Merge pull request #637 from ComputationalCryoEM/develop

garrettwrong · web-flow · commit 1bff8d388418 · 2022-06-02T10:52:46.000-04:00
Develop ~~&gt;  Master 0.9.2
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.1
+current_version = 0.9.2
 commit = True
 tag = True
 
diff --git a/.zenodo.json b/.zenodo.json
@@ -0,0 +1,62 @@
+{
+    "creators": [
+	{
+	    "affiliation": "Princeton University",
+	    "name": "Garrett Wright"
+	},
+	{
+	    "affiliation": "KTH Royal Institute of Technology",
+	    "name": "Joakim And\u00e9n",
+	    "orcid": "0000-0002-3377-813X"
+	},
+	{
+	    "affiliation": "Princeton University",
+	    "name": "Vineet Bansal"
+	},
+	{
+	    "affiliation": "OpenEye Scientific Software Inc",
+	    "name": "Junchao Xia"
+	},
+	{
+	    "affiliation": "Princeton University",
+	    "name": "Chris Langfield",
+	    "orcid": "0000-0003-4151-203X"
+	},
+	{
+	    "affiliation": "Princeton University",
+	    "name": "Josh Carmichael",
+	    "orcid": "0000-0001-9889-349X"
+	},
+        {
+            "name": "Robbie Brook"
+        },
+	{
+	    "affiliation": "Princeton University",
+	    "name": "Yunpeng Shi"
+	},
+	{
+	    "affiliation": "Ariel University",
+	    "name": "Ayelet Heimowitz"
+	},
+	{
+	    "affiliation": "Tel Aviv University",
+	    "name": "Gabi Pragier"
+	},
+	{
+	    "affiliation": "Tel Aviv University",
+	    "name": "Itay Sason"
+	},
+	{
+	    "affiliation": "Tel Aviv University",
+	    "name": "Amit Moscovich"
+	},
+	{
+	    "affiliation": "Tel Aviv University",
+	    "name": "Yoel Shkolnisky"
+	},
+	{
+	    "affiliation": "Princeton University",
+	    "name": "Amit Singer"
+	}
+    ]
+}
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -11,6 +11,7 @@ include pytest.ini
 include tox.ini
 include logging.conf
 include config.ini
+include .zenodo.json
 recursive-include docs *.bat
 recursive-include docs *.bib
 recursive-include docs *.py
diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 [![codecov](https://codecov.io/gh/ComputationalCryoEM/ASPIRE-Python/branch/master/graph/badge.svg?token=3XFC4VONX0)](https://codecov.io/gh/ComputationalCryoEM/ASPIRE-Python)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5657281.svg)](https://doi.org/10.5281/zenodo.5657281)
 
-# ASPIRE - Algorithms for Single Particle Reconstruction - v0.9.1
+# ASPIRE - Algorithms for Single Particle Reconstruction - v0.9.2
 
 This is the Python version to supersede the [Matlab ASPIRE](https://github.com/PrincetonUniversity/aspire).
 
@@ -20,7 +20,7 @@ For more information about the project, algorithms, and related publications ple
 Please cite using the following DOI. This DOI represents all versions, and will always resolve to the latest one.
 
 ```
-ComputationalCryoEM/ASPIRE-Python: v0.9.1 https://doi.org/10.5281/zenodo.5657281
+ComputationalCryoEM/ASPIRE-Python: v0.9.2 https://doi.org/10.5281/zenodo.5657281
 
 ```
 
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -74,7 +74,7 @@
 # built documents.
 #
 # The full version, including alpha/beta/rc tags.
-release = version = "0.9.1"
+release = version = "0.9.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,4 +1,4 @@
-Aspire v0.9.1
+Aspire v0.9.2
 ==============
 
 Algorithms for Single Particle Reconstruction
diff --git a/setup.py b/setup.py
@@ -9,7 +9,7 @@ def read(fname):
 
 setup(
     name="aspire",
-    version="0.9.1",
+    version="0.9.2",
     data_files=[
         ("", ["src/aspire/config.ini"]),
         ("", ["src/aspire/logging.conf"]),
diff --git a/src/aspire/__init__.py b/src/aspire/__init__.py
@@ -9,7 +9,7 @@
 from aspire.exceptions import handle_exception
 
