-master | TrussSymmetry2Dencode.m | .m | TrussOptimization-master/TrussSymmetry2Dencode.m | 10,300 | utf_8 | d2933c7df17e4bf7e74b1008c702cb05 | function [a,b] = TrussSymmetry2Dencode
%Truss2Dencode Declare Global Varaibles and Set Upper and Lower Limit
%Encode PATTERN %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Applied Delaunay Triangulation : Determinate and Indeterminate Structure
% DesignVariable = [FixNodeSet FreeNodeSet]
% By
% a is Low... |
github | greefeet/TrussOptimization-master | TrussSymmetry2Dverify.m | .m | TrussOptimization-master/TrussSymmetry2Dverify.m | 12,745 | utf_8 | 66ef000c930aa600ab4a076517ea776d | function TrussSymmetry2Dverify(indi)
%TrussSymmetry2Dverify %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
global PRB;
bc = PRB.bc;
dv = PRB.dv;
mp = PRB.mp;
prob = PRB.info.prob;
fprintf('[Validate Results]\n');
fitness=TrussSymmetry2D(indi);
fprintf(' fitness: %.0f\n',fitness);
%Transform RAW Dat... |
github | greefeet/TrussOptimization-master | GA.m | .m | TrussOptimization-master/GA.m | 4,246 | utf_8 | 806af84f1b382f4f74ed07286d5a5cf6 | function GA( func,a,b,nloop,nsol)
%GA Start Genetic Algorithm
fprintf('Method : Genetic Algorithms (GA)\n');
% Optimizer's Parameters
nbit=10; % no. of binary bit for one design variable
pc=1.0; % probability of crossover
pm=0.2; % mutation probability
pt=0.05; % transla... |
github | greefeet/TrussOptimization-master | Truss2Dencode.m | .m | TrussOptimization-master/Truss2Dencode.m | 9,456 | utf_8 | 0beea2333f3830022d62c4a1cb9a1e69 | function [a,b] = Truss2Dencode
%Truss2Dencode Declare Global Varaibles and Set Upper and Lower Limit
%Encode PATTERN %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Applied Delaunay Triangulation : Determinate and Indeterminate Structure
% DesignVariable = [FixNodeSet FreeNodeSet]
% By
% a is LowerBounda... |
github | greefeet/TrussOptimization-master | start.m | .m | TrussOptimization-master/start.m | 949 | utf_8 | c3f58c4f66dac0df861225fd84455bfd | function start
%START Start Truss Optimization Framework
%Settings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
prob = 'ProbThaiSymII';
method = 'GA';
nloop = 500;
nsol = 500;
%Start %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fprintf('[Problem] %s\n',prob);
fprintf('[Met... |
github | greefeet/TrussOptimization-master | Truss2D.m | .m | TrussOptimization-master/Truss2D.m | 4,912 | utf_8 | d0d30376bbd622ac71510c44346c5dae | function [fitness, penalty, weight] = Truss2D(indi)
%Truss2D fitness [in] mp,bc,dv [out] fitness,penalty,weight
[node, member]=Truss2Ddecode(indi); %Decode individual
[fitness, penalty, weight]=getFitness(node,member); %Calculate Fitness
end
function [fitness, penalty, weight] = getFitness(node,memb... |
github | greefeet/TrussOptimization-master | initialBinary.m | .m | TrussOptimization-master/initialBinary.m | 726 | utf_8 | 4bdb601b8bfec523400ecfb5f816edb4 | function [bin,x,f] = initialBinary(fun,nvar,nbit,nsol,a,b)
%Randomly initiate the population, design variables
% nvar=no. of variables
% nbit is the number of cell in each variable
% nsol is a number of gene
rng('shuffle');
bin = round(rand(nvar*nbit,nsol));
f = zeros(1,nsol);
x = zeros(nvar,nsol);
for i=1:nsol
for... |
github | greefeet/TrussOptimization-master | Node.m | .m | TrussOptimization-master/Node.m | 4,965 | utf_8 | fa7973ee7d9ef02fa3467e611b04d6b6 | classdef Node
%Node Class is used for Truss2D.m
properties
x
y
noDirectNode
DirectNode
DirectNodeLength
DirectNodeAngle
DirectNodeZone
DirectNodeLayer
DirectNodeSectionIndex
DirectNodeSectionPriority
... |
github | greefeet/TrussOptimization-master | truss2Dverify.m | .m | TrussOptimization-master/truss2Dverify.m | 12,673 | utf_8 | ccc4e4e20968e0e82b67d367ca3265a2 | function Truss2Dverify(indi)
%Truss2Dverify %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
global PRB;
bc = PRB.bc;
dv = PRB.dv;
mp = PRB.mp;
prob = PRB.info.prob;
fprintf('[Validate Results]\n');
fitness=Truss2D(indi);
fprintf(' fitness: %.0f\n',fitness);
%Transform RAW Data to Truss Structure %%%... |
github | hiwonjoon/caffe-master | prepare_batch.m | .m | caffe-master/matlab/caffe/prepare_batch.m | 1,298 | utf_8 | 68088231982895c248aef25b4886eab0 | % ------------------------------------------------------------------------
function images = prepare_batch(image_files,IMAGE_MEAN,batch_size)
% ------------------------------------------------------------------------
if nargin < 2
d = load('ilsvrc_2012_mean');
IMAGE_MEAN = d.image_mean;
end
num_images = length... |
github | hiwonjoon/caffe-master | matcaffe_demo_vgg.m | .m | caffe-master/matlab/caffe/matcaffe_demo_vgg.m | 3,036 | utf_8 | f836eefad26027ac1be6e24421b59543 | function scores = matcaffe_demo_vgg(im, use_gpu, model_def_file, model_file, mean_file)
% scores = matcaffe_demo_vgg(im, use_gpu, model_def_file, model_file, mean_file)
%
% Demo of the matlab wrapper using the networks described in the BMVC-2014 paper "Return of the Devil in the Details: Delving Deep into Convolutional... |
github | hiwonjoon/caffe-master | matcaffe_demo.m | .m | caffe-master/matlab/caffe/matcaffe_demo.m | 3,344 | utf_8 | 669622769508a684210d164ac749a614 | function [scores, maxlabel] = matcaffe_demo(im, use_gpu)
% scores = matcaffe_demo(im, use_gpu)
%
% Demo of the matlab wrapper using the ILSVRC network.
