I successfully build the solution but when I use the binary (ASAP_d.exe) to open a tiff file, the software hints "invalid file type" in the bar below. I have successfully opened this file with the distribution provided by your repository so this tiff is a valid file.
What could be the possible cause of it? Thank you for your attention.

Note that I have changed several projects' library option from Dynamic(dll) to Static(lib) in Visual Studio Properties Panel, otherwise I cannot build it successfully( VS hints unable to find *****.obj files)

I got this error when trying to build the latest Github version. I'm using Ubuntu 14.04 LTS 64 bit.

[ 3%] Building CXX object core/CMakeFiles/core.dir/PathologyEnums.cpp.o
/home/weiliu/packages/ASAP/core/PathologyEnums.cpp:12:3: error: in C++98 ‘pathology::ColorLookupTables’ must be initialized by constructor, not by ‘{...}’
};
^
/home/weiliu/packages/ASAP/core/PathologyEnums.cpp:12:3: warning: extended initializer lists only available with -std=c++11 or -std=gnu++11 [enabled by default]

invalid file type

I use win10 64bit.I download the released ASAP ,ASAP-1.7-win64.exe and install it.I also download Test Data CMU-1.tiff form http://openslide.org/formats/generic-tiff/ .Then I use ASAP to open the CMU-1.tiff but software hints "invalid file type" in the bar below.
I was troubled by this problem for a few days.Can you tell me how to solve it?
Thanks a lot!!

Hi, GeertLitjens, thanks for your last help.  I'v succeeded in introducing support for a new scanning device in ASAP, primarily by modifying openslide library.  It works well in WIN7 system
But when I install it to WIN10 system, it reports errors that need  MSVCR120D.dll and so on.  So I've to compile ASAP in release version.  And I meet a problem in release version, unable to analysis libopenslide-0.dll by dumpbin.exe, erro info below: 
"LINK :  fatal error LNK1328: missing string table "
And when I user original openslide source to compile, the problem remain appears. What's wrong with it? 

》Detail error information is below:

11> -- fixup_bundle
11> -- app='D:/Application/ASAP_new/bin/ASAP.exe'
11> -- libs='D:/Application/ASAP_new/bin/libEGL.dll;D:/Application/ASAP_new/bin/Qt5OpenGL.dll;D:/Application/ASAP_new/bin/plugins/filters/NucleiDetectionFilterPlugin.dll;D:/Application/ASAP_new/bin/formats/openslidefileformat.dll'
11> -- dirs='D:/Applib/Qt5.6.2/5.6/msvc2013_64/lib/cmake/Qt5/../../../bin;D:/Applib/opencv-3.1.0/build/x64/vc12/lib/../bin;D:/Applib/ThirdParty/openslide/include/openslide/../../bin;D:/Applib/ThirdParty/pugixml/include/../bin;D:/Applib/ThirdParty/unittest/include/UnitTest++/../bin;D:/Applib/boost_1_64_0/lib64-msvc-12.0'
11> -- ignoreItems=''
11> -- fixup_bundle: preparing...
11> -- [DBG] gp_cmd=D:/Application/Microsoft Visual Studio 12.0/VC/bin/x86_amd64/dumpbin.exe; gp_cmd_args=/dependents; target=D:/Applib/ThirdParty/openslide/bin/libopenslide-0.dll; gp_cmd_maybe_filter=
11> CMake Error at D:/Application/Cmake/share/cmake-3.9/Modules/GetPrerequisites.cmake:838 (message):
11> D:/Application/Microsoft Visual Studio 12.0/VC/bin/x86_amd64/dumpbin.exe
11> failed: 1328
11>
11>
11>
11> Microsoft (R) COFF/PE Dumper Version 12.00.31101.0
11>
11> Copyright (C) Microsoft Corporation. All rights reserved.
11>
11>
11>
11>
11>
11> Dump of file D:/Applib/ThirdParty/openslide/bin/libopenslide-0.dll
11>
11>
11>
11> File Type: DLL
11>
11>
11>
11> Image has the following dependencies:
11>
11>
11>
11> libcairo-2.dll
11> libgdk_pixbuf-2.0-0.dll
11> libgio-2.0-0.dll
11> libglib-2.0-0.dll
11> libgobject-2.0-0.dll
11> libjpeg-62.dll
11> libopenjp2.dll
11> libpng16-16.dll
11> libsqlite3-0.dll
11> libtiff-5.dll
11> libxml2-2.dll
11> zlib1.dll
11> KERNEL32.dll
11> msvcrt.dll
11>
11>LINK : fatal error LNK1328: missing string table
11>
11> Call Stack (most recent call first):
11> D:/Application/Cmake/share/cmake-3.9/Modules/GetPrerequisites.cmake:969 (get_prerequisites)
11> D:/Application/Cmake/share/cmake-3.9/Modules/BundleUtilities.cmake:585 (get_prerequisites)
11> D:/Application/Cmake/share/cmake-3.9/Modules/BundleUtilities.cmake:903 (get_bundle_keys)
11> buildtools/cmake_install.cmake:83 (fixup_bundle)
11> cmake_install.cmake:81 (include)
11>
11>
11>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(132,5): error MSB3073: The command "setlocal
11>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(132,5): error MSB3073: D:\Application\Cmake\bin\cmake.exe -DBUILD_TYPE=Release -P cmake_install.cmake
11>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(132,5): error MSB3073: if %errorlevel% neq 0 goto :cmEnd
11>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(132,5): error MSB3073: :cmEnd
11>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(132,5): error MSB3073: endlocal & call :cmErrorLevel %errorlevel% & goto :cmDone
11>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(132,5): error MSB3073: :cmErrorLevel
11>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(132,5): error MSB3073: exit /b %1
11>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(132,5): error MSB3073: :cmDone
11>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(132,5): error MSB3073: if %errorlevel% neq 0 goto :VCEnd
11>C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets(132,5): error MSB3073: :VCEnd" exited with code 1.

