From c7b8c3c87fcd89d4a3d86dad4ba5ece72a5362e0 Mon Sep 17 00:00:00 2001
From: hgherzog <henryh@allenai.org>
Date: Tue, 16 Sep 2025 00:53:29 +0000
Subject: [PATCH 01/11] initial pass wip

---
 esrun_data/mangrove/dataset.json              |   0
 esrun_data/mangrove/esrun.yaml                |  34 +++
 esrun_data/mangrove/model.yaml                | 231 ++++++++++++++++++
 .../prediction_request_geometry.geojson       | 142 +++++++++++
 4 files changed, 407 insertions(+)
 create mode 100644 esrun_data/mangrove/dataset.json
 create mode 100644 esrun_data/mangrove/esrun.yaml
 create mode 100644 esrun_data/mangrove/model.yaml
 create mode 100644 esrun_data/mangrove/prediction_request_geometry.geojson

diff --git a/esrun_data/mangrove/dataset.json b/esrun_data/mangrove/dataset.json
new file mode 100644
index 00000000..e69de29b
diff --git a/esrun_data/mangrove/esrun.yaml b/esrun_data/mangrove/esrun.yaml
new file mode 100644
index 00000000..daf94815
--- /dev/null
+++ b/esrun_data/mangrove/esrun.yaml
@@ -0,0 +1,34 @@
+partition_strategies:
+  partition_request_geometry:
+    class_path: esrun.runner.tools.partitioners.grid_partitioner.GridPartitioner
+    init_args:
+      grid_size: 0.15 # Lat lon degrees
+      output_projection:
+        class_path: rslearn.utils.geometry.Projection
+        init_args:
+          crs: EPSG:3857
+          x_resolution: 10
+          y_resolution: -10
+      use_utm: true
+
+  prepare_window_geometries:
+    class_path: esrun.runner.tools.partitioners.grid_partitioner.GridPartitioner
+    init_args:
+      grid_size: 32 # based on the window creation script yawen chose
+      output_projection:
+        class_path: rslearn.utils.geometry.Projection
+        init_args:
+          crs: EPSG:3857
+          x_resolution: 10
+          y_resolution: -10
+      use_utm: true
+
+postprocessing_strategies:
+  process_dataset:
+    class_path: esrun.runner.tools.postprocessors.combine_geotiff.CombineGeotiff
+
+  process_partition:
+    class_path: esrun.runner.tools.postprocessors.combine_geotiff.CombineGeotiff
+
+  process_window:
+    class_path: esrun.runner.tools.postprocessors.noop_raster.NoopRaster
diff --git a/esrun_data/mangrove/model.yaml b/esrun_data/mangrove/model.yaml
new file mode 100644
index 00000000..25f2cdcc
--- /dev/null
+++ b/esrun_data/mangrove/model.yaml
@@ -0,0 +1,231 @@
+model:
+  class_path: rslearn.train.lightning_module.RslearnLightningModule
+  init_args:
+    model:
+      class_path: rslearn.models.multitask.MultiTaskModel
+      init_args:
+        encoder:
+          - class_path: rslp.helios.model.Helios
+            init_args:
+              checkpoint_path: "{CHECKPOINT_PATH}"
+              selector: ["encoder"]
+              forward_kwargs:
+                patch_size: {PATCH_SIZE}
+        decoders:
+          mangrove_classification:
+            - class_path: rslearn.models.pooling_decoder.PoolingDecoder
+              init_args:
+                in_channels: {ENCODER_EMBEDDING_SIZE}
+                out_channels: 3
+            - class_path: rslearn.train.tasks.classification.ClassificationHead
+    lr: 0.0001
+    scheduler:
+      class_path: rslearn.train.scheduler.PlateauScheduler
+      init_args:
+        factor: 0.2
+        patience: 2
+        min_lr: 0
+        cooldown: 10
+data:
+  class_path: rslearn.train.data_module.RslearnDataModule
+  init_args:
+    path: /weka/dfive-default/rslearn-eai/datasets/mangrove/classification/20250626
+    inputs:
+      sentinel2_0:
+        data_type: "raster"
+        layers: ["sentinel2"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      sentinel2_1:
+        data_type: "raster"
+        layers: ["sentinel2.1"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      sentinel2_2:
+        data_type: "raster"
+        layers: ["sentinel2.2"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      sentinel2_3:
+        data_type: "raster"
+        layers: ["sentinel2.3"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      sentinel2_4:
+        data_type: "raster"
+        layers: ["sentinel2.4"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      sentinel2_5:
+        data_type: "raster"
+        layers: ["sentinel2.5"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      sentinel2_6:
+        data_type: "raster"
+        layers: ["sentinel2.6"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      sentinel2_7:
+        data_type: "raster"
+        layers: ["sentinel2.7"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      sentinel2_8:
+        data_type: "raster"
+        layers: ["sentinel2.8"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      sentinel2_9:
+        data_type: "raster"
+        layers: ["sentinel2.9"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      sentinel2_10:
+        data_type: "raster"
+        layers: ["sentinel2.10"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      sentinel2_11:
+        data_type: "raster"
+        layers: ["sentinel2.11"]
+        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        passthrough: true
+        dtype: FLOAT32
+      label:
+        data_type: "vector"
+        layers: ["label"]
+        is_target: true
+    task:
+      class_path: rslearn.train.tasks.multi_task.MultiTask
+      init_args:
+        tasks:
+          mangrove_classification:
+            class_path: rslearn.train.tasks.classification.ClassificationTask
+            init_args:
+              property_name: "category"
+              classes: ["Mangrove", "Water", "Other"]
+              enable_f1_metric: true
+              metric_kwargs:
+                average: "micro"
+        input_mapping:
+          mangrove_classification:
+            label: "targets"
+    batch_size: 32
+    num_workers: 8
+    default_config:
+      transforms:
+        - class_path: rslearn.train.transforms.concatenate.Concatenate
+          init_args:
+            selections:
+              sentinel2_0: []
+              sentinel2_1: []
+              sentinel2_2: []
+              sentinel2_3: []
+              sentinel2_4: []
+              sentinel2_5: []
+              sentinel2_6: []
+              sentinel2_7: []
+              sentinel2_8: []
+              sentinel2_9: []
+              sentinel2_10: []
+              sentinel2_11: []
+            output_selector: sentinel2_l2a
+        - class_path: rslp.helios.norm.HeliosNormalize
+          init_args:
+            config_fname: "/opt/helios/data/norm_configs/computed.json"
+            band_names:
+              sentinel2_l2a: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
+        - class_path: rslearn.train.transforms.pad.Pad
+          init_args:
+            size: 2
+            mode: "center"
+            image_selectors: ["sentinel2_l2a"]
+    train_config:
+      groups: ["sample_100K"]
+      tags:
+        split: "train"
+      num_samples: 10000
+    val_config:
+      groups: ["sample_100K"]
+      tags:
+        split: "val"
+    test_config:
+      groups: ["sample_100K"]
+      tags:
+        split: "val"
+    predict_config:
+      patch_size: 2 #I think this is actually the window size for inference processing
+      overlap_ratio: 0.5
+      load_all_patches: true
+      skip_targets: true
+      transforms:
+      - class_path: rslearn.train.transforms.concatenate.Concatenate
+        init_args:
+          selections:
+            sentinel2_0: []
+            sentinel2_1: []
+            sentinel2_2: []
+            sentinel2_3: []
+            sentinel2_4: []
+            sentinel2_5: []
+            sentinel2_6: []
+            sentinel2_7: []
+            sentinel2_8: []
+            sentinel2_9: []
+            sentinel2_10: []
+            sentinel2_11: []
+          output_selector: sentinel2_l2a
+      # I feel like we really don;t want this
+      - class_path: rslp.helios.norm.HeliosNormalize
+        init_args:
+          band_names:
+            sentinel2_l2a:
+            - B02
+            - B03
+            - B04
+            - B08
+            - B05
+            - B06
+            - B07
+            - B8A
+            - B11
+            - B12
+            - B01
+            - B09
+      - class_path: rslearn.train.transforms.pad.Pad
+        init_args:
+          size: 2
+          mode: "center"
+          image_selectors: ["sentinel2_l2a"]
+
+# Should be independent and unused for inference.
+trainer:
+  max_epochs: 100
+  callbacks:
+    - class_path: lightning.pytorch.callbacks.LearningRateMonitor
+      init_args:
+        logging_interval: "epoch"
+    - class_path: lightning.pytorch.callbacks.ModelCheckpoint
+      init_args:
+        save_top_k: 1
+        save_last: true
+        monitor: val_loss
+        mode: min
+    - class_path: rslearn.train.callbacks.freeze_unfreeze.FreezeUnfreeze
+      init_args:
+        module_selector: ["model", "encoder", 0]
+        unfreeze_at_epoch: 2
+rslp_project: placeholder
+rslp_experiment: placeholder
diff --git a/esrun_data/mangrove/prediction_request_geometry.geojson b/esrun_data/mangrove/prediction_request_geometry.geojson
new file mode 100644
index 00000000..0fd0c9ed
--- /dev/null
+++ b/esrun_data/mangrove/prediction_request_geometry.geojson
@@ -0,0 +1,142 @@
+{
+    "type": "FeatureCollection",
+    "name": "region_of_interests_for_testing",
+    "crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } },
+    "features": [
+    { "type": "Feature", "properties": { "fid": 136, "MinX": 55.0, "MaxX": 56.0, "MinY": 26.0, "MaxY": 27.0, "tile_name": "N27E055", "gmw_tile_name": "GMW_N27E055" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 55.0, 27.0 ], [ 56.0, 27.0 ], [ 56.0, 26.0 ], [ 55.0, 26.0 ], [ 55.0, 27.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 153, "MinX": -82.0, "MaxX": -81.0, "MinY": 25.0, "MaxY": 26.0, "tile_name": "N26W082", "gmw_tile_name": "GMW_N26W082" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -82.0, 26.0 ], [ -81.0, 26.0 ], [ -81.0, 25.0 ], [ -82.0, 25.0 ], [ -82.0, 26.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 154, "MinX": -81.0, "MaxX": -80.0, "MinY": 25.0, "MaxY": 26.0, "tile_name": "N26W081", "gmw_tile_name": "GMW_N26W081" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -81.0, 26.0 ], [ -80.0, 26.0 ], [ -80.0, 25.0 ], [ -81.0, 25.0 ], [ -81.0, 26.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 160, "MinX": 36.0, "MaxX": 37.0, "MinY": 25.0, "MaxY": 26.0, "tile_name": "N26E036", "gmw_tile_name": "GMW_N26E036" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 36.0, 26.0 ], [ 37.0, 26.0 ], [ 37.0, 25.0 ], [ 36.0, 25.0 ], [ 36.0, 26.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 200, "MinX": -79.0, "MaxX": -78.0, "MinY": 24.0, "MaxY": 25.0, "tile_name": "N25W079", "gmw_tile_name": "GMW_N25W079" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -79.0, 25.0 ], [ -78.0, 25.0 ], [ -78.0, 24.0 ], [ -79.0, 24.0 ], [ -79.0, 25.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 201, "MinX": -78.0, "MaxX": -77.0, "MinY": 24.0, "MaxY": 25.0, "tile_name": "N25W078", "gmw_tile_name": "GMW_N25W078" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -78.0, 25.0 ], [ -77.0, 25.0 ], [ -77.0, 24.0 ], [ -78.0, 24.0 ], [ -78.0, 25.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 213, "MinX": 54.0, "MaxX": 55.0, "MinY": 24.0, "MaxY": 25.0, "tile_name": "N25E054", "gmw_tile_name": "GMW_N25E054" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 54.0, 25.0 ], [ 55.0, 25.0 ], [ 55.0, 24.0 ], [ 54.0, 24.0 ], [ 54.0, 25.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 258, "MinX": 70.0, "MaxX": 71.0, "MinY": 23.0, "MaxY": 24.0, "tile_name": "N24E070", "gmw_tile_name": "GMW_N24E070" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 70.0, 24.0 ], [ 71.0, 24.0 ], [ 71.0, 23.0 ], [ 70.0, 23.0 ], [ 70.0, 24.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 277, "MinX": -83.0, "MaxX": -82.0, "MinY": 22.0, "MaxY": 23.0, "tile_name": "N23W083", "gmw_tile_name": "GMW_N23W083" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -83.0, 23.0 ], [ -82.0, 23.0 ], [ -82.0, 22.0 ], [ -83.0, 22.0 ], [ -83.0, 23.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 278, "MinX": -82.0, "MaxX": -81.0, "MinY": 22.0, "MaxY": 23.0, "tile_name": "N23W082", "gmw_tile_name": "GMW_N23W082" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -82.0, 23.0 ], [ -81.0, 23.0 ], [ -81.0, 22.0 ], [ -82.0, 22.0 ], [ -82.0, 23.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 282, "MinX": -78.0, "MaxX": -77.0, "MinY": 22.0, "MaxY": 23.0, "tile_name": "N23W078", "gmw_tile_name": "GMW_N23W078" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -78.0, 23.0 ], [ -77.0, 23.0 ], [ -77.0, 22.0 ], [ -78.0, 22.0 ], [ -78.0, 23.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 294, "MinX": 70.0, "MaxX": 71.0, "MinY": 22.0, "MaxY": 23.0, "tile_name": "N23E070", "gmw_tile_name": "GMW_N23E070" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 70.0, 23.0 ], [ 71.0, 23.0 ], [ 71.0, 22.0 ], [ 70.0, 22.0 ], [ 70.0, 23.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 297, "MinX": 88.0, "MaxX": 89.0, "MinY": 22.0, "MaxY": 23.0, "tile_name": "N23E088", "gmw_tile_name": "GMW_N23E088" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 88.0, 23.0 ], [ 89.0, 23.0 ], [ 89.0, 22.0 ], [ 88.0, 22.0 ], [ 88.0, 23.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 318, "MinX": -89.0, "MaxX": -88.0, "MinY": 21.0, "MaxY": 22.0, "tile_name": "N22W089", "gmw_tile_name": "GMW_N22W089" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -89.0, 22.0 ], [ -88.0, 22.0 ], [ -88.0, 21.0 ], [ -89.0, 21.0 ], [ -89.0, 22.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 328, "MinX": -78.0, "MaxX": -77.0, "MinY": 21.0, "MaxY": 22.0, "tile_name": "N22W078", "gmw_tile_name": "GMW_N22W078" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -78.0, 22.0 ], [ -77.0, 22.0 ], [ -77.0, 21.0 ], [ -78.0, 21.0 ], [ -78.0, 22.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 348, "MinX": 88.0, "MaxX": 89.0, "MinY": 21.0, "MaxY": 22.0, "tile_name": "N22E088", "gmw_tile_name": "GMW_N22E088" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 88.0, 22.0 ], [ 89.0, 22.0 ], [ 89.0, 21.0 ], [ 88.0, 21.0 ], [ 88.0, 22.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 418, "MinX": -88.0, "MaxX": -87.0, "MinY": 19.0, "MaxY": 20.0, "tile_name": "N20W088", "gmw_tile_name": "GMW_N20W088" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -88.0, 20.0 ], [ -87.0, 20.0 ], [ -87.0, 19.0 ], [ -88.0, 19.0 ], [ -88.0, 20.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 427, "MinX": -73.0, "MaxX": -72.0, "MinY": 19.0, "MaxY": 20.0, "tile_name": "N20W073", "gmw_tile_name": "GMW_N20W073" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -73.0, 20.0 ], [ -72.0, 20.0 ], [ -72.0, 19.0 ], [ -73.0, 19.0 ], [ -73.0, 20.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 445, "MinX": 93.0, "MaxX": 94.0, "MinY": 19.0, "MaxY": 20.0, "tile_name": "N20E093", "gmw_tile_name": "GMW_N20E093" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 93.0, 20.0 ], [ 94.0, 20.0 ], [ 94.0, 19.0 ], [ 93.0, 19.0 ], [ 93.0, 20.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 446, "MinX": 94.0, "MaxX": 95.0, "MinY": 19.0, "MaxY": 20.0, "tile_name": "N20E094", "gmw_tile_name": "GMW_N20E094" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 94.0, 20.0 ], [ 95.0, 20.0 ], [ 95.0, 19.0 ], [ 94.0, 19.0 ], [ 94.0, 20.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 468, "MinX": -93.0, "MaxX": -92.0, "MinY": 18.0, "MaxY": 19.0, "tile_name": "N19W093", "gmw_tile_name": "GMW_N19W093" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -93.0, 19.0 ], [ -92.0, 19.0 ], [ -92.0, 18.0 ], [ -93.0, 18.0 ], [ -93.0, 19.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 469, "MinX": -92.0, "MaxX": -91.0, "MinY": 18.0, "MaxY": 19.0, "tile_name": "N19W092", "gmw_tile_name": "GMW_N19W092" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -92.0, 19.0 ], [ -91.0, 19.0 ], [ -91.0, 18.0 ], [ -92.0, 18.0 ], [ -92.0, 19.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 471, "MinX": -89.0, "MaxX": -88.0, "MinY": 18.0, "MaxY": 19.0, "tile_name": "N19W089", "gmw_tile_name": "GMW_N19W089" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -89.0, 19.0 ], [ -88.0, 19.0 ], [ -88.0, 18.0 ], [ -89.0, 18.0 ], [ -89.0, 19.0 ] ] ] } },
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+    { "type": "Feature", "properties": { "fid": 1046, "MinX": 72.0, "MaxX": 73.0, "MinY": 6.0, "MaxY": 7.0, "tile_name": "N07E072", "gmw_tile_name": "GMW_N07E072" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 72.0, 7.0 ], [ 73.0, 7.0 ], [ 73.0, 6.0 ], [ 72.0, 6.0 ], [ 72.0, 7.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 1047, "MinX": 73.0, "MaxX": 74.0, "MinY": 6.0, "MaxY": 7.0, "tile_name": "N07E073", "gmw_tile_name": "GMW_N07E073" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 73.0, 7.0 ], [ 74.0, 7.0 ], [ 74.0, 6.0 ], [ 73.0, 6.0 ], [ 73.0, 7.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 2244, "MinX": 43.0, "MaxX": 44.0, "MinY": -22.0, "MaxY": -21.0, "tile_name": "S21E043", "gmw_tile_name": "GMW_S21E043" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 43.0, -21.0 ], [ 44.0, -21.0 ], [ 44.0, -22.0 ], [ 43.0, -22.0 ], [ 43.0, -21.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 1584, "MinX": 122.0, "MaxX": 123.0, "MinY": -5.0, "MaxY": -4.0, "tile_name": "S04E122", "gmw_tile_name": "GMW_S04E122" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 122.0, -4.0 ], [ 123.0, -4.0 ], [ 123.0, -5.0 ], [ 122.0, -5.0 ], [ 122.0, -4.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 1585, "MinX": 123.0, "MaxX": 124.0, "MinY": -5.0, "MaxY": -4.0, "tile_name": "S04E123", "gmw_tile_name": "GMW_S04E123" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 123.0, -4.0 ], [ 124.0, -4.0 ], [ 124.0, -5.0 ], [ 123.0, -5.0 ], [ 123.0, -4.0 ] ] ] } },
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+    { "type": "Feature", "properties": { "fid": 2333, "MinX": 113.0, "MaxX": 114.0, "MinY": -26.0, "MaxY": -25.0, "tile_name": "S25E113", "gmw_tile_name": "GMW_S25E113" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 113.0, -25.0 ], [ 114.0, -25.0 ], [ 114.0, -26.0 ], [ 113.0, -26.0 ], [ 113.0, -25.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 2303, "MinX": 150.0, "MaxX": 151.0, "MinY": -24.0, "MaxY": -23.0, "tile_name": "S23E150", "gmw_tile_name": "GMW_S23E150" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 150.0, -23.0 ], [ 151.0, -23.0 ], [ 151.0, -24.0 ], [ 150.0, -24.0 ], [ 150.0, -23.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 2304, "MinX": 151.0, "MaxX": 152.0, "MinY": -24.0, "MaxY": -23.0, "tile_name": "S23E151", "gmw_tile_name": "GMW_S23E151" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 151.0, -23.0 ], [ 152.0, -23.0 ], [ 152.0, -24.0 ], [ 151.0, -24.0 ], [ 151.0, -23.0 ] ] ] } }
+    ]
+    }