%
% input
% im color image as uint8 HxWx3
% use_gpu 1 to use the GPU, 0 to use the CPU
%
% output
% scores 1000-dimensional ILSVRC score vector
%
% You m... |
github | hiwonjoon/caffe-master | matcaffe_demo_vgg_mean_pix.m | .m | caffe-master/matlab/caffe/matcaffe_demo_vgg_mean_pix.m | 3,069 | utf_8 | 04b831d0f205ef0932c4f3cfa930d6f9 | function scores = matcaffe_demo_vgg_mean_pix(im, use_gpu, model_def_file, model_file)
% scores = matcaffe_demo_vgg(im, use_gpu, model_def_file, model_file)
%
% Demo of the matlab wrapper based on the networks used for the "VGG" entry
% in the ILSVRC-2014 competition and described in the tech. report
% "Very Deep Convo... |
github | Navendis/geographiclib-master | geodarea.m | .m | geographiclib-master/matlab/geodarea.m | 4,242 | utf_8 | 5e2f0bb2df45f5f8f492c9b3e11c9f7a | function [A, P, N] = geodarea(lats, lons, ellipsoid)
%GEODAREA Surface area of polygon on an ellipsoid
%
% A = GEODAREA(lats, lons)
% [A, P, N] = GEODAREA(lats, lons, ellipsoid)
%
% calculates the surface area A of the geodesic polygon specified by the
% input vectors lats, lons (in degrees). The ellipsoid ve... |
github | Navendis/geographiclib-master | geoddistance.m | .m | geographiclib-master/matlab/geoddistance.m | 17,334 | utf_8 | 9d0f505b52eb3f56ad29f6046a7c568c | function [s12, azi1, azi2, S12, m12, M12, M21, a12] = geoddistance ...
(lat1, lon1, lat2, lon2, ellipsoid)
%GEODDISTANCE Distance between points on an ellipsoid
%
% [s12, azi1, azi2] = GEODDISTANCE(lat1, lon1, lat2, lon2)
% [s12, azi1, azi2, S12, m12, M12, M21, a12] =
% GEODDISTANCE(lat1, lon1, lat2, lo... |
github | Navendis/geographiclib-master | tranmerc_fwd.m | .m | geographiclib-master/matlab/tranmerc_fwd.m | 5,674 | utf_8 | acff0226812f95bc17989337218cdde5 | function [x, y, gam, k] = tranmerc_fwd(lat0, lon0, lat, lon, ellipsoid)
%TRANMERC_FWD Forward transverse Mercator projection
%
% [X, Y] = TRANMERC_FWD(LAT0, LON0, LAT, LON)
% [X, Y, GAM, K] = TRANMERC_FWD(LAT0, LON0, LAT, LON, ELLIPSOID)
%
% performs the forward transverse Mercator projection of points (LAT,LON)... |
github | Navendis/geographiclib-master | tranmerc_inv.m | .m | geographiclib-master/matlab/tranmerc_inv.m | 5,994 | utf_8 | 3ccf6b37ca13daed68a0ae8f166151ce | function [lat, lon, gam, k] = tranmerc_inv(lat0, lon0, x, y, ellipsoid)
%TRANMERC_INV Inverse transverse Mercator projection
%
% [LAT, LON] = TRANMERC_INV(LAT0, LON0, X, Y)
% [LAT, LON, GAM, K] = TRANMERC_INV(LAT0, LON0, X, Y, ELLIPSOID)
%
% performs the inverse transverse Mercator projection of points (X,Y) to
... |
github | tomdoel/pulmonarytoolkit-master | build_executables.m | .m | pulmonarytoolkit-master/build_executables.m | 1,038 | utf_8 | 964b3bb398bfc8565cb2228f76c3fa8e | % Reset path in case it contains folders that will be removed
path(pathdef);
create_empty_dir('./dist');
create_empty_dir('./build');
% Add paths
PTKAddPaths();
% On OSX this variable can cause problems so clear it
setenv('DYLD_LIBRARY_PATH');
% Compile GUI and API into executables
CompilePTK();
% Archive into zip ... |
github | tomdoel/pulmonarytoolkit-master | PTKUpdate.m | .m | pulmonarytoolkit-master/PTKUpdate.m | 4,452 | utf_8 | 344e57dfa02befb25c92b8b927869907 | function updated = PTKUpdate(varargin)
% PTKUpdate. A script to update the PTK codebase via git
%
%
%
% Licence
% -------
% Part of the TD Pulmonary Toolkit. https://github.com/tomdoel/pulmonarytoolkit
% Author: Tom Doel, 2015. www.tomdoel.com
% Distributed under... |
github | tomdoel/pulmonarytoolkit-master | PTKAddPaths.m | .m | pulmonarytoolkit-master/PTKAddPaths.m | 8,174 | utf_8 | 51b30d55eddcbab747fc56bef616b34d | function PTKAddPaths(varargin)
reset = nargin > 0 && strcmp(varargin{1}, 'reset');
force = nargin > 0 && strcmp(varargin{1}, 'force');
if reset
path(pathdef);
force = true;
end
% This version number should be incremented whenever new paths are added to
% the list
... |
github | tomdoel/pulmonarytoolkit-master | PTKImageDivider.m | .m | pulmonarytoolkit-master/Library/PTKImageDivider.m | 10,228 | utf_8 | b2e855a911f29a9abc449d6deacda1f5 | function filtered_image = PTKImageDivider(image_data, filter_function, mask, gaussian_sigma, hessian_filter_gaussian, dont_divide, is_left_lung, reporting)
% PTKImageDivider. Computes a filter for an image, one octant at a time.
%
% This function performs filtering on an image, but
% reduc... |
github | tomdoel/pulmonarytoolkit-master | PTKIsSimplePoint.m | .m | pulmonarytoolkit-master/Library/PTKIsSimplePoint.m | 4,610 | utf_8 | 856f2f913efd9509e69dfb4cf6c177b8 | function is_simple = PTKIsSimplePoint(image)
% PTKIsSimplePoint. Determines if a point in a 3D binary image is a simple point.
%
% A point is simple if removing it does not change the local
% connectivity of the surrounding points.
%
% A faster implementation of this function can be ... |
github | tomdoel/pulmonarytoolkit-master | PTKImageDividerHessian.m | .m | pulmonarytoolkit-master/Library/PTKImageDividerHessian.m | 15,243 | utf_8 | 8d26f78db3f635528f84c08983f95f8e | function filtered_image = PTKImageDividerHessian(image_data, filter_function, mask, gaussian_sigma, hessian_filter_gaussian, dont_divide, dont_calculate_evals, is_left_lung, reporting)
% PTKImageDividerHessian. Computes a Hessian-based filter for an image, one octant at a time.
