diff --git a/.all-contributorsrc b/.all-contributorsrc index 92a3dfb..e6b19fe 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -22,6 +22,31 @@ "infra" ] }, + { + "login": "afni-dglen", + "name": "Daniel Glen", + "avatar_url": "https://avatars.githubusercontent.com/u/10454715?v=4", + "profile": "https://github.com/afni-dglen", + "contributions": [ + "bug", + "code", + "maintenance" + ] + }, + { + "login": "maestroque", + "name": "George Kikas", + "avatar_url": "https://avatars.githubusercontent.com/u/74024609?v=4", + "profile": "https://github.com/maestroque", + "contributions": [ + "bug", + "code", + "ideas", + "infra", + "review", + "test" + ] + }, { "login": "rmarkello", "name": "Ross Markello", @@ -34,12 +59,23 @@ "ideas", "infra", "maintenance", + "mentoring", "projectManagement", "review", "test", "tutorial" ] }, + { + "login": "m-miedema", + "name": "m-miedema", + "avatar_url": "https://avatars.githubusercontent.com/u/39968233?v=4", + "profile": "https://github.com/m-miedema", + "contributions": [ + "review", + "mentoring" + ] + }, { "login": "smoia", "name": "Stefano Moia", @@ -47,11 +83,25 @@ "profile": "https://github.com/smoia", "contributions": [ "review", + "bug", "code", + "ideas", "infra", + "mentoring", "projectManagement" ] }, + { + "login": "me-pic", + "name": "Marie-Eve Picard", + "avatar_url": "https://avatars.githubusercontent.com/u/77584086?v=4", + "profile": "https://github.com/me-pic", + "contributions": [ + "doc", + "review", + "mentoring" + ] + }, { "login": "tsalo", "name": "Taylor Salo", @@ -61,6 +111,17 @@ "infra" ] }, + { + "login": "RayStick", + "name": "Rachael Stickland", + "avatar_url": "https://avatars.githubusercontent.com/u/50215726?v=4", + "profile": "https://github.com/RayStick", + "contributions": [ + "doc", + "infra", + "test" + ] + }, { "login": "mixue-t", "name": "Mi-Xue Tan", diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1831d7e..7b09e15 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ repos: - id: check-case-conflict - id: check-merge-conflict - repo: https://github.com/psf/black - rev: 24.4.2 + rev: 24.8.0 hooks: - id: black - repo: https://github.com/pycqa/isort @@ -19,7 +19,7 @@ repos: hooks: - id: isort - repo: https://github.com/pycqa/flake8 - rev: 7.1.0 + rev: 7.1.1 hooks: - id: flake8 - repo: https://github.com/pycqa/pydocstyle diff --git a/.zenodo.json b/.zenodo.json index 06feda8..23ba575 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -3,19 +3,212 @@ "title": "physiopy/peakdet: A python toolbox for reproducible physiological data analysis", "upload_type": "software", "creators": [ - { - "affiliation": "McGill University", - "name": "Elizabeth DuPre" - }, - { - "affiliation": "McGill University", - "name": "Ross Markello" - }, - { - "orcid": "0000-0002-2553-3327", - "affiliation": "BCBL - Basque Center on Cognition, Brain and Language", - "name": "Stefano Moia" - } + { + "affiliations": [ + { + "name": "Stanford University" + } + ], + "person_or_org": { + "family_name": "DuPre", + "given_name": "Elizabeth", + "identifiers": [ + { + "identifier": "0000-0003-1358-196X", + "scheme": "orcid" + } + ], + "name": "DuPre, Elizabeth", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "National Institute of Mental Health" + } + ], + "person_or_org": { + "family_name": "Glen", + "given_name": "Daniel", + "identifiers": [ + { + "identifier": "0000-0001-8456-5647", + "scheme": "orcid" + } + ], + "name": "Glen, Daniel", + "type": "personal" + } + }, + { + "affiliations": [ + { + "id": "02j61yw88", + "name": "Aristotle University of Thessaloniki" + } + ], + "person_or_org": { + "family_name": "Kikas", + "given_name": "Georgios", + "name": "Kikas, Georgios", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "McGill