Merge pull request #634 from ANTsX/image-from-pointer

ENH: initialize ANTsImage with pointer only

ants/core/ants_image.py

@@ -44,47 +44,74 @@
 
 class ANTsImage(object):
 
-    def __init__(self, pixeltype='float', dimension=3, components=1, pointer=None, is_rgb=False):
+    def __init__(self, pointer):
         """
-        Initialize an ANTsImage
+        Initialize an ANTsImage.
+        
+        Creating an ANTsImage requires a pointer to an underlying ITK image that
+        is stored via a nanobind class wrapping a AntsImage struct.
 
         Arguments
         ---------
-        pixeltype : string
-            ITK pixeltype of image
-
-        dimension : integer
-            number of image dimension. Does NOT include components dimension
-
-        components : integer
-            number of pixel components in the image
-
-        pointer : py::capsule (optional)
-            pybind11 capsule holding the pointer to the underlying ITK image object
+        pointer : nb::class
+            nanobind class wrapping the struct holding the pointer to the underlying ITK image object
 
         """
-        ## Attributes which cant change without creating a new ANTsImage object
         self.pointer = pointer
-        self.pixeltype = pixeltype
-        self.dimension = dimension
-        self.components = components
-        self.has_components = self.components > 1
-        self.dtype = _itk_to_npy_map[self.pixeltype]
-        self.is_rgb = is_rgb
-
-        self._pixelclass = 'vector' if self.has_components else 'scalar'
-        self._shortpclass = 'V' if self._pixelclass == 'vector' else ''
-        if is_rgb:
-            self._pixelclass = 'rgb'
-            self._shortpclass = 'RGB'
-
-        self._libsuffix = '%s%s%i' % (self._shortpclass, utils.short_ptype(self.pixeltype), self.dimension)
-
-        self.shape = tuple(utils.get_lib_fn('getShape')(self.pointer))
-        self.physical_shape = tuple([round(sh*sp,3) for sh,sp in zip(self.shape, self.spacing)])
-
         self._array = None
 
+    @property
+    def _libsuffix(self):
+        return str(type(self.pointer)).split('AntsImage')[-1].split("'")[0]
+
+    @property
+    def shape(self):
+        return tuple(utils.get_lib_fn('getShape')(self.pointer))
+
+    @property
+    def physical_shape(self):
+        return tuple([round(sh*sp,3) for sh,sp in zip(self.shape, self.spacing)])
+
+    @property
+    def is_rgb(self):
+        return 'RGB' in self._libsuffix
+
+    @property
+    def has_components(self):
+        suffix = self._libsuffix
+        return suffix.startswith('V') or suffix.startswith('RGB')
+
+    @property
+    def components(self):
+        if not self.has_components:
+            return 1
+
+        libfn = utils.get_lib_fn('getComponents')
+        return libfn(self.pointer)
+
+    @property
+    def pixeltype(self):
+        ptype = self._libsuffix[:-1]
+        if self.has_components:
+            if self.is_rgb:
+                ptype = ptype[3:]
+            else:
+                ptype = ptype[1:]
+
+        ptype_map = {'UC': 'unsigned char',
+                     'UI': 'unsigned int',
+                     'F': 'float',
+                     'D': 'double'}
+        return ptype_map[ptype]
+
+    @property
+    def dtype(self):
+        return _itk_to_npy_map[self.pixeltype]
+
+    @property
+    def dimension(self):
+        return int(self._libsuffix[-1])
+
     @property
     def spacing(self):
         """
@@ -284,11 +311,7 @@ def clone(self, pixeltype=None):
             fn_suffix = '%s%i' % (p2_short,ndim)
             libfn = utils.get_lib_fn('antsImageClone%s'%fn_suffix)
             pointer_cloned = libfn(self.pointer)
-            return ANTsImage(pixeltype=pixeltype,
-                            dimension=self.dimension,
-                            components=self.components,
-                            is_rgb=self.is_rgb,
-                            pointer=pointer_cloned)
+            return iio2.from_pointer(pointer_cloned)
 
     # pythonic alias for `clone` is `copy`
     copy = clone

ants/core/ants_image_io.py

@@ -3,6 +3,7 @@
 """
 
 __all__ = [
+    'from_pointer',
     "image_header_info",
     "image_clone",
     "image_read",
@@ -66,6 +67,9 @@
             _image_read_dict[itype][p][d] = "imageRead%s%s%i" % (ita, pa, d)
 
