Add batch-wide histogram aggregation, Multi-Otsu thresholding, and QC sweep report

spimquant/workflow/Snakefile

@@ -252,6 +252,59 @@ active ``seg_method`` contains at least one ``otsu+k{}i{}`` entry.
         else [],
 
 
+rule all_batch_otsu_hist_qc:
+    """Target rule to generate batch-wide Otsu threshold sweep QC reports.
+
+Produces one HTML report per stain/method combination (across all subjects)
+for every ``otsu+k{}i{}`` segmentation method.  Each report shows the
+aggregated histogram with Multi-Otsu threshold positions and one mid-volume
+crop per subject at each threshold, enabling visual selection of a threshold
+that generalises across the entire acquisition batch.  Only meaningful when
+the active ``seg_method`` contains at least one ``otsu+k{}i{}`` entry.
+"""
+    input:
+        expand(
+            bids(
+                root=root,
+                datatype="group",
+                stain="{stain}",
+                desc="{desc}",
+                suffix="batchotsuthreshqc.html",
+            ),
+            stain=stains_for_seg,
+            desc=otsu_seg_methods,
+        )
+        if (do_seg and len(otsu_seg_methods) > 0)
+        else [],
+
+
+rule all_batch_otsu_hist_qc_raw:
+    """Target rule to generate batch-wide Otsu threshold sweep QC reports.
+
+Produces one HTML report per stain/method combination (across all subjects)
+for every ``otsu+k{}i{}`` segmentation method.  Each report shows the
+aggregated histogram with Multi-Otsu threshold positions and one mid-volume
+crop per subject at each threshold, enabling visual selection of a threshold
+that generalises across the entire acquisition batch.  Only meaningful when
+the active ``seg_method`` contains at least one ``otsu+k{}i{}`` entry.
+"""
+    input:
+        expand(
+            bids(
+                root=root,
+                datatype="group",
+                stain="{stain}",
+                desc="{desc}",
+                suffix="batchotsuthreshqcraw.html",
+            ),
+            stain=stains_for_seg,
+            desc=otsu_seg_methods,
+        )
+        if (do_seg and len(otsu_seg_methods) > 0)
+        else [],
+
+
+
 rule all_register:
     input:
         inputs["spim"].expand(

spimquant/workflow/rules/qc.smk

@@ -458,6 +458,107 @@ Only applicable when ``seg_method`` uses the ``otsu+k{}i{}`` pattern.
     script:
         "../scripts/qc_otsu_threshold_sweep.py"
 
+rule qc_batch_otsu_threshold_sweep_raw:
+    """Batch threshold sweep QC HTML report for multiotsu segmentation, on raw uncorrected images.
+
+Uses the batch-wide Multi-Otsu thresholds (computed from the aggregated
+histogram across all subjects in the dataset) to sweep over a range of
+threshold values and display one mid-volume 2D crop per subject at each
+threshold.  Subjects are shown as columns so that the user can immediately
+see whether a given threshold generalises across the entire acquisition batch.
+
+The aggregated histogram PNG is embedded at the top of the report.
+
+Only applicable when ``seg_method`` uses the ``otsu+k{}i{}`` pattern.
+"""
+    input:
+        zarrs=inputs["spim"].expand(),
+        thresholds_png=bids(
+            root=root,
+            datatype="group",
+            stain="{stain}",
+            level=str(config["segmentation_level"]),
+            desc="{desc}",
+            suffix="thresholds.png",
+        ),
+    output:
+        html=bids(
+            root=root,
+            datatype="group",
+            stain="{stain}",
+            desc="{desc}",
+            suffix="batchotsuthreshqcraw.html",
+        ),
+    threads: 4
+    resources:
+        mem_mb=32000,
+        runtime=60,
+    params:
+        n_thresholds=10,
+        patch_size=300,
+        level=config["segmentation_level"],
+        hist_percentile_range=[float(x) for x in config["seg_hist_percentile_range"]],
+        zarrnii_kwargs=lambda wildcards: {"orientation": config["orientation"],"channel_labels":[wildcards.stain]},
+    script:
+        "../scripts/qc_batch_otsu_threshold_sweep.py"
+
+
+
+rule qc_batch_otsu_threshold_sweep:
+    """Batch threshold sweep QC HTML report for multiotsu segmentation.
+
+Uses the batch-wide Multi-Otsu thresholds (computed from the aggregated
+histogram across all subjects in the dataset) to sweep over a range of
+threshold values and display one mid-volume 2D crop per subject at each
+threshold.  Subjects are shown as columns so that the user can immediately
+see whether a given threshold generalises across the entire acquisition batch.
+
+The aggregated histogram PNG is embedded at the top of the report.
+
+Only applicable when ``seg_method`` uses the ``otsu+k{}i{}`` pattern.
+"""
+    input:
+        zarrs=inputs["spim"].expand(
+            bids(
+                root=work,
+                datatype="seg",
+                stain="{stain}",
+                level=str(config["segmentation_level"]),
+                desc="corrected{method}".format(method=config["correction_method"]),
+                suffix="SPIM.ome.zarr",
+                **inputs["spim"].wildcards,
+            ),
+            allow_missing=True,
+        ),
+        thresholds_png=bids(
+            root=root,
+            datatype="group",
+            stain="{stain}",
+            level=str(config["segmentation_level"]),
+            desc="{desc}",
+            suffix="thresholds.png",
+        ),
+    output:
+        html=bids(
+            root=root,
+            datatype="group",
+            stain="{stain}",
+            desc="{desc}",
+            suffix="batchotsuthreshqc.html",
+        ),
+    threads: 4
+    resources:
+        mem_mb=32000,
+        runtime=60,
+    params:
+        n_thresholds=10,
+        patch_size=300,
+        level=config["segmentation_level"],
+        hist_percentile_range=[float(x) for x in config["seg_hist_percentile_range"]],
+        zarrnii_kwargs={"orientation": config["orientation"]},
+    script:
+        "../scripts/qc_batch_otsu_threshold_sweep.py"
+
 
 rule qc_roi_summary:
     """Per-ROI summary QC: top-region bar plots for a single subject.