diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 000000000..a242d6f2e --- /dev/null +++ b/.codespellrc @@ -0,0 +1,4 @@ +[codespell] +skip = .git,*.pdf,*.svg +ignore-regex = ("image/png": *".*|hSI) +ignore-words-list = iterm,bloaded diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 000000000..3ebbf5504 --- /dev/null +++ b/.github/workflows/codespell.yml @@ -0,0 +1,22 @@ +--- +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@v3 + - name: Codespell + uses: codespell-project/actions-codespell@v2 diff --git a/conftest.py b/conftest.py index 6109c22be..d1ce5a859 100644 --- a/conftest.py +++ b/conftest.py @@ -37,7 +37,7 @@ def download_cached_inputs(data_path): extract_zip(data_path.joinpath('test_inputs.zip'), cached_inputs_url, data_path) def initialize_ops(tmpdir, data_dir): - """Initializes ops. Used for both the test_ops function above and for generate_test_data script. This function was made to accomodate creation of ops for both pytest and non-pytest settings.""" + """Initializes ops. Used for both the test_ops function above and for generate_test_data script. This function was made to accommodate creation of ops for both pytest and non-pytest settings.""" ops = suite2p.default_ops() ops.update( { diff --git a/docs/settings.rst b/docs/settings.rst index 828b4e8ec..bea54c477 100644 --- a/docs/settings.rst +++ b/docs/settings.rst @@ -54,7 +54,7 @@ These are the essential settings that are dataset-specific. File input/output settings ~~~~~~~~~~~~~~~~~~~~~~~~~~ -Suite2p can accomodate many different file formats. Refer to this +Suite2p can accommodate many different file formats. Refer to this :ref:`page ` for a detailed list of formats suite2p can work with. - **fast_disk**: (*list[str], default: empty list*) specifies location where temporary binary file will be stored. Defaults to ``save_path0`` if no directory is provided by user. diff --git a/helpers/loadFramesBuff.m b/helpers/loadFramesBuff.m index e1bd017bb..5b9fb0ea7 100644 --- a/helpers/loadFramesBuff.m +++ b/helpers/loadFramesBuff.m @@ -2,7 +2,7 @@ %loadFrames Loads the frames of a Tiff file into an array (Y,X,T) % MOVIE = loadFrames(TIFF, [FIRST], [LAST], [STRIDE], []) loads % frames from the Tiff file specified by TIFF, which should be a filename -% or an already open Tiff object. Optionallly FIRST, LAST and STRIDE +% or an already open Tiff object. Optionally FIRST, LAST and STRIDE % specify the range of frame indices to load. if nargin>4 && ~isempty(temp_file) diff --git a/helpers/make_json_config.m b/helpers/make_json_config.m index 0222e5356..c1b84b6dd 100644 --- a/helpers/make_json_config.m +++ b/helpers/make_json_config.m @@ -19,7 +19,7 @@ function make_json_config(root) % fs = hSI.hRoiManager.scanVolumeRate; % fs = 5; -% get relevant infomation for TIFF header +% get relevant information for TIFF header artist_info = header(1).Artist; % retrieve ScanImage ROIs information from json-encoded string diff --git a/helpers/mesoscope_json_from_scanimage.m b/helpers/mesoscope_json_from_scanimage.m index c4e84e1aa..dcbdef6b6 100644 --- a/helpers/mesoscope_json_from_scanimage.m +++ b/helpers/mesoscope_json_from_scanimage.m @@ -20,7 +20,7 @@ fs = 4; end -% get relevant infomation for TIFF header +% get relevant information for TIFF header artist_info = header(1).Artist; % retrieve ScanImage ROIs information from json-encoded string diff --git a/suite2p/__init__.py b/suite2p/__init__.py index 2fa352e50..e4b8c622d 100644 --- a/suite2p/__init__.py +++ b/suite2p/__init__.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from .version import version from .default_ops import default_ops diff --git a/suite2p/__main__.py b/suite2p/__main__.py index 59f7c5c92..045feda8c 100644 --- a/suite2p/__main__.py +++ b/suite2p/__main__.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import argparse import numpy as np diff --git a/suite2p/classification/__init__.py b/suite2p/classification/__init__.py index 84b68e9a4..8cdc1eb11 100644 --- a/suite2p/classification/__init__.py +++ b/suite2p/classification/__init__.