12 load roi id index in order to make classifier work with one trained through the napari ome zarr navigator

docs/_quarto.yml

@@ -45,7 +45,7 @@ quartodoc:
         - tasks.harmony_to_ome_zarr
         - tasks.stardist_segmentation
         - tasks.regionprops_measurement
-        - tasks.label_prediction
+        - tasks.feature_classification
         - tasks.condition_registration
     - title: Input/Output
       desc: "OME-ZARR reader and writer functions"

docs/api/index.qmd

@@ -9,7 +9,7 @@ Modular processing tasks for the Opera/Operetta microscope and drug response pro
 | [tasks.harmony_to_ome_zarr](tasks.harmony_to_ome_zarr.qmd#operetta_compose.tasks.harmony_to_ome_zarr) |  |
 | [tasks.stardist_segmentation](tasks.stardist_segmentation.qmd#operetta_compose.tasks.stardist_segmentation) |  |
 | [tasks.regionprops_measurement](tasks.regionprops_measurement.qmd#operetta_compose.tasks.regionprops_measurement) |  |
-| [tasks.label_prediction](tasks.label_prediction.qmd#operetta_compose.tasks.label_prediction) |  |
+| [tasks.feature_classification](tasks.feature_classification.qmd#operetta_compose.tasks.feature_classification) |  |
 | [tasks.condition_registration](tasks.condition_registration.qmd#operetta_compose.tasks.condition_registration) |  |
 
 ## Input/Output

docs/api/tasks.feature_classification.qmd

@@ -0,0 +1,26 @@
+# tasks.feature_classification { #operetta_compose.tasks.feature_classification }
+
+`tasks.feature_classification`
+
+
+
+## Functions
+
+| Name | Description |
+| --- | --- |
+| [feature_classification](#operetta_compose.tasks.feature_classification.feature_classification) | Classify cells using the [napari-feature-classifier](https://github.com/fractal-napari-plugins-collection/napari-feature-classifier) and write them to the OME-ZARR |
+
+### feature_classification { #operetta_compose.tasks.feature_classification.feature_classification }
+
+`tasks.feature_classification.feature_classification(zarr_url, classifier_path, table_name='regionprops', label_name='nuclei')`
+
+Classify cells using the [napari-feature-classifier](https://github.com/fractal-napari-plugins-collection/napari-feature-classifier) and write them to the OME-ZARR
+
+#### Parameters
+
+| Name              | Type   | Description                                        | Default         |
+|-------------------|--------|----------------------------------------------------|-----------------|
+| `zarr_url`        | str    | Path to an OME-ZARR Image                          | _required_      |
+| `classifier_path` | str    | Path to the pickled scikit-learn classifier        | _required_      |
+| `table_name`      | str    | Folder name of the measured regionprobs features   | `'regionprops'` |
+| `label_name`      | str    | Name of the labels to use for feature measurements | `'nuclei'`      |

