├── .gitignore ├── LICENSE ├── README.md ├── openslide_close.m ├── openslide_detect_vendor.m ├── openslide_example.m ├── openslide_get_associated_image_dimensions.m ├── openslide_get_associated_image_names.m ├── openslide_get_best_level_for_downsample.m ├── openslide_get_error.m ├── openslide_get_level0_dimensions.m ├── openslide_get_level_count.m ├── openslide_get_level_dimensions.m ├── openslide_get_level_downsample.m ├── openslide_get_property_names.m ├── openslide_get_property_value.m ├── openslide_get_slide_properties.m ├── openslide_get_version.m ├── openslide_load_library.m ├── openslide_open.m ├── openslide_read_associated_image.m ├── openslide_read_region.m ├── openslide_unload_library.m └── test_data ├── CMU-1-Small-Region.svs └── README.txt /.gitignore: -------------------------------------------------------------------------------- 1 | openslide-wrapper.h -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | {one line to give the program's name and a brief idea of what it does.} 635 | Copyright (C) {year} {name of author} 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | {project} Copyright (C) {year} {fullname} 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | 676 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | openslide-matlab 2 | ================ 3 | 4 | A MATLAB library providing bindings to the C library OpenSlide 5 | (https://github.com/openslide/openslide) used for reading 6 | whole-slide images. 7 | 8 | Latest tested openslide versions: 3.4.1 9 | 10 | Copyright (c) 2016 Daniel Forsberg 11 | danne.forsberg@outlook.com 12 | 13 | This program is free software: you can redistribute it and/or modify 14 | it under the terms of the GNU General Public License as published by 15 | the Free Software Foundation, either version 3 of the License, or 16 | (at your option) any later version. 17 | 18 | This program is distributed in the hope that it will be useful, 19 | but WITHOUT ANY WARRANTY; without even the implied warranty of 20 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 21 | GNU General Public License for more details. 22 | You should have received a copy of the GNU General Public License 23 | along with this program. If not, see . 24 | 25 | ABOUT 26 | ================ 27 | This library contains MATLAB bindings to the C library OpenSlide, 28 | which is used to read image data from digital whole-slide images. 29 | 30 | INSTALLATION 31 | ================ 32 | Add the folder and any sub folders to the MATLAB path. Also download 33 | source code or binaries for OpenSlide from http://openslide.org/download/. 34 | If downloading the source, make sure to follow instructions provided by 35 | OpenSlide for compiling the binaries. Remember to also add the folders 36 | of these libraries and the include files to the MATLAB path. 37 | 38 | If using release 3.4 or older, make sure to edit the openslide.h 39 | so that '#include ' reads 40 | '#include "openslide-features.h"' instead. 41 | 42 | When running openslide_load_library a wrapper header file will be 43 | created in the openslide MATLAB repository. This file is needed 44 | as wrapper to avoid some issues with gcc function attributes. 45 | 46 | LICENSING 47 | ================ 48 | Source code provided in this repository is generally released under 49 | the GNU GENERAL PUBLIC LICENSE Version 3, if not otherwise stated. 50 | -------------------------------------------------------------------------------- /openslide_close.m: -------------------------------------------------------------------------------- 1 | function openslide_close(openslidePointer) 2 | % OPENSLIDE_CLOSE Closes the currently open whole-slide image 3 | % 4 | % INPUT ARGUMENTS 5 | % openslidePointer - Pointer to the openslide object to close 6 | % 7 | % OPTIONAL INPUT ARGUMENTS 8 | % N/A 9 | % 10 | % OUTPUT 11 | % N/A 12 | 13 | % Copyright (c) 2016 Daniel Forsberg 14 | % danne.forsberg@outlook.com 15 | % 16 | % This program is free software: you can redistribute it and/or modify 17 | % it under the terms of the GNU General Public License as published by 18 | % the Free Software Foundation, either version 3 of the License, or 19 | % (at your option) any later version. 20 | % 21 | % This program is distributed in the hope that it will be useful, 22 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 23 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 24 | % GNU General Public License for more details. 25 | % 26 | % You should have received a copy of the GNU General Public License 27 | % along with this program. If not, see . 28 | 29 | %% 30 | 31 | % Make sure library for openslide is loaded 32 | if ~libisloaded('openslidelib') 33 | warning('OpenSlide library has not been loaded, attempting to load') 34 | openslide_load_library(); 35 | end 36 | 37 | % Close whole-slide image 38 | calllib('openslidelib','openslide_close',openslidePointer); 39 | 40 | disp('Remember to clear the pointer to the openslide object, since it is not valid anymore') -------------------------------------------------------------------------------- /openslide_detect_vendor.m: -------------------------------------------------------------------------------- 1 | function [vendor] = openslide_detect_vendor(slideName) 2 | % OPENSLIDE_DETECT_VENDOR Determine vendor of the whole-slide image 3 | % 4 | % [vendor] = openslide_detect_vendor(slideName) 5 | % 6 | % INPUT ARGUMENTS 7 | % slideName - Full file name of whole-slide image to interact with, i.e. 8 | % including full path and file extension 9 | % 10 | % OPTIONAL INPUT ARGUMENTS 11 | % N/A 12 | % 13 | % OUTPUT 14 | % vendor - Vendor of the whole-slide image 15 | 16 | % Copyright (c) 2016 Daniel Forsberg 17 | % danne.forsberg@outlook.com 18 | % 19 | % This program is free software: you can redistribute it and/or modify 20 | % it under the terms of the GNU General Public License as published by 21 | % the Free Software Foundation, either version 3 of the License, or 22 | % (at your option) any later version. 23 | % 24 | % This program is distributed in the hope that it will be useful, 25 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 26 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 27 | % GNU General Public License for more details. 28 | % 29 | % You should have received a copy of the GNU General Public License 30 | % along with this program. If not, see . 