%
% This function perform... |
github | tomdoel/pulmonarytoolkit-master | PTKGetHessianComponents.m | .m | pulmonarytoolkit-master/Library/PTKGetHessianComponents.m | 3,122 | utf_8 | 26825681d99e041872e738656f27b7d8 | function hessian_components = PTKGetHessianComponents(image_data, mask)
% PTKGetHessianComponents. Computes the Hessian matrices for an image
%
% PTKGetHessianComponents computes the components of the Hessian matrix
% for each voxel in the 3D image specified in the PTKImage class
% image... |
github | tomdoel/pulmonarytoolkit-master | PTKGetPulmonarySegments.m | .m | pulmonarytoolkit-master/Library/Segmentation/PTKGetPulmonarySegments.m | 2,176 | utf_8 | 579cb97a0b1276333d6b6155e0435d51 | function segments = PTKGetPulmonarySegments(lobes, acinar_map, reporting)
% PTKPulmonarySegments.
%
%
%
% Licence
% -------
% Part of the TD Pulmonary Toolkit. https://github.com/tomdoel/pulmonarytoolkit
% Author: Tom Doel, 2012. www.tomdoel.com
% Distributed un... |
github | tomdoel/pulmonarytoolkit-master | PTKFillCoronalHoles.m | .m | pulmonarytoolkit-master/Library/Segmentation/PTKFillCoronalHoles.m | 2,654 | utf_8 | 6ffd53a91a71a3586de2b92dcdd9b716 | function lung_image = PTKFillCoronalHoles(lung_image, is_right, reporting)
% PTKFillCoronalHoles. Operates on each coronal slice, applying a closing
% filter then filling interior holes
%
%
%
% Licence
% -------
% Part of the TD Pulmonary Toolkit. https://github.com/tomdoel/p... |
github | tomdoel/pulmonarytoolkit-master | PTKLevelSets2D.m | .m | pulmonarytoolkit-master/Library/Segmentation/PTKLevelSets2D.m | 7,484 | utf_8 | b3a72a7b7cd75040583a6cb93e9d4753 | function result = PTKLevelSets2D(original_image, initial_mask, bounds, figure_handle, reporting)
% PTKLevelSets2D. 2D level set algorithm based on image gradient
%
%
% Licence
% -------
% Part of the TD Pulmonary Toolkit. https://github.com/tomdoel/pulmonarytoolkit
% Author: ... |
github | tomdoel/pulmonarytoolkit-master | PTKMultipleRegionGrowing.m | .m | pulmonarytoolkit-master/Library/Segmentation/PTKMultipleRegionGrowing.m | 4,439 | utf_8 | acc8b0b689d4455e20dfb20bdad57f57 | function output_image = PTKMultipleRegionGrowing(threshold_image, start_points_global, reporting)
% PTKMultipleRegionGrowing. Performs 3D region growing of several regions
% simultaneously through the supplied binary threshold image, beginning
% at the specified starting points for each region.
... |
github | tomdoel/pulmonarytoolkit-master | PTKSimpleRegionGrowing.m | .m | pulmonarytoolkit-master/Library/Segmentation/PTKSimpleRegionGrowing.m | 3,471 | utf_8 | d215f3968ab952f652c644b4b515b756 | function output_image = PTKSimpleRegionGrowing(threshold_image, start_points_global, reporting)
% PTKSimpleRegionGrowing. Performs 3D region growing through the supplied
% binary threshold image, starting from the specified points
%
%
% Syntax:
% output_image = PTKSimpleRegionGro... |
github | tomdoel/pulmonarytoolkit-master | PTKGetMainRegionExcludingPaddingBorder.m | .m | pulmonarytoolkit-master/Library/Segmentation/PTKGetMainRegionExcludingPaddingBorder.m | 11,025 | utf_8 | 95c65e4f8fe9e67b52ff2db362c10ecc | function main_image = PTKGetMainRegionExcludingPaddingBorder(original_image, threshold_image, minimum_region_volume_mm3, include_interior_regions, reporting)
% PTKGetMainRegionExcludingPaddingBorder. Finds the largest connected region in a
% binary 3D volume, excluding any regions which touch an inner border
... |
github | tomdoel/pulmonarytoolkit-master | PTKFillHolesInImage.m | .m | pulmonarytoolkit-master/Library/Segmentation/PTKFillHolesInImage.m | 2,067 | utf_8 | edd0265fdebdb6974d7be2949a93bed3 | function filled_image = PTKFillHolesInImage(original_image)
% PTKFillHolesInImage. Fills in holes in a binary image.
%
% PTKFillHolesInImage takes in a binary image and fills in any completely
% enclosed holes, where holes are regions of value zero surrounded
% completely by non-zero val... |
github | tomdoel/pulmonarytoolkit-master | PTKGetMainRegionExcludingBorder.m | .m | pulmonarytoolkit-master/Library/Segmentation/PTKGetMainRegionExcludingBorder.m | 6,160 | utf_8 | d1ec3307778169d179c1a1a2db11b3ed | function main_image = PTKGetMainRegionExcludingBorder(threshold_image, minimum_region_volume_mm3, reporting)
% PTKGetMainRegionExcludingBorder. Finds the largest connected region in a
% binary 3D volume, excluding any regions which touch the borders in the
% first and second dimensions.
%
% Syntax:
... |
github | tomdoel/pulmonarytoolkit-master | PTKDivideVolumeUsingScatteredPoints.m | .m | pulmonarytoolkit-master/Library/Lobes/PTKDivideVolumeUsingScatteredPoints.m | 5,622 | utf_8 | b8a30057b263f597539fbd60236b2eb6 | function separated_mask = PTKDivideVolumeUsingScatteredPoints(volume_mask, scattered_points, volume_fraction_threshold, reporting)
% PTKDivideVolumeUsingScatteredPoints. Divides a volume into two regions,
% given a set of points which partly divide the volume
%
%
%
% Licence
% ------... |
github | tomdoel/pulmonarytoolkit-master | PTKGetMaxFissurePoints.m | .m | pulmonarytoolkit-master/Library/Lobes/PTKGetMaxFissurePoints.m | 9,949 | utf_8 | 00c67b4c5df56a674d4ff277a551a334 | function [high_fissure_indices, ref_image] = PTKGetMaxFissurePoints(fissure_approximation, lung_mask, fissureness, image_roi, image_size)
% PTKGetMaxFissurePoints. function for finding candidate points of high
% fissureness given an initial fissure approximation.