From 01445ec598b67fee09b0021176c52878d833f570 Mon Sep 17 00:00:00 2001
From: hgherzog <henryh@allenai.org>
Date: Tue, 16 Sep 2025 00:58:07 +0000
Subject: [PATCH 02/11] ready to start trying esrun steps

---
 esrun_data/mangrove/esrun.yaml                     |  2 +-
 esrun_data/mangrove/model.yaml                     | 11 ++++++-----
 rslp/mangrove/create_windows_for_classification.py |  1 +
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/esrun_data/mangrove/esrun.yaml b/esrun_data/mangrove/esrun.yaml
index daf94815..c4df19e2 100644
--- a/esrun_data/mangrove/esrun.yaml
+++ b/esrun_data/mangrove/esrun.yaml
@@ -2,7 +2,7 @@ partition_strategies:
   partition_request_geometry:
     class_path: esrun.runner.tools.partitioners.grid_partitioner.GridPartitioner
     init_args:
-      grid_size: 0.15 # Lat lon degrees
+      grid_size: 0.01 # Lat lon degrees, a random guess not sure what is really reasonable
       output_projection:
         class_path: rslearn.utils.geometry.Projection
         init_args:
diff --git a/esrun_data/mangrove/model.yaml b/esrun_data/mangrove/model.yaml
index 25f2cdcc..ea8cce8c 100644
--- a/esrun_data/mangrove/model.yaml
+++ b/esrun_data/mangrove/model.yaml
@@ -7,15 +7,16 @@ model:
         encoder:
           - class_path: rslp.helios.model.Helios
             init_args:
-              checkpoint_path: "{CHECKPOINT_PATH}"
+              checkpoint_path: /weka/dfive-default/helios/checkpoints/favyen/v0.2_base_latent_mim_128_alldata_random_fixed_modality_0.5/step320000 # Will need to be copied to gcp for actual inference
+              random_initialization: true
               selector: ["encoder"]
               forward_kwargs:
-                patch_size: {PATCH_SIZE}
+                patch_size: 2
         decoders:
           mangrove_classification:
             - class_path: rslearn.models.pooling_decoder.PoolingDecoder
               init_args:
-                in_channels: {ENCODER_EMBEDDING_SIZE}
+                in_channels: 768
                 out_channels: 3
             - class_path: rslearn.train.tasks.classification.ClassificationHead
     lr: 0.0001
@@ -122,8 +123,8 @@ data:
         input_mapping:
           mangrove_classification:
             label: "targets"
-    batch_size: 32
-    num_workers: 8
+    batch_size: 4
+    num_workers: 2
     default_config:
       transforms:
         - class_path: rslearn.train.transforms.concatenate.Concatenate
diff --git a/rslp/mangrove/create_windows_for_classification.py b/rslp/mangrove/create_windows_for_classification.py
index 0fe6d49b..df5c929c 100644
--- a/rslp/mangrove/create_windows_for_classification.py
+++ b/rslp/mangrove/create_windows_for_classification.py
@@ -25,6 +25,7 @@
 START_TIME = datetime(2020, 6, 15, tzinfo=timezone.utc)
 END_TIME = datetime(2020, 7, 15, tzinfo=timezone.utc)
 
+# For every latlon we get a window of size 32 around the data
 
 def create_window(
     csv_row: pd.Series, ds_path: UPath, window_size: int, group_name: str

