Automated QA during preprocessing

CHANGELOG.md

@@ -4,6 +4,15 @@ Versions follow [Semantic Versioning](https://semver.org) (`<major>.<minor>.<pat
 
 ## Unreleased
 
+### Added
+
+- Add automated QA check results to preprocessing reports ([[#80](https://github.com/DuguidLab/mesoscopy/issues/80)])
+- Add timedelta series to preprocessing report.
+
+### Fixed
+
+- Pin pynwb version to pre-3.0, which currently breaks installs.
+
 ## [0.7.3]
 
 ### Added

src/mesoscopy/preprocess/qa.py

@@ -273,6 +273,30 @@ def plot_timestamps(timestamps: list | npt.NDArray, as_html: bool = False) -> 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.
 

src/mesoscopy/report/__init__.py

@@ -94,10 +94,23 @@ def generate_preprocessing_report(path: str, out_dir: str = ".") -> 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,
         ),
+        "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,

src/mesoscopy/report/templates/preprocessing.html

@@ -7,11 +7,22 @@
         </svg>
         Metadata
     </a> </li>
+<li class="nav-item"> <a class="nav-link d-flex align-items-center gap-2" href="#autoqa">
+        <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-flag"
+            viewBox="0 0 16 16">
+            <path
+                d="M14.778.085A.5.5 0 0 1 15 .5V8a.5.5 0 0 1-.314.464L14.5 8l.186.464-.003.001-.006.003-.023.009a12 12 0 0 1-.397.15c-.264.095-.631.223-1.047.35-.816.252-1.879.523-2.71.523-.847 0-1.548-.28-2.158-.525l-.028-.01C7.68 8.71 7.14 8.5 6.5 8.5c-.7 0-1.638.23-2.437.477A20 20 0 0 0 3 9.342V15.5a.5.5 0 0 1-1 0V.5a.5.5 0 0 1 1 0v.282c.226-.079.496-.17.79-.26C4.606.272 5.67 0 6.5 0c.84 0 1.524.277 2.121.519l.043.018C9.286.788 9.828 1 10.5 1c.7 0 1.638-.23 2.437-.477a20 20 0 0 0 1.349-.476l.019-.007.004-.002h.001M14 1.221c-.22.078-.48.167-.766.255-.81.252-1.872.523-2.734.523-.886 0-1.592-.286-2.203-.534l-.008-.003C7.662 1.21 7.139 1 6.5 1c-.669 0-1.606.229-2.415.478A21 21 0 0 0 3 1.845v6.433c.22-.078.48-.167.766-.255C4.576 7.77 5.638 7.5 6.5 7.5c.847 0 1.548.28 2.158.525l.028.01C9.32 8.29 9.86 8.5 10.5 8.5c.668 0 1.606-.229 2.415-.478A21 21 0 0 0 14 7.655V1.222z" />
+        </svg>
+        Auto-QA
+    </a> </li>
 <li class="nav-item"> <a class="nav-link d-flex align-items-center gap-2" href="#integriy">
-        <svg class="bi" aria-hidden="true">
-            <use xlink:href="#gear-wide-connected"></use>
+        <svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-stopwatch"
+            viewBox="0 0 16 16">
+            <path d="M8.5 5.6a.5.5 0 1 0-1 0v2.9h-3a.5.5 0 0 0 0 1H8a.5.5 0 0 0 .5-.5z" />
+            <path
+                d="M6.5 1A.5.5 0 0 1 7 .5h2a.5.5 0 0 1 0 1v.57c1.36.196 2.594.78 3.584 1.64l.012-.013.354-.354-.354-.353a.5.5 0 0 1 .707-.708l1.414 1.415a.5.5 0 1 1-.707.707l-.353-.354-.354.354-.013.012A7 7 0 1 1 7 2.071V1.5a.5.5 0 0 1-.5-.5M8 3a6 6 0 1 0 .001 12A6 6 0 0 0 8 3" />
         </svg>
-        Integrity
+        Timeseries integriy
     </a>
 </li>
 <li class="nav-item"> <a class="nav-link d-flex align-items-center gap-2" href="#separation">
@@ -72,12 +83,48 @@ <h2 id="metadata">Session metadata</h2>
 </div>
 
 <div class="row mb-3">
-    <h2 id="integrity">Recording integrity</h2>
+    <h2 id="autoqa">Preprocessing auto-QA checks</h2>
 
-    <div class="col-md-12 mb-3 mt-3">
+    <div class="row mb-1">
+        <div class="col-md-4 mb-1">
+            <strong>Histogram separation:</strong> {{ "✅" if qa_histogram_separation else "❌" }}
+        </div>
+        <div class="col-md-4 mb-1">
+            <strong>Timestamp consistency:</strong> {{ "✅" if qa_timestamp_consistency else "❌" }}
+        </div>
+        <div class="col-md-4 mb-1">
+            <strong>Timestamp jumps:</strong> {{ "✅" if qa_timestamp_jump else "❌" }}
+        </div>
+    </div>
+    <div class="row mb-1">
+        <div class="col-md-4 mb-1">
+            <strong>Noise levels:</strong> {{ "✅" if qa_check_noise else "❌" }} (Median noise {{ '%0.2f'|
+            format(qa_median_noise|float) if qa_median_noise is defined else "Unknown" }} %)
+        </div>
+        <div class="col-md-4 mb-1">
+            <strong>Signal-to-Noise:</strong> {{ "✅" if qa_check_snr else "❌" }} ({{ '%0.2f'| format(qa_snr|float) if
+            qa_snr is
+            defined else "Unknown" }} SNR)
+        </div>
+        <div class="col-md-4 mb-1">
+            <strong>Bleaching drift:</strong> {{ "✅" if qa_check_bleaching else "❌" }} ({{ '%0.2f'|
+            format(qa_bleaching_factor|float) if qa_bleaching_factor is defined else "Unknown" }} BF)
+        </div>
+    </div>
+</div>
+
+<div class="row mb-3">
+    <h2 id="integrity">Timeseries integrity</h2>
+
+    <div class="col-md-6 mb-3 mt-3">
         <h6>Timestamp series</h6>
         {{ fig_integrity_timestamps | safe }}
     </div>
+
+    <div class="col-md-6 mb-3 mt-3">
+        <h6>Timedelta series</h6>
+        {{ fig_integrity_timestamp_jumps | safe }}
+    </div>
 </div>
 
 <div class="row mb-3">