I would like to ask if it is possible to extend ASAP functionalities with plug-in based on python. I'm interested in creating some functionality to manage automatic slide cropping.
I was wondering if i need to work with c++ or may i use python.

Thank you,
Francesco Ponzio

When I turn on "BUILD_DIAG_PATHOLOGY_EXECUTABL", I got the following error:

[ 20%] Built target core
[ 50%] Built target multiresolutionimageinterface
[ 76%] Built target annotation
[ 82%] Built target _multiresolutionimageinterface
Linking CXX executable MultiResImageConverter
[ 85%] Built target MultiResImageConverter
Scanning dependencies of target WSIConnectedComponents
[ 88%] Building CXX object executables/WSIConnectedComponents/CMakeFiles/WSIConnectedComponents.dir/WSIConnectedComponents.cpp.o
Linking CXX executable WSIConnectedComponents
/usr/bin/ld: cannot find -lwholeslidefilters
collect2: error: ld returned 1 exit status
make[2]: *** [executables/WSIConnectedComponents/WSIConnectedComponents] Error 1
make[1]: *** [executables/WSIConnectedComponents/CMakeFiles/WSIConnectedComponents.dir/all] Error 2

make: *** [all] Error 2

I use Ubuntu 14.04 LTS 64 bit.

Hello! I compiled all 3rd party libraries. Then successfully added them to CMake paths, configuration was done, and then project was generated for msvc2013, but when I try to compile, then I get single link error from multiresolutionimageinterface module:

error LNK2001: unresolved external symbol jpc_decode JPEG2000Codec.obj

As I understand this problem related to jasper library. Jasper 2.0.10 was successfully built.
Is it сompatibility problems? And should I compile older version of Jasper?

Is the nuclei detection function python supported?

I'll appreciate it if you could answer my question :)

Hello GeertLitjens and community,

I would love to use ASAP, but trying to install via the .deb file on Ubuntu 14.04 fails because several dependencies (e.g. libboost-filesystem1.58) are not available on 14.04 (requires 16.04).

If ASAP's functionality doesn't depend on the version of the uninstallable packages, would you mind compiling against the lower versions? A list of the uninstallable ones is below.

Thanks!