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from .classifier import Classifier from .classify import classify, builtin_classfile, user_classfile \ No newline at end of file diff --git a/suite2p/classification/classifier.py b/suite2p/classification/classifier.py index c9c247031..f8a45ca54 100644 --- a/suite2p/classification/classifier.py +++ b/suite2p/classification/classifier.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from scipy.ndimage import gaussian_filter diff --git a/suite2p/classification/classify.py b/suite2p/classification/classify.py index 73b6bc175..cdf62d68a 100644 --- a/suite2p/classification/classify.py +++ b/suite2p/classification/classify.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from pathlib import Path diff --git a/suite2p/default_ops.py b/suite2p/default_ops.py index ba20ceb51..6b696ffe6 100644 --- a/suite2p/default_ops.py +++ b/suite2p/default_ops.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from .version import version diff --git a/suite2p/detection/__init__.py b/suite2p/detection/__init__.py index 982ca0f59..bb97b8fa6 100644 --- a/suite2p/detection/__init__.py +++ b/suite2p/detection/__init__.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from .detect import detect, detection_wrapper, bin_movie from .stats import roi_stats, ROI \ No newline at end of file diff --git a/suite2p/detection/anatomical.py b/suite2p/detection/anatomical.py index 2872c1cc3..93178317f 100644 --- a/suite2p/detection/anatomical.py +++ b/suite2p/detection/anatomical.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from typing import Any, Dict diff --git a/suite2p/detection/chan2detect.py b/suite2p/detection/chan2detect.py index d9a47679f..de34cf3b2 100644 --- a/suite2p/detection/chan2detect.py +++ b/suite2p/detection/chan2detect.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from scipy.ndimage import gaussian_filter diff --git a/suite2p/detection/denoise.py b/suite2p/detection/denoise.py index 58787c7d2..6eaef7a55 100644 --- a/suite2p/detection/denoise.py +++ b/suite2p/detection/denoise.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from typing import List diff --git a/suite2p/detection/detect.py b/suite2p/detection/detect.py index 3e7089d7c..70d11304e 100644 --- a/suite2p/detection/detect.py +++ b/suite2p/detection/detect.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import time import numpy as np diff --git a/suite2p/detection/metrics.py b/suite2p/detection/metrics.py index cc9319d79..3201cb2e7 100644 --- a/suite2p/detection/metrics.py +++ b/suite2p/detection/metrics.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import time import numpy as np diff --git a/suite2p/detection/sourcery.py b/suite2p/detection/sourcery.py index 308658e02..75886cb64 100644 --- a/suite2p/detection/sourcery.py +++ b/suite2p/detection/sourcery.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import math import time diff --git a/suite2p/detection/sparsedetect.py b/suite2p/detection/sparsedetect.py index 2fd20be2d..cb128ea8b 100644 --- a/suite2p/detection/sparsedetect.py +++ b/suite2p/detection/sparsedetect.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from typing import Tuple, Dict, List, Any from copy import deepcopy @@ -241,7 +241,7 @@ def two_comps(mpix0, lam, Th2): def extend_mask(ypix, xpix, lam, Ly, Lx): - """ extend mask into 8 surrrounding pixels """ + """ extend mask into 8 surrounding pixels """ nel = len(xpix) yx = ((ypix, ypix, ypix, ypix - 1, ypix - 1, ypix - 1, ypix + 1, ypix + 1, ypix + 1), (xpix, xpix + 1, xpix - 1, xpix, xpix + 1, xpix - 1, xpix, diff --git a/suite2p/detection/stats.py b/suite2p/detection/stats.py index d6a9832dc..c1f8774fa 100644 --- a/suite2p/detection/stats.py +++ b/suite2p/detection/stats.