From 988c9c6280de3a5befc3a30efb12edb15146a93f Mon Sep 17 00:00:00 2001
From: hgherzog <henryh@allenai.org>
Date: Tue, 16 Sep 2025 02:13:23 +0000
Subject: [PATCH 03/11] confugre the esrun logger

---
 esrun_data/mangrove/esrun.yaml                |   4 +
 .../prediction_request_geometry.geojson       | 136 +-----------------
 esrun_data/sample/README.md                   |   3 +
 rslp/esrun/esrun.py                           |   9 ++
 4 files changed, 17 insertions(+), 135 deletions(-)

diff --git a/esrun_data/mangrove/esrun.yaml b/esrun_data/mangrove/esrun.yaml
index c4df19e2..33e1aa29 100644
--- a/esrun_data/mangrove/esrun.yaml
+++ b/esrun_data/mangrove/esrun.yaml
@@ -32,3 +32,7 @@ postprocessing_strategies:
 
   process_window:
     class_path: esrun.runner.tools.postprocessors.noop_raster.NoopRaster
+
+
+inference_results_config:
+  data_type: RASTER
\ No newline at end of file
diff --git a/esrun_data/mangrove/prediction_request_geometry.geojson b/esrun_data/mangrove/prediction_request_geometry.geojson
index 0fd0c9ed..07de15f0 100644
--- a/esrun_data/mangrove/prediction_request_geometry.geojson
+++ b/esrun_data/mangrove/prediction_request_geometry.geojson
@@ -3,140 +3,6 @@
     "name": "region_of_interests_for_testing",
     "crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } },
     "features": [
-    { "type": "Feature", "properties": { "fid": 136, "MinX": 55.0, "MaxX": 56.0, "MinY": 26.0, "MaxY": 27.0, "tile_name": "N27E055", "gmw_tile_name": "GMW_N27E055" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 55.0, 27.0 ], [ 56.0, 27.0 ], [ 56.0, 26.0 ], [ 55.0, 26.0 ], [ 55.0, 27.0 ] ] ] } },
-    { "type": "Feature", "properties": { "fid": 153, "MinX": -82.0, "MaxX": -81.0, "MinY": 25.0, "MaxY": 26.0, "tile_name": "N26W082", "gmw_tile_name": "GMW_N26W082" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -82.0, 26.0 ], [ -81.0, 26.0 ], [ -81.0, 25.0 ], [ -82.0, 25.0 ], [ -82.0, 26.0 ] ] ] } },
-    { "type": "Feature", "properties": { "fid": 154, "MinX": -81.0, "MaxX": -80.0, "MinY": 25.0, "MaxY": 26.0, "tile_name": "N26W081", "gmw_tile_name": "GMW_N26W081" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -81.0, 26.0 ], [ -80.0, 26.0 ], [ -80.0, 25.0 ], [ -81.0, 25.0 ], [ -81.0, 26.0 ] ] ] } },
-    { "type": "Feature", "properties": { "fid": 160, "MinX": 36.0, "MaxX": 37.0, "MinY": 25.0, "MaxY": 26.0, "tile_name": "N26E036", "gmw_tile_name": "GMW_N26E036" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 36.0, 26.0 ], [ 37.0, 26.0 ], [ 37.0, 25.0 ], [ 36.0, 25.0 ], [ 36.0, 26.0 ] ] ] } },
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-    { "type": "Feature", "properties": { "fid": 2333, "MinX": 113.0, "MaxX": 114.0, "MinY": -26.0, "MaxY": -25.0, "tile_name": "S25E113", "gmw_tile_name": "GMW_S25E113" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 113.0, -25.0 ], [ 114.0, -25.0 ], [ 114.0, -26.0 ], [ 113.0, -26.0 ], [ 113.0, -25.0 ] ] ] } },
-    { "type": "Feature", "properties": { "fid": 2303, "MinX": 150.0, "MaxX": 151.0, "MinY": -24.0, "MaxY": -23.0, "tile_name": "S23E150", "gmw_tile_name": "GMW_S23E150" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 150.0, -23.0 ], [ 151.0, -23.0 ], [ 151.0, -24.0 ], [ 150.0, -24.0 ], [ 150.0, -23.0 ] ] ] } },
-    { "type": "Feature", "properties": { "fid": 2304, "MinX": 151.0, "MaxX": 152.0, "MinY": -24.0, "MaxY": -23.0, "tile_name": "S23E151", "gmw_tile_name": "GMW_S23E151" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 151.0, -23.0 ], [ 152.0, -23.0 ], [ 152.0, -24.0 ], [ 151.0, -24.0 ], [ 151.0, -23.0 ] ] ] } }
+    { "type": "Feature", "properties": { "fid": 136, "MinX": 55.0, "MaxX": 56.0, "MinY": 26.0, "MaxY": 27.0, "tile_name": "N27E055", "gmw_tile_name": "GMW_N27E055" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 55.0, 27.0 ], [ 56.0, 27.0 ], [ 56.0, 26.0 ], [ 55.0, 26.0 ], [ 55.0, 27.0 ] ] ] } }
     ]
     }
diff --git a/esrun_data/sample/README.md b/esrun_data/sample/README.md
index cc98d6a3..5afead5a 100644
--- a/esrun_data/sample/README.md
+++ b/esrun_data/sample/README.md
@@ -133,6 +133,9 @@ There are 3 different stages to postprocessing:
 
 ### Samples
 
+
+TODO: Add examples with the new rslp cli for this
+
 #### Run a pipeline end-to-end
 
 The simplest way to run a pipeline is to use the `esrun-local-predict` CLI command.  This command will run the entire pipeline end-to-end including partitioning, dataset building, inference, post-processing, and combining the final outputs.
diff --git a/rslp/esrun/esrun.py b/rslp/esrun/esrun.py
index 0a6966ae..beefb5d3 100644
--- a/rslp/esrun/esrun.py
+++ b/rslp/esrun/esrun.py
@@ -1,6 +1,7 @@
 """Run EsPredictRunner inference pipeline."""
 
 import hashlib
+import logging
 import shutil
 import tempfile
 from enum import StrEnum
@@ -9,6 +10,7 @@
 import fsspec
 from esrun.runner.local.fine_tune_runner import EsFineTuneRunner
 from esrun.runner.local.predict_runner import EsPredictRunner
+from esrun.shared.tools.logger import configure_logging
 from upath import UPath
 
 from rslp.log_utils import get_logger
@@ -69,12 +71,16 @@ def esrun(config_path: Path, scratch_path: Path, checkpoint_path: str) -> None:
         scratch_path: directory to use for scratch space.
         checkpoint_path: path to the model checkpoint.
     """
+    # Configure esrun logging before creating the runner
+    configure_logging(log_level=logging.INFO)
+
     runner = EsPredictRunner(
         # ESRun does not work with relative path, so make sure to convert to absolute here.
         project_path=config_path.absolute(),
         scratch_path=scratch_path,
         checkpoint_path=get_local_checkpoint(UPath(checkpoint_path)),
     )
+    logger.info("Partitioning...")
     partitions = runner.partition()
     logger.info(f"Got {len(partitions)} partitions")
 
@@ -122,6 +128,9 @@ def one_stage(
     if stage == EsrunStage.COMBINE and partition_id is not None:
         raise ValueError("partition_id cannot be set for COMBINE stage")
 
+    # Configure esrun logging before creating the runner
+    configure_logging(log_level=logging.INFO)
+
     runner = EsPredictRunner(
         # ESRun does not work with relative path, so make sure to convert to absolute here.
         project_path=config_path,

From 649da4c8d2cd41872699793f9ea824cd056040c4 Mon Sep 17 00:00:00 2001
From: hgherzog <henryh@allenai.org>
Date: Tue, 16 Sep 2025 02:25:49 +0000
Subject: [PATCH 04/11] add all the features back

---
 esrun_data/mangrove/dataset.json              |  87 +++++++++++
 .../prediction_request_geometry.geojson       | 136 +++++++++++++++++-
 2 files changed, 222 insertions(+), 1 deletion(-)