Dennis

The following packages have unmet dependencies:
asap : Depends: libboost-filesystem1.58.0 but it is not installable
Depends: libboost-program-options1.58.0 but it is not installable
Depends: libboost-regex1.58.0 but it is not installable
Depends: libboost-system1.58.0 but it is not installable
Depends: libboost-thread1.58.0 but it is not installable
Depends: libdcmtk5 but it is not installable
Depends: libpugixml1v5 (>= 1.7) but it is not installable
Depends: libpython3.5 (>= 3.5.0~b1) but it is not installable

    ------------------------

    Depends: libqt5core5a (>= 5.5.0) but 5.2.1+dfsg-1ubuntu14.3 is installed
    Depends: libqt5gui5 (>= 5.3.0) but 5.2.1+dfsg-1ubuntu14.3 is installed or
             libqt5gui5-gles (>= 5.3.0) but it is not installable
    Depends: libqt5widgets5 (>= 5.3.0) but 5.2.1+dfsg-1ubuntu14.3 is installed
    Depends: libstdc++6 (>= 5.2) but 4.8.4-2ubuntu1~14.04.3 is installed

The minimal size of the sidebar should be smaller and its docking position should be also configurable as left or right. The latter option would make the use of ASAP on WACOM tablets more comfortable for right handed individuals.

Hi,

I tried to open regular TIFFs using ASAP 1.7.2, but ASAP crashed immediately after I chose the image file on both Windows and Ubuntu (installed the provided .exe and .deb files). I attached the image file which I tried to open (01.zip). Does ASAP support the uploaded image file format or not?

01.zip

Regardless of the zoom level the control points of the annotations are always small rectangles and are quite inconvenient to grab in order to modify the annotation. It would be nice if a (4-8 times) larger circle appeared around the closest control point of the annotation to the cursor for grabbing.

When I use ASAP to view Hamamatsu ndpi WSI files, I cannot load annotation files in the folder. ASAP used a file extension name filter, it only accept .xml file and .ndpa file, but I cannot see my .xml file when I pressed Load button. However, when I pressed Save button, I can see xml file in the folder.

Anybody can help me? Thank you.

Version: 1.7.3
Platform: Ubuntu 16.04
install by deb file

Hello! I compiled all 3rd party libraries. Then successfully added them to CMake paths, configuration was done, and then project was generated for msvc2013, but there is warnings like a

CMake Warning (dev) at core/CMakeLists.txt:6 (ADD_LIBRARY):
  Policy CMP0028 is not set: Double colon in target name means ALIAS or
  IMPORTED target.  Run "cmake --help-policy CMP0028" for policy details.
  Use the cmake_policy command to set the policy and suppress this warning.

  Target "core" links to target "Boost::disable_autolinking" but the target
  was not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
This warning is for project developers.  Use -Wno-dev to suppress it.

And other warnings related to links to boost. If I try to compile project, then I getting:
error LNK1104: cannot open file 'Boost::disable_autolinking.lib' from core module

So I should disable auto linking. I never worked with boost before.
I can't find official documentation related to auto-linking in boost, except little mentions about it, but I found several solutions on stackoverflow and other sites.

Solutions say that for disabling auto-linking I should define macros BOOST_ALL_NO_LIB, but I can't understand where is I should define it. I tried to define it in preprocessor defines of core project, uncomment this define in boost/config/user.hpp, also tried to recompile boost with following options:
b2 -j 4 --toolset=msvc-12.0 addreess-model=64 --build-type=complete define=BOOST_ALL_NO_LIB stage --stage-dir=lib/x64

But no one solution is helped. Also I noticed, that Jamroot file, which configuring boost build, has following lines:

# Disable auto-linking for all targets here, primarily because it caused
      # troubles with V2.
      <define>BOOST_ALL_NO_LIB=1

It looks like auto-linking disabled by default.
Boost version: 1.63.0
CMake version: 3.3.1

If an annotation is moved to a group its color is changed to the color of the group but not until the default color of the group is changed. Also even though the color of the annotation lines between the control points have the color of the group the original (yellow) color of the annotations are shown in the Annotations sidebar. Once an annotation is moved to a group, its color shouldn't be shown on the side bar, just the color of its group.

It would be nice if ASAP was able to show/hide individual annotation groups. The visibility state should be also part of the XML file. There should be a checkbox in front of the annotation group color icon in the Annotations list.