 # version in maj.min.bld format
-__version__ = "0.9.1"
+__version__ = "0.9.2"
 
 # Implements some code that writes out exceptions to 'aspire.err.log'.
 config = Config(read_text(aspire, "config.ini"))
diff --git a/src/aspire/apple/picking.py b/src/aspire/apple/picking.py
@@ -191,9 +191,9 @@ def read_mrc(self):
         size = tuple((np.array(im.shape) / self.mrc_shrink_factor).astype(int))
 
         # Note, float64 required for signal.correlate call accuracy.
-        im = np.asarray(Image.fromarray(im).resize(size, Image.BICUBIC)).astype(
-            np.float64, copy=False
-        )
+        im = np.asarray(
+            Image.fromarray(im).resize(size, Image.Resampling.BICUBIC)
+        ).astype(np.float64, copy=False)
 
         im = signal.correlate(
             im,
diff --git a/src/aspire/basis/__init__.py b/src/aspire/basis/__init__.py
@@ -3,6 +3,7 @@
 
 from .basis import Basis
 from .steerable import SteerableBasis2D
+from .fb import FBBasisMixin
 
 # isort: on
 
diff --git a/src/aspire/basis/basis.py b/src/aspire/basis/basis.py
@@ -3,10 +3,8 @@
 import numpy as np
 from scipy.sparse.linalg import LinearOperator, cg
 
-from aspire.basis.basis_utils import num_besselj_zeros
 from aspire.image import Image
 from aspire.utils import mdim_mat_fun_conj
-from aspire.utils.matlab_compat import m_reshape
 from aspire.volume import Volume
 
 logger = logging.getLogger(__name__)
@@ -47,46 +45,6 @@ def __init__(self, size, ell_max=None, dtype=np.float32):
 
         self._build()
 
-    def _getfbzeros(self):
-        """
-        Generate zeros of Bessel functions
-        """
-        # get upper_bound of zeros of Bessel functions
-        upper_bound = min(self.ell_max + 1, 2 * self.nres + 1)
-
-        # List of number of zeros
-        n = []
-        # List of zero values (each entry is an ndarray; all of possibly different lengths)
-        zeros = []
-
-        # generate zeros of Bessel functions for each ell
-        for ell in range(upper_bound):
-            # for each ell, num_besselj_zeros returns the zeros of the
-            # order ell Bessel function which are less than 2*pi*c*R = nres*pi/2,
-            # the truncation rule for the Fourier-Bessel expansion
-            _n, _zeros = num_besselj_zeros(
-                ell + (self.ndim - 2) / 2, self.nres * np.pi / 2
-            )
-            if _n == 0:
-                break
-            else:
-                n.append(_n)
-                zeros.append(_zeros)
-
-        #  get maximum number of ell
-        self.ell_max = len(n) - 1
-
-        #  set the maximum of k for each ell
-        self.k_max = np.array(n, dtype=int)
-
-        max_num_zeros = max(len(z) for z in zeros)
-        for i, z in enumerate(zeros):
-            zeros[i] = np.hstack(
-                (z, np.zeros(max_num_zeros - len(z), dtype=self.dtype))
-            )
-
-        self.r0 = m_reshape(np.hstack(zeros), (-1, self.ell_max + 1)).astype(self.dtype)
-
     def _build(self):
         """
         Build the internal data structure to represent basis
diff --git a/src/aspire/basis/basis_utils.py b/src/aspire/basis/basis_utils.py
@@ -247,7 +247,7 @@ def besselj_zeros(nu, k):
     return z
 
 
-def num_besselj_zeros(ell, r):
+def all_besselj_zeros(ell, r):
     """
     Compute the zeros of the order `ell` Bessel function which are less than `r`.
 
