From c2d1e09f07d9a828cf259df5d4abe17aedbc114a Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Fri, 26 Jan 2024 07:17:38 -0500 Subject: [PATCH 1/2] Black updates --- gallery/tutorials/tutorials/apple_picker.py | 1 + gallery/tutorials/tutorials/basic_image_array.py | 1 - gallery/tutorials/tutorials/cov3d_simulation.py | 1 + gallery/tutorials/tutorials/preprocess_imgs_sim.py | 1 + src/aspire/basis/fpswf_2d.py | 6 +++--- src/aspire/image/image.py | 4 +--- src/aspire/utils/logging.py | 1 + src/aspire/utils/misc.py | 1 + src/aspire/utils/resolution_estimation.py | 1 + 9 files changed, 10 insertions(+), 7 deletions(-) diff --git a/gallery/tutorials/tutorials/apple_picker.py b/gallery/tutorials/tutorials/apple_picker.py index 701e77dfe0..08ce582a65 100644 --- a/gallery/tutorials/tutorials/apple_picker.py +++ b/gallery/tutorials/tutorials/apple_picker.py @@ -4,6 +4,7 @@ We demonstrate ASPIRE's particle picking methods using the ``Apple`` class. """ + import logging import os diff --git a/gallery/tutorials/tutorials/basic_image_array.py b/gallery/tutorials/tutorials/basic_image_array.py index a5a0dce33f..d82077770f 100644 --- a/gallery/tutorials/tutorials/basic_image_array.py +++ b/gallery/tutorials/tutorials/basic_image_array.py @@ -8,7 +8,6 @@ whiten that noise using some tools from the ASPIRE pipeline. """ - import matplotlib.pyplot as plt import numpy as np from scipy.datasets import face diff --git a/gallery/tutorials/tutorials/cov3d_simulation.py b/gallery/tutorials/tutorials/cov3d_simulation.py index da75f998c8..85b90a8d24 100644 --- a/gallery/tutorials/tutorials/cov3d_simulation.py +++ b/gallery/tutorials/tutorials/cov3d_simulation.py @@ -5,6 +5,7 @@ This script illustrates the example of Covariance 3D estimation using simulation images generated from Gaussian blob volumes. """ + import logging import numpy as np diff --git a/gallery/tutorials/tutorials/preprocess_imgs_sim.py b/gallery/tutorials/tutorials/preprocess_imgs_sim.py index 0d398c6743..a9dd9d78b4 100644 --- a/gallery/tutorials/tutorials/preprocess_imgs_sim.py +++ b/gallery/tutorials/tutorials/preprocess_imgs_sim.py @@ -5,6 +5,7 @@ This script illustrates the preprocess steps implemented prior to starting the pipeline of reconstructing a 3D map using simulated 2D images. """ + import logging import os diff --git a/src/aspire/basis/fpswf_2d.py b/src/aspire/basis/fpswf_2d.py index 5476eed61d..21be9270d2 100644 --- a/src/aspire/basis/fpswf_2d.py +++ b/src/aspire/basis/fpswf_2d.py @@ -361,9 +361,9 @@ def _pswf_integration(self, images_nufft): ) m = self.pswf_radial_quad.shape[1] for i in range(self.n_max): - coef_vec_quad[ - :, self.indices_for_n[i] + np.arange(self.numel_for_n[i]) - ] = np.dot(self.blk_r[i], r_n_eval_mat[i * m : (i + 1) * m, :]).T + coef_vec_quad[:, self.indices_for_n[i] + np.arange(self.numel_for_n[i])] = ( + np.dot(self.blk_r[i], r_n_eval_mat[i * m : (i + 1) * m, :]).T + ) return coef_vec_quad diff --git a/src/aspire/image/image.py b/src/aspire/image/image.py index 11ee7f412a..787725df83 100644 --- a/src/aspire/image/image.py +++ b/src/aspire/image/image.py @@ -360,9 +360,7 @@ def downsample(self, ds_res): # 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.resolution**2 - ) + out = np.real(fft.centered_ifft2(crop_fx)) * (ds_res**2 / self.resolution**2) return self.__class__(out).stack_reshape(original_stack_shape) diff --git a/src/aspire/utils/logging.py b/src/aspire/utils/logging.py index fc60cc6818..7a3151a3ea 100644 --- a/src/aspire/utils/logging.py +++ b/src/aspire/utils/logging.py @@ -1,6 +1,7 @@ """ Miscellaneous Utilities that relate to logging. """ + import logging import os.path import subprocess diff --git a/src/aspire/utils/misc.py b/src/aspire/utils/misc.py index b113bcf85b..f72efbaf14 100644 --- a/src/aspire/utils/misc.py +++ b/src/aspire/utils/misc.py @@ -1,6 +1,7 @@ """ Miscellaneous Utilities that have no better place (yet). """ + import hashlib import importlib.resources import logging diff --git a/src/aspire/utils/resolution_estimation.py b/src/aspire/utils/resolution_estimation.py index 8e2fee99c9..4f97c22e7d 100644 --- a/src/aspire/utils/resolution_estimation.py +++ b/src/aspire/utils/resolution_estimation.py @@ -1,6 +1,7 @@ """ This module contains code for estimating resolution achieved by reconstructions. """ + import logging import warnings From 572ac02c041704359b9cf9d0e86214161aa47b71 Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Fri, 26 Jan 2024 07:09:40 -0500 Subject: [PATCH 2/2] Remove windows FINUFFT workaround, pins to 2.2.0 --- pyproject.toml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 71baee3982..e27e6b2a42 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,9 +31,7 @@ dependencies = [ "click", "confuse >= 2.0.0", "cvxpy", - # finufft 2.2.0 doesn't seemt to run on GHA Windows CI... - "finufft==2.2.0 ; sys_platform != 'win32'", - "finufft==2.1.0 ; sys_platform == 'win32'", + "finufft==2.2.0", "gemmi >= 0.4.8", "grpcio >= 1.54.2", "joblib",