I am trying to install ASAP on ubuntu 16.04 and I get the following error following cmake command

casey@casey-K401LB:~/Downloads/ASAP-1.6$ cmake .
-- Boost version: 1.58.0
-- Found the following Boost libraries:
-- date_time
-- filesystem
-- program_options
-- regex
-- system
-- thread
-- chrono
-- atomic
CMake Error at /usr/share/cmake-3.5/Modules/FindPackageHandleStandardArgs.cmake:148 (message):
Could NOT find OPENSLIDE (missing: OPENSLIDE_LIBRARY OPENSLIDE_INCLUDE_DIR)
Call Stack (most recent call first):
/usr/share/cmake-3.5/Modules/FindPackageHandleStandardArgs.cmake:388 (_FPHSA_FAILURE_MESSAGE)
cmakemodules/FindOPENSLIDE.cmake:14 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
CMakeLists.txt:58 (FIND_PACKAGE)

-- Configuring incomplete, errors occurred!
See also "/home/casey/Downloads/ASAP-1.6/CMakeFiles/CMakeOutput.log".
See also "/home/casey/Downloads/ASAP-1.6/CMakeFiles/CMakeError.log".

However, I have installed openslide using apt-get:
casey@casey-K401LB:~/Downloads/ASAP-1.6$ sudo apt-get install openslide-tools
Reading package lists... Done
Building dependency tree
Reading state information... Done
openslide-tools is already the newest version (3.4.0-1build1).

Any help would be greatly appreciated.

ASAP loads XML with the same file baseneme as of the image file automatically. It would be nice if ASAP offered to load XMLs with the same file name beginning as the name of the loaded image. For example: if the loaded image is my_image.mrxs and there are two XML files in the same directory my_image_aaa.xml and my_image_bbb.xml then ASAP should offer a list of the two mentioned XMLs for loading.

Hi,
I read your paper about stain specific standardization (https://www.ncbi.nlm.nih.gov/labs/articles/26353368/)
, and I found that the code is implemented in this ASAP.

Would you tell me how to try your code??
Thanks a lot!

Hi,

I'm trying to compile ASAP using CMkae and VS 2013 on Windows. I used the files provided in the third-party.7z on the Release page, but I am now getting some similar errors when building in VS2013. Below shows one of those errors:

error LNK2019: unresolved external symbol jpeg8_std_error referenced in function "private: char * __cdecl VSIImage::decodeTile(int,int,int)const " (?decodeTile@VSIImage@@AEBAPEADHHH@Z) C:\ASAP\ASAP-1.7-build\io\multiresolutionimageinterface\VSIImage.obj multiresolutionimageinterface

Does this error result from incorrect linking with some .lib files? Any suggestion for me to try? Thank you.

the error is: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped)

I keep on setting levels to 2, 3...up to 7, and level7 works fine, but only a few nuclei detected.

My system is Ubuntu 16.04, I searched on the Internet, but I still can't figure it out what is wrong.

And I'm still wondering what the method that you use to detect nuclei is? Are there some papers introducing it? Are there any mathematical instructions to read about? I'll appreciate it if you could provide me with some useful materials related!

I tried to load a point annotation xml file which is around ~50MB but ASAP 1.7 and 1.6 become not responding or just freeze for more than an hour.

my laptop spec is i7-6700hq,12gb ram,512gb ssd , 950m 4gb gpu ,windows 10 64bit

i have the coordinate.xml file if you want to check it out for me.

https://drive.google.com/file/d/0B15axUcMKU8eSXlMSlhOdEp0U2s/view?usp=sharing

Hi, I'm running into a problem building on Kubuntu 16.04:

io/multiresolutionimageinterface/VSIImage.cpp:14:44: fatal error: dcmtk/dcmjpeg/libijg8/jpeglib8.h: No such file or directory
 #include "dcmtk/dcmjpeg/libijg8/jpeglib8.h"

I installed the libdcmtk-dev package (xenial 3.6.1~20150924-5), but /usr/include/dcmtk/dcmjpeg doesn't have a libijg8 dir, just a bunch of header files, and I can't find a jpeglib8.h file anywhere. Any recommendations? Thanks!