diff --git a/src/aspire/basis/fb.py b/src/aspire/basis/fb.py
@@ -0,0 +1,56 @@
+import logging
+
+import numpy as np
+
+from aspire.basis.basis_utils import all_besselj_zeros
+from aspire.utils.matlab_compat import m_reshape
+
+logger = logging.getLogger(__name__)
+
+
+class FBBasisMixin(object):
+    """
+    FBBasisMixin is a mixin implementing methods specific to Fourier-Bessel expansions,
+    to be inherited by Fourier-Bessel subclasses of Basis.
+    """
+
+    def _calc_k_max(self):
+        """
+        Generate zeros of Bessel functions
+        """
+        # get upper_bound of zeros of Bessel functions
+        upper_bound = min(self.ell_max + 1, 2 * self.nres + 1)
+
+        # List of number of zeros
+        n = []
+        # List of zero values (each entry is an ndarray; all of possibly different lengths)
+        zeros = []
+
+        for ell in range(upper_bound):
+            # for each ell, num_besselj_zeros returns the zeros of the
+            # order ell Bessel function which are less than 2*pi*c*R = nres*pi/2,
+            # the truncation rule for the Fourier-Bessel expansion
+            if self.ndim == 2:
+                bessel_order = ell
+            elif self.ndim == 3:
+                bessel_order = ell + 1 / 2
+            _n, _zeros = all_besselj_zeros(bessel_order, self.nres * np.pi / 2)
+            if _n == 0:
+                break
+            else:
+                n.append(_n)
+                zeros.append(_zeros)
+
+        #  get maximum number of ell
+        self.ell_max = len(n) - 1
+
+        #  set the maximum of k for each ell
+        self.k_max = np.array(n, dtype=int)
+
+        max_num_zeros = max(len(z) for z in zeros)
+        for i, z in enumerate(zeros):
+            zeros[i] = np.hstack(
+                (z, np.zeros(max_num_zeros - len(z), dtype=self.dtype))
+            )
+
+        self.r0 = m_reshape(np.hstack(zeros), (-1, self.ell_max + 1)).astype(self.dtype)
diff --git a/src/aspire/basis/fb_2d.py b/src/aspire/basis/fb_2d.py
@@ -3,7 +3,7 @@
 import numpy as np
 from scipy.special import jv
 
-from aspire.basis import SteerableBasis2D
+from aspire.basis import FBBasisMixin, SteerableBasis2D
 from aspire.basis.basis_utils import unique_coords_nd
 from aspire.image import Image
 from aspire.utils import complex_type, real_type, roll_dim, unroll_dim
@@ -12,7 +12,7 @@
 logger = logging.getLogger(__name__)
 
 
-class FBBasis2D(SteerableBasis2D):
+class FBBasis2D(SteerableBasis2D, FBBasisMixin):
     """
     Define a derived class using the Fourier-Bessel basis for mapping 2D images
 
@@ -54,7 +54,7 @@ def _build(self):
         )
 
         # get upper bound of zeros, ells, and ks  of Bessel functions
-        self._getfbzeros()
+        self._calc_k_max()
 
         # calculate total number of basis functions
         self.count = self.k_max[0] + sum(2 * self.k_max[1:])
diff --git a/src/aspire/basis/fb_3d.py b/src/aspire/basis/fb_3d.py
@@ -2,15 +2,15 @@
 
 import numpy as np
 
-from aspire.basis import Basis
+from aspire.basis import Basis, FBBasisMixin
 from aspire.basis.basis_utils import real_sph_harmonic, sph_bessel, unique_coords_nd
 from aspire.utils import roll_dim, unroll_dim
 from aspire.utils.matlab_compat import m_flatten, m_reshape
 
 logger = logging.getLogger(__name__)
 
 
-class FBBasis3D(Basis):
+class FBBasis3D(Basis, FBBasisMixin):
     """
     Define a derived class for direct spherical Harmonics Bessel basis expanding 3D volumes
 
@@ -49,7 +49,7 @@ def _build(self):
         )
 
         # get upper bound of zeros, ells, and ks  of Bessel functions
-        self._getfbzeros()
+        self._calc_k_max()
 
         # calculate total number of basis functions
         self.count = sum(self.k_max * (2 * np.arange(0, self.ell_max + 1) + 1))
diff --git a/src/aspire/basis/ffb_2d.py b/src/aspire/basis/ffb_2d.py
@@ -44,7 +44,7 @@ def _build(self):
         self.n_theta = int((n_theta + np.mod(n_theta, 2)) / 2)
 