%
% PTKGetMaxFissurePoints is an... |
github | tomdoel/pulmonarytoolkit-master | PTKGetSegmentsByNearestBronchus.m | .m | pulmonarytoolkit-master/Library/Lobes/PTKGetSegmentsByNearestBronchus.m | 13,424 | utf_8 | 1bc49dfcefe8315f93dc220d5f6cbd81 | function [segment_image_map, labelled_segments] = PTKGetSegmentsByNearestBronchus(airway_root, left_and_right_lungs, segmental_bronchi_by_lobe, lobes, reporting)
% PTKGetSegmentsByNearestBronchus. Allocates each bronchus to a
% pulmonary segment, sets the segmental label of that bronchus, and
% creates an i... |
github | tomdoel/pulmonarytoolkit-master | PTKGetFissurePlane.m | .m | pulmonarytoolkit-master/Library/Lobes/PTKGetFissurePlane.m | 1,634 | utf_8 | 68022d9918227e25eb6b422be038fcbf | function result = PTKGetFissurePlane(max_fissure_points, image_size, extrapolation_multiple)
% PTKGetFissurePlane. Generates fissure curves given candidate points
%
% PTKGetFissurePlane is an intermediate stage in segmenting the
% lobes.
%
% For more information, see
% [Doel ... |
github | tomdoel/pulmonarytoolkit-master | PTKSolveForAffineRegistration.m | .m | pulmonarytoolkit-master/Library/Registration/PTKSolveForAffineRegistration.m | 2,169 | utf_8 | e841030d1712bec1b6ab080cd30b6faf | function [affine_matrix, transformed_matrix] = PTKSolveForAffineRegistration(image_to_transform, reference_image, reporting)
% PTKSolveForAffineRegistration. Computes the transformation matrix to register one
% image segmentation to another based on an solving for an affine
% transformation.
%
... |
github | tomdoel/pulmonarytoolkit-master | PTKSolveForRigidTranslation.m | .m | pulmonarytoolkit-master/Library/Registration/PTKSolveForRigidTranslation.m | 3,440 | utf_8 | 25f0ec23fb67304dc63ecee7f96c0318 | function [affine_matrix, transformed_matrix] = PTKSolveForRigidTranslation(image_to_transform, reference_image, reporting)
% PTKSolveForRigidTranslation. Computes the transformation matrix to register one
% image segmentation to another based on an solving for a rigid
% translation.
%
%
... |
github | tomdoel/pulmonarytoolkit-master | PTKSolveMatchedImagesForFluidRegistration.m | .m | pulmonarytoolkit-master/Library/Registration/PTKSolveMatchedImagesForFluidRegistration.m | 5,050 | utf_8 | 2d427cdfec022ea1a14595bd767c0a7f | function deformation_field = PTKSolveMatchedImagesForFluidRegistration(image_to_transform, reference_image, reporting)
% PTKSolveMatchedImagesForFluidRegistration.
%
%
% Licence
% -------
% Part of the TD Pulmonary Toolkit. https://github.com/tomdoel/pulmonarytoolkit
% Autho... |
github | tomdoel/pulmonarytoolkit-master | PTKSolveForFluidRegistration.m | .m | pulmonarytoolkit-master/Library/Registration/PTKSolveForFluidRegistration.m | 2,126 | utf_8 | 89fff739adc935b99109ec228a9e89c0 | function [deformation_field, deformed_image] = PTKSolveForFluidRegistration(image_to_transform, reference_image, reporting, affine_initial_matrix)
% PTKSolveForFluidRegistration. Computes the deformation field to register one
% image segmentation to another based on solving a fluid registration.
%
%... |
github | tomdoel/pulmonarytoolkit-master | PTKSolveForRigidRegistration.m | .m | pulmonarytoolkit-master/Library/Registration/PTKSolveForRigidRegistration.m | 3,292 | utf_8 | 6e21cfad03bf7930c1d5c7c385cf3b5f | function [affine_matrix, transformed_matrix] = PTKSolveForRigidRegistration(image_to_transform, reference_image, reporting)
% PTKSolveForRigidRegistration. Computes the transformation matrix to register one
% image segmentation to another based on an solving for a rigid
% transformation.
%
%... |
github | tomdoel/pulmonarytoolkit-master | PTKRegisterCentroid.m | .m | pulmonarytoolkit-master/Library/Registration/PTKRegisterCentroid.m | 1,189 | utf_8 | 81d8c35313c58c332ba84b77e1f042c4 | function [affine_matrix, affine_vector] = PTKRegisterCentroid(image_to_transform, reference_image, reporting)
% PTKRegisterCentroid. Computes the transformation matrix to register one
% image segmentation to another based on a rigid translation of the
% centroids.
%
%
% Licence
% ---... |
github | tomdoel/pulmonarytoolkit-master | PTKSegmentLungsMRISagittal2D.m | .m | pulmonarytoolkit-master/Library/Lungs/PTKSegmentLungsMRISagittal2D.m | 5,754 | utf_8 | d819ae7461f16d0670bbacd8d2ac75cb | function [new_image, bounds] = PTKSegmentLungsMRISagittal2D(original_image, filter_size_mm, reporting)
% PTKSegmentLungsMRISagittal2D. Generates an approximate segmentation the lungs
% from MRI images using region growing with a variable threshold.
%
%
% Syntax:
% [new_image, bounds]... |
github | tomdoel/pulmonarytoolkit-master | PTKSeparateAndLabelLungs.m | .m | pulmonarytoolkit-master/Library/Lungs/PTKSeparateAndLabelLungs.m | 8,844 | utf_8 | 9e48c2db5ed988cdd285e999d7e28886 | function both_lungs = PTKSeparateAndLabelLungs(unclosed_lungs, filtered_threshold_lung, lung_roi, trachea_top_local, reporting)
% PTKSeparateAndLabelLungs. Separates left and right lungs from a lung
% segmentation.
%
% The left and right lungs are separated using morphological opening
% ... |
github | tomdoel/pulmonarytoolkit-master | PTKComputeSegmentLungsMRI.m | .m | pulmonarytoolkit-master/Library/Lungs/PTKComputeSegmentLungsMRI.m | 11,508 | utf_8 | 872e12a7d588ffe0b775af9e9c2f5569 | function [new_image, bounds] = PTKComputeSegmentLungsMRI(original_image, filter_size_mm, reporting, start_point_right)
% PTKComputeSegmentLungsMRI. Generates an approximate segmentation the lungs
% from MRI images using region growing with a variable threshold.
%
%
% Syntax:
% [new_i... |
github | tomdoel/pulmonarytoolkit-master | PTKGraphMetricVsDistance.m | .m | pulmonarytoolkit-master/Library/Visualisation/PTKGraphMetricVsDistance.m | 12,136 | utf_8 | e146d2e51ad1e3b149e03e54381cc9b5 | function figure_handle = PTKGraphMetricVsDistance(table, metric, metric_std, context_list, patient_list, distance_label, reporting)
% PTKGraphMetricVsDistance. Plots a graph showing measurement values for images divided into slices along their axes
%
% PTKGraphMetricVsDistance draws a figure based on resul... |
github | tomdoel/pulmonarytoolkit-master | PTKDrawMetricVsMetric.m | .m | pulmonarytoolkit-master/Library/Visualisation/PTKDrawMetricVsMetric.m | 4,793 | utf_8 | 0741192e5d2ca41d57b8a4a36531ad41 | function figure_handle = PTKDrawMetricVsMetric(table, metric_x, metric_y, context_list)
% PTKDrawMetricVsMetric.