docs/contributing.qmd

@@ -24,5 +24,9 @@ harmony_to_ome_zarr(
   zarr_dir="operetta_plate.zarr"
 )
 ```
-
 :::
+
+### Updating the documentation
+1. Make your changes to the documentation under `/docs`
+2. Update the function API with `quartodoc build`
+3. Preview the documentation with `quarto preview`

docs/index.qmd

@@ -14,7 +14,7 @@ Currently the following tasks are part of *operetta-compose*
 | harmony_to_ome_zarr | Convert TIFFs which were exported from Harmony (Operetta/Opera, Perkin-Elmer) to OME-ZARR |
 | stardist_segmentation | Segment cells with Stardist |
 | regionprops_measurement | Take measurements using regionprops and write the features to the OME-ZARR |
-| label_prediction | Make predictions on the selected wells and write them to the OME-ZARR |
+| feature_classification | Classify cells using the [napari-feature-classifier](https://github.com/fractal-napari-plugins-collection/napari-feature-classifier) and write them to the OME-ZARR |
 | condition_registration | Register the experimental conditions in the OME-ZARR |
 
  

docs/objects.json

@@ -1 +1 @@
-{"project": "operetta_compose", "version": "0.0.9999", "count": 24, "items": [{"name": "operetta_compose.tasks.harmony_to_ome_zarr.harmony_to_ome_zarr", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.harmony_to_ome_zarr.html#operetta_compose.tasks.harmony_to_ome_zarr.harmony_to_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.tasks.harmony_to_ome_zarr", "domain": "py", "role": "module", "priority": "1", "uri": "api/tasks.harmony_to_ome_zarr.html#operetta_compose.tasks.harmony_to_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.tasks.stardist_segmentation.stardist_segmentation", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.stardist_segmentation.html#operetta_compose.tasks.stardist_segmentation.stardist_segmentation", "dispname": "-"}, {"name": "operetta_compose.tasks.stardist_segmentation", "domain": "py", "role": "module", "priority": "1", "uri": "api/tasks.stardist_segmentation.html#operetta_compose.tasks.stardist_segmentation", "dispname": "-"}, {"name": "operetta_compose.tasks.regionprops_measurement.feature_table", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.regionprops_measurement.html#operetta_compose.tasks.regionprops_measurement.feature_table", "dispname": "-"}, {"name": "operetta_compose.tasks.regionprops_measurement.regionprops_measurement", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.regionprops_measurement.html#operetta_compose.tasks.regionprops_measurement.regionprops_measurement", "dispname": "-"}, {"name": "operetta_compose.tasks.regionprops_measurement", "domain": "py", "role": "module", "priority": "1", "uri": "api/tasks.regionprops_measurement.html#operetta_compose.tasks.regionprops_measurement", "dispname": "-"}, {"name": "operetta_compose.tasks.label_prediction.label_prediction", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.label_prediction.html#operetta_compose.tasks.label_prediction.label_prediction", "dispname": "-"}, {"name": "operetta_compose.tasks.label_prediction", "domain": "py", "role": "module", "priority": "1", "uri": "api/tasks.label_prediction.html#operetta_compose.tasks.label_prediction", "dispname": "-"}, {"name": "operetta_compose.tasks.condition_registration.condition_registration", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.condition_registration.html#operetta_compose.tasks.condition_registration.condition_registration", "dispname": "-"}, {"name": "operetta_compose.tasks.condition_registration", "domain": "py", "role": "module", "priority": "1", "uri": "api/tasks.condition_registration.html#operetta_compose.tasks.condition_registration", "dispname": "-"}, {"name": "operetta_compose.io.OmeZarrUrl", "domain": "py", "role": "class", "priority": "1", "uri": "api/io.OmeZarrUrl.html#operetta_compose.io.OmeZarrUrl", "dispname": "-"}, {"name": "operetta_compose.io.read_ome_zarr", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.read_ome_zarr.html#operetta_compose.io.read_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.io.parse_zarr_url", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.parse_zarr_url.html#operetta_compose.io.parse_zarr_url", "dispname": "-"}, {"name": "operetta_compose.io.convert_ROI_table_to_indices", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.convert_ROI_table_to_indices.html#operetta_compose.io.convert_ROI_table_to_indices", "dispname": "-"}, {"name": "operetta_compose.io.get_roi", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.get_roi.html#operetta_compose.io.get_roi", "dispname": "-"}, {"name": "operetta_compose.io.load_intensity_roi", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.load_intensity_roi.html#operetta_compose.io.load_intensity_roi", "dispname": "-"}, {"name": "operetta_compose.io.load_label_roi", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.load_label_roi.html#operetta_compose.io.load_label_roi", "dispname": "-"}, {"name": "operetta_compose.io.labels_to_ome_zarr", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.labels_to_ome_zarr.html#operetta_compose.io.labels_to_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.io.features_to_ome_zarr", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.features_to_ome_zarr.html#operetta_compose.io.features_to_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.io.condition_to_ome_zarr", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.condition_to_ome_zarr.html#operetta_compose.io.condition_to_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.utils.colorbrewer", "domain": "py", "role": "function", "priority": "1", "uri": "api/utils.colorbrewer.html#operetta_compose.utils.colorbrewer", "dispname": "-"}, {"name": "operetta_compose.utils.alpha_to_numeric", "domain": "py", "role": "function", "priority": "1", "uri": "api/utils.alpha_to_numeric.html#operetta_compose.utils.alpha_to_numeric", "dispname": "-"}, {"name": "operetta_compose.utils.numeric_to_alpha", "domain": "py", "role": "function", "priority": "1", "uri": "api/utils.numeric_to_alpha.html#operetta_compose.utils.numeric_to_alpha", "dispname": "-"}]}
+{"project": "operetta_compose", "version": "0.0.9999", "count": 24, "items": [{"name": "operetta_compose.tasks.harmony_to_ome_zarr.harmony_to_ome_zarr", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.harmony_to_ome_zarr.html#operetta_compose.tasks.harmony_to_ome_zarr.harmony_to_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.tasks.harmony_to_ome_zarr", "domain": "py", "role": "module", "priority": "1", "uri": "api/tasks.harmony_to_ome_zarr.html#operetta_compose.tasks.harmony_to_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.tasks.stardist_segmentation.stardist_segmentation", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.stardist_segmentation.html#operetta_compose.tasks.stardist_segmentation.stardist_segmentation", "dispname": "-"}, {"name": "operetta_compose.tasks.stardist_segmentation", "domain": "py", "role": "module", "priority": "1", "uri": "api/tasks.stardist_segmentation.html#operetta_compose.tasks.stardist_segmentation", "dispname": "-"}, {"name": "operetta_compose.tasks.regionprops_measurement.feature_table", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.regionprops_measurement.html#operetta_compose.tasks.regionprops_measurement.feature_table", "dispname": "-"}, {"name": "operetta_compose.tasks.regionprops_measurement.regionprops_measurement", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.regionprops_measurement.html#operetta_compose.tasks.regionprops_measurement.regionprops_measurement", "dispname": "-"}, {"name": "operetta_compose.tasks.regionprops_measurement", "domain": "py", "role": "module", "priority": "1", "uri": "api/tasks.regionprops_measurement.html#operetta_compose.tasks.regionprops_measurement", "dispname": "-"}, {"name": "operetta_compose.tasks.feature_classification.feature_classification", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.feature_classification.html#operetta_compose.tasks.feature_classification.feature_classification", "dispname": "-"}, {"name": "operetta_compose.tasks.feature_classification", "domain": "py", "role": "module", "priority": "1", "uri": "api/tasks.feature_classification.html#operetta_compose.tasks.feature_classification", "dispname": "-"}, {"name": "operetta_compose.tasks.condition_registration.condition_registration", "domain": "py", "role": "function", "priority": "1", "uri": "api/tasks.condition_registration.html#operetta_compose.tasks.condition_registration.condition_registration", "dispname": "-"}, {"name": "operetta_compose.tasks.condition_registration", "domain": "py", "role": "module", "priority": "1", "uri": "api/tasks.condition_registration.html#operetta_compose.tasks.condition_registration", "dispname": "-"}, {"name": "operetta_compose.io.OmeZarrUrl", "domain": "py", "role": "class", "priority": "1", "uri": "api/io.OmeZarrUrl.html#operetta_compose.io.OmeZarrUrl", "dispname": "-"}, {"name": "operetta_compose.io.read_ome_zarr", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.read_ome_zarr.html#operetta_compose.io.read_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.io.parse_zarr_url", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.parse_zarr_url.html#operetta_compose.io.parse_zarr_url", "dispname": "-"}, {"name": "operetta_compose.io.convert_ROI_table_to_indices", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.convert_ROI_table_to_indices.html#operetta_compose.io.convert_ROI_table_to_indices", "dispname": "-"}, {"name": "operetta_compose.io.get_roi", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.get_roi.html#operetta_compose.io.get_roi", "dispname": "-"}, {"name": "operetta_compose.io.load_intensity_roi", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.load_intensity_roi.html#operetta_compose.io.load_intensity_roi", "dispname": "-"}, {"name": "operetta_compose.io.load_label_roi", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.load_label_roi.html#operetta_compose.io.load_label_roi", "dispname": "-"}, {"name": "operetta_compose.io.labels_to_ome_zarr", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.labels_to_ome_zarr.html#operetta_compose.io.labels_to_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.io.features_to_ome_zarr", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.features_to_ome_zarr.html#operetta_compose.io.features_to_