I've set this two variable to point same directory which contains "ibUnitTest++.a"
command "cmake" shows one warning
WARNING: Target "patholTestRunner" requests linking to directory "/usr/local/lib/". Targets may link only to libraries. CMake is dropping the item.
and command "make" return error, and it seems that it failed to find unitest++
so my setting should be wrong, can you help me?

the install instruction is too hard for newer. the most hard part is install the dependence. however I installed it also has error. How can I find a detailed instruction about the install

Hello,
I met some errors about compiling ASAS with VS2015
Error LNK1181 cannot open input file '..\Release\ASAP.lib'
Error LNK1181 cannot open input file '....\imgproc\wholeslide\Release\wholeslidefilters.lib'
Could someone tell me how to solve these errors?
Thanks

I've successfully built it with cmake under Ubuntu 14.04 LTS, but could not find any binary executubles. I used the default settings of cmake, which means all 4 flags are turned off:

BUILD_DIAG_PATHOLOGY_EXECUTABL OFF
BUILD_DIAG_PATHOLOGY_IMAGEPROC OFF
BUILD_DIAG_PATHOLOGY_TESTS OFF
BUILD_DIAG_PATHOLOGY_WORKSTATI OFF

Do I need to turn on first flag to build the viewer? I did but got an error, but that will be another issue that I will open.

I spent some time to figure out how to set this variable in cmake. I found I can set it to:

DCMTKJPEG_INCLUDE_DIR /home/weiliu/packages/dcmtk-3.6.1_20160216/build/include

And that works. This is because many files in ASAP include something like "dcmtk/dcmjpeg/libijg8/jpeglib8.h", which assume I should set the above variable so the full path of the .h file is valid.

However, now the name of DCMTKJPEG_INCLUDE_DIR is confusing, because this variable should be the path of all include files of DCMTK, not just DCMJPEG.

Also, I need to copy the libijg8 folder from dcmtk source tree to the installed folder, because the 'make install' command does not do that for me. Not sure if this is a ASAP issue or a dcmtk issue.

Hi,

I'm compiling ASAP on Ubuntu 14.04. May I ask when specifying the third party lib locations in CMake, should the variables point to *.a or *.so files? Thank you very much.

It would be very useful to have to following information displayed on the status line or maybe somewhere at the sidebars:

1. Coordinates of the cursor in millimeters.
2. Coordinates of the cursor in pixels.
3. The current displayed level.
4. Value under the cursor (RGB, unsigned char or float)

And the same for the loaded cancer detection data.

I'm trying to compile ASAP in Win10,VS2013.
I am confused with the link offered (http://libjpeg.sourceforge.net/).
I can't process the files that it link to. There are just some cpp files and I do not know how to set JPEG_LIBRARY and JPEG_INCLUDE_DIR ?

There are the output messages:
CMake Error at C:/Program Files/CMake/share/cmake-3.8/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find JPEG (missing: JPEG_LIBRARY JPEG_INCLUDE_DIR)
Call Stack (most recent call first):
C:/Program Files/CMake/share/cmake-3.8/Modules/FindPackageHandleStandardArgs.cmake:377 (_FPHSA_FAILURE_MESSAGE)
C:/Program Files/CMake/share/cmake-3.8/Modules/FindJPEG.cmake:30 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
CMakeLists.txt:48 (FIND_PACKAGE)

Thanks very much if anyone can help!

I am using patchToMat as follows:

Patch<uchar> p = input->getPatch<uchar>(...);
Mat m = patchToMat(p);

I was getting compilation errors:

error C2440: 'const_cast' : cannot convert from 'const unsigned char *' to 'double *'

I made the following change locally and it is fixed:

 -      T* data = const_cast<double*>(patch.getPointer());
 +      T* data = const_cast<T*>(patch.getPointer());

I haven't tested it yet since I'm using 3 channels anyway. Was there a reason for the double cast?

could you tell me something about the rule of generating a mask file.Because i have no idea of giving a label to my annotation groups,when i save the annotation to a mask file by selecting the save file types as tif. If I don't describe my question clearly, please inform me,thank you!

installed all dependencies. this is output of cmake:

-- Boost version: 1.63.0
-- Found the following Boost libraries:
--   date_time
--   filesystem
--   program_options
--   regex
--   system
--   thread
--   chrono
--   atomic
-- Found DCMTKJPEG: /usr/local/Cellar/dcmtk/3.6.1-20170228/include  
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Configuring done
CMake Warning (dev):
  Policy CMP0042 is not set: MACOSX_RPATH is enabled by default.  Run "cmake
  --help-policy CMP0042" for policy details.  Use the cmake_policy command to
  set the policy and suppress this warning.