31 | 32 | %% 33 | % Check if openslide library is loaded 34 | if ~libisloaded('openslidelib') 35 | warning('OpenSlide library has not been loaded, attempting to load') 36 | openslide_load_library(); 37 | end 38 | 39 | % Call detect vendor 40 | [vendor] = calllib('openslidelib','openslide_detect_vendor',slideName); -------------------------------------------------------------------------------- /openslide_example.m: -------------------------------------------------------------------------------- 1 | % OPENSLIDE_EXAMPLE An example of how to use the MATLAB bindings with 2 | % the OpenSlide library for working with whole-slide images 3 | 4 | % Copyright (c) 2016 Daniel Forsberg 5 | % danne.forsberg@outlook.com 6 | % 7 | % This program is free software: you can redistribute it and/or modify 8 | % it under the terms of the GNU General Public License as published by 9 | % the Free Software Foundation, either version 3 of the License, or 10 | % (at your option) any later version. 11 | % 12 | % This program is distributed in the hope that it will be useful, 13 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 14 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 15 | % GNU General Public License for more details. 16 | % 17 | % You should have received a copy of the GNU General Public License 18 | % along with this program. If not, see . 19 | 20 | close all 21 | 22 | % Get folder of this file 23 | [folder,~,~] = fileparts(mfilename('fullpath')); 24 | 25 | % Load openslide library 26 | openslide_load_library(); 27 | 28 | disp(['OpenSlide version: ',openslide_get_version()]) 29 | 30 | % Set file name of whole-slide image to work with 31 | WSI = [folder,filesep,'test_data',filesep,'CMU-1-Small-Region.svs']; 32 | 33 | % Display vendor of whole-slide image 34 | disp(['Vendor: ',openslide_detect_vendor(WSI)]) 35 | 36 | % Open whole-slide image 37 | slidePtr = openslide_open(WSI); 38 | 39 | % Get whole-slide image properties 40 | [mppX, mppY, width, height, numberOfLevels, ... 41 | downsampleFactors, objectivePower] = openslide_get_slide_properties(slidePtr); 42 | 43 | % Display properties 44 | disp(['mppX: ',num2str(mppX)]) 45 | disp(['mppY: ',num2str(mppY)]) 46 | disp(['width: ',num2str(width)]) 47 | disp(['height: ',num2str(height)]) 48 | disp(['number of levels: ',num2str(numberOfLevels)]) 49 | disp(['downsample factors: ',num2str(downsampleFactors)]) 50 | disp(['objective power: ',num2str(objectivePower)]) 51 | 52 | % Read a part of the image 53 | ARGB = openslide_read_region(slidePtr,512,512,1024,1024,0); 54 | 55 | % Display RGB part 56 | figure(1) 57 | imshow(ARGB(:,:,2:4)) 58 | set(gcf,'Name','WSI','NumberTitle','off') 59 | 60 | % Get property names and display them 61 | propertyNames = openslide_get_property_names(slidePtr); 62 | disp(propertyNames(:)) 63 | 64 | % Get a property value 65 | propertyValue = openslide_get_property_value(slidePtr,propertyNames{21}); 66 | disp(propertyValue) 67 | 68 | % Get associated images 69 | associatedImages = openslide_get_associated_image_names(slidePtr); 70 | disp(associatedImages(:)) 71 | 72 | % Display all associated images 73 | for k = 1 : length(associatedImages) 74 | disp(['Displaying: ',associatedImages{k}]) 75 | label = openslide_read_associated_image(slidePtr,associatedImages{k}); 76 | 77 | % Display label image 78 | figure(1+k) 79 | imshow(label(:,:,2:4)) 80 | set(gcf,'Name',associatedImages{k},'NumberTitle','off') 81 | [w,h] = openslide_get_associated_image_dimensions(slidePtr,associatedImages{k}); 82 | disp(['width: ',num2str(w)]) 83 | disp(['height: ',num2str(h)]) 84 | end 85 | 86 | % Close whole-slide image, note that the slidePtr must be removed manually 87 | openslide_close(slidePtr) 88 | clear slidePtr 89 | 90 | % Unload library 91 | openslide_unload_library -------------------------------------------------------------------------------- /openslide_get_associated_image_dimensions.m: -------------------------------------------------------------------------------- 1 | function [width, height] = openslide_get_associated_image_dimensions(openslidePointer,imageName) 2 | % OPENSLIDE_GET_ASSOCIATED_IMAGE_DIMENSIONS Gets the dimensions of the associated image 3 | % 4 | % [width, height] = openslide_get_associated_image_dimensions(openslidePointer,imageName) 5 | % 6 | % INPUT ARGUMENTS 7 | % openslidePointer - Pointer to openslide object to read from 8 | % imageName - Associated image name to read from 9 | % 10 | % OPTIONAL INPUT ARGUMENTS 11 | % N/A 12 | % 13 | % OUTPUT 14 | % width - Image width 15 | % height - Image Height 16 | 17 | % Copyright (c) 2016 Daniel Forsberg 18 | % danne.forsberg@outlook.com 19 | % 20 | % This program is free software: you can redistribute it and/or modify 21 | % it under the terms of the GNU General Public License as published by 22 | % the Free Software Foundation, either version 3 of the License, or 23 | % (at your option) any later version. 24 | % 25 | % This program is distributed in the hope that it will be useful, 26 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 27 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 28 | % GNU General Public License for more details. 29 | % 30 | % You should have received a copy of the GNU General Public License 31 | % along with this program. If not, see . 32 | 33 | %% 34 | 35 | % Check if library for openslide is already loaded 36 | if ~libisloaded('openslidelib') 37 | warning('OpenSlide library has not been loaded, attempting to load') 38 | openslide_load_library(); 39 | end 40 | 41 | % Check image name 42 | if iscell(imageName) 43 | warning(['Provided imageName argument is a cell object. ',... 44 | 'Attempts to use data from the first cell as imageName argument']); 45 | imageName = imageName{1}; 46 | end 47 | if ~ischar(imageName) 48 | error('openslide:openslide_get_associated_image_dimensions',... 49 | 'Provided imageName argument is not a valid char array.\n') 50 | end 51 | 52 | % See if provided image name is in the list of available associated images 53 | imageNames = openslide_get_associated_image_names(openslidePointer); 54 | if sum(strcmpi(imageName,imageNames)) == 0 55 | error('openslide:openslide_get_associated_image_dimensions',... 56 | 'Provided imageName argument is not a valid associated image name for this openslide object.\n') 57 | end 58 | 59 | % Read size of associated image 60 | width = 0; 61 | height = 0; 62 | [~, ~, width, height] = calllib('openslidelib',... 63 | 'openslide_get_associated_image_dimensions',openslidePointer,imageName,... 64 | width,height); 65 | 66 | % Check for errors 67 | [errorMessage] = openslide_get_error(openslidePointer); 68 | 69 | % Terminate if an error was returned 70 | if ~isempty(errorMessage) 71 | error('openslide:openslide_get_associated_image_dimensions',errorMessage) 72 | end -------------------------------------------------------------------------------- /openslide_get_associated_image_names.m: -------------------------------------------------------------------------------- 1 | function [associatedImages] = openslide_get_associated_image_names(... 