From 2fc4fc4be4c76fc937e6d3a855c32adb6d141b9a Mon Sep 17 00:00:00 2001 From: Constantinos Eleftheriou Date: Mon, 19 Jan 2026 11:45:24 +0000 Subject: [PATCH 1/3] add hotfix entry to changelog --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8271b71..bcca9de 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,10 @@ Versions follow [Semantic Versioning](https://semver.org) (`.. Date: Mon, 19 Jan 2026 15:12:23 +0000 Subject: [PATCH 2/3] add auto qa results to reports --- CHANGELOG.md | 4 ++ src/mesoscopy/report/__init__.py | 9 ++++ .../report/templates/preprocessing.html | 50 +++++++++++++++++-- 3 files changed, 59 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bcca9de..88b92b0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,10 @@ Versions follow [Semantic Versioning](https://semver.org) (`.. str: ), "frame_num": len(preproc.get("F")), # type: ignore[attr-defined] "filesize": preproc.id.get_filesize() / (1024 * 1024), + "qa_histogram_separation": preproc.attrs.get("/qa/checks/histogram_separation"), + "qa_timestamp_consistency": preproc.attrs.get("/qa/checks/timestamp_consistency"), + "qa_timestamp_jump": preproc.attrs.get("/qa/checks/timestamp_jump"), + "qa_check_noise": preproc.attrs.get("/qa/checks/noise_check"), + "qa_median_noise": np.median(np.array(preproc.get("/qa/noise_levels", 0))), + "qa_check_snr": preproc.attrs.get("/qa/checks/snr_check"), + "qa_snr": preproc.attrs.get("/qa/checks/snr"), + "qa_check_bleaching": preproc.attrs.get("/qa/checks/bleaching_check"), + "qa_bleaching_factor": preproc.attrs.get("/qa/checks/bleaching_factor"), "fig_integrity_timestamps": preqa.plot_timestamps( [np.datetime64(ts) for ts in preproc.get("timestamps")], # type: ignore[attr-defined] as_html=True, diff --git a/src/mesoscopy/report/templates/preprocessing.html b/src/mesoscopy/report/templates/preprocessing.html index eb178ad..ea22d2a 100644 --- a/src/mesoscopy/report/templates/preprocessing.html +++ b/src/mesoscopy/report/templates/preprocessing.html @@ -7,11 +7,22 @@ Metadata +
  • + + + + Auto-QA +
  • -
  • @@ -72,7 +83,38 @@

    Session metadata

    -

    Recording integrity

    +

    Preprocessing auto-QA checks

    + +
    +
    + Histogram separation: {{ "✅" if qa_histogram_separation else "❌" }} +
    +
    + Timestamp consistency: {{ "✅" if qa_timestamp_consistency else "❌" }} +
    +
    + Timestamp jumps: {{ "✅" if qa_timestamp_jump else "❌" }} +
    +
    +
    +
    + Noise levels: {{ "✅" if qa_check_noise else "❌" }} (Median noise {{ '%0.2f'| + format(qa_median_noise|float) if qa_median_noise is defined else "Unknown" }} %) +
    +
    + Signal-to-Noise: {{ "✅" if qa_check_snr else "❌" }} ({{ '%0.2f'| format(qa_snr|float) if + qa_snr is + defined else "Unknown" }} SNR) +
    +
    + Bleaching drift: {{ "✅" if qa_check_bleaching else "❌" }} ({{ '%0.2f'| + format(qa_bleaching_factor|float) if qa_bleaching_factor is defined else "Unknown" }} BF) +
    +
    +
    + +
    +

    Timeseries integrity

    Timestamp series
    From 1f67f50851e7b0e78f21d4d78b0aee21b18dd2d0 Mon Sep 17 00:00:00 2001 From: Constantinos Eleftheriou Date: Mon, 19 Jan 2026 15:20:37 +0000 Subject: [PATCH 3/3] add timedelta series to report --- CHANGELOG.md | 1 + src/mesoscopy/preprocess/qa.py | 24 +++++++++++++++++++ src/mesoscopy/report/__init__.py | 4 ++++ .../report/templates/preprocessing.html | 7 +++++- 4 files changed, 35 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 88b92b0..24ce838 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ Versions follow [Semantic Versioning](https://semver.org) (`.. st return fig +def plot_timestamp_jumps( + timestamps: npt.NDArray | list, std_threshold: float = 2.0, as_html: bool = False +) -> str | go.Figure: + try: + timestamps = np.array([datetime.fromisoformat(str(ts, encoding="utf-8")) for ts in np.array(timestamps)]) + except ValueError: + timestamps = np.array([float(ts) for ts in timestamps]) + timedeltas = np.diff(timestamps).astype("timedelta64[ms]").astype(float) + zscored_intervals = stats.zscore(timedeltas) + + fig = go.Figure( + layout=go.Layout( + xaxis={"title": {"text": "Frame index"}}, + yaxis={"title": {"text": "Timedelta (ms)"}}, + margin={"l": 20, "r": 20, "t": 20, "b": 20}, + ) + ) + + fig.add_trace(go.Scatter(y=timedeltas, mode="lines", name="Timestamp")) + if as_html: + return fig.to_html(full_html=False) + return fig + + def plot_raw_timeseries(raw_timeseries: npt.NDArray, as_html: bool = False) -> str | go.Figure: """Plots a raw timeseries signal using Plotly. diff --git a/src/mesoscopy/report/__init__.py b/src/mesoscopy/report/__init__.py index 46b3ea6..ab45573 100644 --- a/src/mesoscopy/report/__init__.py +++ b/src/mesoscopy/report/__init__.py @@ -107,6 +107,10 @@ def generate_preprocessing_report(path: str, out_dir: str = ".") -> str: [np.datetime64(ts) for ts in preproc.get("timestamps")], # type: ignore[attr-defined] as_html=True, ), + "fig_integrity_timestamp_jumps": preqa.plot_timestamp_jumps( + preproc.get("timestamps"), # type: ignore[attr-defined] + as_html=True, + ), "fig_separation_pre_timeseries_mean": preqa.plot_raw_timeseries( preproc.get("qa").get("frame_means_timeseries"), # type: ignore[attr-defined] as_html=True, diff --git a/src/mesoscopy/report/templates/preprocessing.html b/src/mesoscopy/report/templates/preprocessing.html index ea22d2a..750307d 100644 --- a/src/mesoscopy/report/templates/preprocessing.html +++ b/src/mesoscopy/report/templates/preprocessing.html @@ -116,10 +116,15 @@

    Preprocessing auto-QA checks

    Timeseries integrity

    -
    +
    Timestamp series
    {{ fig_integrity_timestamps | safe }}
    + +
    +
    Timedelta series
    + {{ fig_integrity_timestamp_jumps | safe }} +