%
%
%
% Licence
% -------
% Part of the TD Pulmonary Toolkit. https://github.com/tomdoel/pulmonarytoolkit
% Author: Tom Doel, 2014. www.tomdoel.com
% ... |
github | tomdoel/pulmonarytoolkit-master | PTKGraphContextVsMetric.m | .m | pulmonarytoolkit-master/Library/Visualisation/PTKGraphContextVsMetric.m | 12,325 | utf_8 | 24d1897ea3834d6b5f19796231aeaa5e | function figure_handle = PTKGraphContextVsMetric(table, metric, context_list, patient_uids)
% PTKGraphContextVsMetric. Plots a graph showing measurement values against lung regions for one or more subjects
%
% PTKGraphContextVsMetric creates a figure and plots a graph showing measurements for particular lu... |
github | tomdoel/pulmonarytoolkit-master | PTKFindTopOfTrachea.m | .m | pulmonarytoolkit-master/Library/Airways/PTKFindTopOfTrachea.m | 11,676 | utf_8 | ba49772df0049a1e8abf31e9181b6092 | function [top_of_trachea, trachea_voxels] = PTKFindTopOfTrachea(lung_image, reporting, debug_mode)
% PTKFindTopOfTrachea. Finds the trachea from a thresholded lung CT image.
%
% Given a binary image which representes an airway threshold applied to a
% lung CT image, PTKFindTopOfTrachea finds the coordin... |
github | tomdoel/pulmonarytoolkit-master | PTKPruneAirwaysBySegment.m | .m | pulmonarytoolkit-master/Library/Airways/PTKPruneAirwaysBySegment.m | 1,004 | utf_8 | 36417950bd02d59400900758d13d342a | function start_branches = PTKPruneAirwaysBySegment(start_branches)
% PTKPruneAirwaysBySegment. Prunes branches from an airway
% tree at the end of each segmental bronchus
%
%
% Licence
% -------
% Part of the TD Pulmonary Toolkit. https://github.com/tomdoel/pulmonarytoolkit
... |
github | tomdoel/pulmonarytoolkit-master | PTKCloseBranchesInTree.m | .m | pulmonarytoolkit-master/Library/Airways/PTKCloseBranchesInTree.m | 3,507 | utf_8 | 777b3b64095b9f762a1a32e19c2c39cb | function airway_tree = PTKCloseBranchesInTree(airway_tree, closing_size_mm, image_size, reporting)
% PTKCloseBranchesInTree. Takes a segmented airway tree and
% performs a morphological closing on each segment, and between each segment
% and its child segments.
%
% This function is used by P... |
github | tomdoel/pulmonarytoolkit-master | PTKMapSegmentalParameters.m | .m | pulmonarytoolkit-master/Library/Airways/PTKMapSegmentalParameters.m | 3,996 | utf_8 | 6bb602b02fab26bb3543b105a597bc8a | function airway_tree_without_segmental_labels = PTKMapSegmentalParameters(airway_tree_with_segmental_labels, airway_tree_without_segmental_labels, reporting)
% PTKMapSegmentalParameters. Copies segmental labels from one airway tree to
% another
%
%
% Licence
% -------
% Part of t... |
github | tomdoel/pulmonarytoolkit-master | PTKAirwayRegionGrowingWithExplosionControl.m | .m | pulmonarytoolkit-master/Library/Airways/PTKAirwayRegionGrowingWithExplosionControl.m | 18,602 | utf_8 | 32831b70ea0af66f5d9b7b6c6e8d7e73 | function results = PTKAirwayRegionGrowingWithExplosionControl(threshold_image, start_point_global, maximum_number_of_generations, explosion_multiplier, coronal_mode, reporting, debug_mode)
% PTKAirwayRegionGrowingWithExplosionControl. Segments the airways from a
% threshold image using a region growing meth... |
github | tomdoel/pulmonarytoolkit-master | PTKReallocateAirwaysByLobe.m | .m | pulmonarytoolkit-master/Library/Airways/PTKReallocateAirwaysByLobe.m | 2,069 | utf_8 | 69cbaa3eddccec9109c1edaf61b1b602 | function start_branches = PTKReallocateAirwaysByLobe(start_branches, lobes, reporting)
% PTKReallocateAirwaysByLobe. Given a segmented airway tree and lobar
% segmentations, finds the bronchus corresponding to each pulmonary lobe
%
%
% Licence
% -------
% Part of the TD Pulmo... |
github | tomdoel/pulmonarytoolkit-master | PTKDivideAirwayTreeByCentrelineBranches.m | .m | pulmonarytoolkit-master/Library/Airways/PTKDivideAirwayTreeByCentrelineBranches.m | 2,701 | utf_8 | b4f49edc14bb13c5addb04ce83c16ca5 | function results_image = PTKDivideAirwayTreeByCentrelineBranches(start_branches, airway_tree, template)
% PTKDivideAirwayTreeByCentrelineBranches. Given a set of branches, this
% creates an output image which divides an airway tree into the subtrees
% serving each branch
%
% PTKDivideAir... |
github | tomdoel/pulmonarytoolkit-master | PTKColourBranchesBelowLobe.m | .m | pulmonarytoolkit-master/Library/Airways/PTKColourBranchesBelowLobe.m | 3,747 | utf_8 | c5a69d039c64a6b0383f8d04860456b6 | function results_image = PTKColourBranchesBelowLobe(start_branches, airway_tree, template)
% PTKColourBranchesBelowLobe. Given a set of labelled branches, this creates an output image with all the subtrees coloured by lobe
%
%
% Licence
% -------
% Part of the TD Pulmonary Toolkit. h... |
github | tomdoel/pulmonarytoolkit-master | PTKSaveSmoothedCentrelineTreeAsNodes.m | .m | pulmonarytoolkit-master/Library/Airways/PTKSaveSmoothedCentrelineTreeAsNodes.m | 5,238 | utf_8 | 398f06e57454cfd93a41d313f9450d7b | function PTKSaveSmoothedCentrelineTreeAsNodes(tree_root, file_path, filename_prefix, coordinate_system, template_image, reporting)
% PTKSaveSmoothedCentrelineTreeAsNodes. Exports a centreline tree structure into node and element files
%
% Syntax
% ------
%
% PTKSaveSmoothedCentre... |
github | tomdoel/pulmonarytoolkit-master | PTKSkeletonise.m | .m | pulmonarytoolkit-master/Library/Airways/PTKSkeletonise.m | 4,405 | utf_8 | 48f8f3bd9a5dbcbaf90408ea17929639 | function binary_image = PTKSkeletonise(binary_image, fixed_points_global, reporting)
% PTKSkeletonise. Performs a skeletonisation on a segmented airway tree.