2 | openslidePointer) 3 | % OPENSLIDE_GET_ASSOCIATED_IMAGE_NAMES Returns a list of associated images 4 | % 5 | % [associatedImages] = openslide_get_associated_image_names(openslidePointer) 6 | % 7 | % INPUT ARGUMENTS 8 | % openslidePointer - Pointer to the openslide object to read associated 9 | % image names from 10 | % 11 | % OPTIONAL INPUT ARGUMENTS 12 | % N/A 13 | % 14 | % OUTPUT 15 | % associatedImages - Cell list with names of associated images 16 | 17 | % Copyright (c) 2016 Daniel Forsberg 18 | % danne.forsberg@outlook.com 19 | % 20 | % This program is free software: you can redistribute it and/or modify 21 | % it under the terms of the GNU General Public License as published by 22 | % the Free Software Foundation, either version 3 of the License, or 23 | % (at your option) any later version. 24 | % 25 | % This program is distributed in the hope that it will be useful, 26 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 27 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 28 | % GNU General Public License for more details. 29 | % 30 | % You should have received a copy of the GNU General Public License 31 | % along with this program. If not, see . 32 | 33 | %% 34 | 35 | % Check if library for openslide is already loaded 36 | if ~libisloaded('openslidelib') 37 | warning('OpenSlide library has not been loaded, attempting to load') 38 | openslide_load_library(); 39 | end 40 | 41 | % Read list of associated image names 42 | [stringArray, ~] = calllib('openslidelib','openslide_get_associated_image_names',... 43 | openslidePointer); 44 | 45 | % Check for errors 46 | [errorMessage] = openslide_get_error(openslidePointer); 47 | 48 | % Terminate if an error was returned 49 | if ~isempty(errorMessage) 50 | error('openslide:openslide_get_associated_image_names',errorMessage) 51 | end 52 | 53 | % Parse the array 54 | ptrInd = stringArray; 55 | ind = 1; 56 | 57 | % Stop at end of list (NULL) 58 | while ischar(ptrInd.value{1}) 59 | associatedImages{ind} = ptrInd.value{1}; 60 | % Increment pointer 61 | ptrInd = ptrInd + 1; 62 | % Increment array index 63 | ind = ind + 1; 64 | end 65 | -------------------------------------------------------------------------------- /openslide_get_best_level_for_downsample.m: -------------------------------------------------------------------------------- 1 | function [level] = openslide_get_best_level_for_downsample(openslidePointer, downsamplingFactor) 2 | % OPENSLIDE_GET_BEST_LEVEL_FOR_DOWNSAMPLE Determine the most suitable level given a downsampling factor 3 | % 4 | % [level] = openslide_get_best_level_for_downsample(openslidePointer, downsamplingFactor) 5 | % 6 | % INPUT ARGUMENTS 7 | % openslidePointer - Pointer to openslide object to read from 8 | % downsamplingFactor - Preferred downsampling factor 9 | % 10 | % OPTIONAL INPUT ARGUMENTS 11 | % N/A 12 | % 13 | % OUTPUT 14 | % level - Most suitable level 15 | 16 | 17 | % Copyright (c) 2016 Daniel Forsberg 18 | % danne.forsberg@outlook.com 19 | % 20 | % This program is free software: you can redistribute it and/or modify 21 | % it under the terms of the GNU General Public License as published by 22 | % the Free Software Foundation, either version 3 of the License, or 23 | % (at your option) any later version. 24 | % 25 | % This program is distributed in the hope that it will be useful, 26 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 27 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 28 | % GNU General Public License for more details. 29 | % 30 | % You should have received a copy of the GNU General Public License 31 | % along with this program. If not, see . 32 | 33 | %% 34 | % Make sure library for openslide is loaded 35 | if ~libisloaded('openslidelib') 36 | warning('OpenSlide library has not been loaded, attempting to load') 37 | openslide_load_library(); 38 | end 39 | 40 | % Call get best level for downsample 41 | [level] = calllib('openslidelib',... 42 | 'openslide_get_best_level_for_downsample',openslidePointer,downsamplingFactor); 43 | 44 | % Check for errors 45 | [errorMessage] = openslide_get_error(openslidePointer); 46 | 47 | % Terminate if an error was returned 48 | if ~isempty(errorMessage) 49 | error('openslide:openslide_get_best_level_for_downsample',errorMessage) 50 | end 51 | -------------------------------------------------------------------------------- /openslide_get_error.m: -------------------------------------------------------------------------------- 1 | function [errorMessage] = openslide_get_error(openslidePointer) 2 | % OPENSLIDE_GET_ERROR Retrieves an error message related to current openslide object 3 | % 4 | % [errorMessage] = openslide_get_error(openslidePointer) 5 | % 6 | % INPUT ARGUMENTS 7 | % openslidePointer - Pointer to openslide object to retrieve error for 8 | % 9 | % OPTIONAL INPUT ARGUMENTS 10 | % N/A 11 | % 12 | % OUTPUT 13 | % errorMessage - Retrieved error message, NULL if none is available 14 | 15 | % Copyright (c) 2016 Daniel Forsberg 16 | % danne.forsberg@outlook.com 17 | % 18 | % This program is free software: you can redistribute it and/or modify 19 | % it under the terms of the GNU General Public License as published by 20 | % the Free Software Foundation, either version 3 of the License, or 21 | % (at your option) any later version. 22 | % 23 | % This program is distributed in the hope that it will be useful, 24 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 25 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 26 | % GNU General Public License for more details. 27 | % 28 | % You should have received a copy of the GNU General Public License 29 | % along with this program. If not, see . 30 | 31 | %% 32 | % Check if openslide library is opened 33 | if ~libisloaded('openslidelib') 34 | error('openslide:openslide_read_region',... 35 | 'Make sure to load the openslide library first\n') 36 | end 37 | 38 | % Retrieve error message associated with current slide 39 | [errorMessage] = calllib('openslidelib','openslide_get_error',openslidePointer); -------------------------------------------------------------------------------- /openslide_get_level0_dimensions.m: -------------------------------------------------------------------------------- 1 | function [width, height] = openslide_get_level0_dimensions(openslidePointer) 2 | % OPENSLIDE_GET_LEVEL0_DIMENSIONS Determine size of level 0 image 3 | % 4 | % [width, height] = openslide_get_level0_dimensions(openslidePointer) 5 | % 6 | % INPUT ARGUMENTS 7 | % openslidePointer - Pointer to openslide object to read from 8 | % 9 | % OPTIONAL INPUT ARGUMENTS 10 | % N/A 11 | % 12 | % OUTPUT 13 | % width - Image level 0 width 14 | % height - Image level 0 Height 15 | 16 | % Copyright (c) 2016 Daniel Forsberg 17 | % danne.forsberg@outlook.com 18 | % 19 | % This program is free software: you can redistribute it and/or modify 20 | % it under the terms of the GNU General Public License as published by 21 | % the Free Software Foundation, either version 3 of the License, or 22 | % (at your option) any later version. 