Merge pull request #533 from ANTsX/explicit-inits

Explicit imports

README.md

@@ -16,8 +16,10 @@
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/stnava/ANTsPyDocker/master)
 [![PubMed](https://img.shields.io/badge/ANTsX_paper-Open_Access-8DABFF?logo=pubmed)](https://pubmed.ncbi.nlm.nih.gov/33907199/)
 
+
 ## About ANTsPy
 
+
 Search [ANTsPy documentation at read the docs.](https://antspyx.readthedocs.io/en/latest/?badge=latest)
 
 <i>ANTsPy</i> is a Python library which wraps the C++ biomedical image processing library <i>[ANTs](https://github.com/ANTsX/ANTs)</i>,

ants/__init__.py

@@ -11,4 +11,4 @@
 from .learn import *
 from .viz import *
 
-from . import contrib
+from . import contrib

ants/core/__init__.py

@@ -1,9 +1,66 @@
 
-from .ants_image import *
-from .ants_image_io import *
+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,
+    LabelImage,
+    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_transform import *
-from .ants_transform_io import *
 
-from .ants_metric import *
-from .ants_metric_io import *

ants/learn/__init__.py

@@ -1,2 +1,6 @@
 
-from .decomposition import *
+from .decomposition import (
+    eig_seg,
+    initialize_eigenanatomy,
+    sparse_decom2
+)

ants/registration/__init__.py

@@ -1,18 +1,22 @@
 
 
-from .affine_initializer import *
-from .apply_transforms import *
+from .affine_initializer import affine_initializer
+from .apply_transforms import (apply_transforms,apply_transforms_to_points)
 from .create_jacobian_determinant_image import create_jacobian_determinant_image
 from .create_jacobian_determinant_image import deformation_gradient
-from .create_warped_grid import *
-from .fsl2antstransform import *
-from .make_points_image import *
-from .metrics import *
-from .reflect_image import *
-from .reorient_image import *
-from .resample_image import *
-from .symmetrize_image import *
-from .build_template import *
-from .landmark_transforms import *
+from .create_warped_grid import create_warped_grid
+from .fsl2antstransform import fsl2antstransform
+from .make_points_image import make_points_image
+from .metrics import image_mutual_information
+from .reflect_image import reflect_image
+from .reorient_image import (get_orientation,
+           reorient_image2,
+           get_possible_orientations,
+           get_center_of_mass)
+from .resample_image import (resample_image,
+           resample_image_to_target)
+from .symmetrize_image import symmetrize_image
+from .build_template import build_template
+from .landmark_transforms import (fit_transform_to_paired_points, fit_time_varying_transform_to_point_sets)
 
-from .interface import *
+from .interface import (registration, motion_correction)

ants/segmentation/__init__.py

@@ -1,11 +1,10 @@
-from .anti_alias import *
-from .atropos import *
-from .kmeans import *
-from .functional_lung_segmentation import *
-from .fuzzy_spatial_cmeans_segmentation import *
-from .kelly_kapowski import *
-from .joint_label_fusion import joint_label_fusion
-from .joint_label_fusion import local_joint_label_fusion
-from .label_geometry_measures import *
-from .otsu import *
-from .prior_based_segmentation import *
+from .anti_alias import anti_alias
+from .atropos import atropos
+from .kmeans import kmeans_segmentation
+from .functional_lung_segmentation import functional_lung_segmentation
+from .fuzzy_spatial_cmeans_segmentation import fuzzy_spatial_cmeans_segmentation
+from .kelly_kapowski import kelly_kapowski
+from .joint_label_fusion import joint_label_fusion, local_joint_label_fusion
+from .label_geometry_measures import label_geometry_measures
+from .otsu import otsu_segmentation
+from .prior_based_segmentation import prior_based_segmentation

