Add aspire.utils.coor_trans.crop_2d and move coor_trans objects to second-level API access (#565)

* utils.coor_trans methods accessible from second level

* crop_2d method

* crop2d test

* clarify flooring behavior for centering and add apdding

* tests finished

* isort shenanigans

* fix even to odd n->n+1 padding bug

* slightly better comment

* better behavior for dtype

* remove mistaken characters

* fixes after merge

* last ensure removed

* rect tests

* padding tests and fill value test

* better comments

* even better comments

* np.diag

* crop_pad_2d

* clarifying comment when padding

Author: chris-langfield

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__)