Add aspire.utils.coor_trans.crop_2d and move coor_trans objects to second-level API access

gallery/tutorials/lecture_feature_demo.py

@@ -42,8 +42,8 @@
 from aspire.noise import AnisotropicNoiseEstimator, WhiteNoiseEstimator
 from aspire.operators import FunctionFilter, RadialCTFFilter, ScalarFilter
 from aspire.source import RelionSource, Simulation
-from aspire.utils import Rotation
-from aspire.utils.coor_trans import (
+from aspire.utils import (
+    Rotation,
     get_aligned_rotations,
     get_rots_mse,
     register_rotations,

gallery/tutorials/orient3d_simulation.py

@@ -15,11 +15,7 @@
 from aspire.abinitio import CLSyncVoting
 from aspire.operators import RadialCTFFilter
 from aspire.source.simulation import Simulation
-from aspire.utils.coor_trans import (
-    get_aligned_rotations,
-    get_rots_mse,
-    register_rotations,
-)
+from aspire.utils import get_aligned_rotations, get_rots_mse, register_rotations
 from aspire.volume import Volume
 
 logger = logging.getLogger(__name__)

src/aspire/abinitio/commonline_base.py

@@ -6,7 +6,7 @@
 
 from aspire.abinitio.orientation_src import OrientEstSource
 from aspire.basis import PolarBasis2D
-from aspire.utils.coor_trans import common_line_from_rots
+from aspire.utils import common_line_from_rots
 from aspire.utils.random import choice
 
 logger = logging.getLogger(__name__)

src/aspire/basis/basis_utils.py

@@ -10,7 +10,7 @@
 from numpy.polynomial.legendre import leggauss
 from scipy.special import jn, jv, sph_harm
 
-from aspire.utils.coor_trans import grid_2d, grid_3d
+from aspire.utils import grid_2d, grid_3d
 
 logger = logging.getLogger(__name__)
 

src/aspire/ctf/ctf_estimator.py

@@ -21,8 +21,7 @@
 from aspire.numeric import fft
 from aspire.operators import voltage_to_wavelength
 from aspire.storage import StarFile
-from aspire.utils import abs2, complex_type
-from aspire.utils.coor_trans import grid_1d, grid_2d
+from aspire.utils import abs2, complex_type, grid_1d, grid_2d
 
 logger = logging.getLogger(__name__)
 

src/aspire/denoising/adaptive_support.py

@@ -5,7 +5,7 @@
 from aspire.noise import WhiteNoiseEstimator
 from aspire.numeric import fft
 from aspire.source import ImageSource
-from aspire.utils.coor_trans import grid_2d
+from aspire.utils import grid_2d
 
 logger = logging.getLogger(__name__)
 

src/aspire/image/image.py

@@ -9,7 +9,7 @@
 import aspire.volume
 from aspire.nufft import anufft
 from aspire.numeric import fft, xp
-from aspire.utils.coor_trans import grid_2d
+from aspire.utils import grid_2d
 from aspire.utils.matrix import anorm
 
 logger = logging.getLogger(__name__)

src/aspire/noise/noise.py

@@ -4,7 +4,7 @@
 
 from aspire.numeric import fft, xp
 from aspire.operators import ArrayFilter, ScalarFilter
-from aspire.utils.coor_trans import grid_2d
+from aspire.utils import grid_2d
 
 logger = logging.getLogger(__name__)
 

src/aspire/operators/filters.py

@@ -5,7 +5,7 @@
 import numpy as np
 from scipy.interpolate import RegularGridInterpolator
 