         # get upper bound of zeros, ells, and ks  of Bessel functions
-        self._getfbzeros()
+        self._calc_k_max()
 
         # calculate total number of basis functions
         self.count = self.k_max[0] + sum(2 * self.k_max[1:])
diff --git a/src/aspire/basis/ffb_3d.py b/src/aspire/basis/ffb_3d.py
@@ -33,7 +33,7 @@ def _build(self):
         self.kcut = 0.5
 
         # get upper bound of zeros, ells, and ks  of Bessel functions
-        self._getfbzeros()
+        self._calc_k_max()
 
         # calculate total number of basis functions
         self.count = sum(self.k_max * (2 * np.arange(0, self.ell_max + 1) + 1))
diff --git a/src/aspire/image/image.py b/src/aspire/image/image.py
@@ -3,13 +3,12 @@
 import matplotlib.pyplot as plt
 import mrcfile
 import numpy as np
-from scipy.interpolate import RegularGridInterpolator
 from scipy.linalg import lstsq
 
 import aspire.volume
 from aspire.nufft import anufft
 from aspire.numeric import fft, xp
-from aspire.utils import grid_2d
+from aspire.utils import crop_pad_2d, grid_2d
 from aspire.utils.matrix import anorm
 
 logger = logging.getLogger(__name__)
@@ -209,30 +208,14 @@ def downsample(self, ds_res):
             of this Image
         :return: The downsampled Image object.
         """
-        grid = grid_2d(self.res, indexing="yx")
-        grid_ds = grid_2d(ds_res, indexing="yx")
-
-        im_ds = np.zeros((self.n_images, ds_res, ds_res), dtype=self.dtype)
-
-        # x, y values corresponding to 'grid'. This is what scipy interpolator needs to function.
-        res_by_2 = self.res / 2
-        x = y = np.ceil(np.arange(-res_by_2, res_by_2)) / res_by_2
-
-        mask = (np.abs(grid["x"]) < ds_res / self.res) & (
-            np.abs(grid["y"]) < ds_res / self.res
-        )
-        im_shifted = fft.centered_ifft2(
-            fft.centered_fft2(xp.asarray(self.data)) * xp.asarray(mask)
-        )
-        im = np.real(xp.asnumpy(im_shifted))
-
-        for s in range(im_ds.shape[0]):
-            interpolator = RegularGridInterpolator(
-                (x, y), im[s], bounds_error=False, fill_value=0
-            )
-            im_ds[s] = interpolator(np.dstack([grid_ds["y"], grid_ds["x"]]))
-
-        return Image(im_ds)
+        # compute FT with centered 0-frequency
+        fx = fft.centered_fft2(self.data)
+        # crop 2D Fourier transform for each image
+        crop_fx = np.array([crop_pad_2d(fx[i], ds_res) for i in range(self.n_images)])
+        # take back to real space, discard complex part, and scale
+        out = np.real(fft.centered_ifft2(crop_fx)) * (ds_res**2 / self.res**2)
+
+        return Image(out)
 
     def filter(self, filter):
         """
diff --git a/src/aspire/numeric/complex_pca/validation.py b/src/aspire/numeric/complex_pca/validation.py
diff --git a/src/aspire/storage/micrograph.py b/src/aspire/storage/micrograph.py
diff --git a/tests/test_basis_utils.py b/tests/test_basis_utils.py
diff --git a/tests/test_complexPCA.py b/tests/test_complexPCA.py
diff --git a/tests/test_downsample.py b/tests/test_downsample.py
diff --git a/tox.ini b/tox.ini

Original file line number	Diff line number	Diff line change
`@@ -74,7 +74,7 @@`
`74`	`74`	`# built documents.`
`75`	`75`	`#`
`76`	`76`	`# The full version, including alpha/beta/rc tags.`
`77`		`-release = version = "0.9.1"`
	`77`	`+release = version = "0.9.2"`
`78`	`78`
`79`	`79`	`# The language for content autogenerated by Sphinx. Refer to documentation`
`80`	`80`	`# for a list of supported languages.`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-Aspire v0.9.1`
	`1`	`+Aspire v0.9.2`
`2`	`2`	`==============`
`3`	`3`
`4`	`4`	`Algorithms for Single Particle Reconstruction`