%
%
%
% Licence
% -------
% Part of the TD Pulmonary Toolkit. https://github.com/tomdoel/pulmonarytoolkit
% Author... |
github | tomdoel/pulmonarytoolkit-master | PTKGetAirwaysLabelledByLobe.m | .m | pulmonarytoolkit-master/Library/Airways/PTKGetAirwaysLabelledByLobe.m | 21,744 | utf_8 | a98b3a1709e202c93c90f07f47b86d27 | function start_branches = PTKGetAirwaysLabelledByLobe(template, airway_centreline_tree, reporting)
% PTKGetAirwaysLabelledByLobe. Label segmented bronchi according to the
% lobes they serve.
%
% Usage:
%
% [results_image, start_branches] = PTKGetAirwaysLabelledByLobe(template, airway_result... |
github | tomdoel/pulmonarytoolkit-master | PTKSaveTreeAsNodes.m | .m | pulmonarytoolkit-master/Library/Airways/PTKSaveTreeAsNodes.m | 6,996 | utf_8 | 72c30fbb4a159bc621c2c5013de3f938 | function PTKSaveTreeAsNodes(tree_root, file_path, filename_prefix, coordinate_system, template_image, reporting)
% PTKSaveTreeAsNodes. Exports a tree structure into node and element files
%
% Two text files are produced; a node file and an element file.
%
% The node file describes points which compr... |
github | tomdoel/pulmonarytoolkit-master | PTKProcessAirwaySkeleton.m | .m | pulmonarytoolkit-master/Library/Airways/PTKProcessAirwaySkeleton.m | 8,134 | utf_8 | 752615f5538a78effce941be593ea1b0 | function results = PTKProcessAirwaySkeleton(skeleton_image, start_point, reporting)
% PTKProcessAirwaySkeleton. Processes a skeletonised image of the airway
% tree, beginning from start_point and returning a data structure containing
% the processed informtion
%
% Syntax:
% results = PTKProc... |
github | tomdoel/pulmonarytoolkit-master | PTKSaveCentrelineTreeAsNodes.m | .m | pulmonarytoolkit-master/Library/Airways/PTKSaveCentrelineTreeAsNodes.m | 4,838 | utf_8 | d6bfdb92073c1b7ab0d11999e6e96187 | function PTKSaveCentrelineTreeAsNodes(tree_root, file_path, filename_prefix, coordinate_system, template_image, reporting)
% PTKSaveCentrelineTreeAsNodes. Exports a centreline tree structure into node and element files
%
% Syntax
% ------
%
% PTKSaveCentrelineTreeAsNodes(tree_roo... |
github | tomdoel/pulmonarytoolkit-master | PTKGetSegmentalBronchiCentrelinesForEachLobe.m | .m | pulmonarytoolkit-master/Library/Airways/PTKGetSegmentalBronchiCentrelinesForEachLobe.m | 9,855 | utf_8 | f7fee892b85a1fad3b008a020351e964 | function start_branches = PTKGetSegmentalBronchiCentrelinesForEachLobe(airway_tree, lobes, template, reporting)
% PTKGetSegmentalBronchiCentrelinesForEachLobe. Given a segmented airway tree, finds the bronchus
% corresponding to each pulmonary segment
%
%
% Licence
% -------
% ... |
github | tomdoel/pulmonarytoolkit-master | PTKGetRadiusForAirways.m | .m | pulmonarytoolkit-master/Library/Airways/PTKGetRadiusForAirways.m | 1,874 | utf_8 | cf16941d9e77aa3c9601e3895c23aa69 | function results = PTKGetRadiusForAirways(centreline_results, lung_image, radius_approximation, reporting, figure_airways_3d)
% PTKGetRadiusForAirways. Computes the radius for a segmented airway tree.
%
%
%
% Licence
% -------
% Part of the TD Pulmonary Toolkit. https://github.co... |
github | tomdoel/pulmonarytoolkit-master | PTKGetWallThicknessForBranch.m | .m | pulmonarytoolkit-master/Library/Airways/PTKGetWallThicknessForBranch.m | 43,003 | utf_8 | 725a071ada27971ad51e15bcb9d314e4 | function results = PTKGetWallThicknessForBranch(bronchus, image_roi, context, figure_airways_3d, segmented_image)
if isempty(bronchus)
results = [];
else
segment_label = PTKPulmonarySegmentLabels(bronchus.SegmentIndex);
centreline = bronchus.Centreline;
radius_guess = br... |
github | tomdoel/pulmonarytoolkit-master | PTKSaveTreeAsVTK.m | .m | pulmonarytoolkit-master/Library/Airways/PTKSaveTreeAsVTK.m | 9,826 | utf_8 | 182ef7ab4ddcedd1b9ad09c003435b7d | function PTKSaveTreeAsVTK(tree_root, file_path, filename_prefix, coordinate_system, template_image, reporting)
% PTKSaveTreeAsVTK. Exports a tree structure into a VTK file
%
% PTKSaveTreeAsVTK saves the tree whose root branch is tree_root into a
% .vtk file which can be viewed with ParaView.
... |
github | tomdoel/pulmonarytoolkit-master | PTKComputeRadiusForBranch.m | .m | pulmonarytoolkit-master/Library/Airways/PTKComputeRadiusForBranch.m | 22,348 | utf_8 | 8179304a81cf19233068988a8d204d39 | function next_result = PTKComputeRadiusForBranch(next_segment, lung_image_as_double, radius_approximation, figure_airways_3d, reporting)
% PTKComputeRadiusForBranch. Image-derived radius estimation of an airway.