23 | % 24 | % This program is distributed in the hope that it will be useful, 25 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 26 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 27 | % GNU General Public License for more details. 28 | % 29 | % You should have received a copy of the GNU General Public License 30 | % along with this program. If not, see . 31 | 32 | %% 33 | % Make sure library for openslide is loaded 34 | if ~libisloaded('openslidelib') 35 | warning('OpenSlide library has not been loaded, attempting to load') 36 | openslide_load_library(); 37 | end 38 | 39 | % Call get level 0 dimensions 40 | width = 0; 41 | height = 0; 42 | [~, width, height] = calllib('openslidelib',... 43 | 'openslide_get_level0_dimensions',openslidePointer,width,height); 44 | 45 | % Check for errors 46 | [errorMessage] = openslide_get_error(openslidePointer); 47 | 48 | % Terminate if an error was returned 49 | if ~isempty(errorMessage) 50 | error('openslide:openslide_get_level0_dimensions',errorMessage) 51 | end -------------------------------------------------------------------------------- /openslide_get_level_count.m: -------------------------------------------------------------------------------- 1 | function [numberOfLevels] = openslide_get_level_count(openslidePointer) 2 | % OPENSLIDE_GET_LEVEL_COUNT Determine number of available image levels 3 | % 4 | % [numberOfLevels] = openslide_get_level_count(openslidePointer) 5 | % 6 | % INPUT ARGUMENTS 7 | % openslidePointer - Pointer to openslide object to read from 8 | % 9 | % OPTIONAL INPUT ARGUMENTS 10 | % N/A 11 | % 12 | % OUTPUT 13 | % numberOfLevels - Number of levels available 14 | 15 | % Copyright (c) 2016 Daniel Forsberg 16 | % danne.forsberg@outlook.com 17 | % 18 | % This program is free software: you can redistribute it and/or modify 19 | % it under the terms of the GNU General Public License as published by 20 | % the Free Software Foundation, either version 3 of the License, or 21 | % (at your option) any later version. 22 | % 23 | % This program is distributed in the hope that it will be useful, 24 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 25 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 26 | % GNU General Public License for more details. 27 | % 28 | % You should have received a copy of the GNU General Public License 29 | % along with this program. If not, see . 30 | 31 | %% 32 | % Make sure library for openslide is loaded 33 | if ~libisloaded('openslidelib') 34 | warning('OpenSlide library has not been loaded, attempting to load') 35 | openslide_load_library(); 36 | end 37 | 38 | % Call get level count 39 | [numberOfLevels] = calllib('openslidelib','openslide_get_level_count',... 40 | openslidePointer); 41 | 42 | % Check for errors 43 | [errorMessage] = openslide_get_error(openslidePointer); 44 | 45 | % Terminate if an error was returned 46 | if ~isempty(errorMessage) 47 | error('openslide:openslide_get_level_count',errorMessage) 48 | end 49 | -------------------------------------------------------------------------------- /openslide_get_level_dimensions.m: -------------------------------------------------------------------------------- 1 | function [width, height] = openslide_get_level_dimensions(openslidePointer, level) 2 | % OPENSLIDE_GET_LEVEL_DIMENSIONS Determine size of level image 3 | % 4 | % [width, height] = openslide_get_level_dimensions(openslidePointer, level) 5 | % 6 | % INPUT ARGUMENTS 7 | % openslidePointer - Pointer to openslide object to read from 8 | % level - Level to query dimensions for 9 | % 10 | % OPTIONAL INPUT ARGUMENTS 11 | % N/A 12 | % 13 | % OUTPUT 14 | % width - Image level width 15 | % height - Image level Height 16 | 17 | % Copyright (c) 2016 Daniel Forsberg 18 | % danne.forsberg@outlook.com 19 | % 20 | % This program is free software: you can redistribute it and/or modify 21 | % it under the terms of the GNU General Public License as published by 22 | % the Free Software Foundation, either version 3 of the License, or 23 | % (at your option) any later version. 24 | % 25 | % This program is distributed in the hope that it will be useful, 26 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 27 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 28 | % GNU General Public License for more details. 29 | % 30 | % You should have received a copy of the GNU General Public License 31 | % along with this program. If not, see . 32 | 33 | %% 34 | % Make sure library for openslide is loaded 35 | if ~libisloaded('openslidelib') 36 | warning('OpenSlide library has not been loaded, attempting to load') 37 | openslide_load_library(); 38 | end 39 | 40 | % Check that specified level is available 41 | numberOfLevels = calllib('openslidelib','openslide_get_level_count',... 42 | openslidePointer); 43 | if level >= numberOfLevels 44 | error('openslide:openslide_get_level_dimensions',... 45 | 'Specified level is not available in the current whole-slide image\n') 46 | end 47 | 48 | % Call get level dimensions 49 | width = 0; 50 | height = 0; 51 | [~, width, height] = calllib('openslidelib',... 52 | 'openslide_get_level_dimensions',openslidePointer,level,width,height); 53 | 54 | % Check for errors 55 | [errorMessage] = openslide_get_error(openslidePointer); 56 | 57 | % Terminate if an error was returned 58 | if ~isempty(errorMessage) 59 | error('openslide:openslide_get_level_dimensions',errorMessage) 60 | end 61 | -------------------------------------------------------------------------------- /openslide_get_level_downsample.m: -------------------------------------------------------------------------------- 1 | function [downsamplingFactor] = openslide_get_level_downsample(openslidePointer, level) 2 | % OPENSLIDE_GET_LEVEL_DOWNSAMPLE Determine downsampling factor of level image 3 | % 4 | % [downsamplingFactor] = openslide_get_level_downsample(openslidePointer, level) 5 | % 6 | % INPUT ARGUMENTS 7 | % openslidePointer - Pointer to openslide object to read from 8 | % level - Level to query downsampling facotr for 9 | % 10 | % OPTIONAL INPUT ARGUMENTS 11 | % N/A 12 | % 13 | % OUTPUT 14 | % downsamplingFactor - Downsampling factor 15 | 16 | % Copyright (c) 2016 Daniel Forsberg 17 | % danne.forsberg@outlook.com 18 | % 19 | % This program is free software: you can redistribute it and/or modify 20 | % it under the terms of the GNU General Public License as published by 21 | % the Free Software Foundation, either version 3 of the License, or 22 | % (at your option) any later version. 