From eee5ef3405e3613b84a65ee5bea5a9235d2c8d1e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 17 Nov 2025 13:59:21 -0800 Subject: [PATCH 1/6] Add github action to codespell main on push and PRs --- .github/workflows/codespell.yml | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 .github/workflows/codespell.yml diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 0000000..489bbcc --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,25 @@ +# Codespell configuration is within setup.cfg +--- +name: Codespell + +on: + push: + branches: [main] + pull_request: + branches: [main] + +permissions: + contents: read + +jobs: + codespell: + name: Check for spelling errors + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Annotate locations with typos + uses: codespell-project/codespell-problem-matcher@v1 + - name: Codespell + uses: codespell-project/actions-codespell@v2 From c170f874d800a4d14659674e69a54d608f878ca9 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 17 Nov 2025 14:07:19 -0800 Subject: [PATCH 2/6] [DATALAD RUNCMD] Fix common Copyright typo === Do not change lines below === { "chain": [], "cmd": "git-sedi Copright Copyright", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- docs/conf.py | 2 +- facemap/__init__.py | 2 +- facemap/__main__.py | 2 +- facemap/gui/cluster.py | 2 +- facemap/gui/gui.py | 2 +- facemap/gui/guiparts.py | 2 +- facemap/gui/help_windows.py | 2 +- facemap/gui/io.py | 2 +- facemap/gui/menus.py | 2 +- facemap/keypoints.py | 2 +- facemap/neural_prediction/keypoints_utils.py | 2 +- facemap/neural_prediction/neural_activity.py | 2 +- facemap/neural_prediction/neural_model.py | 2 +- facemap/neural_prediction/prediction_utils.py | 2 +- facemap/pose/datasets.py | 2 +- facemap/pose/facemap_network.py | 2 +- facemap/pose/model_loader.py | 2 +- facemap/pose/model_training.py | 2 +- facemap/pose/pose.py | 2 +- facemap/pose/pose_gui.py | 2 +- facemap/pose/pose_helper_functions.py | 2 +- facemap/pose/refine_pose.py | 2 +- facemap/pose/transforms.py | 2 +- facemap/process.py | 2 +- facemap/pupil.py | 2 +- facemap/roi.py | 2 +- facemap/running.py | 2 +- facemap/utils.py | 2 +- facemap/version.py | 2 +- paper/fig1.py | 2 +- paper/fig3.py | 2 +- paper/fig4.py | 2 +- paper/fig_utils.py | 2 +- paper/kpsproc.py | 2 +- paper/neuralpred.py | 2 +- paper/suppfigs.py | 2 +- setup.py | 2 +- tests/conftest.py | 2 +- tests/test_import.py | 2 +- tests/test_neural_prediction_output.py | 2 +- tests/test_pose_estimation_output.py | 2 +- tests/test_svd_output.py | 2 +- 42 files changed, 42 insertions(+), 42 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index a939caf..3a38620 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ # Configuration file for the Sphinx documentation builder. # diff --git a/facemap/__init__.py b/facemap/__init__.py index bf670cd..00e4c1f 100644 --- a/facemap/__init__.py +++ b/facemap/__init__.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ name = "facemap" from facemap.version import version, version_str \ No newline at end of file diff --git a/facemap/__main__.py b/facemap/__main__.py index f2bd05b..857c23b 100644 --- a/facemap/__main__.py +++ b/facemap/__main__.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import argparse import time diff --git a/facemap/gui/cluster.py b/facemap/gui/cluster.py index 8aaba8b..3f71509 100644 --- a/facemap/gui/cluster.py +++ b/facemap/gui/cluster.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os diff --git a/facemap/gui/gui.py b/facemap/gui/gui.py index ee60f65..acc8204 100644 --- a/facemap/gui/gui.py +++ b/facemap/gui/gui.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os import sys diff --git a/facemap/gui/guiparts.py b/facemap/gui/guiparts.py index 0024771..ce97c29 100644 --- a/facemap/gui/guiparts.py +++ b/facemap/gui/guiparts.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import numpy as np import pyqtgraph as pg diff --git a/facemap/gui/help_windows.py b/facemap/gui/help_windows.py index fbd1fc0..b5303ef 100644 --- a/facemap/gui/help_windows.py +++ b/facemap/gui/help_windows.