%
% PTKComputeRadiusForBranch creates a projection of the lung image
% perpendicular... |
github | tomdoel/pulmonarytoolkit-master | PTKSaveTreeAsCMISS.m | .m | pulmonarytoolkit-master/Library/Airways/PTKSaveTreeAsCMISS.m | 15,414 | utf_8 | c3750e21860971a3ddaef4e128616d3c | function PTKSaveTreeAsCMISS(tree_root, file_path, filename_prefix, coordinate_system, template_image, reporting)
% PTKSaveTreeAsCMISS. Exports a tree structure into ipnode and ipelem files
%
% Syntax
% ------
%
% PTKSaveTreeAsCMISS(tree_root, file_path, base_filename, reporting)
... |
github | tomdoel/pulmonarytoolkit-master | CompilePTK.m | .m | pulmonarytoolkit-master/Framework/CompilePTK.m | 6,251 | utf_8 | 5061cb9616d5f0b8d8cf053d74e1b7f5 | function CompilePTK
Compile(true); % Compile GUI
Compile(false); % Compile API
end
function Compile(is_gui)
if is_gui
main_function_file = 'PulmonaryToolkit.m';
compiled_output_subfolder = 'compiled';
else
main_function_file = 'PulmonaryToolkitAPI.m';
compiled_output_su... |
github | tomdoel/pulmonarytoolkit-master | CoreAddPaths.m | .m | pulmonarytoolkit-master/External/coremat/CoreAddPaths.m | 1,610 | utf_8 | a47046a1b9ec175354d17a12284ed6f1 | function CoreAddPaths(varargin)
force = nargin > 0 && strcmp(varargin{1}, 'force');
% This version number should be incremented whenever new paths are added to
% the list
CoreAddPaths_Version_Number = 3;
persistent Core_PathsHaveBeenSet
full_path = mfilename('fullpath');
... |
github | tomdoel/pulmonarytoolkit-master | CoreCompileMexFiles.m | .m | pulmonarytoolkit-master/External/coremat/MexCompile/CoreCompileMexFiles.m | 15,568 | utf_8 | ef87e006cdffadce377683918e8f16d5 | function CoreCompileMexFiles(mex_cache, output_directory, mex_files_to_compile, force_recompile, retry_instructions, reporting)
% CoreCompileMexFiles. Checks if mex files are up to date and re-compiles if
% necessary
%
% CoreCompileMexFiles takes in a list of mex files to be compiled,
% with... |
github | tomdoel/pulmonarytoolkit-master | CoreFindCudaCompiler.m | .m | pulmonarytoolkit-master/External/coremat/MexCompile/CoreFindCudaCompiler.m | 1,697 | utf_8 | e4ab0bd3355cd46299278920aa952902 | function cuda_compiler = CoreFindCudaCompiler()
% CoreFindCudaCompiler Attempts to locate the cuda compiler
%
%
%
% Licence
% -------
% Part of CoreMat. https://github.com/tomdoel/coremat
% Author: Tom Doel, 2013. www.tomdoel.com
% Distributed under the MIT licen... |
github | tomdoel/pulmonarytoolkit-master | CoreSaveXmlSimplified.m | .m | pulmonarytoolkit-master/External/coremat/Xml/CoreSaveXmlSimplified.m | 9,063 | utf_8 | 96ae0c41643984540eb69ca8530ba471 | function CoreSaveXmlSimplified(data, name, file_name, alias_mapping, reporting)
% CoreSaveXmlSimplified. Saves a data structure as an XML file
%
% CoreSaveXmlSimplified saves data into an XML file in a simplified format. The data may include arrays,
% cell arrays, structures, maps and classes wh... |
github | tomdoel/pulmonarytoolkit-master | CoreLoadXml.m | .m | pulmonarytoolkit-master/External/coremat/Xml/CoreLoadXml.m | 12,344 | utf_8 | d57fab94971630438beb11b4400fb9db | function data = CoreLoadXml(file_name, reporting, conversion_map)
% CoreLoadXml. Loads data structure from an XML file
%
% CoreLoadXml loads data which has been serialised to an XML file using
% CoreSaveXml. The data may include arrays, cell arrays, structures, maps and
% classes which s... |
github | tomdoel/pulmonarytoolkit-master | CoreSaveXml.m | .m | pulmonarytoolkit-master/External/coremat/Xml/CoreSaveXml.m | 8,652 | utf_8 | 476b4558ce2a78dc1b1bbe4b5ed00452 | function CoreSaveXml(data, name, file_name, reporting)
% CoreSaveXml. Saves a data structure as an XML file
%
% CoreSaveXml saves data into an XML file. The data may include arrays,
% cell arrays, structures, maps and classes which support serialisation.
%
% Syntax:
% Cor... |
github | tomdoel/pulmonarytoolkit-master | CoreSaveRawImage.m | .m | pulmonarytoolkit-master/External/coremat/File/CoreSaveRawImage.m | 3,021 | utf_8 | a6c5843f98055a9f489cf05c73e8593c | function CoreSaveRawImage(raw_image, file_path, raw_filename, compression, reporting)
% CoreSaveRawImage. Saves raw image data from disk
%
%
%
% Licence
% -------
% Part of CoreMat. https://github.com/tomdoel/coremat
% Author: Tom Doel, 2013. www.tomdoel.com
% Di... |
github | tomdoel/pulmonarytoolkit-master | CoreLoadRawImage.m | .m | pulmonarytoolkit-master/External/coremat/File/CoreLoadRawImage.m | 2,622 | utf_8 | f4376852841463a9bfadfa4af5c070d4 | function raw_image = CoreLoadRawImage(file_path, raw_filename, data_type, image_size, compression, reporting)
% CoreLoadRawImage. Loads raw image data from disk
%
%
%
% Licence
% -------
% Part of CoreMat. https://github.com/tomdoel/coremat
% Author: Tom Doel, 2013. www.... |
github | tomdoel/pulmonarytoolkit-master | CoreRunTests.m | .m | pulmonarytoolkit-master/External/coremat/MTest/CoreRunTests.m | 2,086 | utf_8 | 68002cbc63bff70d805bce725b0b2a60 | function CoreRunTests(testsOrDirectory)
% CoreRunTests Runs MTest unit tests for Matlab
%
% Executes the specified unit tests and reports on the sucess and
% failures.