University" + } + ], + "person_or_org": { + "family_name": "Markello", + "given_name": "Ross", + "identifiers": [ + { + "identifier": "0000-0003-1057-1336", + "scheme": "orcid" + } + ], + "name": "Markello, Ross", + "type": "personal" + } + }, + { + "affiliations": [ + { + "id": "01pxwe438", + "name": "McGill University" + } + ], + "person_or_org": { + "family_name": "Miedema", + "given_name": "Mary", + "identifiers": [ + { + "identifier": "0009-0008-3263-731X", + "scheme": "orcid" + } + ], + "name": "Miedema, Mary", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "Maastricht University" + } + ], + "person_or_org": { + "family_name": "Moia", + "given_name": "Stefano", + "identifiers": [ + { + "identifier": "0000-0002-2553-3327", + "scheme": "orcid" + } + ], + "name": "Moia, Stefano", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "Universit\u00e9 de Montr\u00e9al" + } + ], + "person_or_org": { + "family_name": "Picard", + "given_name": "Marie-\u00c8ve", + "identifiers": [ + { + "identifier": "0000-0002-4316-2830", + "scheme": "orcid" + } + ], + "name": "Picard, Marie-\u00c8ve", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "University of Pennsylvania" + } + ], + "person_or_org": { + "family_name": "Salo", + "given_name": "Taylor", + "identifiers": [ + { + "identifier": "0000-0001-9813-3167", + "scheme": "orcid" + } + ], + "name": "Salo, Taylor", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "The Alan Turing Institute" + } + ], + "person_or_org": { + "family_name": "Stickland", + "given_name": "Rachael", + "identifiers": [ + { + "identifier": "0000-0003-3398-4272", + "scheme": "orcid" + } + ], + "name": "Stickland, Rachael", + "type": "personal" + } + }, + { + "affiliations": [ + { + "name": "University of Geneva" + } + ], + "person_or_org": { + "family_name": "Tan", + "given_name": "Mi Xue", + "identifiers": [ + { + "identifier": "0000-0002-8214-2146", + "scheme": "orcid" + } + ], + "name": "Tan, Mi Xue", + "type": "personal" + } + }, + { + "affiliations": [ + { + "id": "01a28zg77", + "name": "Basque Center on Cognition, Brain and Language" + } + ], + "person_or_org": { + "family_name": "Uru\u00f1uela", + "given_name": "Eneko", + "identifiers": [ + { + "identifier": "0000-0001-6849-9088", + "scheme": "orcid" + } + ], + "name": "Uru\u00f1uela, Eneko", + "type": "personal" + } + } ], "access_right": "open" } diff --git a/CHANGELOG.md b/CHANGELOG.md index f640380..0ea063a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,45 @@ +# 0.5.2 (Wed Oct 09 2024) + +#### πŸ› Bug Fix + +- Make sure peak detection works with negative signals [#84](https://github.com/physiopy/peakdet/pull/84) ([@smoia](https://github.com/smoia)) + +#### 🏠 Internal + +- [pre-commit.ci] pre-commit autoupdate [#75](https://github.com/physiopy/peakdet/pull/75) ([@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot])) + +#### Authors: 2 + +- [@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot]) +- Stefano Moia ([@smoia](https://github.com/smoia)) + +--- + +# 0.5.1 (Tue Aug 27 2024) + +:tada: This release contains work from a new contributor! :tada: + +Thank you, Marie-Eve Picard ([@me-pic](https://github.com/me-pic)), for all your work! + +#### πŸ› Bug Fix + +- Fix type errors in exporting history after manually adding peaks [#79](https://github.com/physiopy/peakdet/pull/79) ([@smoia](https://github.com/smoia)) + +#### πŸ“ Documentation + +- Update contributors [#82](https://github.com/physiopy/peakdet/pull/82) ([@smoia](https://github.com/smoia)) + +#### 🏠 Internal + +- Add contribution [#81](https://github.com/physiopy/peakdet/pull/81) ([@me-pic](https://github.com/me-pic)) + +#### Authors: 2 + +- Marie-Eve Picard ([@me-pic](https://github.com/me-pic)) +- Stefano Moia ([@smoia](https://github.com/smoia)) + +--- + # 0.5.0 (Fri Jul 19 2024) #### πŸš€ Enhancement diff --git a/README.md b/README.md index 489b3f7..6b6b21f 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ peakdet: A toolbox for physiological peak detection analyses [![See the documentation at: http://peakdet.readthedocs.io](https://readthedocs.org/projects/peakdet/badge/?version=latest)](http://peakdet.readthedocs.io/en/latest) -[![All Contributors](https://img.shields.io/badge/all_contributors-7-orange.svg?style=flat)](#contributors) +[![All Contributors](https://img.shields.io/badge/all_contributors-12-orange.svg?style=flat)](#contributors) This package is designed for use in the reproducible processing and analysis of @@ -55,11 +55,18 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d Elizabeth DuPre
Elizabeth DuPre
πŸ’» πŸš‡ - Ross Markello
Ross Markello
πŸ› πŸ’» πŸ“– πŸ€” πŸš‡ 🚧 πŸ“† πŸ‘€ ⚠️ βœ… - Stefano Moia
Stefano Moia
πŸ‘€ πŸ’» πŸš‡ πŸ“† + Daniel Glen
Daniel Glen
πŸ› πŸ’» 🚧 + George Kikas
George Kikas
πŸ› πŸ’» πŸ€” πŸš‡ πŸ‘€ ⚠️ + Ross Markello
Ross Markello
πŸ› πŸ’» πŸ“– πŸ€” πŸš‡ 🚧 πŸ§‘β€πŸ« πŸ“† πŸ‘€ ⚠️ βœ… + + + m-miedema
m-miedema
πŸ‘€ πŸ§‘β€πŸ« + Stefano Moia
Stefano Moia
πŸ‘€ πŸ› πŸ’» πŸ€” πŸš‡ πŸ§‘β€πŸ« πŸ“† + Marie-Eve Picard
Marie-Eve Picard
πŸ“– πŸ‘€ πŸ§‘β€πŸ« Taylor Salo
Taylor Salo
πŸš‡ + Rachael Stickland
Rachael Stickland
πŸ“– πŸš‡ ⚠️ Mi-Xue Tan
Mi-Xue Tan
πŸ’» πŸ““ πŸ”Œ Eneko UruΓ±uela
Eneko UruΓ±uela
πŸš‡ xl624
xl624
πŸ’» diff --git a/peakdet/editor.py b/peakdet/editor.py index e3cd0ba..c4d69b8 100644 --- a/peakdet/editor.py +++ b/peakdet/editor.py @@ -161,7 +161,7 @@ def on_edit(self, xmin, xmax, *, method): if method == "insert": tmp = np.argmax(self.data.data[tmin:tmax]) if tmin != tmax else 0 - newpeak = tmin + tmp + newpeak = int(tmin + tmp) if newpeak == tmin: self.plot_signals() return diff --git a/peakdet/operations.py b/peakdet/operations.py index 480b0c0..36d0511 100644 --- a/peakdet/operations.py +++ b/peakdet/operations.py @@ -144,8 +144,15 @@ def peakfind_physio(data, *, thresh=0.2, dist=None): data = utils.check_physio(data, ensure_fs=ensure_fs, copy=True) # first pass peak detection to get approximate distance between peaks cdist = data.fs // 4 if dist is None else dist - thresh = np.squeeze(np.diff(np.percentile(data, [5, 95]))) * thresh - locs, heights = signal.find_peaks(data[:], distance=cdist, height=thresh) + + # check if data is negative, if so make it all positive and continue with signal + phys_signal = data.data - data.data.min() if data.data.min() < 0 else data.data + logger.debug( + f"Negative signal detected (min = {data.data.min()}), working with positive signal for peak detection." + ) + + thresh = np.squeeze(np.diff(np.percentile(phys_signal, [5, 95]))) * thresh + locs, heights = signal.find_peaks(phys_signal, distance=cdist, height=thresh) logger.debug( f"First peak detection iteration. Acquiring approximate distance between peaks (Number of peaks: {len(locs)})" ) @@ -153,7 +160,7 @@ def peakfind_physio(data, *, thresh=0.2, dist=None): # second, more thorough peak detection cdist = np.diff(locs).mean() // 2 heights = np.percentile(heights["peak_heights"], 1) - locs, heights = signal.find_peaks(data[:], distance=cdist, height=heights) + locs, heights = signal.find_peaks(phys_signal, distance=cdist, height=heights) data._metadata["peaks"] = locs logger.debug( f"Second peak detection iteration. Acquiring more precise peak locations (Number of peaks: {len(locs)})"