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from __future__ import annotations @@ -87,7 +87,7 @@ def stats_dicts_to_3d_array(cls, stats: Sequence[Dict[str, Any]], Ly: int, Lx: i stats : List of dictionary "ypix", "xpix", "lam" Ly : y size of frame Lx : x size of frame - label_id : whether array should be an integer value indicating ROI id or just 1 (indicating precence of ROI). + label_id : whether array should be an integer value indicating ROI id or just 1 (indicating presence of ROI). """ arrays = [] for i, stat in enumerate(stats): diff --git a/suite2p/detection/utils.py b/suite2p/detection/utils.py index cccb80942..b5d5cecb7 100644 --- a/suite2p/detection/utils.py +++ b/suite2p/detection/utils.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from numba import jit diff --git a/suite2p/extraction/__init__.py b/suite2p/extraction/__init__.py index e0e880562..a3f53115c 100644 --- a/suite2p/extraction/__init__.py +++ b/suite2p/extraction/__init__.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from .dcnv import preprocess, oasis from .extract import create_masks_and_extract, enhanced_mean_image, extract_traces_from_masks, extraction_wrapper diff --git a/suite2p/extraction/dcnv.py b/suite2p/extraction/dcnv.py index 524a825e5..45d8f55c0 100644 --- a/suite2p/extraction/dcnv.py +++ b/suite2p/extraction/dcnv.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from numba import njit, prange diff --git a/suite2p/extraction/extract.py b/suite2p/extraction/extract.py index 49914397e..8a5093453 100644 --- a/suite2p/extraction/extract.py +++ b/suite2p/extraction/extract.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import os import time diff --git a/suite2p/extraction/masks.py b/suite2p/extraction/masks.py index f3941093d..ba1cc22e5 100644 --- a/suite2p/extraction/masks.py +++ b/suite2p/extraction/masks.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from typing import List, Tuple, Dict, Any from itertools import count diff --git a/suite2p/gui/__init__.py b/suite2p/gui/__init__.py index 1b3469a5d..0af7de0f3 100644 --- a/suite2p/gui/__init__.py +++ b/suite2p/gui/__init__.py @@ -1,4 +1,4 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from .gui2p import run \ No newline at end of file diff --git a/suite2p/gui/buttons.py b/suite2p/gui/buttons.py index 6e25ec336..351cc9e7a 100644 --- a/suite2p/gui/buttons.py +++ b/suite2p/gui/buttons.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from PyQt5 import QtGui, QtCore diff --git a/suite2p/gui/classgui.py b/suite2p/gui/classgui.py index e507ca87d..0030e63ad 100644 --- a/suite2p/gui/classgui.py +++ b/suite2p/gui/classgui.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import os import shutil diff --git a/suite2p/gui/drawroi.py b/suite2p/gui/drawroi.py index bee73fb40..77795750d 100644 --- a/suite2p/gui/drawroi.py +++ b/suite2p/gui/drawroi.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import os import time @@ -233,7 +233,7 @@ def closeEvent(self, event): def check_proc(self, event): cproc = QMessageBox.question( self, "PROC", - "Would you like to save traces before closing? (if you havent extracted the traces, click Cancel and extract!)", + "Would you like to save traces before closing? (if you haven't extracted the traces, click Cancel and extract!)", QMessageBox.Yes | QMessageBox.No | QMessageBox.Cancel) if cproc == QMessageBox.Yes: self.close_GUI() diff --git a/suite2p/gui/graphics.py b/suite2p/gui/graphics.py index 9d22c4051..59826c20c 100644 --- a/suite2p/gui/graphics.py +++ b/suite2p/gui/graphics.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np import pyqtgraph as pg diff --git a/suite2p/gui/gui2p.py b/suite2p/gui/gui2p.py index 531801b6f..c950771e4 100644 --- a/suite2p/gui/gui2p.py +++ b/suite2p/gui/gui2p.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import os, pathlib, shutil, sys, warnings diff --git a/suite2p/gui/io.py b/suite2p/gui/io.py index 23cab4cfc..d40d0e158 100644 --- a/suite2p/gui/io.py +++ b/suite2p/gui/io.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import os, time import numpy as np diff --git a/suite2p/gui/masks.py b/suite2p/gui/masks.py index b9637f51f..bc6967397 100644 --- a/suite2p/gui/masks.py +++ b/suite2p/gui/masks.