Merge pull request #357 from ComputationalCryoEM/develop

Merge Develop

Author: garrettwrong

.bumpversion.cfg

@@ -1,23 +1,23 @@
 [bumpversion]
-current_version = 0.6.0
+current_version = 0.6.1
 commit = True
 tag = True
 
 [bumpversion:file:setup.py]
-search = version='{current_version}'
-replace = version='{new_version}'
+search = version="{current_version}"
+replace = version="{new_version}"
 
 [bumpversion:file:README.md]
 search = v{current_version}
 replace = v{new_version}
 
 [bumpversion:file:src/aspire/__init__.py]
-search = __version__ = '{current_version}'
-replace = __version__ = '{new_version}'
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"
 
 [bumpversion:file:docs/source/conf.py]
-search = release = version = '{current_version}'
-replace = release = version = '{new_version}'
+search = release = version = "{current_version}"
+replace = release = version = "{new_version}"
 
 [bumpversion:file:docs/source/index.rst]
 search = v{current_version}

MANIFEST.in

@@ -16,15 +16,6 @@ recursive-include docs *.bib
 recursive-include docs *.py
 recursive-include docs *.rst
 recursive-include docs Makefile
-recursive-include tests *.mrc
-recursive-include tests *.mrcs
-recursive-include tests *.npy
-recursive-include tests *.py
-recursive-include tests *.star
-recursive-include tutorials *.dontrun
-recursive-include tutorials *.ipynb
-recursive-include tutorials *.mat
-recursive-include tutorials *.mrc
-recursive-include tutorials *.npy
-recursive-include tutorials *.py
 prune docs/source
+prune tests
+prune tutorials

README.md

@@ -4,7 +4,7 @@
 [![Travis Build Status](https://travis-ci.org/ComputationalCryoEM/ASPIRE-Python.svg?branch=master)](https://travis-ci.org/ComputationalCryoEM/ASPIRE-Python)
 [![Coverage Status](https://coveralls.io/repos/github/ComputationalCryoEM/ASPIRE-Python/badge.svg?branch=master)](https://coveralls.io/github/ComputationalCryoEM/ASPIRE-Python?branch=master)
 
-# ASPIRE - Algorithms for Single Particle Reconstruction - v0.6.0
+# ASPIRE - Algorithms for Single Particle Reconstruction - v0.6.1
 
 This is the Python version to supersede the [Matlab ASPIRE](https://github.com/PrincetonUniversity/aspire).
 

docs/source/conf.py

@@ -62,7 +62,7 @@
 # built documents.
 #
 # The full version, including alpha/beta/rc tags.
-release = version = "0.6.0"
+release = version = "0.6.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/index.rst

@@ -1,4 +1,4 @@
-Aspire v0.6.0
+Aspire v0.6.1
 ==============
 
 Algorithms for Single Particle Reconstruction

setup.py

@@ -9,7 +9,7 @@ def read(fname):
 
 setup(
     name="aspire",
-    version="0.6.0",
+    version="0.6.1",
     data_files=[
         ("", ["src/aspire/config.ini"]),
         ("", ["src/aspire/logging.conf"]),

src/aspire/__init__.py

@@ -10,7 +10,7 @@
 from aspire.exceptions import handle_exception
 
 # version in maj.min.bld format
-__version__ = "0.6.0"
+__version__ = "0.6.1"
 
 # Implements some code that writes out exceptions to 'aspire.err.log'.
 config = Config(read_text(aspire, "config.ini"))

src/aspire/basis/basis_utils.py

@@ -8,7 +8,7 @@
 import numpy as np
 from numpy import diff, exp, log, pi
 from numpy.polynomial.legendre import leggauss
-from scipy.special import jn, jv, lpmv
+from scipy.special import jn, jv, lpmv, sph_harm
 
 from aspire.utils import ensure
 from aspire.utils.coor_trans import grid_2d, grid_3d
@@ -126,26 +126,14 @@ def real_sph_harmonic(j, m, theta, phi):
     :return: The real spherical harmonics evaluated at the points (theta, phi).
     """
     abs_m = abs(m)
-    y = lpmv(abs_m, j, np.cos(theta))
-
-    # Beware of using just np.prod in the denominator here
-    # Unless we use float64, values in the denominator > 13! will be incorrect
-    try:
-        y = (
-            np.sqrt(
-                (2 * j + 1)
-                / (4 * pi)
-                / np.prod(range(j - abs_m + 1, j + abs_m + 1), dtype=np.float64)
-            )
-            * y
-        )
-    except RuntimeWarning:
-        logger.error("debug")
 
+    y = sph_harm(abs_m, j, phi, theta)
     if m < 0:
-        y = np.sqrt(2) * np.sin(abs_m * phi) * y
+        y = np.sqrt(2) * np.imag(y)
     elif m > 0:
-        y = np.sqrt(2) * np.cos(abs_m * phi) * y
+        y = np.sqrt(2) * np.real(y)
+    else:
+        y = np.real(y)
 
     return y
 

src/aspire/denoising/denoised_src.py

@@ -40,11 +40,13 @@ def _images(self, start=0, num=np.inf, indices=None, batch_size=512):
             start = indices.min()
         end = indices.max()
 
-        im = np.empty((self.L, self.L, len(indices)))
+        nimgs = len(indices)
+        im = np.empty((nimgs, self.L, self.L))
 
-        logger.info(f"Loading {len(indices)} images complete")
-        for istart in range(start, end, batch_size):
+        logger.info(f"Loading {nimgs} images complete")
+        for istart in range(start, end + 1, batch_size):
             imgs_denoised = self.denoiser.images(istart, batch_size)
-            im = imgs_denoised.data
+            iend = min(istart + batch_size, end + 1)
+            im[istart:iend] = imgs_denoised.data
 
         return Image(im)

src/aspire/denoising/denoiser_cov2d.py

@@ -130,9 +130,7 @@ def denoise(self, covar_opt=None, batch_size=512):
 
         # Initialize the rotationally invariant covariance matrix of 2D images
         # A fixed batch size is used to go through each image
-        self.cov2d = BatchedRotCov2D(
-            self.src, self.basis, batch_size=batch_size, dtype=self.dtype
-        )
+        self.cov2d = BatchedRotCov2D(self.src, self.basis, batch_size=batch_size)
 
         default_opt = {
             "shrinker": "frobenius_norm",