diff --git a/esrun_data/mangrove/dataset.json b/esrun_data/mangrove/dataset.json
index e69de29b..1bb48774 100644
--- a/esrun_data/mangrove/dataset.json
+++ b/esrun_data/mangrove/dataset.json
@@ -0,0 +1,87 @@
+{
+    "layers": {
+      "label": {
+        "type": "vector"
+      },
+      "sentinel1": {
+        "band_sets": [
+          {
+            "bands": [
+              "vv",
+              "vh"
+            ],
+            "dtype": "float32"
+          }
+        ],
+        "data_source": {
+          "time_offset": "-180d",
+          "duration": "366d",
+          "cache_dir": "cache/planetary_computer",
+          "ingest": false,
+          "name": "rslp.satlas.data_sources.MonthlySentinel1",
+          "query": {
+            "sar:instrument_mode": {
+              "eq": "IW"
+            },
+            "sar:polarizations": {
+              "eq": [
+                "VV",
+                "VH"
+              ]
+            }
+          },
+          "query_config": {
+            "max_matches": 12
+          }
+        },
+        "type": "raster"
+      },
+      "sentinel2": {
+        "band_sets": [
+          {
+            "bands": [
+              "B02",
+              "B03",
+              "B04",
+              "B08"
+            ],
+            "dtype": "uint16"
+          },
+          {
+            "bands": [
+              "B05",
+              "B06",
+              "B07",
+              "B8A",
+              "B11",
+              "B12"
+            ],
+            "dtype": "uint16",
+            "zoom_offset": -1
+          },
+          {
+            "bands": [
+              "B01",
+              "B09"
+            ],
+            "dtype": "uint16",
+            "zoom_offset": -2
+          }
+        ],
+        "data_source": {
+          "time_offset": "-180d",
+          "duration": "366d",
+          "cache_dir": "cache/planetary_computer",
+          "harmonize": true,
+          "ingest": false,
+          "max_cloud_cover": 50,
+          "name": "rslp.satlas.data_sources.MonthlyAzureSentinel2",
+          "query_config": {
+            "max_matches": 12
+          },
+          "sort_by": "eo:cloud_cover"
+        },
+        "type": "raster"
+      }
+    }
+  }
\ No newline at end of file
diff --git a/esrun_data/mangrove/prediction_request_geometry.geojson b/esrun_data/mangrove/prediction_request_geometry.geojson
index 07de15f0..0fd0c9ed 100644
--- a/esrun_data/mangrove/prediction_request_geometry.geojson
+++ b/esrun_data/mangrove/prediction_request_geometry.geojson
@@ -3,6 +3,140 @@
     "name": "region_of_interests_for_testing",
     "crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } },
     "features": [
-    { "type": "Feature", "properties": { "fid": 136, "MinX": 55.0, "MaxX": 56.0, "MinY": 26.0, "MaxY": 27.0, "tile_name": "N27E055", "gmw_tile_name": "GMW_N27E055" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 55.0, 27.0 ], [ 56.0, 27.0 ], [ 56.0, 26.0 ], [ 55.0, 26.0 ], [ 55.0, 27.0 ] ] ] } }
+    { "type": "Feature", "properties": { "fid": 136, "MinX": 55.0, "MaxX": 56.0, "MinY": 26.0, "MaxY": 27.0, "tile_name": "N27E055", "gmw_tile_name": "GMW_N27E055" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 55.0, 27.0 ], [ 56.0, 27.0 ], [ 56.0, 26.0 ], [ 55.0, 26.0 ], [ 55.0, 27.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 153, "MinX": -82.0, "MaxX": -81.0, "MinY": 25.0, "MaxY": 26.0, "tile_name": "N26W082", "gmw_tile_name": "GMW_N26W082" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -82.0, 26.0 ], [ -81.0, 26.0 ], [ -81.0, 25.0 ], [ -82.0, 25.0 ], [ -82.0, 26.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 154, "MinX": -81.0, "MaxX": -80.0, "MinY": 25.0, "MaxY": 26.0, "tile_name": "N26W081", "gmw_tile_name": "GMW_N26W081" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -81.0, 26.0 ], [ -80.0, 26.0 ], [ -80.0, 25.0 ], [ -81.0, 25.0 ], [ -81.0, 26.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 160, "MinX": 36.0, "MaxX": 37.0, "MinY": 25.0, "MaxY": 26.0, "tile_name": "N26E036", "gmw_tile_name": "GMW_N26E036" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 36.0, 26.0 ], [ 37.0, 26.0 ], [ 37.0, 25.0 ], [ 36.0, 25.0 ], [ 36.0, 26.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 200, "MinX": -79.0, "MaxX": -78.0, "MinY": 24.0, "MaxY": 25.0, "tile_name": "N25W079", "gmw_tile_name": "GMW_N25W079" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -79.0, 25.0 ], [ -78.0, 25.0 ], [ -78.0, 24.0 ], [ -79.0, 24.0 ], [ -79.0, 25.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 201, "MinX": -78.0, "MaxX": -77.0, "MinY": 24.0, "MaxY": 25.0, "tile_name": "N25W078", "gmw_tile_name": "GMW_N25W078" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -78.0, 25.0 ], [ -77.0, 25.0 ], [ -77.0, 24.0 ], [ -78.0, 24.0 ], [ -78.0, 25.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 213, "MinX": 54.0, "MaxX": 55.0, "MinY": 24.0, "MaxY": 25.0, "tile_name": "N25E054", "gmw_tile_name": "GMW_N25E054" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 54.0, 25.0 ], [ 55.0, 25.0 ], [ 55.0, 24.0 ], [ 54.0, 24.0 ], [ 54.0, 25.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 258, "MinX": 70.0, "MaxX": 71.0, "MinY": 23.0, "MaxY": 24.0, "tile_name": "N24E070", "gmw_tile_name": "GMW_N24E070" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 70.0, 24.0 ], [ 71.0, 24.0 ], [ 71.0, 23.0 ], [ 70.0, 23.0 ], [ 70.0, 24.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 277, "MinX": -83.0, "MaxX": -82.0, "MinY": 22.0, "MaxY": 23.0, "tile_name": "N23W083", "gmw_tile_name": "GMW_N23W083" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -83.0, 23.0 ], [ -82.0, 23.0 ], [ -82.0, 22.0 ], [ -83.0, 22.0 ], [ -83.0, 23.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 278, "MinX": -82.0, "MaxX": -81.0, "MinY": 22.0, "MaxY": 23.0, "tile_name": "N23W082", "gmw_tile_name": "GMW_N23W082" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -82.0, 23.0 ], [ -81.0, 23.0 ], [ -81.0, 22.0 ], [ -82.0, 22.0 ], [ -82.0, 23.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 282, "MinX": -78.0, "MaxX": -77.0, "MinY": 22.0, "MaxY": 23.0, "tile_name": "N23W078", "gmw_tile_name": "GMW_N23W078" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -78.0, 23.0 ], [ -77.0, 23.0 ], [ -77.0, 22.0 ], [ -78.0, 22.0 ], [ -78.0, 23.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 294, "MinX": 70.0, "MaxX": 71.0, "MinY": 22.0, "MaxY": 23.0, "tile_name": "N23E070", "gmw_tile_name": "GMW_N23E070" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 70.0, 23.0 ], [ 71.0, 23.0 ], [ 71.0, 22.0 ], [ 70.0, 22.0 ], [ 70.0, 23.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 297, "MinX": 88.0, "MaxX": 89.0, "MinY": 22.0, "MaxY": 23.0, "tile_name": "N23E088", "gmw_tile_name": "GMW_N23E088" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ 88.0, 23.0 ], [ 89.0, 23.0 ], [ 89.0, 22.0 ], [ 88.0, 22.0 ], [ 88.0, 23.0 ] ] ] } },
+    { "type": "Feature", "properties": { "fid": 318, "MinX": -89.0, "MaxX": -88.0, "MinY": 21.0, "MaxY": 22.0, "tile_name": "N22W089", "gmw_tile_name": "GMW_N22W089" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -89.0, 22.0 ], [ -88.0, 22.0 ], [ -88.0, 21.0 ], [ -89.0, 21.0 ], [ -89.0, 22.0 ] ] ] } },
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From 02066ccb69448d3fa280f5e9a46db644fa406671 Mon Sep 17 00:00:00 2001
From: hgherzog <henryh@allenai.org>
Date: Tue, 16 Sep 2025 04:15:47 +0000
Subject: [PATCH 05/11] add times to the prediciton request geometry

---
 .../prediction_request_geometry.geojson       | 5679 ++++++++++++++++-
 1 file changed, 5542 insertions(+), 137 deletions(-)

diff --git a/esrun_data/mangrove/prediction_request_geometry.geojson b/esrun_data/mangrove/prediction_request_geometry.geojson
index 0fd0c9ed..a11d7034 100644
--- a/esrun_data/mangrove/prediction_request_geometry.geojson
+++ b/esrun_data/mangrove/prediction_request_geometry.geojson
@@ -1,142 +1,5547 @@
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+    "crs": {
+      "type": "name",
+      "properties": {
+        "name": "urn:ogc:def:crs:OGC:1.3:CRS84"
+      }
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+          "gmw_tile_name": "GMW_S04E122",
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+              [
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+                -23.0
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+      {
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+          "MaxY": -23.0,
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+          "gmw_tile_name": "GMW_S23E151",
+          "es_start_time": "2018-01-01T00:00:00Z",
+          "es_end_time": "2024-12-31T23:59:59Z"
+        },
+        "geometry": {
+          "type": "Polygon",
+          "coordinates": [
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+                -24.0
+              ],
+              [
+                151.0,
+                -23.0
+              ]
+            ]
+          ]
+        }
+      }
     ]
-    }
+  }
\ No newline at end of file

From 7d3ad2a1d3a0d855edda8c4daaee639ad96ba879 Mon Sep 17 00:00:00 2001
From: hgherzog <henryh@allenai.org>
Date: Wed, 17 Sep 2025 00:34:21 +0000
Subject: [PATCH 06/11] mangrove stuff

---
 esrun_data/mangrove/dataset.json              |   11 +
 esrun_data/mangrove/esrun.yaml                |   14 +-
 esrun_data/mangrove/model.yaml                |  686 +-
 .../prediction_request_geometry.geojson       | 5494 -----------------
 rslp/esrun/esrun.py                           |   17 +-
 5 files changed, 557 insertions(+), 5665 deletions(-)

diff --git a/esrun_data/mangrove/dataset.json b/esrun_data/mangrove/dataset.json
index 1bb48774..a6c9cec5 100644
--- a/esrun_data/mangrove/dataset.json
+++ b/esrun_data/mangrove/dataset.json
@@ -82,6 +82,17 @@
           "sort_by": "eo:cloud_cover"
         },
         "type": "raster"
+      },
+      "output": {
+        "band_sets": [
+          {
+            "bands": [
+              "output"
+            ],
+            "dtype": "uint8"
+          }
+        ],
+        "type": "raster"
       }
     }
   }
\ No newline at end of file
diff --git a/esrun_data/mangrove/esrun.yaml b/esrun_data/mangrove/esrun.yaml
index 33e1aa29..4112ffc4 100644
--- a/esrun_data/mangrove/esrun.yaml
+++ b/esrun_data/mangrove/esrun.yaml
@@ -2,7 +2,7 @@ partition_strategies:
   partition_request_geometry:
     class_path: esrun.runner.tools.partitioners.grid_partitioner.GridPartitioner
     init_args:
-      grid_size: 0.01 # Lat lon degrees, a random guess not sure what is really reasonable
+      grid_size: .1 # Lat lon degrees, a random guess not sure what is really reasonable
       output_projection:
         class_path: rslearn.utils.geometry.Projection
         init_args:
@@ -14,7 +14,7 @@ partition_strategies:
   prepare_window_geometries:
     class_path: esrun.runner.tools.partitioners.grid_partitioner.GridPartitioner
     init_args:
-      grid_size: 32 # based on the window creation script yawen chose
+      grid_size: 32 # 32 based on the window creation script yawen made
       output_projection:
         class_path: rslearn.utils.geometry.Projection
         init_args:
@@ -35,4 +35,12 @@ postprocessing_strategies:
 
