Use itk::ReadImage and itk::WriteImage

[thewtex]

Use the new functions, itk::ReadImage and itk::WriteImage, available in ITK 5.2 for simplicity over itk::ImageFileReader and itk::ImageFileWriter throughout the examples. See #225
for an illustration of the changes required.

[josetascon]

Hi @thewtex,
I would like to contribute. I have a question. Is this desired for all the examples?. If that is the case, should I make individual commits for every example?

For instance, If I check how many example files uses itkImageFileReader there are 212, while itkImageFileWriter 210. It may be convenient to commit per module (Core, Numerics, ...)

For now, I will make a single commit with the example at src/Core/Transform/ScaleAnImage/Code.cxx

[dzenanz]

commit per module

This sounds good. Or change all in one commit. There would be too many commits with one commit per example. #302 is just what we are looking for. This should be done for great majority of the examples. If reader or writer are being used to demonstrate streaming or in some other unusual way, they should be left alone.

[josetascon]

Ok. New commit #303 with changes of examples at src/Core.
I have some notes. Some of comments are just to mention the unchanged, another file changed, some examples without test, and finally some examples that import header files but they are unnecessary.

Unchaged
* ImportPixelBufferIntoAnImage unchanged because demonstrate filter connection
* MiniPipeline unchanged because demonstrate itk pipeline
* StoreNonPixelDataInImage unchanged because reader calls reader->GetMetaDataDictionary()
* MakePartOfImageTransparent unchanged because sets extra writer parameters
* TryCatchException unchanged because use the reader to catch an exception

Changed
* ConvertArrayToImage change output format to mhd

Missing compiled binary (not added in cmake) and without test files
* MultipleInputsOfDifferentType
* MultipleOutputsOfDifferentType
* FilterImageUsingMultipleThreads
* IterateRegionWithNeighborhood
* MakeOutOfBoundsPixelsReturnConstValue
* GetOrSetMemberVariableOfITKClass
* InPlaceFilterOfImage

Not working as intended, all test passed but the output is a black image
* ContourSpatialObject
* CreateALineSpatialObject

Unused header
Import file reader and writer headers but are not used:
* FilterImage
* GetOrSetMemberVariableOfITKClass
* MultipleInputsOfSameType
* FilterImageWithoutCopying

Import file writer but unused:
* IterateImageStartingAtSeed

Import file reader but unused:
* ScaleAnImage
* CropImageBySpecifyingRegion
* IterateOverSpecificRegion
* RandomSelectPixelFromRegionWithoutReplacee
* IterateLineThroughImageWithoutWriteAccess
* MakeOutOfBoundsPixelsReturnConstValue
* RandomSelectOfPixelsFromRegion

Question, although importing the itkImageFileReader.h or itkImageFileWriter.h in those files do not create conflicts should I delete them?

[dzenanz]

If the includes are unused, they should be deleted. I guess this was created by starting a new example by copying an old one, which had some unnecessary includes.

[dzenanz]

I think it is desirable to update the non-working examples along with the working ones. Unless reading or writing are the problematic part of the example.

[dzenanz]

Perhaps the broken/unindexed examples should be updated in a separate commit?

[josetascon]

able to update the non-working examples along with the working ones. Unless reading or writing are the problematic part of the example.

I am currently doing this.

[josetascon]

Perhaps the broken/unindexed examples should be updated in a separate commit?

Agree, I am just reporting those for now.

[josetascon]

If the includes are unused, they should be deleted. I guess this was created by starting a new example by copying an old one, which had some unnecessary includes.

Got it, I will include them in #303

[thewtex]

@josetascon thank you for your contributions! 🙏

[josetascon]

@josetascon thank you for your contributions! pray

I am happy to help :)

[josetascon]

New commit #305.
The notes.

Unchaged:
src/Filtering/ImageGrid/ChangeImageOriginSpacingOrDirection/Code.cxx unchanged because use image reader to demonstrate update information

Missing compiled binary (cmake) and without test files:
src/Filtering/ImageStatistics/ComputePCAShapeFromSample/Code.cxx
src/Filtering/Convolution/NormalizedCorrelation/Code.cxx
src/Filtering/Convolution/ColorNormalizedCorrelation/Code.cxx
src/Filtering/ImageFeature/ApplyAFilterToASpecifiedRegionOfAnImage/Code.cxx
src/Filtering/ImageFeature/SharpenImage/Code.cxx
src/Filtering/ImageIntensity/SubtractTwoImages/Code.cxx
src/Filtering/ImageGrid/Stack2DImagesInto3DImage/Code.cxx
src/Filtering/ImageGradient/ComputeGradientMagnitude/Code.cxx
src/Filtering/ImageGradient/ComputeAndDisplayGradient/Code.cxx
src/Filtering/ImageGradient/ComputeGradientMagnitudeRecursiveGaussian/Code.cxx
src/Filtering/ImageGradient/ApplyGradientRecursiveGaussian/Code.cxx
src/Filtering/ImageGradient/ApplyGradientRecursiveGaussianWithVectorInput/Code.cxx
src/Filtering/ImageGradient/ImplementationOfSnakes/Code.cxx

[josetascon]

New commit #306.
The notes:

Missing compiled binary (cmake) and without test files:
src/Segmentation/KLMRegionGrowing/BasicRegionGrowing/Code.cxx
src/Segmentation/ConnectedComponents/LabelConnectComponentsInBinaryImage/Code.cxx
src/Segmentation/RegionGrowing/ConnectedComponentsInImage/Code.cxx
src/Segmentation/Classifiers/KMeansClusterOfPixelsInImage/Code.cxx
src/Segmentation/Classifiers/KMeansClustering/Code.cxx
src/Segmentation/Classifiers/ClusterPixelsInGrayscaleImage/Code.cxx
src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Code.cxx
src/Numerics/Statistics/DistributionOfPixelsUsingGMM/Code.cxx
src/Numerics/Statistics/ComputeHistogramOfMaskedRegion/Code.cxx
src/Registration/Common/WatchRegistration/Code.cxx
src/Registration/Common/Perform2DTranslationRegistrationWithMeanSquares/Code.cxx

[josetascon]

Final commit #307.

The notes:
Unchaged files:
src/IO/ImageBase/ReadAnImage/Code.cxx unchanged because this example show the reader filter
src/IO/ImageBase/WriteAnImage/Code.cxx unchanged because this example show the writer filter
src/IO/ImageBase/RegisterIOFactories/Code.cxx unchanged because use the reader to get different metadata
src/IO/ImageBase/ReadUnknownImageType/Code.cxx unchanged because creates a function to read the image
src/IO/TIFF/WriteATIFFImage/Code.cxx unchaged because use the writer filter to SetImageIO
src/Video/BridgeOpenCV/ConvertAnITKGrayScaleImageToCVMat/Code.cxx unchanged because catch exception when reading

Missing compiled binary (cmake) and without test files:
All examples in src/Developer/ require a cmake file.