23 | % 24 | % This program is distributed in the hope that it will be useful, 25 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 26 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 27 | % GNU General Public License for more details. 28 | % 29 | % You should have received a copy of the GNU General Public License 30 | % along with this program. If not, see . 31 | 32 | %% 33 | % Make sure library for openslide is loaded 34 | if ~libisloaded('openslidelib') 35 | warning('OpenSlide library has not been loaded, attempting to load') 36 | openslide_load_library(); 37 | end 38 | 39 | % Check that specified level is available 40 | numberOfLevels = calllib('openslidelib','openslide_get_level_count',... 41 | openslidePointer); 42 | if level >= numberOfLevels 43 | error('openslide:openslide_get_level_downsample',... 44 | 'Specified level is not available in the current whole-slide image\n') 45 | end 46 | 47 | % Call get level downsample 48 | [downsamplingFactor] = calllib('openslidelib',... 49 | 'openslide_get_level_downsample',openslidePointer,level); 50 | 51 | % Check for errors 52 | [errorMessage] = openslide_get_error(openslidePointer); 53 | 54 | % Terminate if an error was returned 55 | if ~isempty(errorMessage) 56 | error('openslide:openslide_get_level_downsample',errorMessage) 57 | end 58 | -------------------------------------------------------------------------------- /openslide_get_property_names.m: -------------------------------------------------------------------------------- 1 | function [propertyNames] = ... 2 | openslide_get_property_names(openslidePointer) 3 | % OPENSLIDE_GET_PROPERTY_NAMES Returns a list of all available property names for current openslide objects 4 | % 5 | % [propertyNames] = openslide_get_property_names(openslidePointer) 6 | % 7 | % INPUT ARGUMENTS 8 | % openslidePointer - Pointer to the openslide object to read properties from 9 | % 10 | % OPTIONAL INPUT ARGUMENTS 11 | % N/A 12 | % 13 | % OUTPUT 14 | % propertyNames - Cell list with all avaiable property names 15 | 16 | % Copyright (c) 2016 Daniel Forsberg 17 | % danne.forsberg@outlook.com 18 | % 19 | % This program is free software: you can redistribute it and/or modify 20 | % it under the terms of the GNU General Public License as published by 21 | % the Free Software Foundation, either version 3 of the License, or 22 | % (at your option) any later version. 23 | % 24 | % This program is distributed in the hope that it will be useful, 25 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 26 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 27 | % GNU General Public License for more details. 28 | % 29 | % You should have received a copy of the GNU General Public License 30 | % along with this program. If not, see . 31 | 32 | %% 33 | 34 | % Make sure library for openslide is loaded 35 | if ~libisloaded('openslidelib') 36 | warning('OpenSlide library has not been loaded, attempting to load') 37 | openslide_load_library(); 38 | end 39 | 40 | % Read list of available properties 41 | [stringArray, ~] = calllib('openslidelib','openslide_get_property_names',... 42 | openslidePointer); 43 | 44 | % Check for errors 45 | [errorMessage] = openslide_get_error(openslidePointer); 46 | 47 | % Terminate if an error was returned 48 | if ~isempty(errorMessage) 49 | error('openslide:openslide_get_property_names',errorMessage) 50 | end 51 | 52 | % Parse the array 53 | ptrInd = stringArray; 54 | ind = 1; 55 | 56 | % Stop at end of list (NULL) 57 | while ischar(ptrInd.value{1}) 58 | propertyNames{ind} = ptrInd.value{1}; 59 | % Increment pointer 60 | ptrInd = ptrInd + 1; 61 | % Increment array index 62 | ind = ind + 1; 63 | end -------------------------------------------------------------------------------- /openslide_get_property_value.m: -------------------------------------------------------------------------------- 1 | function [propertyValue] = ... 2 | openslide_get_property_value(openslidePointer, propertyName) 3 | % OPENSLIDE_GET_PROPERTY_VALUE Returns the value of a single property from the openslide object 4 | % 5 | % [propertyValue] = openslide_get_property_value(openslidePointer, propertyName) 6 | % 7 | % INPUT ARGUMENTS 8 | % openslidePointer - Pointer to the openslide object to read properties from 9 | % propertyName - Property to retrieve value for 10 | % 11 | % OPTIONAL INPUT ARGUMENTS 12 | % N/A 13 | % 14 | % OUTPUT 15 | % propertyValue - Value of specified property name. Note that 16 | % this value might have to be type casted 17 | % before it can be used. 18 | 19 | % Copyright (c) 2016 Daniel Forsberg 20 | % danne.forsberg@outlook.com 21 | % 22 | % This program is free software: you can redistribute it and/or modify 23 | % it under the terms of the GNU General Public License as published by 24 | % the Free Software Foundation, either version 3 of the License, or 25 | % (at your option) any later version. 26 | % 27 | % This program is distributed in the hope that it will be useful, 28 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 29 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 30 | % GNU General Public License for more details. 31 | % 32 | % You should have received a copy of the GNU General Public License 33 | % along with this program. If not, see . 34 | 35 | %% 36 | 37 | % Make sure library for openslide is loaded 38 | if ~libisloaded('openslidelib') 39 | warning('OpenSlide library has not been loaded, attempting to load') 40 | openslide_load_library(); 41 | end 42 | 43 | % Check property name 44 | if iscell(propertyName) 45 | warning(['Provided propertyName argument is a cell object. ',... 46 | 'Attempts to use data from the first cell as propertyName argument']); 47 | propertyName = propertyName{1}; 48 | end 49 | if ~ischar(propertyName) 50 | error('openslide:openslide_get_property_value',... 51 | 'Provided propertyName argument is not a valid char array.\n') 52 | end 53 | 54 | % See if provided property name is in the list of available properties 55 | propertyNames = openslide_get_property_names(openslidePointer); 56 | if sum(strcmpi(propertyName,propertyNames)) == 0 57 | error('openslide:openslide_get_property_value',... 58 | 'Provided propertyName argument is not a valid property name for this openslide object.\n') 59 | end 60 | 61 | % Read property value 62 | [propertyValue, ~] = calllib('openslidelib','openslide_get_property_value',... 63 | openslidePointer,propertyName); 64 | 65 | % Check for errors 66 | [errorMessage] = openslide_get_error(openslidePointer); 67 | 68 | % Terminate if an error was returned 69 | if ~isempty(errorMessage) 70 | error('openslide:openslide_get_property_value',errorMessage) 71 | end -------------------------------------------------------------------------------- /openslide_get_slide_properties.m: -------------------------------------------------------------------------------- 1 | function [mppX,mppY,width,height,numberOfLevels,... 