 
 inference_results_config:
-  data_type: RASTER
\ No newline at end of file
+  data_type: RASTER
+
+
+inference_writer:
+  selector: ["mangrove_classification"]
+  merger:
+    class_path: rslearn.train.prediction_writer.RasterMerger
+    init_args:
+      padding: 2
\ No newline at end of file
diff --git a/esrun_data/mangrove/model.yaml b/esrun_data/mangrove/model.yaml
index ea8cce8c..ce192989 100644
--- a/esrun_data/mangrove/model.yaml
+++ b/esrun_data/mangrove/model.yaml
@@ -1,3 +1,5 @@
+# lightning.pytorch==2.5.1.post0
+seed_everything: 0
 model:
   class_path: rslearn.train.lightning_module.RslearnLightningModule
   init_args:
@@ -5,167 +7,342 @@ model:
       class_path: rslearn.models.multitask.MultiTaskModel
       init_args:
         encoder:
-          - class_path: rslp.helios.model.Helios
-            init_args:
-              checkpoint_path: /weka/dfive-default/helios/checkpoints/favyen/v0.2_base_latent_mim_128_alldata_random_fixed_modality_0.5/step320000 # Will need to be copied to gcp for actual inference
-              random_initialization: true
-              selector: ["encoder"]
-              forward_kwargs:
-                patch_size: 2
+        - class_path: rslp.helios.model.Helios
+          init_args:
+            checkpoint_path: /weka/dfive-default/helios/checkpoints/yawenzzzz/latent_mim_cross_random_per_modality_patchdisc_add_contrastive_0.1_1/step300000
+            selector:
+            - encoder
+            forward_kwargs:
+              patch_size: 2
+            random_initialization: false
+            embedding_size: null
+            patch_size: null
+            autocast_dtype: bfloat16
         decoders:
           mangrove_classification:
-            - class_path: rslearn.models.pooling_decoder.PoolingDecoder
-              init_args:
-                in_channels: 768
-                out_channels: 3
-            - class_path: rslearn.train.tasks.classification.ClassificationHead
+          - class_path: rslp.crop.kenya_nandi.train.SegmentationPoolingDecoder
+            init_args:
+              in_channels: 768
+              out_channels: 4
+              num_conv_layers: 0
+              num_fc_layers: 0
+              conv_channels: 128
+              fc_channels: 512
+          - class_path: rslearn.train.tasks.segmentation.SegmentationHead
+        lazy_decode: false
+        loss_weights: null
+    optimizer: null
+    scheduler: null
+    visualize_dir: null
+    metrics_file: null
+    restore_config: null
+    print_parameters: false
+    print_model: false
     lr: 0.0001
-    scheduler:
-      class_path: rslearn.train.scheduler.PlateauScheduler
-      init_args:
-        factor: 0.2
-        patience: 2
-        min_lr: 0
-        cooldown: 10
+    plateau: true
+    plateau_factor: 0.2
+    plateau_patience: 2
+    plateau_min_lr: 0.0
+    plateau_cooldown: 10
 data:
   class_path: rslearn.train.data_module.RslearnDataModule
   init_args:
-    path: /weka/dfive-default/rslearn-eai/datasets/mangrove/classification/20250626
     inputs:
-      sentinel2_0:
-        data_type: "raster"
-        layers: ["sentinel2"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
-      sentinel2_1:
-        data_type: "raster"
-        layers: ["sentinel2.1"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
-      sentinel2_2:
-        data_type: "raster"
-        layers: ["sentinel2.2"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
-      sentinel2_3:
-        data_type: "raster"
-        layers: ["sentinel2.3"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
-      sentinel2_4:
-        data_type: "raster"
-        layers: ["sentinel2.4"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
-      sentinel2_5:
-        data_type: "raster"
-        layers: ["sentinel2.5"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
-      sentinel2_6:
-        data_type: "raster"
-        layers: ["sentinel2.6"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
-      sentinel2_7:
-        data_type: "raster"
-        layers: ["sentinel2.7"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
-      sentinel2_8:
-        data_type: "raster"
-        layers: ["sentinel2.8"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
-      sentinel2_9:
-        data_type: "raster"
-        layers: ["sentinel2.9"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
-      sentinel2_10:
-        data_type: "raster"
-        layers: ["sentinel2.10"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
-      sentinel2_11:
-        data_type: "raster"
-        layers: ["sentinel2.11"]
-        bands: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        passthrough: true
-        dtype: FLOAT32
       label:
-        data_type: "vector"
-        layers: ["label"]
-        is_target: true
+        class_path: rslearn.train.dataset.DataInput
+        init_args:
+          data_type: raster
+          layers:
+          - label_raster
+          bands:
+          - label
+          required: true
+          passthrough: false
+          is_target: true
+          dtype: INT32
+          load_all_layers: false
+          load_all_item_groups: false
+      sentinel2_l2a:
+        class_path: rslearn.train.dataset.DataInput
+        init_args:
+          data_type: raster
+          layers:
+          - sentinel2
+          bands:
+          - B02
+          - B03
+          - B04
+          - B08
+          - B05
+          - B06
+          - B07
+          - B8A
+          - B11
+          - B12
+          - B01
+          - B09
+          required: true
+          passthrough: true
+          is_target: false
+          dtype: FLOAT32
+          load_all_layers: true
+          load_all_item_groups: true
     task:
       class_path: rslearn.train.tasks.multi_task.MultiTask
       init_args:
         tasks:
           mangrove_classification:
-            class_path: rslearn.train.tasks.classification.ClassificationTask
+            class_path: rslearn.train.tasks.segmentation.SegmentationTask
             init_args:
-              property_name: "category"
-              classes: ["Mangrove", "Water", "Other"]
-              enable_f1_metric: true
+              num_classes: 4
+              colors: # what is this?
+              - - 255
+                - 0
+                - 0
+              - - 0
+                - 255
+                - 0
+              - - 0
+                - 0
+                - 255
+              - - 255
+                - 255
+                - 0
+              - - 0
+                - 255
+                - 255
+              - - 255
+                - 0
+                - 255
+              - - 0
+                - 128
+                - 0
+              - - 255
+                - 160
+                - 122
+              - - 139
+                - 69
+                - 19
+              - - 128
+                - 128
+                - 128
+              - - 255
+                - 255
+                - 255
+              - - 143
+                - 188
+                - 143
+              - - 95
+                - 158
+                - 160
+              - - 255
+                - 200
+                - 0
+              - - 128
+                - 0
+                - 0
+              zero_is_invalid: true
+              enable_accuracy_metric: true
+              enable_miou_metric: false
+              enable_f1_metric: false
+              f1_metric_thresholds:
+              - - 0.5
               metric_kwargs:
-                average: "micro"
+                average: micro
+              miou_metric_kwargs: {}
+              prob_scales: null
+              other_metrics:
+                mangrove_precision:
+                  class_path: rslearn.train.tasks.segmentation.SegmentationMetric
+                  init_args:
+                    metric:
+                      class_path: torchmetrics.classification.MulticlassPrecision
+                      init_args:
+                        num_classes: 4
+                        top_k: 1
+                        average: null
+                        multidim_average: global
+                        ignore_index: null
+                        validate_args: true
+                        zero_division: 0
+                    pass_probabilities: true
+                    class_idx: 1
+                mangrove_recall:
+                  class_path: rslearn.train.tasks.segmentation.SegmentationMetric
+                  init_args:
+                    metric:
+                      class_path: torchmetrics.classification.MulticlassRecall
+                      init_args:
+                        num_classes: 4
+                        top_k: 1
+                        average: null
+                        multidim_average: global
+                        ignore_index: null
+                        validate_args: true
+                        zero_division: 0
+                    pass_probabilities: true
+                    class_idx: 1
+                other_precision:
+                  class_path: rslearn.train.tasks.segmentation.SegmentationMetric
+                  init_args:
+                    metric:
+                      class_path: torchmetrics.classification.MulticlassPrecision
+                      init_args:
+                        num_classes: 4
+                        top_k: 1
+                        average: null
+                        multidim_average: global
+                        ignore_index: null
+                        validate_args: true
+                        zero_division: 0
+                    pass_probabilities: true
+                    class_idx: 3
+                other_recall:
+                  class_path: rslearn.train.tasks.segmentation.SegmentationMetric
+                  init_args:
+                    metric:
+                      class_path: torchmetrics.classification.MulticlassRecall
+                      init_args:
+                        num_classes: 4
+                        top_k: 1
+                        average: null
+                        multidim_average: global
+                        ignore_index: null
+                        validate_args: true
+                        zero_division: 0
+                    pass_probabilities: true
+                    class_idx: 3
+                water_precision:
+                  class_path: rslearn.train.tasks.segmentation.SegmentationMetric
+                  init_args:
+                    metric:
+                      class_path: torchmetrics.classification.MulticlassPrecision
+                      init_args:
+                        num_classes: 4
+                        top_k: 1
+                        average: null
+                        multidim_average: global
+                        ignore_index: null
+                        validate_args: true
+                        zero_division: 0
+                    pass_probabilities: true
+                    class_idx: 2
+                water_recall:
+                  class_path: rslearn.train.tasks.segmentation.SegmentationMetric
+                  init_args:
+                    metric:
+                      class_path: torchmetrics.classification.MulticlassRecall
+                      init_args:
+                        num_classes: 4
+                        top_k: 1
+                        average: null
+                        multidim_average: global
+                        ignore_index: null
+                        validate_args: true
+                        zero_division: 0
+                    pass_probabilities: true
+                    class_idx: 2
+              image_bands:
+              - 0
+              - 1
+              - 2
+              remap_values: null
         input_mapping:
           mangrove_classification:
-            label: "targets"
-    batch_size: 4
-    num_workers: 2
+            label: targets
+    path: /weka/dfive-default/rslearn-eai/datasets/mangrove/classification/20250626
+    path_options: {}
+    batch_size: 128 # Modified for testing
+    num_workers: 16 # This is overridedn by envrionment variable within esrun
+    init_workers: 0
     default_config:
-      transforms:
-        - class_path: rslearn.train.transforms.concatenate.Concatenate
+      class_path: rslearn.train.dataset.SplitConfig
+      init_args:
+        groups: null
+        names: null
+        tags: null
+        num_samples: null
+        num_patches: null
+        transforms:
+        - class_path: rslearn.train.transforms.pad.Pad
           init_args:
-            selections:
-              sentinel2_0: []
-              sentinel2_1: []
-              sentinel2_2: []
-              sentinel2_3: []
-              sentinel2_4: []
-              sentinel2_5: []
-              sentinel2_6: []
-              sentinel2_7: []
-              sentinel2_8: []
-              sentinel2_9: []
-              sentinel2_10: []
-              sentinel2_11: []
-            output_selector: sentinel2_l2a
+            size: 2
+            mode: center
+            image_selectors:
+            - sentinel2_l2a
+            - target/mangrove_classification/classes
+            - target/mangrove_classification/valid
+            box_selectors: []
         - class_path: rslp.helios.norm.HeliosNormalize
           init_args:
-            config_fname: "/opt/helios/data/norm_configs/computed.json"
             band_names:
-              sentinel2_l2a: ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"]
-        - class_path: rslearn.train.transforms.pad.Pad
-          init_args:
-            size: 2
-            mode: "center"
-            image_selectors: ["sentinel2_l2a"]
+              sentinel2_l2a:
+              - B02
+              - B03
+              - B04
+              - B08
+              - B05
+              - B06
+              - B07
+              - B8A
+              - B11
+              - B12
+              - B01
+              - B09
+            std_multiplier: 2.0
+        sampler: null
+        patch_size: null
+        overlap_ratio: null
+        load_all_patches: null
+        skip_targets: null
     train_config:
-      groups: ["sample_100K"]
-      tags:
-        split: "train"
-      num_samples: 10000
+      class_path: rslearn.train.dataset.SplitConfig
+      init_args:
+        groups:
+        - sample_100K
+        names: null
+        tags:
+          split: train
+        num_samples: 10000
+        num_patches: null
+        transforms: null
+        sampler: null
+        patch_size: null
+        overlap_ratio: null
+        load_all_patches: null
+        skip_targets: null
     val_config:
-      groups: ["sample_100K"]
-      tags:
-        split: "val"
+      class_path: rslearn.train.dataset.SplitConfig
+      init_args:
+        groups:
+        - sample_100K
+        names: null
+        tags:
+          split: val
+        num_samples: null
+        num_patches: null
+        transforms: null
+        sampler: null
+        patch_size: null
+        overlap_ratio: null
+        load_all_patches: null
+        skip_targets: null
     test_config:
-      groups: ["sample_100K"]
-      tags:
-        split: "val"
+      class_path: rslearn.train.dataset.SplitConfig
+      init_args:
+        groups:
+        - sample_100K
+        names: null
+        tags:
+          split: val
+        num_samples: null
+        num_patches: null
+        transforms: null
+        sampler: null
+        patch_size: null
+        overlap_ratio: null
+        load_all_patches: null
+        skip_targets: null
     predict_config:
       patch_size: 2 #I think this is actually the window size for inference processing
       overlap_ratio: 0.5
@@ -175,18 +352,7 @@ data:
       - class_path: rslearn.train.transforms.concatenate.Concatenate
         init_args:
           selections:
-            sentinel2_0: []
-            sentinel2_1: []
-            sentinel2_2: []
-            sentinel2_3: []
-            sentinel2_4: []
-            sentinel2_5: []
-            sentinel2_6: []