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os import typing diff --git a/facemap/gui/io.py b/facemap/gui/io.py index ba54401..57e7979 100644 --- a/facemap/gui/io.py +++ b/facemap/gui/io.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import glob import os diff --git a/facemap/gui/menus.py b/facemap/gui/menus.py index 6291705..4c668ee 100644 --- a/facemap/gui/menus.py +++ b/facemap/gui/menus.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ from qtpy.QtWidgets import QAction from qtpy.QtGui import QGuiApplication diff --git a/facemap/keypoints.py b/facemap/keypoints.py index ae8b087..a7d1e61 100644 --- a/facemap/keypoints.py +++ b/facemap/keypoints.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os diff --git a/facemap/neural_prediction/keypoints_utils.py b/facemap/neural_prediction/keypoints_utils.py index 05d9f20..d4e25b9 100644 --- a/facemap/neural_prediction/keypoints_utils.py +++ b/facemap/neural_prediction/keypoints_utils.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os diff --git a/facemap/neural_prediction/neural_activity.py b/facemap/neural_prediction/neural_activity.py index c651f24..0004159 100644 --- a/facemap/neural_prediction/neural_activity.py +++ b/facemap/neural_prediction/neural_activity.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import numpy as np diff --git a/facemap/neural_prediction/neural_model.py b/facemap/neural_prediction/neural_model.py index 87294f6..3aa2f17 100644 --- a/facemap/neural_prediction/neural_model.py +++ b/facemap/neural_prediction/neural_model.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import time from io import StringIO diff --git a/facemap/neural_prediction/prediction_utils.py b/facemap/neural_prediction/prediction_utils.py index b294452..e4fd16d 100644 --- a/facemap/neural_prediction/prediction_utils.py +++ b/facemap/neural_prediction/prediction_utils.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os import time diff --git a/facemap/pose/datasets.py b/facemap/pose/datasets.py index 63eff9b..ce4ca33 100644 --- a/facemap/pose/datasets.py +++ b/facemap/pose/datasets.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os from glob import glob diff --git a/facemap/pose/facemap_network.py b/facemap/pose/facemap_network.py index 729053f..867398e 100644 --- a/facemap/pose/facemap_network.py +++ b/facemap/pose/facemap_network.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Network ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ import numpy as np diff --git a/facemap/pose/model_loader.py b/facemap/pose/model_loader.py index 9599b33..23b5b8a 100644 --- a/facemap/pose/model_loader.py +++ b/facemap/pose/model_loader.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ """ Facemap model trained for generating pose estimates. Contains functions for: diff --git a/facemap/pose/model_training.py b/facemap/pose/model_training.py index 34df575..4288ff1 100644 --- a/facemap/pose/model_training.py +++ b/facemap/pose/model_training.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ ## Import packages import os diff --git a/facemap/pose/pose.py b/facemap/pose/pose.py index 2dd42c0..b3bd102 100644 --- a/facemap/pose/pose.py +++ b/facemap/pose/pose.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os import pickle diff --git a/facemap/pose/pose_gui.py b/facemap/pose/pose_gui.py index 0a06fe7..bc63d79 100644 --- a/facemap/pose/pose_gui.py +++ b/facemap/pose/pose_gui.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import numpy as np import pyqtgraph as pg diff --git a/facemap/pose/pose_helper_functions.py b/facemap/pose/pose_helper_functions.py index 99d4517..a71e6f8 100644 --- a/facemap/pose/pose_helper_functions.py +++ b/facemap/pose/pose_helper_functions.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import random from platform import python_version diff --git a/facemap/pose/refine_pose.py b/facemap/pose/refine_pose.py index 24caf4a..c43d82a 100644 --- a/facemap/pose/refine_pose.py +++ b/facemap/pose/refine_pose.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os import shutil diff --git a/facemap/pose/transforms.py b/facemap/pose/transforms.py index 8d4fa10..36d1601 100644 --- a/facemap/pose/transforms.py +++ b/facemap/pose/transforms.