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.io.condition_to_ome_zarr", "domain": "py", "role": "function", "priority": "1", "uri": "api/io.condition_to_ome_zarr.html#operetta_compose.io.condition_to_ome_zarr", "dispname": "-"}, {"name": "operetta_compose.utils.colorbrewer", "domain": "py", "role": "function", "priority": "1", "uri": "api/utils.colorbrewer.html#operetta_compose.utils.colorbrewer", "dispname": "-"}, {"name": "operetta_compose.utils.alpha_to_numeric", "domain": "py", "role": "function", "priority": "1", "uri": "api/utils.alpha_to_numeric.html#operetta_compose.utils.alpha_to_numeric", "dispname": "-"}, {"name": "operetta_compose.utils.numeric_to_alpha", "domain": "py", "role": "function", "priority": "1", "uri": "api/utils.numeric_to_alpha.html#operetta_compose.utils.numeric_to_alpha", "dispname": "-"}]}

src/operetta_compose/__FRACTAL_MANIFEST__.json

@@ -291,8 +291,8 @@
       "docs_link": "https://leukemia-kispi.github.io/operetta-compose/"
     },
     {
-      "name": "Label prediction",
-      "executable_parallel": "tasks/label_prediction.py",
+      "name": "Feature classification",
+      "executable_parallel": "tasks/feature_classification.py",
       "meta_parallel": {
         "cpus_per_task": 1,
         "mem": 4000
@@ -328,9 +328,9 @@
           "classifier_path"
         ],
         "type": "object",
-        "title": "LabelPrediction"
+        "title": "FeatureClassification"
       },
-      "docs_info": "## label_prediction\nMake predictions on the selected wells and write them to the OME-ZARR\n",
+      "docs_info": "## feature_classification\nClassify cells using the [napari-feature-classifier](https://github.com/fractal-napari-plugins-collection/napari-feature-classifier)\nand write them to the OME-ZARR\n",
       "docs_link": "https://leukemia-kispi.github.io/operetta-compose/"
     },
     {

src/operetta_compose/dev/task_list.py

@@ -17,8 +17,8 @@
         meta={"cpus_per_task": 1, "mem": 4000},
     ),
     ParallelTask(
-        name="Label prediction",
-        executable="tasks/label_prediction.py",
+        name="Feature classification",
+        executable="tasks/feature_classification.py",
         meta={"cpus_per_task": 1, "mem": 4000},
     ),
     ParallelTask(

src/operetta_compose/tasks/label_prediction.py → src/operetta_compose/tasks/feature_classification.py

@@ -17,14 +17,14 @@
 
 
 @validate_call
-def label_prediction(
+def feature_classification(
     *,
     zarr_url: str,
     classifier_path: str,
     table_name: str = "regionprops",
     label_name: str = "nuclei",
 ) -> None:
-    """Make predictions on the selected wells and write them to the OME-ZARR
+    """Classify cells using the [napari-feature-classifier](https://github.com/fractal-napari-plugins-collection/napari-feature-classifier) and write them to the OME-ZARR
 
     Args:
         zarr_url: Path to an OME-ZARR Image
@@ -42,11 +42,23 @@ def label_prediction(
             f"No measurements exist at the specified zarr URL in the table {table_name}."
         )
     features = ann_tbl.to_df()
+    roi_id_cols = ann_tbl.obs.drop(
+        columns=["roi_id", "label", "prediction"], errors="ignore"
+    )
+    if "roi_id" not in ann_tbl.obs.columns:
+        ann_tbl.obs["roi_id"] = f"{zarr_url}:" + roi_id_cols.astype(str).agg(
+            ":".join, axis=1
+        )
+
+    # Select feature subset in expected order
+    features = features[clf.get_feature_names()]
+
+    # Add index columns
     features_with_annotations = pd.concat(
         (ann_tbl.obs[["roi_id", "label"]], features), axis=1
     )
     predictions = clf.predict(features_with_annotations).reset_index()
-    ann_tbl.obs = predictions
+    ann_tbl.obs = pd.concat((roi_id_cols.reset_index(drop=True), predictions), axis=1)
     ann_tbl.obs_names = ann_tbl.obs.index.map(str)
     ann_tbl.write_zarr(f"{zarr_url}/tables/{table_name}")
     io.write_table_metadata(zarr_url, "feature_table", table_name, label_name)
@@ -56,6 +68,6 @@ def label_prediction(
     from fractal_tasks_core.tasks._utils import run_fractal_task
 
     run_fractal_task(
-        task_function=label_prediction,
+        task_function=feature_classification,
         logger_name=logger.name,
     )

tests/test_compose.py

@@ -7,7 +7,7 @@
 from operetta_compose.tasks.harmony_to_ome_zarr import harmony_to_ome_zarr
 from operetta_compose.tasks.stardist_segmentation import stardist_segmentation
 from operetta_compose.tasks.regionprops_measurement import regionprops_measurement
-from operetta_compose.tasks.label_prediction import label_prediction
+from operetta_compose.tasks.feature_classification import feature_classification
 from operetta_compose.tasks.condition_registration import condition_registration
 
 from operetta_compose.io import OmeroNgffChannel, OmeroNgffWindow
@@ -78,7 +78,7 @@ def test_measure():
 @pytest.mark.dependency(depends=["test_converter", "test_stardist", "test_measure"])
 # @pytest.mark.skip
 def test_predict():
-    label_prediction(
+    feature_classification(
         zarr_url=str(ZARR_DIR.joinpath(PLATE_ZARR, "C", "3", "0")),
         classifier_path=str(Path(TEST_DIR).joinpath("fixtures", "classifier.pkl")),
         table_name="regionprops",