-            sentinel2_7: []
-            sentinel2_8: []
-            sentinel2_9: []
-            sentinel2_10: []
-            sentinel2_11: []
+            sentinel2_l2a: []
           output_selector: sentinel2_l2a
       # I feel like we really don;t want this
       - class_path: rslp.helios.norm.HeliosNormalize
@@ -210,23 +376,211 @@ data:
           size: 2
           mode: "center"
           image_selectors: ["sentinel2_l2a"]
-
-# Should be independent and unused for inference.
+    name: null
+    retries: 0
 trainer:
-  max_epochs: 100
+  profiler: simple
+  accelerator: auto
+  strategy:
+    class_path: lightning.pytorch.strategies.DDPStrategy
+    init_args:
+      find_unused_parameters: true
+  devices: auto
+  num_nodes: 1
+  # precision: null
   callbacks:
-    - class_path: lightning.pytorch.callbacks.LearningRateMonitor
-      init_args:
-        logging_interval: "epoch"
-    - class_path: lightning.pytorch.callbacks.ModelCheckpoint
-      init_args:
-        save_top_k: 1
-        save_last: true
-        monitor: val_loss
-        mode: min
-    - class_path: rslearn.train.callbacks.freeze_unfreeze.FreezeUnfreeze
-      init_args:
-        module_selector: ["model", "encoder", 0]
-        unfreeze_at_epoch: 2
-rslp_project: placeholder
-rslp_experiment: placeholder
+  # - class_path: lightning.pytorch.callbacks.LearningRateMonitor
+  #   init_args:
+  #     logging_interval: epoch
+  #     log_momentum: false
+  #     log_weight_decay: false
+  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
+    init_args:
+      dirpath: gs://rslearn-eai/projects/2025_09_15_mangrove_classification/mangrove_classification_segment_helios_base_S2_ts_ws2_ps2/checkpoints
+      filename: null
+      monitor: val_loss
+      verbose: false
+      save_last: true
+      save_top_k: 1
+      save_weights_only: false
+      mode: min
+      auto_insert_metric_name: true
+      every_n_train_steps: null
+      train_time_interval: null
+      every_n_epochs: null
+      save_on_train_epoch_end: null
+      enable_version_counter: true
+# lighning wants these other
+  - class_path: rslearn.train.callbacks.freeze_unfreeze.FreezeUnfreeze
+    init_args:
+      module_selector:
+      - model
+      - encoder
+      - 0
+      unfreeze_at_epoch: 20
+      unfreeze_lr_factor: 10.0
+  # - class_path: rslp.lightning_cli.SaveWandbRunIdCallback
+  #   init_args:
+  #     project_id: 2025_09_15_mangrove_classification
+  #     experiment_id: mangrove_classification_segment_helios_base_S2_ts_ws2_ps2
+  #     run_id: ''
+  #     config_str: '{"config": ["<not serializable>"], "seed_everything": 0, "trainer":
+  #       {"accelerator": "auto", "strategy": {"class_path": "lightning.pytorch.strategies.DDPStrategy",
+  #       "init_args": {"find_unused_parameters": true}}, "devices": "auto", "num_nodes":
+  #       1, "precision": null, "logger": {"class_path": "lightning.pytorch.loggers.WandbLogger",
+  #       "init_args": {"project": "2025_09_15_mangrove_classification", "name": "mangrove_classification_segment_helios_base_S2_ts_ws2_ps2"}},
+  #       "callbacks": [{"class_path": "lightning.pytorch.callbacks.LearningRateMonitor",
+  #       "init_args": {"logging_interval": "epoch", "log_momentum": false, "log_weight_decay":
+  #       false}}, {"class_path": "lightning.pytorch.callbacks.ModelCheckpoint", "init_args":
+  #       {"dirpath": "gs://rslearn-eai/projects/2025_09_15_mangrove_classification/mangrove_classification_segment_helios_base_S2_ts_ws2_ps2/checkpoints",
+  #       "filename": null, "monitor": "val_loss", "verbose": false, "save_last": true,
+  #       "save_top_k": 1, "save_weights_only": false, "mode": "min", "auto_insert_metric_name":
+  #       true, "every_n_train_steps": null, "train_time_interval": null, "every_n_epochs":
+  #       null, "save_on_train_epoch_end": null, "enable_version_counter": true}}, {"class_path":
+  #       "rslearn.train.callbacks.freeze_unfreeze.FreezeUnfreeze", "init_args": {"module_selector":
+  #       ["model", "encoder", 0], "unfreeze_at_epoch": 20, "unfreeze_lr_factor": 10.0}}],
+  #       "fast_dev_run": false, "max_epochs": 100, "min_epochs": null, "max_steps":
+  #       -1, "min_steps": null, "max_time": null, "limit_train_batches": null, "limit_val_batches":
+  #       null, "limit_test_batches": null, "limit_predict_batches": null, "overfit_batches":
+  #       0.0, "val_check_interval": null, "check_val_every_n_epoch": 1, "num_sanity_val_steps":
+  #       null, "log_every_n_steps": null, "enable_checkpointing": null, "enable_progress_bar":
+  #       null, "enable_model_summary": null, "accumulate_grad_batches": 1, "gradient_clip_val":
+  #       null, "gradient_clip_algorithm": null, "deterministic": null, "benchmark":
+  #       null, "inference_mode": true, "use_distributed_sampler": false, "profiler":
+  #       null, "detect_anomaly": false, "barebones": false, "plugins": null, "sync_batchnorm":
+  #       false, "reload_dataloaders_every_n_epochs": 0, "default_root_dir": null, "model_registry":
+  #       null}, "model": {"class_path": "rslearn.train.lightning_module.RslearnLightningModule",
+  #       "init_args": {"model": {"class_path": "rslearn.models.multitask.MultiTaskModel",
+  #       "init_args": {"encoder": [{"class_path": "rslp.helios.model.Helios", "init_args":
+  #       {"checkpoint_path": "/weka/dfive-default/helios/checkpoints/yawenzzzz/latent_mim_cross_random_per_modality_patchdisc_add_contrastive_0.1_1/step300000",
+  #       "selector": ["encoder"], "forward_kwargs": {"patch_size": 2}, "random_initialization":
+  #       false, "embedding_size": null, "patch_size": null, "autocast_dtype": "bfloat16"}}],
+  #       "decoders": {"mangrove_classification": ["<not serializable>", "<not serializable>"]},
+  #       "lazy_decode": false, "loss_weights": null}}, "task": null, "optimizer": null,
+  #       "scheduler": null, "visualize_dir": null, "metrics_file": null, "restore_config":
+  #       null, "print_parameters": false, "print_model": false, "lr": 0.0001, "plateau":
+  #       true, "plateau_factor": 0.2, "plateau_patience": 2, "plateau_min_lr": 0.0,
+  #       "plateau_cooldown": 10}}, "data": {"class_path": "rslearn.train.data_module.RslearnDataModule",
+  #       "init_args": {"inputs": {"label": {"class_path": "rslearn.train.dataset.DataInput",
+  #       "init_args": {"data_type": "raster", "layers": ["label_raster"], "bands":
+  #       ["label"], "required": true, "passthrough": false, "is_target": true, "dtype":
+  #       "<not serializable>", "load_all_layers": false, "load_all_item_groups": false}},
+  #       "sentinel2_l2a": {"class_path": "rslearn.train.dataset.DataInput", "init_args":
+  #       {"data_type": "raster", "layers": ["sentinel2"], "bands": ["B02", "B03", "B04",
+  #       "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"], "required":
+  #       true, "passthrough": true, "is_target": false, "dtype": "<not serializable>",
+  #       "load_all_layers": true, "load_all_item_groups": true}}}, "task": {"class_path":
+  #       "rslearn.train.tasks.multi_task.MultiTask", "init_args": {"tasks": {"mangrove_classification":
+  #       {"class_path": "rslearn.train.tasks.segmentation.SegmentationTask", "init_args":
+  #       {"num_classes": 4, "colors": [[255, 0, 0], [0, 255, 0], [0, 0, 255], [255,
+  #       255, 0], [0, 255, 255], [255, 0, 255], [0, 128, 0], [255, 160, 122], [139,
+  #       69, 19], [128, 128, 128], [255, 255, 255], [143, 188, 143], [95, 158, 160],
+  #       [255, 200, 0], [128, 0, 0]], "zero_is_invalid": true, "enable_accuracy_metric":
+  #       true, "enable_miou_metric": false, "enable_f1_metric": false, "f1_metric_thresholds":
+  #       [[0.5]], "metric_kwargs": {"average": "micro"}, "miou_metric_kwargs": {},
+  #       "prob_scales": null, "other_metrics": {"mangrove_precision": {"class_path":
+  #       "rslearn.train.tasks.segmentation.SegmentationMetric", "init_args": {"metric":
+  #       {"class_path": "torchmetrics.classification.MulticlassPrecision", "init_args":
+  #       {"num_classes": 4, "top_k": 1, "average": null, "multidim_average": "global",
+  #       "ignore_index": null, "validate_args": true, "zero_division": 0}}, "pass_probabilities":
+  #       true, "class_idx": 1}}, "mangrove_recall": {"class_path": "rslearn.train.tasks.segmentation.SegmentationMetric",
+  #       "init_args": {"metric": {"class_path": "torchmetrics.classification.MulticlassRecall",
+  #       "init_args": {"num_classes": 4, "top_k": 1, "average": null, "multidim_average":
+  #       "global", "ignore_index": null, "validate_args": true, "zero_division": 0}},
+  #       "pass_probabilities": true, "class_idx": 1}}, "other_precision": {"class_path":
+  #       "rslearn.train.tasks.segmentation.SegmentationMetric", "init_args": {"metric":
+  #       {"class_path": "torchmetrics.classification.MulticlassPrecision", "init_args":
+  #       {"num_classes": 4, "top_k": 1, "average": null, "multidim_average": "global",
+  #       "ignore_index": null, "validate_args": true, "zero_division": 0}}, "pass_probabilities":
+  #       true, "class_idx": 3}}, "other_recall": {"class_path": "rslearn.train.tasks.segmentation.SegmentationMetric",
+  #       "init_args": {"metric": {"class_path": "torchmetrics.classification.MulticlassRecall",
+  #       "init_args": {"num_classes": 4, "top_k": 1, "average": null, "multidim_average":
+  #       "global", "ignore_index": null, "validate_args": true, "zero_division": 0}},
+  #       "pass_probabilities": true, "class_idx": 3}}, "water_precision": {"class_path":
+  #       "rslearn.train.tasks.segmentation.SegmentationMetric", "init_args": {"metric":
+  #       {"class_path": "torchmetrics.classification.MulticlassPrecision", "init_args":
+  #       {"num_classes": 4, "top_k": 1, "average": null, "multidim_average": "global",
+  #       "ignore_index": null, "validate_args": true, "zero_division": 0}}, "pass_probabilities":
+  #       true, "class_idx": 2}}, "water_recall": {"class_path": "rslearn.train.tasks.segmentation.SegmentationMetric",
+  #       "init_args": {"metric": {"class_path": "torchmetrics.classification.MulticlassRecall",
+  #       "init_args": {"num_classes": 4, "top_k": 1, "average": null, "multidim_average":
+  #       "global", "ignore_index": null, "validate_args": true, "zero_division": 0}},
+  #       "pass_probabilities": true, "class_idx": 2}}}, "image_bands": [0, 1, 2], "remap_values":
+  #       null}}}, "input_mapping": {"mangrove_classification": {"label": "targets"}}}},
+  #       "path": "/weka/dfive-default/rslearn-eai/datasets/mangrove/classification/20250626",
+  #       "path_options": {}, "batch_size": 32, "num_workers": 32, "init_workers": 0,
+  #       "default_config": {"class_path": "rslearn.train.dataset.SplitConfig", "init_args":
+  #       {"groups": null, "names": null, "tags": null, "num_samples": null, "num_patches":
+  #       null, "transforms": [{"class_path": "rslearn.train.transforms.pad.Pad", "init_args":
+  #       {"size": 2, "mode": "center", "image_selectors": ["sentinel2_l2a", "target/mangrove_classification/classes",
+  #       "target/mangrove_classification/valid"], "box_selectors": []}}, {"class_path":
+  #       "rslp.helios.norm.HeliosNormalize", "init_args": {"band_names": {"sentinel2_l2a":
+  #       ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01",
+  #       "B09"]}, "std_multiplier": 2.0, "config_fname": "/opt/helios/data/norm_configs/computed.json"}}],
+  #       "sampler": null, "patch_size": null, "overlap_ratio": null, "load_all_patches":
+  #       null, "skip_targets": null}}, "train_config": {"class_path": "rslearn.train.dataset.SplitConfig",
+  #       "init_args": {"groups": ["sample_100K"], "names": null, "tags": {"split":
+  #       "train"}, "num_samples": 10000, "num_patches": null, "transforms": null, "sampler":
+  #       null, "patch_size": null, "overlap_ratio": null, "load_all_patches": null,
+  #       "skip_targets": null}}, "val_config": {"class_path": "rslearn.train.dataset.SplitConfig",
+  #       "init_args": {"groups": ["sample_100K"], "names": null, "tags": {"split":
+  #       "val"}, "num_samples": null, "num_patches": null, "transforms": null, "sampler":
+  #       null, "patch_size": null, "overlap_ratio": null, "load_all_patches": null,
+  #       "skip_targets": null}}, "test_config": {"class_path": "rslearn.train.dataset.SplitConfig",
+  #       "init_args": {"groups": ["sample_100K"], "names": null, "tags": {"split":
+  #       "val"}, "num_samples": null, "num_patches": null, "transforms": null, "sampler":
+  #       null, "patch_size": null, "overlap_ratio": null, "load_all_patches": null,
+  #       "skip_targets": null}}, "predict_config": {"class_path": "rslearn.train.dataset.SplitConfig",
+  #       "init_args": {"groups": null, "names": null, "tags": null, "num_samples":
+  #       null, "num_patches": null, "transforms": null, "sampler": null, "patch_size":
+  #       null, "overlap_ratio": null, "load_all_patches": null, "skip_targets": null}},
+  #       "name": null, "retries": 0}}, "rslp_project": "2025_09_15_mangrove_classification",
+  #       "rslp_experiment": "mangrove_classification_segment_helios_base_S2_ts_ws2_ps2",
+  #       "rslp_description": "", "autoresume": true, "load_best": false, "force_log":
+  #       false, "no_log": false, "profiler": null, "allow_missing_weights": false,
+  #       "optimizer": null, "lr_scheduler": null, "ckpt_path": null}'
+  fast_dev_run: false
+  max_epochs: 100
+  min_epochs: null
+  max_steps: -1
+  min_steps: null
+  max_time: null
+  limit_train_batches: null
+  limit_val_batches: null
+  limit_test_batches: null
+  limit_predict_batches: null
+  overfit_batches: 0.0
+  val_check_interval: null
+  check_val_every_n_epoch: 1
+  num_sanity_val_steps: null
+  log_every_n_steps: null
+  enable_checkpointing: null
+  enable_progress_bar: null
+  enable_model_summary: null
+  accumulate_grad_batches: 1
+  gradient_clip_val: null
+  gradient_clip_algorithm: null
+  deterministic: null
+  benchmark: null
+  inference_mode: true
+  use_distributed_sampler: false
+  profiler: null
+  detect_anomaly: false
+  barebones: false
+  plugins: null
+  sync_batchnorm: false
+  reload_dataloaders_every_n_epochs: 0
+  default_root_dir: null
+  model_registry: null
+# rslp_project: 2025_09_15_mangrove_classification
+# rslp_experiment: mangrove_classification_segment_helios_base_S2_ts_ws2_ps2
+# rslp_description: ''
+# autoresume: true
+# load_best: false
+# force_log: false
+# no_log: false
+# profiler: null
+# allow_missing_weights: false
+# optimizer: null
+# lr_scheduler: null
+# ckpt_path: null
\ No newline at end of file
diff --git a/esrun_data/mangrove/prediction_request_geometry.geojson b/esrun_data/mangrove/prediction_request_geometry.geojson
index a11d7034..d245fe67 100644
--- a/esrun_data/mangrove/prediction_request_geometry.geojson
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-          "es_end_time": "2024-12-31T23:59:59Z"
-        },
-        "geometry": {
-          "type": "Polygon",
-          "coordinates": [
-            [
-              [
-                151.0,
-                -23.0
-              ],
-              [
-                152.0,
-                -23.0
-              ],
-              [
-                152.0,
-                -24.0
-              ],
-              [
-                151.0,
-                -24.0
-              ],
-              [
-                151.0,
-                -23.0
-              ]
-            ]
-          ]
-        }
       }
     ]
   }
\ No newline at end of file
diff --git a/rslp/esrun/esrun.py b/rslp/esrun/esrun.py
index beefb5d3..29683682 100644
--- a/rslp/esrun/esrun.py
+++ b/rslp/esrun/esrun.py
@@ -10,6 +10,7 @@
 import fsspec
 from esrun.runner.local.fine_tune_runner import EsFineTuneRunner
 from esrun.runner.local.predict_runner import EsPredictRunner
+from esrun.shared.models.task_results import InferenceResultsDataType
 from esrun.shared.tools.logger import configure_logging
 from upath import UPath
 