2 | downsampleFactors,objectivePower] = ... 3 | openslide_get_slide_properties(openslidePointer) 4 | % OPENSLIDE_GET_SLIDE_PROPERTIES Reads some basics properties from openslide object 5 | % 6 | % [mppX,mppY,width,height,numberOfLevels,... 7 | % downsampleFactors,objectivePower] = ... 8 | % openslide_get_slide_properties(openslidePointer) 9 | % 10 | % INPUT ARGUMENTS 11 | % openslidePointer - Pointer to the openslide object to read properties from 12 | % 13 | % OPTIONAL INPUT ARGUMENTS 14 | % N/A 15 | % 16 | % OUTPUT 17 | % mppX - Resolution, microns per pixel 18 | % mppY - Resolution, microns per pixel 19 | % width - Size in pixels 20 | % height - Size in pixels 21 | % numberOfLevels - Number of levels available 22 | % downsampleFactors - Downsample factors of the levels available 23 | % objectivePower - Magnification factor for level 0 24 | 25 | % Copyright (c) 2016 Daniel Forsberg 26 | % danne.forsberg@outlook.com 27 | % 28 | % This program is free software: you can redistribute it and/or modify 29 | % it under the terms of the GNU General Public License as published by 30 | % the Free Software Foundation, either version 3 of the License, or 31 | % (at your option) any later version. 32 | % 33 | % This program is distributed in the hope that it will be useful, 34 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 35 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 36 | % GNU General Public License for more details. 37 | % 38 | % You should have received a copy of the GNU General Public License 39 | % along with this program. If not, see . 40 | 41 | %% 42 | 43 | % Check if library for openslide is already loaded 44 | if ~libisloaded('openslidelib') 45 | warning('OpenSlide library has not been loaded, attempting to load') 46 | openslide_load_library(); 47 | end 48 | 49 | %% mpp 50 | % Read microns per pixel along x-axis 51 | mppX = str2double(openslide_get_property_value(openslidePointer,'openslide.mpp-x')); 52 | 53 | % Read microns per pixel along y-axis 54 | mppY = str2double(openslide_get_property_value(openslidePointer,'openslide.mpp-y')); 55 | 56 | %% size 57 | % Read size of whole-slide image 58 | [width, height] = openslide_get_level0_dimensions(openslidePointer); 59 | 60 | %% number of zoom levels 61 | % Read number of zoom levels 62 | [numberOfLevels] = openslide_get_level_count(openslidePointer); 63 | 64 | %% downsample factors 65 | % Read downsample factors for each available zoom level 66 | downsampleFactors = zeros(numberOfLevels,1); 67 | for level = 0 : numberOfLevels - 1 68 | downsampleFactors(level+1) = openslide_get_level_downsample(openslidePointer,level); 69 | end 70 | 71 | %% objective power 72 | % Read objective power of level 0 73 | objectivePower = str2double(openslide_get_property_value(... 74 | openslidePointer,'openslide.objective-power')); 75 | -------------------------------------------------------------------------------- /openslide_get_version.m: -------------------------------------------------------------------------------- 1 | function [openslideVersion] = openslide_get_version() 2 | % OPENSLIDE_GET_VERSION Determine version of used openslide library 3 | % 4 | % [openslideVersion] = openslide_get_version() 5 | % 6 | % INPUT ARGUMENTS 7 | % N/a 8 | % 9 | % OPTIONAL INPUT ARGUMENTS 10 | % N/A 11 | % 12 | % OUTPUT 13 | % openslideVersion - Current openslide library version 14 | 15 | 16 | % Copyright (c) 2016 Daniel Forsberg 17 | % danne.forsberg@outlook.com 18 | % 19 | % This program is free software: you can redistribute it and/or modify 20 | % it under the terms of the GNU General Public License as published by 21 | % the Free Software Foundation, either version 3 of the License, or 22 | % (at your option) any later version. 23 | % 24 | % This program is distributed in the hope that it will be useful, 25 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 26 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 27 | % GNU General Public License for more details. 28 | % 29 | % You should have received a copy of the GNU General Public License 30 | % along with this program. If not, see . 31 | 32 | %% 33 | % Make sure library for openslide is loaded 34 | if ~libisloaded('openslidelib') 35 | warning('OpenSlide library has not been loaded, attempting to load') 36 | openslide_load_library(); 37 | end 38 | 39 | % Call get version 40 | [openslideVersion] = calllib('openslidelib','openslide_get_version'); -------------------------------------------------------------------------------- /openslide_load_library.m: -------------------------------------------------------------------------------- 1 | function openslide_load_library() 2 | % OPENSLIDE_LOAD_LIBRARY Loads the openslide library 3 | % 4 | % openslide_load_library() 5 | % 6 | % INPUT ARGUMENTS 7 | % N/A 8 | % 9 | % OPTIONAL INPUT ARGUMENTS 10 | % N/A 11 | % 12 | % OUTPUT 13 | % N/A 14 | 15 | % Copyright (c) 2016 Daniel Forsberg 16 | % danne.forsberg@outlook.com 17 | % 18 | % This program is free software: you can redistribute it and/or modify 19 | % it under the terms of the GNU General Public License as published by 20 | % the Free Software Foundation, either version 3 of the License, or 21 | % (at your option) any later version. 22 | % 23 | % This program is distributed in the hope that it will be useful, 24 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 25 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 26 | % GNU General Public License for more details. 27 | % 28 | % You should have received a copy of the GNU General Public License 29 | % along with this program. If not, see . 30 | 31 | %% 32 | 33 | % Check if library is already loaded 34 | if libisloaded('openslidelib'); 35 | disp('Openslide library is already loaded') 36 | return 37 | end 38 | 39 | % Set name of library, platform dependent 40 | if ismac 41 | libName = 'libopenslide.0.dylib'; 42 | elseif ispc 43 | libName = 'libopenslide-0.dll'; 44 | else 45 | libName = 'libopenslide.so.0'; 46 | end 47 | if isempty(which(libName)) 48 | error('openslide:openslide_load_library',... 49 | [libName,' not available on the MATLAB path\n']) 50 | end 51 | 52 | % Get location of openslide.h 53 | openslideHeaderLocation = which('openslide.h'); 54 | if isempty(openslideHeaderLocation) 55 | error('openslide:openslide_load_library',... 