Develop~~>Main v0.14.2

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.14.1
+current_version = 0.14.2
 commit = True
 tag = True
 

.github/workflows/workflow.yml

@@ -156,7 +156,7 @@ jobs:
         shell: bash -el {0}
     strategy:
       matrix:
-        os: [ubuntu-latest, ubuntu-22.04, macOS-latest, macOS-13]
+        os: [ubuntu-latest, ubuntu-22.04, macOS-latest, macOS-14]
         backend: [default, openblas]
         python-version: ['3.9']
         include:

README.md

@@ -5,7 +5,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5657281.svg)](https://doi.org/10.5281/zenodo.5657281)
 [![Downloads](https://static.pepy.tech/badge/aspire/month)](https://pepy.tech/project/aspire)
 
-# ASPIRE - Algorithms for Single Particle Reconstruction - v0.14.1
+# ASPIRE - Algorithms for Single Particle Reconstruction - v0.14.2
 
 The ASPIRE-Python project supersedes [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: v0.14.1 https://doi.org/10.5281/zenodo.5657281
+ComputationalCryoEM/ASPIRE-Python: v0.14.2 https://doi.org/10.5281/zenodo.5657281
 
 ```
 

docs/source/conf.py

@@ -86,7 +86,7 @@
 # built documents.
 #
 # The full version, including alpha/beta/rc tags.
-release = version = "0.14.1"
+release = version = "0.14.2"
 
 # 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 v0.14.1
+Aspire v0.14.2
 ==============
 
 Algorithms for Single Particle Reconstruction

environment-accelerate.yml

@@ -7,8 +7,8 @@ channels:
 dependencies:
   - pip
   - python=3.9
-  - numpy=1.24.1
-  - scipy=1.10.1
+  - numpy=1.25.0
+  - scipy=1.13.1
   - scikit-learn
   - scikit-image
   - libblas=*=*accelerate

environment-default.yml

@@ -7,7 +7,7 @@ channels:
 dependencies:
   - pip
   - python=3.9
-  - numpy=1.23.5
-  - scipy=1.9.3
+  - numpy=1.25.0
+  - scipy=1.13.1
   - scikit-learn
   - scikit-image

environment-intel.yml

@@ -7,8 +7,8 @@ channels:
 dependencies:
   - pip
   - python=3.9
-  - numpy=1.23.5
-  - scipy=1.9.3
+  - numpy=1.25.0
+  - scipy=1.13.1
   - scikit-learn
   - scikit-image
   - mkl_fft

environment-openblas.yml

@@ -7,8 +7,8 @@ channels:
 dependencies:
   - pip
   - python=3.9
-  - numpy=1.23.5
-  - scipy=1.9.3
+  - numpy=1.25.0
+  - scipy=1.13.1
   - scikit-learn
   - scikit-image
   - libblas=*=*openblas

environment-win64.yml

@@ -7,8 +7,8 @@ channels:
 dependencies:
   - pip
   - python=3.9
-  - numpy=1.23.5
-  - scipy=1.9.3
+  - numpy=1.25.0
+  - scipy=1.13.1
   - scikit-learn
   - scikit-image
   - mkl=2024.1.*  # possible regression impacts eig solver in later versions up to 2025.0

gallery/experiments/save_simulation_relion_reconstruct.py

@@ -0,0 +1,80 @@
+"""
+Simulated Stack to RELION Reconstruction
+========================================
+
+This experiment shows how to:
+
+1. build a synthetic dataset with ASPIRE,
+2. write the stack via ``ImageSource.save`` so RELION can consume it, and
+3. call :code:`relion_reconstruct` on the saved STAR file.
+"""
+
+# %%
+# Imports
+# -------
+
+import logging
+from pathlib import Path
+
+import numpy as np
+
+from aspire.downloader import emdb_2660
+from aspire.noise import WhiteNoiseAdder
+from aspire.operators import RadialCTFFilter
+from aspire.source import Simulation
+
+logger = logging.getLogger(__name__)
+
+
+# %%
+# Configuration
+# -------------
+# We set a few parameters to initialize the Simulation.
+# You can safely alter ``n_particles`` (or change the defocus values, etc.) when
+# trying this interactively; the defaults here are chosen for demonstrative purposes.
+
+output_dir = Path("relion_save_demo")
+output_dir.mkdir(exist_ok=True)
+
+n_particles = 512
+snr = 0.5
+defocus = np.linspace(
+    15000, 25000, 7
+)  # defocus values for the radial CTF filters (angstroms)
+star_file = f"sim_n{n_particles}.star"
+star_path = output_dir / star_file
+
+# %%
+# Volume and Filters
+# ------------------
+# Start from the EMDB-2660 ribosome map and build a small set of radial CTF filters
+# that RELION will recover as optics groups.
+
+vol = emdb_2660()
+ctf_filters = [RadialCTFFilter(defocus=d) for d in defocus]
+
+
+# %%
+# Simulate, Add Noise, Save
+# -------------------------
+# Initialize the Simulation:
+# mix the CTFs across the stack, add white noise at a target SNR,
+# and write the particles and metadata to a RELION-compatible STAR/MRC stack.
+
+sim = Simulation(
+    n=n_particles,
+    vols=vol,
+    unique_filters=ctf_filters,
+    noise_adder=WhiteNoiseAdder.from_snr(snr),
+)
+sim.save(star_path, overwrite=True)
+
+
+# %%
+# Running ``relion_reconstruct``
+# ------------------------------
+# ``relion_reconstruct`` is an external RELION command, so we just show the call.
+# Run this, from the output directory, in a RELION-enabled shell after generating
+# the STAR file above.
+
+logger.info(f"relion_reconstruct --i {star_file} " f"--o 'relion_recon.mrc' --ctf")

gallery/tutorials/tutorials/class_averaging.py

@@ -226,6 +226,7 @@
 est_shifts = avgs.averager.shifts
 est_dot_products = avgs.averager.dot_products
 
+# These are dictionaries mapping each class to arrays of attributes.
 print(f"Estimated Rotations: {est_rotations}")
 print(f"Estimated Shifts: {est_shifts}")
 print(f"Estimated Dot Products: {est_dot_products}")
@@ -241,7 +242,12 @@
 original_img_nbr = noisy_src.images[original_img_nbr_idx].asnumpy()[0]
 
 # Rotate using estimated rotations.
-angle = est_rotations[0, nbr] * 180 / np.pi
+# First retrieve all angles for the `review_class` (original_img_0_idx),
+#   then lookup the specific neighbor `nbr`
+assert (
+    original_img_0_idx == review_class
+), "DebugClassAvgSource should retain original source image ordering"
+angle = est_rotations[original_img_0_idx][nbr] * 180 / np.pi
 if reflections[nbr]:
     print("Reflection reported.")
     original_img_nbr = np.flipud(original_img_nbr)

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aspire"
-version = "0.14.1"
+version = "0.14.2"
 description = "Algorithms for Single Particle Reconstruction"
 readme = "README.md" # Optional
 requires-python = ">=3.9"
@@ -37,7 +37,7 @@ dependencies = [
     "joblib",
     "matplotlib >= 3.2.0",
     "mrcfile",
-    "numpy>=1.21.5",
+    "numpy>=1.25.0",
     "packaging",
     "pooch>=1.7.0",
     "pillow",

src/aspire/__init__.py

@@ -15,7 +15,7 @@
 from aspire.exceptions import handle_exception
 
 # version in maj.min.bld format
-__version__ = "0.14.1"
+__version__ = "0.14.2"
 
 
 # Setup `confuse` config