@@ -62,7 +63,7 @@ def prepare_labeled_windows(project_path: Path, scratch_path: Path) -> None:
     runner.prepare_labeled_windows()
 
 
-def esrun(config_path: Path, scratch_path: Path, checkpoint_path: str) -> None:
+def esrun(config_path: Path, scratch_path: Path, checkpoint_path: str, num_workers_partition: int | None = None, num_workers_inference: int | None = None, num_workers_postprocess: int | None = None, num_workers_combine: int | None = None) -> None:
     """Run EsPredictRunner inference pipeline.
 
     Args:
@@ -79,6 +80,10 @@ def esrun(config_path: Path, scratch_path: Path, checkpoint_path: str) -> None:
         project_path=config_path.absolute(),
         scratch_path=scratch_path,
         checkpoint_path=get_local_checkpoint(UPath(checkpoint_path)),
+        num_workers_partition=num_workers_partition,
+        num_workers_inference=num_workers_inference,
+        num_workers_postprocess=num_workers_postprocess,
+        num_workers_combine=num_workers_combine,
     )
     logger.info("Partitioning...")
     partitions = runner.partition()
@@ -114,6 +119,8 @@ def one_stage(
     checkpoint_path: str,
     stage: EsrunStage,
     partition_id: str | None = None,
+    num_workers: int | None = None,
+    inference_results_data_type: InferenceResultsDataType = InferenceResultsDataType.RASTER,
 ) -> None:
     """Run EsPredictRunner inference pipeline.
 
@@ -129,13 +136,18 @@ def one_stage(
         raise ValueError("partition_id cannot be set for COMBINE stage")
 
     # Configure esrun logging before creating the runner
-    configure_logging(log_level=logging.INFO)
+    configure_logging(log_level=logging.WARNING)
 
     runner = EsPredictRunner(
         # ESRun does not work with relative path, so make sure to convert to absolute here.
         project_path=config_path,
         scratch_path=scratch_path,
         checkpoint_path=get_local_checkpoint(UPath(checkpoint_path)),
+        # only running one stage so we just override the workers for that stage
+        num_workers_partition=num_workers,
+        num_workers_inference=num_workers,
+        num_workers_postprocess=num_workers,
+        num_workers_combine=num_workers,
     )
     partitions = runner.partition()
 
@@ -150,6 +162,7 @@ def one_stage(
         elif stage == EsrunStage.RUN_INFERENCE:
             fn = runner.run_inference
         elif stage == EsrunStage.POSTPROCESS:
+            runner.inference_results_data_type = inference_results_data_type
             fn = runner.postprocess
         else:
             assert False

From 52368ebf0ee24bf6bdfed62fa72e58bea692f6c6 Mon Sep 17 00:00:00 2001
From: hgherzog <henryh@allenai.org>
Date: Wed, 1 Oct 2025 20:44:17 +0000
Subject: [PATCH 07/11] wip before merging favyen pr

---
 esrun_data/mangrove/model.yaml                | 156 ++----------------
 .../prediction_request_geometry.geojson       |   2 +-
 rslp/esrun/esrun.py                           |  13 +-
 3 files changed, 19 insertions(+), 152 deletions(-)