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ """ Facemap functions for: diff --git a/facemap/process.py b/facemap/process.py index b688dac..049b650 100644 --- a/facemap/process.py +++ b/facemap/process.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os import time diff --git a/facemap/pupil.py b/facemap/pupil.py index e9eb78e..a0dd074 100644 --- a/facemap/pupil.py +++ b/facemap/pupil.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import numpy as np from scipy.ndimage import gaussian_filter diff --git a/facemap/roi.py b/facemap/roi.py index c8782ca..ece978d 100644 --- a/facemap/roi.py +++ b/facemap/roi.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import numpy as np import pyqtgraph as pg diff --git a/facemap/running.py b/facemap/running.py index f08a162..ca76a5e 100644 --- a/facemap/running.py +++ b/facemap/running.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ # outputs the dx, dy offsets between frames by registering frame N to frame # N-1. If the movement is larger than half the frame size, outputs NaN. diff --git a/facemap/utils.py b/facemap/utils.py index 65bf905..5519144 100644 --- a/facemap/utils.py +++ b/facemap/utils.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import cv2 import h5py diff --git a/facemap/version.py b/facemap/version.py index 50515d4..472aa68 100644 --- a/facemap/version.py +++ b/facemap/version.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import sys diff --git a/paper/fig1.py b/paper/fig1.py index 2e05ace..3e38beb 100644 --- a/paper/fig1.py +++ b/paper/fig1.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import cv2 import matplotlib diff --git a/paper/fig3.py b/paper/fig3.py index b834876..a7aea67 100644 --- a/paper/fig3.py +++ b/paper/fig3.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import matplotlib.pyplot as plt import torch diff --git a/paper/fig4.py b/paper/fig4.py index d546c20..dff4fd4 100644 --- a/paper/fig4.py +++ b/paper/fig4.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import matplotlib.pyplot as plt import torch diff --git a/paper/fig_utils.py b/paper/fig_utils.py index df39755..2e50fc4 100644 --- a/paper/fig_utils.py +++ b/paper/fig_utils.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import string diff --git a/paper/kpsproc.py b/paper/kpsproc.py index e10fc38..3e8c017 100644 --- a/paper/kpsproc.py +++ b/paper/kpsproc.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os diff --git a/paper/neuralpred.py b/paper/neuralpred.py index 8a279c3..1abbd20 100644 --- a/paper/neuralpred.py +++ b/paper/neuralpred.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os import sys diff --git a/paper/suppfigs.py b/paper/suppfigs.py index e860a3c..750830d 100644 --- a/paper/suppfigs.py +++ b/paper/suppfigs.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import fig4 import matplotlib.pyplot as plt diff --git a/setup.py b/setup.py index 8f258d1..92a15d0 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import setuptools diff --git a/tests/conftest.py b/tests/conftest.py index db458f1..ffb792d 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ import os import shutil diff --git a/tests/test_import.py b/tests/test_import.py index 6083f32..d7900bc 100644 --- a/tests/test_import.py +++ b/tests/test_import.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ " Test imports for facemap package " diff --git a/tests/test_neural_prediction_output.py b/tests/test_neural_prediction_output.py index 44d9a40..caabbd2 100644 --- a/tests/test_neural_prediction_output.py +++ b/tests/test_neural_prediction_output.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ " Test Facemap neural prediction output " diff --git a/tests/test_pose_estimation_output.py b/tests/test_pose_estimation_output.py index 4adb6da..87e2ff7 100644 --- a/tests/test_pose_estimation_output.py +++ b/tests/test_pose_estimation_output.