56 | 'openslide.h not available on the MATLAB path\n') 57 | end 58 | if ispc 59 | % Need to add \ to openslideHeaderLocation when writing to file for windows 60 | openslideHeaderLocation = strrep(openslideHeaderLocation,'\','\\'); 61 | end 62 | 63 | % Create openslide-wrapper.h add location of openslide.h 64 | % Wrapper is needed to avoid some issues with MATLAB parsing openslide.h on mac 65 | % and linux systems 66 | [pathStr,~,~] = fileparts(mfilename('fullpath')); 67 | fid = fopen([pathStr,filesep,'openslide-wrapper.h'],'w'); 68 | fprintf(fid,'#ifndef MATLAB_OPENSLIDE_WRAPPER_H\n'); 69 | fprintf(fid,'#define MATLAB_OPENSLIDE_WRAPPER_H\n'); 70 | fprintf(fid,'#define OPENSLIDE_SIMPLIFY_HEADERS\n'); 71 | fprintf(fid,['#include "',openslideHeaderLocation,'"\n']); 72 | fprintf(fid,'#endif\n'); 73 | fclose(fid); 74 | 75 | % Load library 76 | loadlibrary(libName,'openslide-wrapper.h','alias','openslidelib',... 77 | 'addheader','openslide.h'); 78 | 79 | % Check success of load 80 | success = libisloaded('openslidelib'); 81 | 82 | % Notify user of success 83 | if success 84 | disp('Openslide library has been loaded') 85 | else 86 | error('openslide:openslide_load_library',... 87 | 'Failure to load openslide library\n') 88 | end -------------------------------------------------------------------------------- /openslide_open.m: -------------------------------------------------------------------------------- 1 | function openslidePointer = openslide_open(slideName) 2 | % OPENSLIDE_OPEN Opens a whole-slide image for interaction 3 | % 4 | % openslidePointer = openslide_open(slideName) 5 | % 6 | % INPUT ARGUMENTS 7 | % slideName - Full file name of whole-slide image to interact with, i.e. 8 | % including path and file extension 9 | % 10 | % OPTIONAL INPUT ARGUMENTS 11 | % N/A 12 | % 13 | % OUTPUT 14 | % openslidePointer - Pointer to whole-slide image to interact with, to be used 15 | % as input argument in other openslide funcions 16 | 17 | % Copyright (c) 2016 Daniel Forsberg 18 | % danne.forsberg@outlook.com 19 | % 20 | % This program is free software: you can redistribute it and/or modify 21 | % it under the terms of the GNU General Public License as published by 22 | % the Free Software Foundation, either version 3 of the License, or 23 | % (at your option) any later version. 24 | % 25 | % This program is distributed in the hope that it will be useful, 26 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 27 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 28 | % GNU General Public License for more details. 29 | % 30 | % You should have received a copy of the GNU General Public License 31 | % along with this program. If not, see . 32 | 33 | %% 34 | 35 | % Check if library for openslide is already loaded 36 | if ~libisloaded('openslidelib') 37 | warning('OpenSlide library has not been loaded, attempting to load') 38 | openslide_load_library(); 39 | end 40 | 41 | % Get pointer to whole-slide image 42 | openslidePointer = calllib('openslidelib','openslide_open',slideName); 43 | 44 | % Check validity of returned pointer 45 | if isempty(openslidePointer) 46 | errorMessage = ['Unable to open the specified slide: ',slideName,'\n']; 47 | error('openslide:openslide_open',errorMessage) 48 | end 49 | 50 | % Check for errors 51 | [errorMessage] = openslide_get_error(openslidePointer); 52 | 53 | % Terminate if an error was returned 54 | if ~isempty(errorMessage) 55 | error('openslide:openslide_open',errorMessage) 56 | end -------------------------------------------------------------------------------- /openslide_read_associated_image.m: -------------------------------------------------------------------------------- 1 | function [ARGB] = openslide_read_associated_image(openslidePointer,imageName) 2 | % OPENSLIDE_READ_ASSOCIATED_IMAGE Reads an associated image 3 | % 4 | % [ARGB] = openslide_read_associated_image(openslidePointer,imageName) 5 | % 6 | % INPUT ARGUMENTS 7 | % openslidePointer - Pointer to openslide object to read from 8 | % imageName - Associated image name to read 9 | % 10 | % OPTIONAL INPUT ARGUMENTS 11 | % N/A 12 | % 13 | % OUTPUT 14 | % ARGB - Read ARGB image 15 | 16 | % Copyright (c) 2016 Daniel Forsberg 17 | % danne.forsberg@outlook.com 18 | % 19 | % This program is free software: you can redistribute it and/or modify 20 | % it under the terms of the GNU General Public License as published by 21 | % the Free Software Foundation, either version 3 of the License, or 22 | % (at your option) any later version. 23 | % 24 | % This program is distributed in the hope that it will be useful, 25 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 26 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 27 | % GNU General Public License for more details. 28 | % 29 | % You should have received a copy of the GNU General Public License 30 | % along with this program. If not, see . 31 | 32 | %% 33 | 34 | % Check if library for openslide is already loaded 35 | if ~libisloaded('openslidelib') 36 | warning('OpenSlide library has not been loaded, attempting to load') 37 | openslide_load_library(); 38 | end 39 | 40 | % Check image name 41 | if iscell(imageName) 42 | warning(['Provided imageName argument is a cell object. ',... 43 | 'Attempts to use data from the first cell as imageName argument']); 44 | imageName = imageName{1}; 45 | end 46 | if ~ischar(imageName) 47 | error('openslide:openslide_read_associated_image',... 48 | 'Provided imageName argument is not a valid char array.\n') 49 | end 50 | 51 | % See if provided image name is in the list of available associated images 52 | imageNames = openslide_get_associated_image_names(openslidePointer); 53 | if sum(strcmpi(imageName,imageNames)) == 0 54 | error('openslide:openslide_read_associated_image',... 55 | 'Provided imageName argument is not a valid associated image name for this openslide object.\n') 56 | end 57 | 58 | % Read size of associated image 59 | [width, height] = openslide_get_associated_image_dimensions(openslidePointer,imageName); 60 | 61 | % Read image 62 | data = uint32(zeros(width*height,1)); 63 | region = libpointer('uint32Ptr',data); 64 | [~, ~, region] = calllib('openslidelib',... 