MultiResolutionImageReader.open(file_name) will return None

[zengyh1900]

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)

[GeertLitjens]

Could you try putting in the full path to the file instead of a relative one?

[zengyh1900]

@GeertLitjens I once tried that but failed. The data is a tif file from Camelyon16. Can ASAP open the files defined by in Camelyon16 or not ?

MultiResolutionImage* MultiResolutionImageFactory::openImage(const std::string& fileName) {
  MultiResolutionImageFactory::registerExternalFileFormats();
  std::string extension = core::extractFileExtension(fileName);
  for (std::map<std::string, MultiResolutionImageFactory*>::const_iterator it = registry().begin(); it != registry().end(); ++it) {
    std::vector<std::string> factoryExtensions;
    core::split(it->first, factoryExtensions, ";");
    if (std::find(factoryExtensions.begin(), factoryExtensions.end(), extension) != factoryExtensions.end()) {
      MultiResolutionImage* img = it->second->readImage(fileName);
      if (img) {

#ifdef HAS_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT
        if ((img->getNumberOfLevels() > 1 || dynamic_cast<VSIImage*>(img) != NULL) || (img->getNumberOfLevels() == 1 && img->getLevelDimensions(0)[0] < 4096)) {
#else
        if ((img->getNumberOfLevels() > 1) || (img->getNumberOfLevels() == 1 && img->getLevelDimensions(0)[0] < 4096)) {
#endif
          return img;
        }
        else {
          delete img;
        }
      }
    }
  }
  return NULL;
}

I guess ASAP cannot deal with the data from Camelyon because of the format. But why it could work in Windows? I have no idea.

[GeertLitjens]

Yes, it can open those files. Which file specifically are you trying to open? My guess is that you have an old version of OpenSlide. See this ticket and others for solutions:

https://github.com/GeertLitjens/ASAP/issues/33

[zengyh1900]

@GeertLitjens Thanks a lot! I have installed the latest openslide and everything goes well now.

Openslide Installation Instruction: http://openslide.org/download/

[tomi2077]

Yes, it can open those files. Which file specifically are you trying to open? My guess is that you have an old version of OpenSlide. See this ticket and others for solutions:

33

Hi, Please I want to read large very biomedical images. I can currently open and view them via Openslide but I want to use ASAP to prepare them. Do you know how ASAP is downloaded?

Thanks, Tom