ENH: simpler imports, image decorator, and better code organization

CONTRIBUTING.md

@@ -74,7 +74,7 @@ The general workflow for wrapping a library calls involves the following steps:
 
 - write a wrapper python function (e.g. `def atropos(...)`)
 - build up a list or dictionary of string argument names as in ANTs
-- pass those raw arguments through the function `utils._int_antsProcessArguments(args)`
+- pass those raw arguments through the function `process_arguments(args)`
 - pass those processed arguments into the library call (e.g. `lib.Atropos(processed_args)`).
 
 ## Writing custom code for antspy

ants/__init__.py

@@ -2,10 +2,11 @@
 __version__ = '0.5.3'
 
 from .core import *
-from .utils import *
-from .segmentation import *
-from .registration import *
+from .label import *
 from .learn import *
-from .viz import *
-
-from . import contrib
+from .math import *
+from .ops import *
+from .plotting import *
+from .registration import *
+from .segmentation import *
+from .utils import *

ants/core/__init__.py

@@ -1,65 +1,40 @@
-
-from .ants_image_io import (
-    image_header_info,
-    image_clone,
-    image_read,
-    dicom_read,
-    image_write,
-    make_image,
-    matrix_to_images,
-    images_from_matrix,
-    image_list_to_matrix,
-    images_to_matrix,
-    matrix_from_images,
-    timeseries_to_matrix,
-    matrix_to_timeseries,
-    from_numpy,
-    _from_numpy
-)
-
-from .ants_image import (
-    ANTsImage,
-    copy_image_info,
-    set_origin,
-    get_origin,
-    set_direction,
-    get_direction,
-    set_spacing,
-    get_spacing,
-    image_physical_space_consistency,
-    image_type_cast,
-    allclose
-)
-
-from .ants_metric_io import (
-    new_ants_metric,
-    create_ants_metric,
-    supported_metrics
-)
-
-from .ants_transform_io import (
-    create_ants_transform,
-    new_ants_transform,
-    read_transform,
-    write_transform,
-    transform_from_displacement_field,
-    transform_to_displacement_field
-)
-
-from .ants_transform import (
-    ANTsTransform,
-    set_ants_transform_parameters,
-    get_ants_transform_parameters,
-    get_ants_transform_fixed_parameters,
-    set_ants_transform_fixed_parameters,
-    apply_ants_transform,
-    apply_ants_transform_to_point,
-    apply_ants_transform_to_vector,
-    apply_ants_transform_to_image,
-    invert_ants_transform,
-    compose_ants_transforms,
-    transform_index_to_physical_point,
-    transform_physical_point_to_index
-)
-
-
+from .ants_image_io import (image_header_info,
+                            image_clone,
+                            image_read,
+                            dicom_read,
+                            image_write,
+                            make_image,
+                            from_numpy,
+                            new_image_like)
+from .ants_image import (copy_image_info,
+                         set_origin,
+                         get_origin,
+                         set_direction,
+                         get_direction,
+                         set_spacing,
+                         get_spacing,
+                         is_image,
+                         from_pointer)
+from .ants_metric_io import (new_ants_metric,
+                             create_ants_metric,
+                             supported_metrics)
+from .ants_transform_io import (create_ants_transform,
+                                new_ants_transform,
+                                read_transform,
+                                write_transform,
+                                transform_from_displacement_field,
+                                transform_to_displacement_field,
+                                fsl2antstransform)
+from .ants_transform import (ANTsTransform,
+                             set_ants_transform_parameters,
+                             get_ants_transform_parameters,
+                             get_ants_transform_fixed_parameters,
+                             set_ants_transform_fixed_parameters,
+                             apply_ants_transform,
+                             apply_ants_transform_to_point,
+                             apply_ants_transform_to_vector,
+                             apply_ants_transform_to_image,
+                             invert_ants_transform,
+                             compose_ants_transforms,
+                             transform_index_to_physical_point,
+                             transform_physical_point_to_index)