65 | 'openslide_read_associated_image',openslidePointer,imageName,region); 66 | 67 | % Check for errors 68 | [errorMessage] = openslide_get_error(openslidePointer); 69 | 70 | % Terminate if an error was returned 71 | if ~isempty(errorMessage) 72 | error('openslide:openslide_read_associated_image',errorMessage) 73 | end 74 | 75 | % Cast and reformat read data 76 | RGBA = typecast(region,'uint8'); 77 | ARGB = uint8(zeros(width,height,4)); 78 | ARGB(:,:,1) = reshape(RGBA(4:4:end),width,height); 79 | ARGB(:,:,2) = reshape(RGBA(3:4:end),width,height); 80 | ARGB(:,:,3) = reshape(RGBA(2:4:end),width,height); 81 | ARGB(:,:,4) = reshape(RGBA(1:4:end),width,height); 82 | 83 | % Permute image to make sure it is according to standard MATLAB format 84 | ARGB = permute(ARGB,[2 1 3]); -------------------------------------------------------------------------------- /openslide_read_region.m: -------------------------------------------------------------------------------- 1 | function [ARGB] = openslide_read_region(openslidePointer,xPos,yPos,width,height,varargin) 2 | % OPENSLIDE_READ_REGION Reads a region according to specified coordinates and with specified size 3 | % 4 | % [ARGB] = openslide_read_region(openslidePointer,xPos,yPos,width,height) 5 | % 6 | % INPUT ARGUMENTS 7 | % openslidePointer - Pointer to openslide object to read from 8 | % xPos - Pixel position, with first position as 0 and in 9 | % the specified level reference frame 10 | % yPos - Pixel position, with first position as 0 and in 11 | % the specified level reference frame 12 | % width - Widht of region to read in pixels 13 | % height - Height of region to read in pixels 14 | % 15 | % OPTIONAL INPUT ARGUMENTS 16 | % 'level' - Image level to read, 0 refers to original 17 | % level 18 | % 19 | % OUTPUT 20 | % ARGB - Read ARGB image 21 | 22 | % Copyright (c) 2016 Daniel Forsberg 23 | % danne.forsberg@outlook.com 24 | % 25 | % This program is free software: you can redistribute it and/or modify 26 | % it under the terms of the GNU General Public License as published by 27 | % the Free Software Foundation, either version 3 of the License, or 28 | % (at your option) any later version. 29 | % 30 | % This program is distributed in the hope that it will be useful, 31 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 32 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 33 | % GNU General Public License for more details. 34 | % 35 | % You should have received a copy of the GNU General Public License 36 | % along with this program. If not, see . 37 | 38 | %% Default parameters 39 | level = 0; 40 | 41 | % Overwrites default parameter 42 | for k=1:2:length(varargin) 43 | eval([varargin{k},'=varargin{',int2str(k+1),'};']); 44 | end 45 | 46 | %% 47 | % Make sure library for openslide is loaded 48 | if ~libisloaded('openslidelib') 49 | warning('OpenSlide library has not been loaded, attempting to load') 50 | openslide_load_library(); 51 | end 52 | 53 | % Check that specified level is available 54 | numberOfLevels = openslide_get_level_count(openslidePointer); 55 | if level >= numberOfLevels 56 | error('openslide:openslide_read_region',... 57 | 'Specified level is not available in the current whole-slide image\n') 58 | end 59 | 60 | % Check that it is possible to read the specified region 61 | [widthLevel, heightLevel] = openslide_get_level_dimensions(openslidePointer,level); 62 | 63 | if xPos + width - 1 >= widthLevel 64 | error('openslide:openslide_read_region',... 65 | 'Specified x-pos and width yields an invalid end position\n') 66 | end 67 | if xPos < 0 68 | error('openslide:openslide_read_region',... 69 | 'Specified x-pos yields an invalid start position\n') 70 | end 71 | if yPos + height - 1 >= heightLevel 72 | error('openslide:openslide_read_region',... 73 | 'Specified y-pos and height yields an invalid end position\n') 74 | end 75 | if yPos < 0 76 | error('openslide:openslide_read_region',... 77 | 'Specified y-pos yields an invalid start position\n') 78 | end 79 | 80 | % Adjust position according to downsampling factor of desired level 81 | downsamplingFactor = openslide_get_level_downsample(openslidePointer,level); 82 | xPos = xPos * downsamplingFactor; 83 | yPos = yPos * downsamplingFactor; 84 | 85 | % Read region 86 | data = uint32(zeros(width*height,1)); 87 | region = libpointer('uint32Ptr',data); 88 | [~, region] = calllib('openslidelib','openslide_read_region',openslidePointer,region,int64(xPos),int64(yPos),int32(level),int64(width),int64(height)); 89 | 90 | % Check for errors 91 | [errorMessage] = openslide_get_error(openslidePointer); 92 | 93 | % Terminate if an error was returned 94 | if ~isempty(errorMessage) 95 | error('openslide:openslide_read_region',... 96 | errorMessage) 97 | end 98 | 99 | % Cast and reformat read data 100 | RGBA = typecast(region,'uint8'); 101 | ARGB = uint8(zeros(width,height,4)); 102 | ARGB(:,:,1) = reshape(RGBA(4:4:end),width,height); 103 | ARGB(:,:,2) = reshape(RGBA(3:4:end),width,height); 104 | ARGB(:,:,3) = reshape(RGBA(2:4:end),width,height); 105 | ARGB(:,:,4) = reshape(RGBA(1:4:end),width,height); 106 | 107 | % Permute image to make sure it is according to standard MATLAB format 108 | ARGB = permute(ARGB,[2 1 3]); -------------------------------------------------------------------------------- /openslide_unload_library.m: -------------------------------------------------------------------------------- 1 | function openslide_unload_library() 2 | % OPENSLIDE_UNLOAD_LIBRARY Unloads the open slide library 3 | % 4 | % openslide_unload_library() 5 | % 6 | % INPUT ARGUMENTS 7 | % N/A 8 | % 9 | % OPTIONAL INPUT ARGUMENTS 10 | % N/A 11 | % 12 | % OUTPUT 13 | % N/A 14 | 15 | % Copyright (c) 2016 Daniel Forsberg 16 | % danne.forsberg@outlook.com 17 | % 18 | % This program is free software: you can redistribute it and/or modify 19 | % it under the terms of the GNU General Public License as published by 20 | % the Free Software Foundation, either version 3 of the License, or 21 | % (at your option) any later version. 22 | % 23 | % This program is distributed in the hope that it will be useful, 24 | % but WITHOUT ANY WARRANTY; without even the implied warranty of 25 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 26 | % GNU General Public License for more details. 27 | % 28 | % You should have received a copy of the GNU General Public License 29 | % along with this program. If not, see . 30 | 31 | %% 32 | 33 | % Check if library is already loaded 34 | if ~libisloaded('openslidelib'); 35 | disp('Openslide library is not loaded') 36 | return 37 | end 38 | 39 | % Unload library 40 | unloadlibrary('openslidelib') 41 | 42 | % Check success of unload 43 | if libisloaded('openslidelib'); 44 | error('openslide:openslide_unload_library',... 45 | 'Failure to unload openslide library\n') 46 | else 47 | disp('Openslide library has been unloaded') 48 | end -------------------------------------------------------------------------------- /test_data/CMU-1-Small-Region.svs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fordanic/openslide-matlab/240c223fac8db81e96084a189ad6c8327b2b26e3/test_data/CMU-1-Small-Region.svs -------------------------------------------------------------------------------- /test_data/README.txt: -------------------------------------------------------------------------------- 1 | This test data has been downloaded from http://openslide.cs.cmu.edu/download/openslide-testdata/. 2 | 3 | More test data from various vendors can be found on this site. --------------------------------------------------------------------------------