Changing the S3cimg/pixset class to the magick-image
Applying the morphological operations using image_morphology()
The data structures
I am currently using two S3 classes from imager. These are cimg and pixset. Both are layers over arrays of numeric or logical values. The advantage here is that the two classes can be transformed from one to the other and math operations can be directly applied to them.
magick-image is an externalptr and I think would relace cimg(I am not sure what to do about the pixset, or whether an equivalent would be needed at all). I am having a hard time getting data in and out of magick-image. This certainly needs more work on my part. I wish there were more information in the magick's vignette on how to manipulate the image objects.
These changes will obviously affect all the functions in colocr as which objects they dispatch on, the way the manipulations are done and the return value.
Applying morphological operations
The main functions I use from imager are grow, shrink, fill and clean. In the development version of magick there is image_morphology() which can these operations and more https://github.com/ropensci/onboarding/issues/243#issuecomment-425673974. These changes would mainly affect roi_select().
Other
Two other functions I use from imager and still don't see how to replace them are
label to label each pixel for the region they belong to
highlight to highlight the selected area on the image
Summary
As it stands,
colocris functional but switching the main dependency fromimagertomagickhas been proposed https://github.com/ropensci/onboarding/issues/243#issuecomment-425357850. The two main changes would include:cimg/pixsetclass to themagick-imageimage_morphology()The data structures
I am currently using two S3 classes from
imager. These arecimgandpixset. Both are layers over arrays ofnumericorlogicalvalues. The advantage here is that the two classes can be transformed from one to the other and math operations can be directly applied to them.magick-imageis anexternalptrand I think would relacecimg(I am not sure what to do about thepixset, or whether an equivalent would be needed at all). I am having a hard time getting data in and out ofmagick-image. This certainly needs more work on my part. I wish there were more information in themagick's vignette on how to manipulate the image objects. These changes will obviously affect all the functions incolocras which objects they dispatch on, the way the manipulations are done and the return value.Applying morphological operations
The main functions I use from
imageraregrow,shrink,fillandclean. In the development version ofmagickthere isimage_morphology()which can these operations and more https://github.com/ropensci/onboarding/issues/243#issuecomment-425673974. These changes would mainly affectroi_select().Other
Two other functions I use from
imagerand still don't see how to replace them arelabelto label each pixel for the region they belong tohighlightto highlight the selected area on the image