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from pathlib import Path import matplotlib.cm diff --git a/suite2p/gui/menus.py b/suite2p/gui/menus.py index 318ed3b0c..6f68d4dea 100644 --- a/suite2p/gui/menus.py +++ b/suite2p/gui/menus.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from PyQt5 import QtGui from PyQt5.QtWidgets import QAction, QMenu diff --git a/suite2p/gui/merge.py b/suite2p/gui/merge.py index a5291ac49..0b1014238 100644 --- a/suite2p/gui/merge.py +++ b/suite2p/gui/merge.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import os import numpy as np diff --git a/suite2p/gui/reggui.py b/suite2p/gui/reggui.py index 30e213cbd..fa50f90ec 100644 --- a/suite2p/gui/reggui.py +++ b/suite2p/gui/reggui.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ # heavily modified script from a pyqt4 release import os diff --git a/suite2p/gui/rungui.py b/suite2p/gui/rungui.py index 601aba913..c5883a337 100644 --- a/suite2p/gui/rungui.py +++ b/suite2p/gui/rungui.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import glob, json, os, shutil, pathlib from datetime import datetime diff --git a/suite2p/gui/traces.py b/suite2p/gui/traces.py index 980bd3eef..558a21b99 100644 --- a/suite2p/gui/traces.py +++ b/suite2p/gui/traces.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from PyQt5 import QtGui, QtCore diff --git a/suite2p/gui/utils.py b/suite2p/gui/utils.py index 44ebccbca..80293ea58 100644 --- a/suite2p/gui/utils.py +++ b/suite2p/gui/utils.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from scipy.ndimage.morphology import binary_dilation, binary_fill_holes diff --git a/suite2p/gui/views.py b/suite2p/gui/views.py index 22edc2325..20ccc77fe 100644 --- a/suite2p/gui/views.py +++ b/suite2p/gui/views.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from PyQt5 import QtGui, QtCore diff --git a/suite2p/gui/visualize.py b/suite2p/gui/visualize.py index 53bf46f68..55d9672fb 100644 --- a/suite2p/gui/visualize.py +++ b/suite2p/gui/visualize.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import sys import time diff --git a/suite2p/io/__init__.py b/suite2p/io/__init__.py index affdfacda..1b8dbe3ab 100644 --- a/suite2p/io/__init__.py +++ b/suite2p/io/__init__.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from .h5 import h5py_to_binary from .nwb import save_nwb, read_nwb, nwb_to_binary diff --git a/suite2p/io/binary.py b/suite2p/io/binary.py index ea21ef400..1aec258d2 100644 --- a/suite2p/io/binary.py +++ b/suite2p/io/binary.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from typing import Optional, Tuple, Sequence from contextlib import contextmanager diff --git a/suite2p/io/h5.py b/suite2p/io/h5.py index 95d1ab3bf..fbfe53e8f 100644 --- a/suite2p/io/h5.py +++ b/suite2p/io/h5.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import math diff --git a/suite2p/io/nd2.py b/suite2p/io/nd2.py index e8a8bbac0..7a2c722bc 100644 --- a/suite2p/io/nd2.py +++ b/suite2p/io/nd2.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import os import gc diff --git a/suite2p/io/nwb.py b/suite2p/io/nwb.py index 97b044fd6..1f009764b 100644 --- a/suite2p/io/nwb.py +++ b/suite2p/io/nwb.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import datetime import gc diff --git a/suite2p/io/save.py b/suite2p/io/save.py index 08eb7fcf1..74e20b4ef 100644 --- a/suite2p/io/save.py +++ b/suite2p/io/save.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import os from natsort import natsorted diff --git a/suite2p/io/sbx.py b/suite2p/io/sbx.py index 693e60aa0..bd1e1ce57 100644 --- a/suite2p/io/sbx.py +++ b/suite2p/io/sbx.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import os diff --git a/suite2p/io/server.py b/suite2p/io/server.py index 951eb3f70..da4c9c954 100644 --- a/suite2p/io/server.py +++ b/suite2p/io/server.