%
% Syntax:
% CoreRunTests(testsOrDirectory);
%
% testsOrDirectory - a folder or a cell array of strings... |
github | tomdoel/pulmonarytoolkit-master | ReadData3D.m | .m | pulmonarytoolkit-master/External/ReadData3D/ReadData3D.m | 14,709 | utf_8 | 75ee6dd1c85876b0cbdd092f7693c5ce | function varargout = ReadData3D(varargin)
% This function ReadData3D allows the user to open medical 3D files. It
% supports the following formats :
%
% Dicom Files ( .dcm , .dicom )
% V3D Philips Scanner ( .v3d )
% GIPL Guys Image Processing Lab ( .gipl )
% HDR/IMG Analyze ( .hdr )
% ISI Files ( .isi )
% N... |
github | tomdoel/pulmonarytoolkit-master | dicom_folder_info.m | .m | pulmonarytoolkit-master/External/ReadData3D/dicom/dicom_folder_info.m | 8,441 | utf_8 | b8e07058d3c4b9890f08da8053d9216e | function datasets=dicom_folder_info(link,subfolders)
% Function DICOM_FOLDER_INFO gives information about all Dicom files
% in a certain folder (and subfolders), or of a certain dataset
%
% datasets=dicom_folder_info(link,subfolders)
%
% inputs,
% link : A link to a folder like "C:\temp" or a link to the first... |
github | tomdoel/pulmonarytoolkit-master | dicom_write_volume.m | .m | pulmonarytoolkit-master/External/ReadData3D/dicom/dicom_write_volume.m | 2,219 | utf_8 | a3f41a386dcd02f121e040857f26b55a | function dicom_write_volume(Volume,filename,volscale,info)
% This function DICOM_WRITE_VOLUME will write a Matlab 3D volume as
% a stack of 2D slices in separate dicom files.
%
% dicom_write_volume(Volume,Filename,Scales,Info)
%
% inputs,
% Volume: The 3D Matlab volume
% Filename: The name of the dicom file... |
github | tomdoel/pulmonarytoolkit-master | choose_from_list.m | .m | pulmonarytoolkit-master/External/ReadData3D/dicom/choose_from_list.m | 1,062 | utf_8 | 9a5736ab8c4022c2092521054615df27 | function [id,name] = choose_from_list(varargin)
%
% example :
%
% c{1}='apple'
% c{2}='orange'
% c{3}='berries'
% [id,name]=choose_from_list(c,'Select a Fruit');
%
if(strcmp(varargin{1},'press'))
handles=guihandles;
id=get(handles.listbox1,'Value');
setMyData(id);
uiresume
return
end
% listbox1 Positio... |
github | tomdoel/pulmonarytoolkit-master | mha_read_volume.m | .m | pulmonarytoolkit-master/External/ReadData3D/mha/mha_read_volume.m | 2,868 | utf_8 | 9475c2dea18daaf73262042ce8be7b50 | function V = mha_read_volume(info)
% Function for reading the volume of a Insight Meta-Image (.mha, .mhd) file
%
% volume = tk_read_volume(file-header)
%
% examples:
% 1: info = mha_read_header()
% V = mha_read_volume(info);
% imshow(squeeze(V(:,:,round(end/2))),[]);
%
% 2: V = mha_read_volume('test.mh... |
github | tomdoel/pulmonarytoolkit-master | raw_read_header.m | .m | pulmonarytoolkit-master/External/ReadData3D/raw/raw_read_header.m | 19,605 | utf_8 | 4012e947c5ae87248c1a2034fb83864e | function varargout = raw_read_header(varargin)
% function for reading header of raw volume file
%
% info = raw_read_header(filename);
%
% examples:
% 1, info=raw_read_header()
% 2, info=raw_read_header('volume.raw');
% Edit the above text to modify the response to help raw_read_header
% Last Modified by GUIDE v2.5 ... |
github | tomdoel/pulmonarytoolkit-master | par_read_header.m | .m | pulmonarytoolkit-master/External/ReadData3D/par/par_read_header.m | 9,281 | utf_8 | d35b414f478ff294a6ca3ab889e04551 | function info =par_read_header(filename)
% Function for reading the header of a Philips Par / Rec MR V4.* file
%
% info = par_read_header(filename);
%
% examples:
% 1, info=par_read_header()
% 2, info=par_read_header('volume.par');
if(exist('filename','var')==0)
[filename, pathname] = uigetfile('*.p... |
github | tomdoel/pulmonarytoolkit-master | hdr_read_volume.m | .m | pulmonarytoolkit-master/External/ReadData3D/hdr/hdr_read_volume.m | 1,429 | utf_8 | ddbf082bf0adb5cc48c5ad55a65a4f07 | function V=hdr_read_volume(info)
% function for reading volume of HDR/IMG Analyze ( .hdr ) volume file
%
% volume = hdr_read_volume(file-header)
%
% examples:
% 1: info = hdr_read_volume(()
% V = hdr_read_volume(info);
% imshow(squeeze(V(:,:,round(end/2))),[]);
%
% 2: V = hdr_read_volume(('test.hdr');
... |
github | tomdoel/pulmonarytoolkit-master | hdr_read_header.m | .m | pulmonarytoolkit-master/External/ReadData3D/hdr/hdr_read_header.m | 4,707 | utf_8 | a2dc54e78b103557c78fd2f7652f1bfe | function info=hdr_read_header(filename)
% function for reading header of HDR/IMG Analyze ( .hdr ) volume file
%
% info = hdr_read_header(filename);
%
% examples:
% 1, info=hdr_read_header()
% 2, info=hdr_read_header('volume.hdr');
if(exist('filename','var')==0)
[filename, pathname] = uigetfile('*.hdr',... |
github | tomdoel/pulmonarytoolkit-master | ErrorData3D.m | .m | pulmonarytoolkit-master/External/ReadData3D/subfunctions/ErrorData3D.m | 3,246 | utf_8 | 66924055ba5a507e5363c6d4666bdac8 | function varargout = ErrorData3D(varargin)
% ERRORDATA3D M-file for ErrorData3D.fig
% ERRORDATA3D, by itself, creates a new ERRORDATA3D or raises the existing
% singleton*.
%
% H = ERRORDATA3D returns the handle to a new ERRORDATA3D or the handle to
% the existing singleton*.
%
% ERRORDATA3D('C... |
github | tomdoel/pulmonarytoolkit-master | InfoData3D.m | .m | pulmonarytoolkit-master/External/ReadData3D/subfunctions/InfoData3D.m | 3,553 | utf_8 | da6f4f6491166d601be56e443974a131 | function varargout = InfoData3D(varargin)
% INFODATA3D M-file for InfoData3D.fig
% INFODATA3D, by itself, creates a new INFODATA3D or raises the existing
% singleton*.
%
% H = INFODATA3D returns the handle to a new INFODATA3D or the handle to
% the existing singleton*.
%
% INFODATA3D('CALLBACK'... |
github | tomdoel/pulmonarytoolkit-master | load_nii_ext.m | .m | pulmonarytoolkit-master/External/Nifti_tools/load_nii_ext.m | 5,337 | utf_8 | fa0e831b0a596c3208b21bddc1c6d812 | % Load NIFTI header extension after its header is loaded using load_nii_hdr.
%
% Usage: ext = load_nii_ext(filename)
%
% filename - NIFTI file name.
%
% Returned values:
%
% ext - Structure of NIFTI header extension, which includes num_ext,
% and all the extended header sections in the header extension.
% ... |
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