-from aspire.utils.coor_trans import grid_2d
+from aspire.utils import grid_2d
 from aspire.utils.filter_to_fb_mat import filter_to_fb_mat
 
 logger = logging.getLogger(__name__)

src/aspire/source/image.py

@@ -22,8 +22,7 @@
     PowerFilter,
 )
 from aspire.storage import MrcStats, StarFile
-from aspire.utils import Rotation
-from aspire.utils.coor_trans import grid_2d
+from aspire.utils import Rotation, grid_2d
 
 logger = logging.getLogger(__name__)
 

src/aspire/source/simulation.py

@@ -8,8 +8,14 @@
 from aspire.image.xform import NoiseAdder
 from aspire.operators import ZeroFilter
 from aspire.source import ImageSource
-from aspire.utils import acorr, ainner, anorm, make_symmat, vecmat_to_volmat
-from aspire.utils.coor_trans import uniform_random_angles
+from aspire.utils import (
+    acorr,
+    ainner,
+    anorm,
+    make_symmat,
+    uniform_random_angles,
+    vecmat_to_volmat,
+)
 from aspire.utils.random import rand, randi, randn
 from aspire.volume import Volume, gaussian_blob_vols
 

src/aspire/utils/__init__.py

@@ -1,4 +1,23 @@
-from .misc import abs2, get_full_version, powerset, sha256sum  # isort:skip
+from .coor_trans import (  # isort:skip
+    common_line_from_rots,
+    crop_pad_2d,
+    get_aligned_rotations,
+    get_rots_mse,
+    grid_1d,
+    grid_2d,
+    grid_3d,
+    register_rotations,
+    uniform_random_angles,
+)
+from .misc import (  # isort:skip
+    abs2,
+    circ,
+    gaussian_2d,
+    get_full_version,
+    inverse_r,
+    powerset,
+    sha256sum,
+)
 from .matrix import (
     acorr,
     ainner,
@@ -23,6 +42,5 @@
     vol_to_vec,
     volmat_to_vecmat,
 )
-from .misc import circ, gaussian_2d, inverse_r
 from .rotation import Rotation
 from .types import complex_type, real_type, utest_tolerance

src/aspire/utils/coor_trans.py

@@ -2,6 +2,8 @@
 General purpose math functions, mostly geometric in nature.
 """
 
+import math
+
 import numpy as np
 from numpy.linalg import norm
 from scipy.linalg import svd
@@ -302,3 +304,32 @@ def common_line_from_rots(r1, r2, ell):
     ell_ji = int(np.mod(np.round(ell_ji), ell))
 
     return ell_ij, ell_ji
+
+
+def crop_pad_2d(im, size, fill_value=0):
+    """
+    :param im: A 2-dimensional numpy array
+    :param size: Integer size of cropped/padded output
+    :return: A numpy array of shape (size, size)
+    """
+
+    im_y, im_x = im.shape
+    # shift terms
+    start_x = math.floor(im_x / 2) - math.floor(size / 2)
+    start_y = math.floor(im_y / 2) - math.floor(size / 2)
+
+    # cropping
+    if size <= min(im_y, im_x):
+        return im[start_y : start_y + size, start_x : start_x + size]
+    # padding
+    elif size >= max(im_y, im_x):
+        # ensure that we return in the same dtype as the input
+        to_return = fill_value * np.ones((size, size), dtype=im.dtype)
+        # when padding, start_x and start_y are negative since size is larger
+        # than im_x and im_y; the below line calculates where the original image
+        # is placed in relation to the (now-larger) box size
+        to_return[-start_y : im_y - start_y, -start_x : im_x - start_x] = im
+        return to_return
+    else:
+        # target size is between mat_x and mat_y
+        raise ValueError("Cannot crop and pad an image at the same time.")

src/aspire/utils/misc.py

@@ -9,7 +9,7 @@
 
 import numpy as np
 
-from aspire.utils.coor_trans import grid_1d, grid_2d, grid_3d
+from aspire.utils import grid_1d, grid_2d, grid_3d
 
 logger = logging.getLogger(__name__)
 

src/aspire/volume/__init__.py

@@ -7,8 +7,7 @@
 import aspire.image
 from aspire.nufft import nufft
 from aspire.numeric import fft, xp
-from aspire.utils import Rotation, mat_to_vec, vec_to_mat
-from aspire.utils.coor_trans import grid_2d, grid_3d
+from aspire.utils import Rotation, grid_2d, grid_3d, mat_to_vec, vec_to_mat
 from aspire.utils.matlab_compat import m_reshape
 from aspire.utils.random import Random, randn
 from aspire.utils.types import complex_type