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ "Test Facemap's pose estimation output " import os diff --git a/tests/test_svd_output.py b/tests/test_svd_output.py index e1a51c7..82b5ac2 100644 --- a/tests/test_svd_output.py +++ b/tests/test_svd_output.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ "Test facemap SVD processing outputs for single and multiple videos" import os From 1f1e30b5d668047503aaa60cb727e3de74146cc8 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 17 Nov 2025 13:59:21 -0800 Subject: [PATCH 3/6] Add rudimentary codespell config --- setup.cfg | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/setup.cfg b/setup.cfg index bb08343..2b84524 100644 --- a/setup.cfg +++ b/setup.cfg @@ -10,3 +10,11 @@ extend-ignore=E203 per-file-ignores = */__init__.py: F401, F403 + +[codespell] +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +skip = .git* +check-hidden = true +ignore-regex = ^\s*"image/\S+": ".*|.{300,}|\bTung\b +# some unfortunate names of variables +ignore-words-list = dout,nd,gaus,dum,gaus' From df6c55e3f8c4a691141b7afbebb90ecb83ba422e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 17 Nov 2025 14:09:55 -0800 Subject: [PATCH 4/6] pragma to ignore mot --- facemap/process.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/facemap/process.py b/facemap/process.py index 049b650..2c2b85e 100644 --- a/facemap/process.py +++ b/facemap/process.py @@ -710,7 +710,7 @@ def run( Lybin, Lxbin, iinds = binned_inds(Ly, Lx, sbin) LYbin, LXbin, sybin, sxbin = utils.video_placement(Lybin, Lxbin) - # number of mot/mov ROIs + # number of mot/mov ROIs # codespell:ignore nroi = 0 if rois is not None: for r in rois: From a69940d82fc5b8ca8dc97a1b7cd27d1cd8b00419 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 17 Nov 2025 14:10:00 -0800 Subject: [PATCH 5/6] [DATALAD RUNCMD] run codespell throughout fixing typos automagically (but ignoring overall fail due to ambigous ones) === Do not change lines below === { "chain": [], "cmd": "codespell -w || :", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- README.md | 4 ++-- docs/installation.md | 2 +- docs/pose_tracking_gui_tutorial.md | 4 ++-- docs/pose_tracking_gui_tutorial.rst | 2 +- docs/svd_matlab_tutorial.md | 2 +- facemap/gui/gui.py | 4 ++-- facemap/pose/datasets.py | 2 +- facemap/pose/transforms.py | 2 +- matlab/pupil/fitMVGaus.m | 4 ++-- 9 files changed, 13 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index cbcfa68..e829c71 100644 --- a/README.md +++ b/README.md @@ -121,7 +121,7 @@ Next you can extract information from the videos like track keypoints, compute m ## I. Pose tracking -tracker +tracker Facemap provides a trained network for tracking distinct keypoints on the mouse face from different camera views (some examples shown below). Check the `keypoints` box then click `process`. Next a bounding box will appear -- focus this on the face as shown below. Then the processed keypoints `*.h5` file will be saved in the output folder along with the corresponding metadata file `*.pkl`. @@ -131,7 +131,7 @@ For more details on using the tracker, please refer to the [GUI Instructions](ht

view1 -view2 +view2

### 📢 User contributions 📹 📷 diff --git a/docs/installation.md b/docs/installation.md index 836b00a..835b826 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -19,7 +19,7 @@ If you are on Yosemite Mac OS, PyQt doesn't work, and you won't be able to insta The software has been heavily tested on Ubuntu 18.04, and less well tested on Windows 10 and Mac OS. Please post an issue if you have installation problems. -### Pyhton dependencies +### Python dependencies Facemap python relies on these awesome packages: - [pyqtgraph](http://pyqtgraph.org/) diff --git a/docs/pose_tracking_gui_tutorial.md b/docs/pose_tracking_gui_tutorial.md index 7f811db..988533d 100644 --- a/docs/pose_tracking_gui_tutorial.md +++ b/docs/pose_tracking_gui_tutorial.md @@ -1,12 +1,12 @@ # Pose tracking **(GUI)** :mouse: -tracker +tracker The latest python version is integrated with Facemap network for tracking 14 distinct keypoints on mouse face and an additional point for tracking paw. The keypoints can be tracked from different camera views (some examples shown below).