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import sys, os, time, glob from pathlib import Path diff --git a/suite2p/io/tiff.py b/suite2p/io/tiff.py index d1ab68f54..fbb1c326f 100644 --- a/suite2p/io/tiff.py +++ b/suite2p/io/tiff.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import gc import glob diff --git a/suite2p/io/utils.py b/suite2p/io/utils.py index e812f6232..325902654 100644 --- a/suite2p/io/utils.py +++ b/suite2p/io/utils.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import glob import os diff --git a/suite2p/ops/clean.py b/suite2p/ops/clean.py index 19f8312bc..e91c7275a 100644 --- a/suite2p/ops/clean.py +++ b/suite2p/ops/clean.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import argparse diff --git a/suite2p/registration/__init__.py b/suite2p/registration/__init__.py index 76844f97c..b3ae9a00d 100644 --- a/suite2p/registration/__init__.py +++ b/suite2p/registration/__init__.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from .register import (registration_wrapper, save_registration_outputs_to_ops, compute_enhanced_mean_image) diff --git a/suite2p/registration/bidiphase.py b/suite2p/registration/bidiphase.py index be5cdba0a..5a15326ef 100644 --- a/suite2p/registration/bidiphase.py +++ b/suite2p/registration/bidiphase.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import numpy as np from numpy import fft diff --git a/suite2p/registration/metrics.py b/suite2p/registration/metrics.py index 73697e842..cb56dfacf 100644 --- a/suite2p/registration/metrics.py +++ b/suite2p/registration/metrics.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from multiprocessing import Pool diff --git a/suite2p/registration/nonrigid.py b/suite2p/registration/nonrigid.py index 593031cfe..ae0809968 100644 --- a/suite2p/registration/nonrigid.py +++ b/suite2p/registration/nonrigid.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import warnings from typing import Tuple diff --git a/suite2p/registration/register.py b/suite2p/registration/register.py index a2af254fb..781d9107c 100644 --- a/suite2p/registration/register.py +++ b/suite2p/registration/register.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import time from os import path @@ -77,7 +77,7 @@ def pick_initial_reference(frames: np.ndarray): the seed frame is the frame with the largest correlations with other frames; the average of the seed frame with its top 20 correlated pairs is the - inital reference frame returned + initial reference frame returned Parameters ---------- diff --git a/suite2p/registration/rigid.py b/suite2p/registration/rigid.py index 94b4f4526..94402e987 100644 --- a/suite2p/registration/rigid.py +++ b/suite2p/registration/rigid.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from typing import Tuple @@ -22,7 +22,7 @@ def compute_masks(refImg, maskSlope) -> Tuple[np.ndarray, np.ndarray]: Returns ------- - maskMul: float arrray + maskMul: float array maskOffset: float array """ Ly, Lx = refImg.shape diff --git a/suite2p/registration/utils.py b/suite2p/registration/utils.py index 77804133f..cc49569e2 100644 --- a/suite2p/registration/utils.py +++ b/suite2p/registration/utils.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import warnings from functools import lru_cache diff --git a/suite2p/registration/zalign.py b/suite2p/registration/zalign.py index aa2db5662..b9df99b64 100644 --- a/suite2p/registration/zalign.py +++ b/suite2p/registration/zalign.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import os import time diff --git a/suite2p/run_s2p.py b/suite2p/run_s2p.py index 022068025..45e516893 100644 --- a/suite2p/run_s2p.py +++ b/suite2p/run_s2p.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ import os import shutil diff --git a/suite2p/version.py b/suite2p/version.py index dcf14e201..087f15270 100644 --- a/suite2p/version.py +++ b/suite2p/version.py @@ -1,5 +1,5 @@ """ -Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. +Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu. """ from importlib_metadata import metadata as _metadata