  MACOSX_RPATH is not specified for the following targets:

   annotation
   core
   multiresolutionimageinterface
   openslidefileformat

This warning is for project developers.  Use -Wno-dev to suppress it.

-- Generating done
-- Build files have been written to: /Users/ehosseiniasl/Downloads/ASAP

finally, make failed,

~/ASAP/io/multiresolutionimageinterface/VSIImage.cpp:14:10: fatal error: 'dcmtk/dcmjpeg/libijg8/jpeglib8.h' file not found

I finished the CMake steps and get the VS solution, I open DIAGPathology.sln and hit "Build Solution" and successfully build the project, then try to run the program, only to find an error message box which says "Unable to start program E:\code\ASAP-VS2013\Debug\ALL_BUILD".
I have already set ethe ALL_BUILD project as StartUp Project.
In my ALL_BUILD vs project, there is only one CMakeList.txt and no cpp files. It seems that such a project cannot produce a executable program.

What should I do to run an ASAP compiled by my self?

Setting the right Window and Level values for visualizing heat maps is not straightforward. It would be nice to have some kind of default settings for ranges: [0, 255] uint8 and [0.0, 1.0] float32. A more clear setting method or at least a formula description in a tool tip for any arbitrary interval would be also very useful.

Hi,

I have been using ASAP for a while, I was able to compile it from source when their was no deb file and now i just install with the deb file and I am currently using ASAP 1.7 (but I had this problem with 1.4) on a ubuntu 16.04 machine.

I have a problem and the source of it is unknown to me. I downloaded from a Phillips scanner, slides that I wish to visualize with ASAP, some files work just fine, but however for many files the image just disappears when I zoom in.
Here are some visual examples:

I have loaded my file:

and then I just scroll once with my mouse and the tissue is then replaced by black like this:

Wierdly ( ? ), if I analyze the image with some c++ library and rewrite it with vips, I have no issues during the analysis and during the visualization with ASAP. This final point ensures me that it is not a problem with the file but points to maybe some library issues or some compatibility issues.

Any help would be nice as it is super annoying to switch back to windows just to check my slides... (I have had no problem with ASAP under windows tho, for any image)

Thanks,

Peter

I try

import multiresolutionimageinterface as mir
reader = mir.MultiResolutionImageReader()
mr_image = reader.open('camelyon17/centre_0/patient_000_node_0.tif')

there is no error message but when I print the mr_image, it will be None.

It is ASAP-1.7-Linux-python27.deb on Ubuntu16.04 (python2.7)

There are duplicate fragments on the border of the image opened, but after I zoom it, the repetition disappears. I generate that.tif image by convert .jpeg using Imagemagick.

Hi, Geert. I'm sorry to bother you again.
For some reason, I cleaned my VS2013 project generated by CMAKE, and executed CMAKE again, but something is wrong with the new VS2013 project. I got warnings and errors like below. I googled some answers but they does not work well. Could you help me? Thanks a lot.

》boost config for CMAKE
Boost_DEBUG=ON
Boost_NO_BOOST_CMAKE=ON
Boost_USE_STATIC_LIBS=ON
BOOST_ROOT=D:/Applib/boost_1_64_0
BOOST_INCLUDE_DIR=D:/Applib/boost_1_64_0

》Boost library is found OK by CMAKE, detailed log while configuring cmake:
Boost version: 1.64.0
Found the following Boost libraries:
date_time
filesystem
program_options
regex
system
thread
chrono
atomic

》detailed warnings
1>MultiResImageConverter.obj : warning LNK4217: locally defined symbol ??0validation_error@program_options@boost@@QEAA@W4kind_t@012@AEBV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@1H@Z (public: __cdecl boost::program_options::validation_error::validation_error(enum boost::program_options::validation_error::kind_t,class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > const &,class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > const &,int)) imported in function "class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > const & __cdecl boost::program_options::validators::get_single_string<char>(class std::vector<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> >,class std::allocator<class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > > > const &,bool)" (??$get_single_string@D@validators@program_options@boost@@YAAEBV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@AEBV?$vector@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@V?$allocator@V?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@@2@@4@_N@Z)