view1 -view2 +view2

## Generate keypoints diff --git a/docs/pose_tracking_gui_tutorial.rst b/docs/pose_tracking_gui_tutorial.rst index fa2f1a2..029a46b 100644 --- a/docs/pose_tracking_gui_tutorial.rst +++ b/docs/pose_tracking_gui_tutorial.rst @@ -38,7 +38,7 @@ Follow the steps below to generate keypoints for your videos: - A dialog box for selecting a bounding box for the face will appear. Drag the red rectangle to select region of interest on the frame where the keypoints will be tracked. Please ensure that the - bouding box is focused on the face where all the keypoints will be + bounding box is focused on the face where all the keypoints will be visible. See example frames `here `__. If a ‘Face (pose)’ ROI has already been added then this step will be skipped. diff --git a/docs/svd_matlab_tutorial.md b/docs/svd_matlab_tutorial.md index db4b6aa..9d1ccd5 100644 --- a/docs/svd_matlab_tutorial.md +++ b/docs/svd_matlab_tutorial.md @@ -97,7 +97,7 @@ You can draw areas to be included and excluded in the multivideo SVD (or single The motion energy is then computed from these non-red pixels. -### Proccessed output +### Processed output The GUIs create one file for all videos (saved in current folder), the processed mat file has name "videofile_proc.mat". diff --git a/facemap/gui/gui.py b/facemap/gui/gui.py index acc8204..f8d6b8b 100644 --- a/facemap/gui/gui.py +++ b/facemap/gui/gui.py @@ -836,7 +836,7 @@ def add_pose_model(self, pose_model_path=None): msg = QMessageBox() msg.setIcon(QMessageBox.Icon.Critical) msg.setText("Pose model not added. Error: " + str(e)) - msg.setWindowTitle("Eror") + msg.setWindowTitle("Error") msg.setStandardButtons(QMessageBox.StandardButton.Ok) msg.exec_() @@ -2250,7 +2250,7 @@ def update_ROI_vis_comboBox(self): def display_ROI(self): """ - Plot selected ROI on visualizaiton window + Plot selected ROI on visualization window """ self.roi_display_combobox.show() roi_request = self.roi_display_combobox.currentText() diff --git a/facemap/pose/datasets.py b/facemap/pose/datasets.py index ce4ca33..e78eebb 100644 --- a/facemap/pose/datasets.py +++ b/facemap/pose/datasets.py @@ -254,7 +254,7 @@ def load_keypoints_h5(self): if len(annotation_files) == 0: raise ValueError("No .h5 files found in the directory") - # Landmarks dataframe concatentation + # Landmarks dataframe concatenation landmarks = pd.DataFrame() for f in annotation_files: df = pd.read_hdf(f) diff --git a/facemap/pose/transforms.py b/facemap/pose/transforms.py index 36d1601..baabee0 100644 --- a/facemap/pose/transforms.py +++ b/facemap/pose/transforms.py @@ -82,7 +82,7 @@ def randomize_bbox_coordinates(bbox, im_shape, random_factor_range=(0.1, 0.3)): im_shape: tuple of size (2,) image shape in order Ly, Lx random_factor_range: tuple of size (2,) - range of random factor to use for expaning bounding box + range of random factor to use for expanding bounding box Returns ------- bbox: tuple of size (4,) diff --git a/matlab/pupil/fitMVGaus.m b/matlab/pupil/fitMVGaus.m index c751657..316635c 100644 --- a/matlab/pupil/fitMVGaus.m +++ b/matlab/pupil/fitMVGaus.m @@ -1,10 +1,10 @@ % fit 2D gaussian to cell with lam pixel weights function params = fitMVGaus(iy, ix, lam0, thres) -% normalize pixel weigths +% normalize pixel weights lam = lam0; -% iteratively fit the Guassian, excluding outliers +% iteratively fit the Gaussian, excluding outliers for k = 1:5 lam = lam / sum(lam); mu = [sum(lam.*iy) sum(lam.*ix)]; From 41f53729db01eebb644108354a7efe82100f2f02 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Mon, 17 Nov 2025 14:10:49 -0800 Subject: [PATCH 6/6] [DATALAD RUNCMD] chore: run codespell throughout fixing a few typos interactively === Do not change lines below === { "chain": [], "cmd": "codespell -w -i 3 -C 4", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- docs/pose_tracking_gui_tutorial.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/pose_tracking_gui_tutorial.rst b/docs/pose_tracking_gui_tutorial.rst index 029a46b..72f4f6b 100644 --- a/docs/pose_tracking_gui_tutorial.rst +++ b/docs/pose_tracking_gui_tutorial.rst @@ -17,7 +17,7 @@ Follow the steps below to generate keypoints for your videos: - For processing single video, select ``Load video``. Alternatively, for processing multiple videos, select ``Load multiple videos`` to select the folder containing the videos. (Note: Pose estimation - for multipl videos is only supported for videos recorded + for multiple videos is only supported for videos recorded simultaneously i.e. have the same time duration and frame rate). (Optional) Set output folder