 
+def from_pointer(pointer):
+    return iio.ANTsImage(pointer)
+
 def from_numpy(
     data, origin=None, spacing=None, direction=None, has_components=False, is_rgb=False
 ):
@@ -128,9 +132,7 @@ def _from_numpy(
 
     if not has_components:
         itk_image = libfn(data, data.shape[::-1])
-        ants_image = iio.ANTsImage(
-            pixeltype=ptype, dimension=ndim, components=1, pointer=itk_image
-        )
+        ants_image = from_pointer(itk_image)
         ants_image.set_origin(origin)
         ants_image.set_spacing(spacing)
         ants_image.set_direction(direction)
@@ -141,9 +143,7 @@ def _from_numpy(
         ants_images = []
         for i in range(len(arrays)):
             tmp_ptr = libfn(arrays[i], data_shape[::-1])
-            tmp_img = iio.ANTsImage(
-                pixeltype=ptype, dimension=ndim, components=1, pointer=tmp_ptr
-            )
+            tmp_img = from_pointer(tmp_ptr)
             tmp_img.set_origin(origin)
             tmp_img.set_spacing(spacing)
             tmp_img.set_direction(direction)
@@ -547,13 +547,7 @@ def image_read(filename, dimension=None, pixeltype="float", reorient=False):
         libfn = utils.get_lib_fn(_image_read_dict[pclass][ptype][ndim])
         itk_pointer = libfn(filename)
 
-        ants_image = iio.ANTsImage(
-            pixeltype=ptype,
-            dimension=ndim,
-            components=ncomp,
-            pointer=itk_pointer,
-            is_rgb=is_rgb,
-        )
+        ants_image = from_pointer(itk_pointer)
 
         if pixeltype is not None:
             ants_image = ants_image.clone(pixeltype)

ants/core/ants_transform.py

@@ -16,7 +16,7 @@
            'transform_index_to_physical_point',
            'transform_physical_point_to_index']
 
-from . import ants_image as iio
+from . import ants_image as iio, ants_image_io as iio2
 from .. import utils
 
 
@@ -188,10 +188,7 @@ def apply_to_image(self, image, reference=None, interpolation='linear'):
         reference = reference.clone(image.pixeltype)
 
         img_ptr = tform_fn(self.pointer, image.pointer, reference.pointer, interpolation)
-        return iio.ANTsImage(pixeltype=image.pixeltype,
-                            dimension=image.dimension,
-                            components=image.components,
-                            pointer=img_ptr)
+        return iio2.from_pointer(img_ptr)
 
     def __repr__(self):
         s = "ANTsTransform\n" +\

ants/core/ants_transform_io.py

@@ -10,7 +10,7 @@
 import os
 import numpy as np
 
-from . import ants_image as iio
+from . import ants_image as iio, ants_image_io as iio2
 from . import ants_transform as tio
 from .. import utils
 
@@ -297,10 +297,7 @@ def transform_to_displacement_field(xfrm, ref):
         raise ValueError("Transform must be of DisplacementFieldTransform type")
     libfn = utils.get_lib_fn("antsTransformToDisplacementField")
     field_ptr = libfn(xfrm.pointer, ref.pointer)
-    return iio.ANTsImage( pixeltype=xfrm.precision,
-                          dimension=xfrm.dimension,
-                          components=xfrm.dimension,
-                          pointer=field_ptr)
+    return iio2.from_pointer(field_ptr)
 
 def read_transform(filename, precision="float"):
     """

ants/registration/reorient_image.py

@@ -11,7 +11,7 @@
 
 from . import apply_transforms
 from .. import utils
-from ..core import ants_image as iio
+from ..core import ants_image as iio, ants_image_io as iio2
 
 
 _possible_orientations = ['RIP','LIP',  'RSP',  'LSP',  'RIA',  'LIA',
@@ -72,8 +72,7 @@ def reorient_image2(image, orientation='RAS'):
      libfn = utils.get_lib_fn('reorientImage2')
      itkimage = libfn(image.pointer, orientation)
 
-     new_img = iio.ANTsImage(pixeltype='float', dimension=ndim,
-                          components=image.components, pointer=itkimage)#.clone(inpixeltype)
+     new_img = iio2.from_pointer(itkimage)
      if inpixeltype != 'float':
          new_img = new_img.clone(inpixeltype)
      return new_img

ants/segmentation/anti_alias.py

@@ -40,5 +40,4 @@ def anti_alias(image):
 
     libfn = utils.get_lib_fn('antiAlias%s' % image._libsuffix)
     new_ptr = libfn(image.pointer)
-    return iio.ANTsImage(pixeltype='float', dimension=image.dimension, 
-                         components=image.components, pointer=new_ptr)
+    return iio2.from_pointer(new_ptr)

ants/utils/add_noise_to_image.py

@@ -1,7 +1,7 @@
 __all__ = ["add_noise_to_image"]
 
 from .. import utils
-from ..core import ants_image as iio
+from ..core import ants_image as iio, ants_image_io as iio2
 
 def add_noise_to_image(image,
                        noise_model,
@@ -47,39 +47,31 @@ def add_noise_to_image(image,
 
         libfn = utils.get_lib_fn("additiveGaussianNoise")
         noise = libfn(image.pointer, noise_parameters[0], noise_parameters[1])
-        output_image = iio.ANTsImage(pixeltype='float', 
-            dimension=image_dimension, components=1,
-            pointer=noise).clone('float')
+        output_image = iio2.from_pointer(noise).clone('float')
         return output_image
     elif noise_model == 'saltandpepper':
         if len(noise_parameters) != 3:
             raise ValueError("Incorrect number of parameters.")
 