ants/utils/__init__.py

@@ -1,45 +1,91 @@
-from .add_noise_to_image import *
-from .bias_correction import *
-from .channels import *
-from .compose_displacement_fields import *
-from .convert_nibabel import *
-from .crop_image import *
-from .denoise_image import *
-from .fit_bspline_object_to_scattered_data import *
-from .fit_bspline_displacement_field import *
-from .fit_thin_plate_spline_displacement_field import *
-from .get_ants_data import *
-from .get_centroids import *
-from .get_mask import *
-from .get_neighborhood import *
-from .histogram_match_image import *
-from .hausdorff_distance import *
-from .image_similarity import *
-from .image_to_cluster_images import *
-from .iMath import *
-from .impute import *
-from .integrate_velocity_field import *
-from .invariant_image_similarity import *
-from .invert_displacement_field import *
-from .label_clusters import *
-from .label_image_centroids import *
-from .label_overlap_measures import *
-from .label_stats import *
-from .labels_to_matrix import *
-from .mask_image import *
-from .mni2tal import *
-from .morphology import *
-from .multi_label_morphology import *
-from .ndimage_to_list import *
-from .pad_image import *
-from .process_args import *
-from .quantile import *
-from .scalar_rgb_vector import *
-from .simulate_displacement_field import *
-from .slice_image import *
-from .smooth_image import *
-from .threshold_image import *
-from .weingarten_image_curvature import *
-from .average_transform import *
+from .add_noise_to_image import add_noise_to_image
+from .bias_correction import (n3_bias_field_correction, n3_bias_field_correction2, n4_bias_field_correction, abp_n4)
+from .channels import merge_channels, split_channels
+from .compose_displacement_fields import compose_displacement_fields
+from .convert_nibabel import (to_nibabel, from_nibabel, nifti_to_ants)
+from .crop_image import (crop_image, 
+           crop_indices,
+           decrop_image)
+from .denoise_image import denoise_image
+from .fit_bspline_object_to_scattered_data import fit_bspline_object_to_scattered_data
+from .fit_bspline_displacement_field import fit_bspline_displacement_field
+from .fit_thin_plate_spline_displacement_field import fit_thin_plate_spline_displacement_field
+from .get_ants_data import (get_ants_data,
+           get_data)
+from .get_centroids import get_centroids
+from .get_mask import get_mask
+from .get_neighborhood import (get_neighborhood_in_mask,
+            get_neighborhood_at_voxel)
+from .histogram_match_image import histogram_match_image
+from .hausdorff_distance import hausdorff_distance
+from .image_similarity import image_similarity
+from .image_to_cluster_images import image_to_cluster_images
+from .iMath import (iMath,
+           image_math,
+           multiply_images,
+           iMath_get_largest_component,
+           iMath_normalize,
+           iMath_truncate_intensity,
+           iMath_sharpen,
+           iMath_pad,
+           iMath_maurer_distance,
+           iMath_perona_malik,
+           iMath_grad,
+           iMath_laplacian,
+           iMath_canny,
+           iMath_histogram_equalization,
+           iMath_MD,
+           iMath_ME,
+           iMath_MO,
+           iMath_MC,
+           iMath_GD,
+           iMath_GE,
+           iMath_GO,
+           iMath_GC,
+           iMath_fill_holes,
+           iMath_get_largest_component,
+           iMath_normalize,
+           iMath_truncate_intensity,
+           iMath_sharpen,
+           iMath_propagate_labels_through_mask)
+from .impute import impute
+from .integrate_velocity_field import integrate_velocity_field
+from .invariant_image_similarity import (invariant_image_similarity,
+           convolve_image)
+from .invert_displacement_field import invert_displacement_field
+from .label_clusters import label_clusters
+from .label_image_centroids import label_image_centroids
+from .label_overlap_measures import label_overlap_measures
+from .label_stats import label_stats
+from .labels_to_matrix import labels_to_matrix
+from .mask_image import mask_image
+from .mni2tal import mni2tal
+from .morphology import morphology
+from .multi_label_morphology import multi_label_morphology
+from .ndimage_to_list import (ndimage_to_list,
+           list_to_ndimage)
+from .pad_image import pad_image
+from .process_args import (
+    get_pointer_string,
+    short_ptype,
+    _ptrstr,
+    _int_antsProcessArguments,
+    get_lib_fn,
+)
+from .quantile import (ilr,
+           rank_intensity,
+           quantile,
+           regress_poly,
+           regress_components,
+           get_average_of_timeseries,
+           compcor,
+           bandpass_filter_matrix )
+from .scalar_rgb_vector import (rgb_to_vector, vector_to_rgb, scalar_to_rgb)
+from .simulate_displacement_field import simulate_displacement_field
+from .slice_image import slice_image
+from .smooth_image import smooth_image
+from .threshold_image import threshold_image
+from .weingarten_image_curvature import weingarten_image_curvature
+from .average_transform import average_affine_transform, average_affine_transform_no_rigid
 from .averaging import average_images
 

ants/utils/average_transform.py

@@ -2,6 +2,7 @@
 from tempfile import mktemp
 import os
 
+__all__ = ['average_affine_transform', 'average_affine_transform_no_rigid']
 
 
 def _average_affine_transform_driver(transformlist, referencetransform=None, funcname="AverageAffineTransform"):

ants/utils/averaging.py

@@ -8,6 +8,7 @@
 from ..core import ants_image_io as iio2
 from .. import registration as reg
 
+__all__ = ['average_images']
 ########################
 def average_images( x, normalize=True, mask=None, imagetype=0, sum_image_threshold=3, return_sum_image=False, verbose=False ):
     """

ants/viz/__init__.py

@@ -1,5 +1,14 @@
-from .create_tiled_mosaic import *
-from .plot import *
-from .render_surface_function import *
-from .surface import *
-from .volume import *
+from .create_tiled_mosaic import create_tiled_mosaic
+from .plot import (
+    plot,
+    movie,
+    plot_hist,
+    plot_grid,
+    plot_ortho,
+    plot_ortho_double,
+    plot_ortho_stack,
+    plot_directory,
+)
+from .render_surface_function import render_surface_function
+from .surface import (surf, surf_fold, surf_smooth, get_canonical_views)
+from .volume import (vol, vol_fold)