AttributeError: module 'multiresolutionimageinterface' has no attribute 'MultiResolutionImageReader'

[CapitalZe]

Running Ubuntu 16.04 via VMware on a Macbook Pro. Tried in both Terminal and Jupyter NB.

I believe all env variables and directories are in order.

when I run:

import multiresolutionimageinterface as mir
reader = mir.MultiResolutionImageReader()
mr_image = reader.open('/media/XXX/book/camelyon17/centre_0/patient_000_node_0.tif')
level = 2
ds = mr_image.getLevelDownsample(level)
image_patch = mr_image.getUCharPatch(int(568 * ds), int(732 * ds), 300, 200, level)

I get the following output:

ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-3-2e258b46d239> in <module>
----> 1 import multiresolutionimageinterface as mir
      2 reader = mir.MultiResolutionImageReader()
      3 mr_image = reader.open('/media/XXX/book/camelyon17/centre_0/patient_000_node_0.tif')
      4 level = 2
      5 ds = mr_image.getLevelDownsample(level)

ModuleNotFoundError: No module named 'multiresolutionimageinterface'

I've checked and the module is within the ASAP-1.9 folder. Within ASAP-1.9 ls reads out:

(MIDI) XXX@ubuntu:~/ASAP-1.9$ ls
annotation                  cmakemodules   License.txt
ASAP                        config         Manual.docx
ASAPConfig.cmake.in         Copyright.txt  multiresolutionimageinterface
ASAPConfigVersion.cmake.in  core           Readme.md
buildtools                  executables    runASAP.py
CMakeLists.txt              imgproc        WorklistInterface

I've tried numerous approaches, namely around env vars.

Does anyone have a clue why this is happening?

I'm attempting to process the CAMELYON17 dataset and cannot overcome this impasse.

Thanks in advance.

[GeertLitjens]

Two things: Python needs to find the multiresolutionimage.py file, so you have to make sure the PYTHONPATH environmental variable has a reference to the ASAP bin dir. Second, the kernel needs to know where to look for multiresolutionimage.dll. For this, you need (on Linux) to set the LD_LIBRARY_PATH environmental variable to include the ASAP bin folder

[CapitalZe]

Thank you for the reply. It worked and got me beyond that point.

Now, however, I am faced with this:

AttributeError                            Traceback (most recent call last)
<ipython-input-2-2e258b46d239> in <module>
      3 mr_image = reader.open('/media/XXX/book/camelyon17/centre_0/patient_000_node_0.tif')
      4 level = 2
----> 5 ds = mr_image.getLevelDownsample(level)
      6 image_patch = mr_image.getUCharPatch(int(568 * ds), int(732 * ds), 300, 200, level)

AttributeError: 'NoneType' object has no attribute 'getLevelDownsample'

I decided to go through the entire installation again in a separate environment, and this time when I run sudo cmake . I receive the following:

CMake Error at CMakeLists.txt:44 (find_package):
  By not providing "FindOpenJPEG.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "OpenJPEG",
  but CMake did not find one.

  Could not find a package configuration file provided by "OpenJPEG" with any
  of the following names:

   OpenJPEGConfig.cmake
    openjpeg-config.cmake

  Add the installation prefix of "OpenJPEG" to CMAKE_PREFIX_PATH or set
  "OpenJPEG_DIR" to a directory containing one of the above files.  If
  "OpenJPEG" provides a separate development package or SDK, be sure it has
  been installed.

-- Configuring incomplete, errors occurred!
See also "/home/XXX/ASAP-1.9/CMakeFiles/CMakeOutput.log".

I've reinstalled OpenJPEG and sufficiently followed the variable instructions in the output:

(MIDI) XXX@ubuntu:~/ASAP-1.9$ echo $CMAKE_PREFIX_PATH
/home/XXX/openjpeg/

As well as:

(MIDI) XXX@ubuntu:~/ASAP-1.9$ echo $OpenJPEG_DIR
/home/XXX/openjpeg/build

Constructing FindOpenJPEG.cmake and placing it in /home/XXX/ASAP-1.9/cmakemodules just lead to more errors.

Any ideas?

[CapitalZe]

This was resolved. The problem was, for most of the dependencies it was required to install the 'dev' version or 'tools' version.

This was probably made clear somewhere and I overlooked it.

Issue can be closed.

[eternaldolphin]

AttributeError: 'NoneType' object has no attribute 'getLevelDownsample' So I need install which one ?ASAP-1.9-Linux-Ubuntu1804.deb?