Merge pull request #455 from ComputationalCryoEM/develop

Develop ~~> Master

Author: garrettwrong

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.7.0
+current_version = 0.8.0
 commit = True
 tag = True
 

.codecov.yml

@@ -1,2 +1,13 @@
+# We take the defaults except for treating as informational only.
+# This provides feedback without erroring the entire CI pipeline.
+
+coverage:
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true
 ignore:
-  - "*/tests/*”
+  - "*/tests/*"

README.md

@@ -4,7 +4,7 @@
 [![Github Actions Status](https://github.com/ComputationalCryoEM/ASPIRE-Python/actions/workflows/workflow.yml/badge.svg)](https://github.com/ComputationalCryoEM/ASPIRE-Python/actions/workflows/workflow.yml)
 [![codecov](https://codecov.io/gh/ComputationalCryoEM/ASPIRE-Python/branch/master/graph/badge.svg?token=3XFC4VONX0)](https://codecov.io/gh/ComputationalCryoEM/ASPIRE-Python)
 
-# ASPIRE - Algorithms for Single Particle Reconstruction - v0.7.0
+# ASPIRE - Algorithms for Single Particle Reconstruction - v0.8.0
 
 This is the Python version to supersede the [Matlab ASPIRE](https://github.com/PrincetonUniversity/aspire).
 
@@ -41,26 +41,26 @@ After cloning this repo, the simplest option is to use Anaconda 64-bit for your
 ```
 cd /path/to/git/clone/folder
 
-# Create's the conda environment and installs base dependencies.
+# Creates the conda environment and installs base dependencies.
 conda env create -f environment.yml --name aspire_dev
 
 # Enable the environment
 conda activate aspire_dev
 
-# Install the aspire package in a locally editable way:
-pip install -e .
+# Install the aspire package in a locally editable way,
+# and additionally installs the developer tools extras:
+pip install -e ".[dev]"
+
 ```
 
 If you prefer not to use Anaconda, or want to manage environments yourself, you should be able to use `pip` with Python >= 3.6.
 Please see the full documentation for details.
 
-You may optionally install additional packages:
+You may optionally install additional packages for GPU extensions:
 
 ```
-# Additional GPU packages (reqires CUDA)
+# Additional GPU packages (requires CUDA)
 pip install -e ".[gpu]"
-# Additional developer tools
-pip install -e ".[dev]"
 ```
 
 ### Make sure everything works

docs/source/conf.py

@@ -64,7 +64,7 @@
 # built documents.
 #
 # The full version, including alpha/beta/rc tags.
-release = version = "0.7.0"
+release = version = "0.8.0"
 
 # 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 v0.7.0
+Aspire v0.8.0
 ==============
 
 Algorithms for Single Particle Reconstruction

setup.py

@@ -9,7 +9,7 @@ def read(fname):
 
 setup(
     name="aspire",
-    version="0.7.0",
+    version="0.8.0",
     data_files=[
         ("", ["src/aspire/config.ini"]),
         ("", ["src/aspire/logging.conf"]),
@@ -24,14 +24,15 @@ def read(fname):
     author_email="[email protected]",
     install_requires=[
         "click",
-        "finufft",
+        "finufft==2.0.0",
         "importlib_resources>=1.0.2",
         "joblib",
         "matplotlib",
         "mrcfile",
         "numpy==1.16",
         "pandas==0.25.3",
         "pyfftw",
+        "PyWavelets",
         "pillow",
         "scipy==1.4.0",
         "scikit-learn",

src/aspire/__init__.py

@@ -10,7 +10,7 @@
 from aspire.exceptions import handle_exception
 
 # version in maj.min.bld format
-__version__ = "0.7.0"
+__version__ = "0.8.0"
 
 # Implements some code that writes out exceptions to 'aspire.err.log'.
 config = Config(read_text(aspire, "config.ini"))

src/aspire/apple/picking.py

@@ -1,5 +1,6 @@
 import logging
 import os
+import warnings
 from concurrent import futures
 
 import mrcfile
@@ -104,8 +105,34 @@ def read_mrc(self):
             Micrograph image.
         """
 
-        with mrcfile.open(self.filename, mode="r+", permissive=True) as mrc:
-            im = mrc.data.astype("float")
+        # mrcfile tends to yield many warnings about EMPIAR datasets being corrupt
+        # These warnings generally seem benign, and the message could be clearer
+        # The following code handles the warnings via ASPIRE's logger
+        with warnings.catch_warnings(record=True) as ws:
+            # Cause all warnings to always be triggered in this context
+            warnings.simplefilter("always")
+
+            # Try to open the mrcfile
+            with mrcfile.open(self.filename, mode="r", permissive=True) as mrc:
+                im = mrc.data.astype("float")
+
+            # Log each mrcfile warning to debug log, noting the associated file
+            for w in ws:
+                logger.debug(
+                    "In APPLE.picking mrcfile.open reports corruption for"
+                    f" {self.filename} warning: {w.message}"
+                )
+
+            # Log a single warning to user
+            # Give context and note assocated filename
+            if len(ws) > 0:
+                logger.warning(
+                    f"APPLE.picking mrcfile reporting {len(ws)} corruptions."
+                    " Most likely this is a problem with the header contents."
+                    " Details written to debug log."
+                    f" APPLE will attempt to continue processing {self.filename}"
+                )
+
         self.original_im = im
 
         # Discard outer pixels
@@ -121,7 +148,9 @@ def read_mrc(self):
         size = tuple((np.array(im.shape) / config.apple.mrc_shrink_factor).astype(int))
 
         # Note, float64 required for signal.correlate call accuracy.
-        im = np.array(Image.fromarray(im).resize(size, Image.BICUBIC), dtype=np.float64)
+        im = np.asarray(Image.fromarray(im).resize(size, Image.BICUBIC)).astype(
+            np.float64, copy=False
+        )
 
         im = signal.correlate(
             im,

src/aspire/basis/__init__.py

@@ -1,11 +1,19 @@
+# We'll tell isort not to sort these base classes
+# isort: off
+
 from .basis import Basis
+from .steerable import SteerableBasis2D
+
+# isort: on
+
 from .dirac import DiracBasis
 from .fb_2d import FBBasis2D
 from .fb_3d import FBBasis3D
 from .ffb_2d import FFBBasis2D
 from .ffb_3d import FFBBasis3D
 from .fpswf_2d import FPSWFBasis2D
 from .fpswf_3d import FPSWFBasis3D
+from .fspca import FSPCABasis
 from .polar_2d import PolarBasis2D
 from .pswf_2d import PSWFBasis2D
 from .pswf_3d import PSWFBasis3D

src/aspire/basis/basis.py

@@ -80,7 +80,7 @@ def _getfbzeros(self):
                 (z, np.zeros(max_num_zeros - len(z), dtype=self.dtype))
             )
 
-        self.r0 = m_reshape(np.hstack(zeros), (-1, self.ell_max + 1))
+        self.r0 = m_reshape(np.hstack(zeros), (-1, self.ell_max + 1)).astype(self.dtype)
 
     def _build(self):
         """