IO in python module

simon.rit · March 17, 2020, 8:57pm

I have started to work on the wrapping of IO in RTK:

There is something which is not clear to me. When working with C++, I can register IO factories so that this is quite transparent for the user, the adequate ImageIO is automatically detected:

github.com

SimonRit/RTK/blob/master/src/rtkIOFactories.cxx#L59-L68


rtk::HndImageIOFactory::RegisterOneFactory();
rtk::HncImageIOFactory::RegisterOneFactory();
rtk::XimImageIOFactory::RegisterOneFactory();
rtk::HisImageIOFactory::RegisterOneFactory();
rtk::ImagXImageIOFactory::RegisterOneFactory();
rtk::DCMImagXImageIOFactory::RegisterOneFactory();
rtk::EdfImageIOFactory::RegisterOneFactory();
rtk::XRadImageIOFactory::RegisterOneFactory();
rtk::OraImageIOFactory::RegisterOneFactory();
itk::GDCMImageIOFactory::RegisterOneFactory();

In an example that I found, it seems that one has to specify manually the IO using the SetImageIO method of the image reader. Is there a way to avoid this and to register factories in a module? My PR attempted to do this with the rtk::HisImageIO but that does not work so far…

dzenanz · March 17, 2020, 9:28pm

Specifying FACTORY_NAMES like this should do it:

github.com

InsightSoftwareConsortium/ITK/blob/99b11184c89a15ec50daf1086d720c63fd33d2b0/Modules/IO/BMP/itk-module.cmake#L11


set(DOCUMENTATION "This module contains ImageIO classes for reading the
Microsoft Bitmap File Format (BMP).")


itk_module(ITKIOBMP
  ENABLE_SHARED
  DEPENDS
    ITKIOImageBase
  TEST_DEPENDS
    ITKTestKernel
  FACTORY_NAMES
    ImageIO::BMP
  DESCRIPTION
    "${DOCUMENTATION}"
)

simon.rit · March 17, 2020, 9:57pm

Thanks. That’s what I tried for one factory in my PR but that did not seem to work, I haven’t found what’s wrong yet. Is it supposed to work even if a separate wheel package is created for the module? If yes, why is this not used in ITKIOScanco example?

dzenanz · March 18, 2020, 1:39am

FACTORY_NAMES might only work at compile time? @matt.mccormick can probably explain better.

simon.rit · March 18, 2020, 1:27pm

I confirm that it works if I compile all the wrappings. I guess it comes down to this generated file

github.com

InsightSoftwareConsortium/ITK/blob/master/CMake/itkImageIOFactoryRegisterManager.h.in

/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/

#ifndef itkImageIOFactoryRegisterManager_h
#define itkImageIOFactoryRegisterManager_h

This file has been truncated. show original

which cannot contain the factories added by a module. I see no obvious solution for this…

matt.mccormick · March 18, 2020, 5:47pm

Yes, the itk::ImageIOFactoryRegisterManager is configured at ITK build time, so externally built remote modules will not be in the list of registered factories.

I will work on a patch to register remote module IO factories at runtime.