         libfn = utils.get_lib_fn("saltAndPepperNoise")
         noise = libfn(image.pointer, noise_parameters[0], noise_parameters[1], noise_parameters[2])
-        output_image = iio.ANTsImage(pixeltype='float', 
-            dimension=image_dimension, components=1,
-            pointer=noise).clone('float')
+        output_image = iio2.from_pointer(noise).clone('float')
         return output_image
     elif noise_model == 'shot':
         if not isinstance(noise_parameters, (int, float)):
             raise ValueError("Incorrect parameter specification.")
 
         libfn = utils.get_lib_fn("shotNoise")
         noise = libfn(image.pointer, noise_parameters)
-        output_image = iio.ANTsImage(pixeltype='float', 
-            dimension=image_dimension, components=1,
-            pointer=noise).clone('float')
+        output_image = iio2.from_pointer(noise).clone('float')
         return output_image
     elif noise_model == 'speckle':
         if not isinstance(noise_parameters, (int, float)):
             raise ValueError("Incorrect parameter specification.")
 
         libfn = utils.get_lib_fn("speckleNoise")
         noise = libfn(image.pointer, noise_parameters)
-        output_image = iio.ANTsImage(pixeltype='float', 
-            dimension=image_dimension, components=1,
-            pointer=noise).clone('float')
+        output_image = iio2.from_pointer(noise).clone('float')
         return output_image
     else:
         raise ValueError("Unknown noise model.")    

ants/utils/channels.py

@@ -4,7 +4,7 @@
 __all__ = ['merge_channels',
            'split_channels']
 
-from ..core import ants_image as iio
+from ..core import ants_image as iio, ants_image_io as iio2
 from .. import utils
 
 
@@ -45,10 +45,7 @@ def merge_channels(image_list):
     libfn = utils.get_lib_fn('mergeChannels')
     image_ptr = libfn([image.pointer for image in image_list])
 
-    return iio.ANTsImage(pixeltype=inpixeltype,
-                         dimension=dimension,
-                         components=components,
-                         pointer=image_ptr)
+    return iio2.from_pointer(image_ptr)
 
 
 def split_channels(image):
@@ -82,8 +79,7 @@ def split_channels(image):
 
     libfn = utils.get_lib_fn('splitChannels')
     itkimages = libfn(image.pointer)
-    antsimages = [iio.ANTsImage(pixeltype=inpixeltype, dimension=dimension, 
-                              components=components, pointer=itkimage) for itkimage in itkimages]
+    antsimages = [iio2.from_pointer(itkimage) for itkimage in itkimages]
     return antsimages
 
 

ants/utils/compose_displacement_fields.py

@@ -1,7 +1,7 @@
 
 __all__ = ['compose_displacement_fields']
 
-from ..core import ants_image as iio
+from ..core import ants_image as iio, ants_image_io as iio2
 from .. import utils
 
 
@@ -27,8 +27,7 @@ def compose_displacement_fields(displacement_field,
     libfn = utils.get_lib_fn('composeDisplacementFieldsD%i' % displacement_field.dimension)
     comp_field = libfn(displacement_field.pointer, warping_field.pointer)
 
-    new_image = iio.ANTsImage(pixeltype='float', dimension=displacement_field.dimension, 
-                         components=displacement_field.dimension, pointer=comp_field).clone('float')
+    new_image = iio2.from_pointer(comp_field).clone('float')
     return new_image
 
 

ants/utils/crop_image.py

@@ -7,7 +7,7 @@
 
 
 from .get_mask import get_mask
-from ..core import ants_image as iio
+from ..core import ants_image as iio, ants_image_io as iio2
 from .. import utils
 
 
@@ -52,8 +52,7 @@ def crop_image(image, label_image=None, label=1):
 
     libfn = utils.get_lib_fn('cropImage')
     itkimage = libfn(image.pointer, label_image.pointer, label, 0, [], [])
-    return iio.ANTsImage(pixeltype='float', dimension=ndim, 
-                        components=image.components, pointer=itkimage).clone(inpixeltype)
+    return iio2.from_pointer(itkimage).clone(inpixeltype)
 
 
 def crop_indices(image, lowerind, upperind):
@@ -98,8 +97,7 @@ def crop_indices(image, lowerind, upperind):
 
     libfn = utils.get_lib_fn('cropImage')
     itkimage = libfn(image.pointer, image.pointer, 1, 2, lowerind, upperind)
-    ants_image = iio.ANTsImage(pixeltype='float', dimension=image.dimension,
-                        components=image.components, pointer=itkimage)
+    ants_image = iio2.from_pointer(itkimage)
     if inpixeltype != 'float':
         ants_image = ants_image.clone(inpixeltype)
     return ants_image
@@ -141,8 +139,7 @@ def decrop_image(cropped_image, full_image):
 
     libfn = utils.get_lib_fn('cropImage')
     itkimage = libfn(cropped_image.pointer, full_image.pointer, 1, 1, [], [])
-    ants_image = iio.ANTsImage(pixeltype='float', dimension=cropped_image.dimension,
-                        components=cropped_image.components, pointer=itkimage)
+    ants_image = iio2.from_pointer(itkimage)
     if inpixeltype != 'float':
         ants_image = ants_image.clone(inpixeltype)