》detailed errors
1>MultiResImageConverter.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) public: __cdecl boost::program_options::invalid_option_value::invalid_option_value(class boost::program_options::invalid_option_value const &)" (_imp??0invalid_option_value@program_options@boost@@qeaa@AEBV012@@z) referenced in function "struct boost::exception_detail::error_info_injector __cdecl boost::enable_error_info(class boost::program_options::invalid_option_value const &)" (??$enable_error_info@Vinvalid_option_value@program_options@boost@@@boost@@ya?AU?$error_info_injector@Vinvalid_option_value@program_options@boost@@@exception_detail@0@AEBVinvalid_option_value@program_options@0@@z)

When the python wrapper is imported and used before matplotlib is imported, every plot call to matplotlib crashes the python process. My guess is that the python wrapper somehow prevents matplotlib loading the correct Qt backend. It is a minor issue as loading all modules first does not trigger the problem. Nonetheless, in interactive sessions users will expect that the order of imports does not matter.

Debugging gives the following exception:

Traceback (most recent call last):
  File "C:\Program Files (x86)\JetBrains\PyCharm Community Edition 2017.1\helpers\pydev\pydevd.py", line 1578, in <module>
    globals = debugger.run(setup['file'], None, None, is_module)
  File "C:\Program Files (x86)\JetBrains\PyCharm Community Edition 2017.1\helpers\pydev\pydevd.py", line 1015, in run
    pydev_imports.execfile(file, globals, locals)  # execute the script
  File "D:/Projects/prostate-epithelium-segmentation/main.py", line 70, in <module>
    import matplotlib.pyplot as plt
  File "C:\Users\wouterbulten\Anaconda2\envs\cadcourse\lib\site-packages\matplotlib\pyplot.py", line 115, in <module>
    _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
  File "C:\Users\wouterbulten\Anaconda2\envs\cadcourse\lib\site-packages\matplotlib\backends\__init__.py", line 32, in pylab_setup
    globals(),locals(),[backend_name],0)
  File "C:\Users\wouterbulten\Anaconda2\envs\cadcourse\lib\site-packages\matplotlib\backends\backend_qt5agg.py", line 16, in <module>
    from .backend_qt5 import QtCore
  File "C:\Users\wouterbulten\Anaconda2\envs\cadcourse\lib\site-packages\matplotlib\backends\backend_qt5.py", line 26, in <module>
    import matplotlib.backends.qt_editor.figureoptions as figureoptions
  File "C:\Users\wouterbulten\Anaconda2\envs\cadcourse\lib\site-packages\matplotlib\backends\qt_editor\figureoptions.py", line 20, in <module>
    import matplotlib.backends.qt_editor.formlayout as formlayout
  File "C:\Users\wouterbulten\Anaconda2\envs\cadcourse\lib\site-packages\matplotlib\backends\qt_editor\formlayout.py", line 56, in <module>
    from matplotlib.backends.qt_compat import QtGui, QtWidgets, QtCore
  File "C:\Users\wouterbulten\Anaconda2\envs\cadcourse\lib\site-packages\matplotlib\backends\qt_compat.py", line 137, in <module>
    from PyQt4 import QtCore, QtGui
ImportError: No module named PyQt4

As Qt5 is installed there is no need for matplotlib to load Qt4.

Code example that tiggers error:

import multiresolutionimageinterface as mrimage

reader = mrimage.MultiResolutionImageReader()
img = reader.open( ... some path ..)

import matplotlib.pyplot as plt
plt.plot(range(10))

Code that works:

import matplotlib.pyplot as plt
import multiresolutionimageinterface as mrimage
reader = mrimage.MultiResolutionImageReader()
img = reader.open( ... some path ..)

plt.plot(range(10))

Setting the backend explictely in a interactive session (i.e. %matplotlib qt5) also solves the problem.

I'm curious if you have worked with cloud-hosted datasets yet and/or if ASAP could be run on Google VMs accessing images in Google Cloud Storage.

The ISB-CGC (www.isb-cgc.org) is an NCI funded effort to make data generated from NCI research programs available in the cloud. Our initial focus was on genomic and molecular data, but now we have two large sets of images available -- a set of tissue slide images (SVS format) and a set of radiology images (DICOM format). We have "cloud credits" to give researchers "free" compute in the cloud for exploratory purposes. We are also interested in knowing about machine-learning applications that make use of these types of images.

