From ec3293247573603c549482a787e5f54ac6e21621 Mon Sep 17 00:00:00 2001 From: Michal Grzadkowski Date: Thu, 19 Dec 2024 19:55:55 -0500 Subject: [PATCH] fixing logging typos and updating documentation --- README.md | 7 ++++--- cryodrgn/commands/abinit_het.py | 2 +- cryodrgn/commands/train_vae.py | 2 +- cryodrgn/commands_utils/make_movies.py | 6 ++++-- 4 files changed, 10 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 95f6bd7f..7d988fe7 100644 --- a/README.md +++ b/README.md @@ -19,8 +19,9 @@ cryoDRGN installation, training and analysis. A brief quick start is provided be For any feedback, questions, or bugs, please file a Github issue or start a Github discussion. -### New in Version 3.4.x -* [NEW] `cryodrgn plot_classes` for analysis visualizations colored by a given set of class labels +### Updates in Version 3.4.x +* [NEW] `cryodrgn_utils plot_classes` for analysis visualizations colored by a given set of class labels +* [NEW] `cryodrgn_utils make_movies` for animations of `analyze*` output volumes * implementing [automatic mixed-precision training](https://pytorch.org/docs/stable/amp.html) for ab-initio reconstruction for 2-4x speedup * support for RELION 3.1 .star files with separate optics tables, np.float16 number formats used in RELION .mrcs outputs @@ -33,7 +34,7 @@ For any feedback, questions, or bugs, please file a Github issue or start a Gith * official support for Python 3.11 -### New in Version 3.x +### Updates in Version 3.x The official release of [cryoDRGN-ET](https://www.biorxiv.org/content/10.1101/2023.08.18.553799v1) for heterogeneous subtomogram analysis. diff --git a/cryodrgn/commands/abinit_het.py b/cryodrgn/commands/abinit_het.py index f165d550..4d9e9c97 100644 --- a/cryodrgn/commands/abinit_het.py +++ b/cryodrgn/commands/abinit_het.py @@ -901,7 +901,7 @@ def main(args): ) if in_dim % 8 != 0: logger.warning( - f"Masked input image dimension {in_dim} is not a mutiple of 8 " + f"Masked input image dimension {in_dim} is not a multiple of 8 " "-- AMP training speedup is not optimized!" ) diff --git a/cryodrgn/commands/train_vae.py b/cryodrgn/commands/train_vae.py index 75535127..88f6506d 100755 --- a/cryodrgn/commands/train_vae.py +++ b/cryodrgn/commands/train_vae.py @@ -855,7 +855,7 @@ def main(args: argparse.Namespace) -> None: ) if in_dim % 8 != 0: logger.warning( - f"Masked input image dimension {in_dim} is not a mutiple of 8 " + f"Masked input image dimension {in_dim} is not a multiple of 8 " "-- AMP training speedup is not optimized!" ) diff --git a/cryodrgn/commands_utils/make_movies.py b/cryodrgn/commands_utils/make_movies.py index 34e0fc57..ae64b515 100644 --- a/cryodrgn/commands_utils/make_movies.py +++ b/cryodrgn/commands_utils/make_movies.py @@ -1,4 +1,7 @@ -"""Make mp4 movies of .mrc's produced by analyze* commands +"""Make MP4 movies of .mrc volumes produced by cryodrgn analyze* commands. + +You must install ChimeraX under the alias `chimerax` before running this command, see: +https://www.cgl.ucsf.edu/chimerax/download.html Example usage ------------- @@ -9,7 +12,6 @@ $ cryodrgn_utils make_movies spr_runs/07/out 19 volume --name=front --iso=210 --camera="0.12868,-0.9576,0.25778,95.4,-0.85972,-0.23728,-0.45231,15.356,0.4943,-0.16341,-0.8538,-33.755" """ - import argparse import os from datetime import datetime as dt