ants.read_transform fails for syn warp file

[rueberger]

antspy 0.2.7

There are a couple wacky things going on with ants.read_transform. For one, the dimension kwarg is ignored, as dimension is reassigned on line 293. Should make another issue for that.

Here's the bug:

tx = ants.read_transform('warp.nii.gz', dimension=3)
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-34-c277abb66a46> in <module>
----> 1 tx = ants.read_transform('warp.nii.gz', dimension=3)

~/.local/lib/python3.6/site-packages/ants/core/ants_transform_io.py in read_transform(filename, dimension, precision)
    291
    292     libfn1 = utils.get_lib_fn("getTransformDimensionFromFile")
--> 293     dimension = libfn1(filename)
    294
    295     libfn2 = utils.get_lib_fn("getTransformNameFromFile")

RuntimeError: /build101/ANTsPy/itksource/Modules/IO/TransformBase/src/itkTransformFileReader.cxx:128:
itk::ERROR: itk::ERROR: TransformFileReaderTemplate(0x154c5520): Could not create Transform IO object for reading file warp.nii.gz
  Tried to create one of the following:
    HDF5TransformIOTemplate
    HDF5TransformIOTemplate
    MatlabTransformIOTemplate
    MatlabTransformIOTemplate
    TxtTransformIOTemplate
    TxtTransformIOTemplate
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

I thought this might just be an issue with getTransformDimensionFromFile, so I tried running

read_transform = utils.get_lib_fn('readTransform%s%i' % (utils.short_ptype(precision), dimension))
tx = read_transform('warp.nii.gz', dimension, precision)

Same error.

Also tried removing the suffix, using the absolute path, using the absolute path and removing the suffix, none of that worked.

ants.apply_transform works fine with the same file. Using ants.read_transform because I need to apply the transform to a point.

To Reproduce Run ants.registration, rename syn forward warp to warp.nii.gz (probably unnecessary), try to load transform

[stnava]

the intended approach is:

import ants
reg=ants.registration( ants.image_read( ants.get_data("r16" ) ),  ants.image_read( ants.get_data("r16" ) ), 'SyN')
warp=ants.image_read( reg['fwdtransforms'][0] )  # image not transform
warptx = ants.transform_from_displacement_field( warp )

now you have a transformation object. 2 ways to apply to points:

help(ants.apply_transforms_to_points)  # on disk transforms

and for tx objects

help( ants.apply_ants_transform_to_point )

[rueberger]

That's very helpful, thanks.

Is there any reason we can't dispatch to transform_from_displacement_field from read_transform?

[stnava]

the objects saved in the reg['fwdtransforms'][0] is not explicitly coded as a transformation .... so we'd have to guess that it represents an actual deformation field ......

[rueberger]

True, but if I'm trying to read a .nii as a transform I presumably already know it's own. What do you think about dispatching and printing a warning? Or at least a more descriptive error

[stnava]

we would welcome any contributions that improve clarity and usability.