For more information, have a look at this page in our documentation:
http://isb-cancer-genomics-cloud.readthedocs.io/en/latest/sections/TCGA-images.html

I'd be very interested in hearing from you -- please also feel free to distribute this information to anyone who might be interested. Thanks in advance.

-- Sheila

Hi,

I am using ASAP 1.7.2 on Ubuntu, but having the display problem as shown in the following screen shot. It is happening on every .tif image on Ubuntu.

Thanks,
scarletvv

When many loose dot annotations (approx. >200) are made and you would like to modify one of the annotations (move or delete) ASAP 1.7.3 crashes.

All functions on the toolbar should be mapped to F1-F12 function keys. This would make ASAP comfortable to use on WACOM tablets.

I've been following the process for compiling ASAP using CMake on Ubuntu (defining each LIBRARY and INCLUDE variable as they come up after each Configure iteration), and I think I've managed to do that correctly. However, I am stuck with the following error:

CMake Error at core/CMakeLists.txt:12 (target_compile_features):
target_compile_features no known features for CXX compiler

"GNU"

version 4.8.4.

Is a different version of g++ required? Is it something to do with c++11? I'm currently using CMake 3.2.2, if that might be relevant to the issue.

When building asap on WINDOWS, some errors like below are encountered：
I searched for "_ITERATOR_DEBUG_LEVEL" error, and rebuild boost as debug, but error is still existing. I need help about this. Thanks

》build info
system: WIN7
compile tools : visual studio 2013 community
boost version: 1.64.0
boost build command: b2.exe --prefix=C:\Boost --build-type=complete --build-dir=output address-model=64 runtime-link=static variant=debug stage
ASAP source version：1.7.2

》error info:
2>libboost_filesystem-vc120-mt-s-1_64.lib(path_traits.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_filesystem-vc120-mt-s-1_64.lib(path_traits.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>libboost_filesystem-vc120-mt-s-1_64.lib(path.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_filesystem-vc120-mt-s-1_64.lib(path.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>libboost_filesystem-vc120-mt-s-1_64.lib(operations.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_filesystem-vc120-mt-s-1_64.lib(operations.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>libboost_filesystem-vc120-mt-s-1_64.lib(codecvt_error_category.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_filesystem-vc120-mt-s-1_64.lib(codecvt_error_category.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>libboost_filesystem-vc120-mt-s-1_64.lib(windows_file_codecvt.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_filesystem-vc120-mt-s-1_64.lib(windows_file_codecvt.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>libboost_system-vc120-mt-s-1_64.lib(error_code.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_system-vc120-mt-s-1_64.lib(error_code.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(instances.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(instances.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(regex.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(regex.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(regex_traits_defaults.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(regex_traits_defaults.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(static_mutex.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(static_mutex.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(w32_regex_traits.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(w32_regex_traits.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(regex_raw_buffer.obj) : error LNK2038: mismatch detected for '_ITERATOR_DEBUG_LEVEL': value '0' doesn't match value '2' in filetools.obj
2>libboost_regex-vc120-mt-s-1_64.lib(regex_raw_buffer.obj) : error LNK2038: mismatch detected for 'RuntimeLibrary': value 'MT_StaticRelease' doesn't match value 'MDd_DynamicDebug' in filetools.obj
2>msvcprtd.lib(MSVCP120D.dll) : error LNK2005: "public: __cdecl std::locale::id::id(unsigned __int64)" (??0id@locale@std@@qeaa@_K@Z) already defined in libboost_filesystem-vc120-mt-s-1_64.lib(path_traits.obj)
2>msvcprtd.lib(MSVCP120D.dll) : error LNK2005: "public: __cdecl std::locale::id::operator unsigned __int64(void)" (??Bid@locale@std@@QEAA_KXZ) already defined in libboost_filesystem-vc120-mt-s-1_64.lib(path.obj)

The documentation says :

The easiest way to install the software is to download the binary installer or .DEB package from the release page.

But, where is this release page. Can you please provide a link to that. @GeertLitjens

The text on the "Add new group" button on the Annotations sidebar should be simply "New Group".