diff --git a/esrun_data/mangrove/model.yaml b/esrun_data/mangrove/model.yaml
index ce192989..d6c0ca10 100644
--- a/esrun_data/mangrove/model.yaml
+++ b/esrun_data/mangrove/model.yaml
@@ -250,10 +250,10 @@ data:
         input_mapping:
           mangrove_classification:
             label: targets
-    path: /weka/dfive-default/rslearn-eai/datasets/mangrove/classification/20250626
+    path: ${DATASET_PATH}
     path_options: {}
     batch_size: 128 # Modified for testing
-    num_workers: 16 # This is overridedn by envrionment variable within esrun
+    num_workers: ${NUM_WORKERS}
     init_workers: 0
     default_config:
       class_path: rslearn.train.dataset.SplitConfig
@@ -387,13 +387,16 @@ trainer:
       find_unused_parameters: true
   devices: auto
   num_nodes: 1
-  # precision: null
   callbacks:
-  # - class_path: lightning.pytorch.callbacks.LearningRateMonitor
-  #   init_args:
-  #     logging_interval: epoch
-  #     log_momentum: false
-  #     log_weight_decay: false
+  - class_path: rslearn.train.prediction_writer.RslearnWriter
+    init_args:
+      path: ${DATASET_PATH}
+      output_layer: ${PREDICTION_OUTPUT_LAYER}
+      selector: ["mangrove_classification"]
+      merger:
+        class_path: rslearn.train.prediction_writer.RasterMerger
+        init_args:
+          padding: 2
   - class_path: lightning.pytorch.callbacks.ModelCheckpoint
     init_args:
       dirpath: gs://rslearn-eai/projects/2025_09_15_mangrove_classification/mangrove_classification_segment_helios_base_S2_ts_ws2_ps2/checkpoints
@@ -419,126 +422,6 @@ trainer:
       - 0
       unfreeze_at_epoch: 20
       unfreeze_lr_factor: 10.0
-  # - class_path: rslp.lightning_cli.SaveWandbRunIdCallback
-  #   init_args:
-  #     project_id: 2025_09_15_mangrove_classification
-  #     experiment_id: mangrove_classification_segment_helios_base_S2_ts_ws2_ps2
-  #     run_id: ''
-  #     config_str: '{"config": ["<not serializable>"], "seed_everything": 0, "trainer":
-  #       {"accelerator": "auto", "strategy": {"class_path": "lightning.pytorch.strategies.DDPStrategy",
-  #       "init_args": {"find_unused_parameters": true}}, "devices": "auto", "num_nodes":
-  #       1, "precision": null, "logger": {"class_path": "lightning.pytorch.loggers.WandbLogger",
-  #       "init_args": {"project": "2025_09_15_mangrove_classification", "name": "mangrove_classification_segment_helios_base_S2_ts_ws2_ps2"}},
-  #       "callbacks": [{"class_path": "lightning.pytorch.callbacks.LearningRateMonitor",
-  #       "init_args": {"logging_interval": "epoch", "log_momentum": false, "log_weight_decay":
-  #       false}}, {"class_path": "lightning.pytorch.callbacks.ModelCheckpoint", "init_args":
-  #       {"dirpath": "gs://rslearn-eai/projects/2025_09_15_mangrove_classification/mangrove_classification_segment_helios_base_S2_ts_ws2_ps2/checkpoints",
-  #       "filename": null, "monitor": "val_loss", "verbose": false, "save_last": true,
-  #       "save_top_k": 1, "save_weights_only": false, "mode": "min", "auto_insert_metric_name":
-  #       true, "every_n_train_steps": null, "train_time_interval": null, "every_n_epochs":
-  #       null, "save_on_train_epoch_end": null, "enable_version_counter": true}}, {"class_path":
-  #       "rslearn.train.callbacks.freeze_unfreeze.FreezeUnfreeze", "init_args": {"module_selector":
-  #       ["model", "encoder", 0], "unfreeze_at_epoch": 20, "unfreeze_lr_factor": 10.0}}],
-  #       "fast_dev_run": false, "max_epochs": 100, "min_epochs": null, "max_steps":
-  #       -1, "min_steps": null, "max_time": null, "limit_train_batches": null, "limit_val_batches":
-  #       null, "limit_test_batches": null, "limit_predict_batches": null, "overfit_batches":
-  #       0.0, "val_check_interval": null, "check_val_every_n_epoch": 1, "num_sanity_val_steps":
-  #       null, "log_every_n_steps": null, "enable_checkpointing": null, "enable_progress_bar":
-  #       null, "enable_model_summary": null, "accumulate_grad_batches": 1, "gradient_clip_val":
-  #       null, "gradient_clip_algorithm": null, "deterministic": null, "benchmark":
-  #       null, "inference_mode": true, "use_distributed_sampler": false, "profiler":
-  #       null, "detect_anomaly": false, "barebones": false, "plugins": null, "sync_batchnorm":
-  #       false, "reload_dataloaders_every_n_epochs": 0, "default_root_dir": null, "model_registry":
-  #       null}, "model": {"class_path": "rslearn.train.lightning_module.RslearnLightningModule",
-  #       "init_args": {"model": {"class_path": "rslearn.models.multitask.MultiTaskModel",
-  #       "init_args": {"encoder": [{"class_path": "rslp.helios.model.Helios", "init_args":
-  #       {"checkpoint_path": "/weka/dfive-default/helios/checkpoints/yawenzzzz/latent_mim_cross_random_per_modality_patchdisc_add_contrastive_0.1_1/step300000",
-  #       "selector": ["encoder"], "forward_kwargs": {"patch_size": 2}, "random_initialization":
-  #       false, "embedding_size": null, "patch_size": null, "autocast_dtype": "bfloat16"}}],
-  #       "decoders": {"mangrove_classification": ["<not serializable>", "<not serializable>"]},
-  #       "lazy_decode": false, "loss_weights": null}}, "task": null, "optimizer": null,
-  #       "scheduler": null, "visualize_dir": null, "metrics_file": null, "restore_config":
-  #       null, "print_parameters": false, "print_model": false, "lr": 0.0001, "plateau":
-  #       true, "plateau_factor": 0.2, "plateau_patience": 2, "plateau_min_lr": 0.0,
-  #       "plateau_cooldown": 10}}, "data": {"class_path": "rslearn.train.data_module.RslearnDataModule",
-  #       "init_args": {"inputs": {"label": {"class_path": "rslearn.train.dataset.DataInput",
-  #       "init_args": {"data_type": "raster", "layers": ["label_raster"], "bands":
-  #       ["label"], "required": true, "passthrough": false, "is_target": true, "dtype":
-  #       "<not serializable>", "load_all_layers": false, "load_all_item_groups": false}},
-  #       "sentinel2_l2a": {"class_path": "rslearn.train.dataset.DataInput", "init_args":
-  #       {"data_type": "raster", "layers": ["sentinel2"], "bands": ["B02", "B03", "B04",
-  #       "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01", "B09"], "required":
-  #       true, "passthrough": true, "is_target": false, "dtype": "<not serializable>",
-  #       "load_all_layers": true, "load_all_item_groups": true}}}, "task": {"class_path":
-  #       "rslearn.train.tasks.multi_task.MultiTask", "init_args": {"tasks": {"mangrove_classification":
-  #       {"class_path": "rslearn.train.tasks.segmentation.SegmentationTask", "init_args":
-  #       {"num_classes": 4, "colors": [[255, 0, 0], [0, 255, 0], [0, 0, 255], [255,
-  #       255, 0], [0, 255, 255], [255, 0, 255], [0, 128, 0], [255, 160, 122], [139,
-  #       69, 19], [128, 128, 128], [255, 255, 255], [143, 188, 143], [95, 158, 160],
-  #       [255, 200, 0], [128, 0, 0]], "zero_is_invalid": true, "enable_accuracy_metric":
-  #       true, "enable_miou_metric": false, "enable_f1_metric": false, "f1_metric_thresholds":
-  #       [[0.5]], "metric_kwargs": {"average": "micro"}, "miou_metric_kwargs": {},
-  #       "prob_scales": null, "other_metrics": {"mangrove_precision": {"class_path":
-  #       "rslearn.train.tasks.segmentation.SegmentationMetric", "init_args": {"metric":
-  #       {"class_path": "torchmetrics.classification.MulticlassPrecision", "init_args":
-  #       {"num_classes": 4, "top_k": 1, "average": null, "multidim_average": "global",
-  #       "ignore_index": null, "validate_args": true, "zero_division": 0}}, "pass_probabilities":
-  #       true, "class_idx": 1}}, "mangrove_recall": {"class_path": "rslearn.train.tasks.segmentation.SegmentationMetric",
-  #       "init_args": {"metric": {"class_path": "torchmetrics.classification.MulticlassRecall",
-  #       "init_args": {"num_classes": 4, "top_k": 1, "average": null, "multidim_average":
-  #       "global", "ignore_index": null, "validate_args": true, "zero_division": 0}},
-  #       "pass_probabilities": true, "class_idx": 1}}, "other_precision": {"class_path":
-  #       "rslearn.train.tasks.segmentation.SegmentationMetric", "init_args": {"metric":
-  #       {"class_path": "torchmetrics.classification.MulticlassPrecision", "init_args":
-  #       {"num_classes": 4, "top_k": 1, "average": null, "multidim_average": "global",
-  #       "ignore_index": null, "validate_args": true, "zero_division": 0}}, "pass_probabilities":
-  #       true, "class_idx": 3}}, "other_recall": {"class_path": "rslearn.train.tasks.segmentation.SegmentationMetric",
-  #       "init_args": {"metric": {"class_path": "torchmetrics.classification.MulticlassRecall",
-  #       "init_args": {"num_classes": 4, "top_k": 1, "average": null, "multidim_average":
-  #       "global", "ignore_index": null, "validate_args": true, "zero_division": 0}},
-  #       "pass_probabilities": true, "class_idx": 3}}, "water_precision": {"class_path":
-  #       "rslearn.train.tasks.segmentation.SegmentationMetric", "init_args": {"metric":
-  #       {"class_path": "torchmetrics.classification.MulticlassPrecision", "init_args":
-  #       {"num_classes": 4, "top_k": 1, "average": null, "multidim_average": "global",
-  #       "ignore_index": null, "validate_args": true, "zero_division": 0}}, "pass_probabilities":
-  #       true, "class_idx": 2}}, "water_recall": {"class_path": "rslearn.train.tasks.segmentation.SegmentationMetric",
-  #       "init_args": {"metric": {"class_path": "torchmetrics.classification.MulticlassRecall",
-  #       "init_args": {"num_classes": 4, "top_k": 1, "average": null, "multidim_average":
-  #       "global", "ignore_index": null, "validate_args": true, "zero_division": 0}},
-  #       "pass_probabilities": true, "class_idx": 2}}}, "image_bands": [0, 1, 2], "remap_values":
-  #       null}}}, "input_mapping": {"mangrove_classification": {"label": "targets"}}}},
-  #       "path": "/weka/dfive-default/rslearn-eai/datasets/mangrove/classification/20250626",
-  #       "path_options": {}, "batch_size": 32, "num_workers": 32, "init_workers": 0,
-  #       "default_config": {"class_path": "rslearn.train.dataset.SplitConfig", "init_args":
-  #       {"groups": null, "names": null, "tags": null, "num_samples": null, "num_patches":
-  #       null, "transforms": [{"class_path": "rslearn.train.transforms.pad.Pad", "init_args":
-  #       {"size": 2, "mode": "center", "image_selectors": ["sentinel2_l2a", "target/mangrove_classification/classes",
-  #       "target/mangrove_classification/valid"], "box_selectors": []}}, {"class_path":
-  #       "rslp.helios.norm.HeliosNormalize", "init_args": {"band_names": {"sentinel2_l2a":
-  #       ["B02", "B03", "B04", "B08", "B05", "B06", "B07", "B8A", "B11", "B12", "B01",
-  #       "B09"]}, "std_multiplier": 2.0, "config_fname": "/opt/helios/data/norm_configs/computed.json"}}],
-  #       "sampler": null, "patch_size": null, "overlap_ratio": null, "load_all_patches":
-  #       null, "skip_targets": null}}, "train_config": {"class_path": "rslearn.train.dataset.SplitConfig",
-  #       "init_args": {"groups": ["sample_100K"], "names": null, "tags": {"split":
-  #       "train"}, "num_samples": 10000, "num_patches": null, "transforms": null, "sampler":
-  #       null, "patch_size": null, "overlap_ratio": null, "load_all_patches": null,
-  #       "skip_targets": null}}, "val_config": {"class_path": "rslearn.train.dataset.SplitConfig",
-  #       "init_args": {"groups": ["sample_100K"], "names": null, "tags": {"split":
-  #       "val"}, "num_samples": null, "num_patches": null, "transforms": null, "sampler":
-  #       null, "patch_size": null, "overlap_ratio": null, "load_all_patches": null,
-  #       "skip_targets": null}}, "test_config": {"class_path": "rslearn.train.dataset.SplitConfig",
-  #       "init_args": {"groups": ["sample_100K"], "names": null, "tags": {"split":
-  #       "val"}, "num_samples": null, "num_patches": null, "transforms": null, "sampler":
-  #       null, "patch_size": null, "overlap_ratio": null, "load_all_patches": null,
-  #       "skip_targets": null}}, "predict_config": {"class_path": "rslearn.train.dataset.SplitConfig",
-  #       "init_args": {"groups": null, "names": null, "tags": null, "num_samples":
-  #       null, "num_patches": null, "transforms": null, "sampler": null, "patch_size":
-  #       null, "overlap_ratio": null, "load_all_patches": null, "skip_targets": null}},
-  #       "name": null, "retries": 0}}, "rslp_project": "2025_09_15_mangrove_classification",
-  #       "rslp_experiment": "mangrove_classification_segment_helios_base_S2_ts_ws2_ps2",
-  #       "rslp_description": "", "autoresume": true, "load_best": false, "force_log":
-  #       false, "no_log": false, "profiler": null, "allow_missing_weights": false,
-  #       "optimizer": null, "lr_scheduler": null, "ckpt_path": null}'
   fast_dev_run: false
   max_epochs: 100
   min_epochs: null
@@ -572,15 +455,8 @@ trainer:
   reload_dataloaders_every_n_epochs: 0
   default_root_dir: null
   model_registry: null
-# rslp_project: 2025_09_15_mangrove_classification
-# rslp_experiment: mangrove_classification_segment_helios_base_S2_ts_ws2_ps2
-# rslp_description: ''
-# autoresume: true
-# load_best: false
-# force_log: false
-# no_log: false
-# profiler: null
-# allow_missing_weights: false
-# optimizer: null
-# lr_scheduler: null
-# ckpt_path: null
\ No newline at end of file
+rslp_project: ${WANDB_PROJECT}
+rslp_experiment: ${WANDB_NAME}
+# ${EXTRA_FILES_PATH}: Path to the extra pretrained model/data preprocessing config files
+# ${TRAINER_DATA_PATH}: Path to the rslearn trainer data directory. For intermediate checkpoints, trainer state, etc.
+# ${WANDB_ENTITY}: wandb entity for the trainer to log metrics to
\ No newline at end of file
diff --git a/esrun_data/mangrove/prediction_request_geometry.geojson b/esrun_data/mangrove/prediction_request_geometry.geojson
index d245fe67..01e2faaf 100644
--- a/esrun_data/mangrove/prediction_request_geometry.geojson
+++ b/esrun_data/mangrove/prediction_request_geometry.geojson
@@ -19,7 +19,7 @@
           "tile_name": "N27E055",
           "gmw_tile_name": "GMW_N27E055",
           "es_start_time": "2018-01-01T00:00:00Z",
-          "es_end_time": "2024-12-31T23:59:59Z"
+          "es_end_time": "2019-12-31T23:59:59Z"
         },
         "geometry": {
           "type": "Polygon",
diff --git a/rslp/esrun/esrun.py b/rslp/esrun/esrun.py
index 29683682..f7397fd5 100644
--- a/rslp/esrun/esrun.py
+++ b/rslp/esrun/esrun.py
@@ -63,7 +63,7 @@ def prepare_labeled_windows(project_path: Path, scratch_path: Path) -> None:
     runner.prepare_labeled_windows()
 
 
-def esrun(config_path: Path, scratch_path: Path, checkpoint_path: str, num_workers_partition: int | None = None, num_workers_inference: int | None = None, num_workers_postprocess: int | None = None, num_workers_combine: int | None = None) -> None:
+def esrun(config_path: Path, scratch_path: Path, checkpoint_path: str) -> None:
     """Run EsPredictRunner inference pipeline.
 
     Args:
@@ -80,10 +80,6 @@ def esrun(config_path: Path, scratch_path: Path, checkpoint_path: str, num_worke
         project_path=config_path.absolute(),
         scratch_path=scratch_path,
         checkpoint_path=get_local_checkpoint(UPath(checkpoint_path)),
-        num_workers_partition=num_workers_partition,
-        num_workers_inference=num_workers_inference,
-        num_workers_postprocess=num_workers_postprocess,
-        num_workers_combine=num_workers_combine,
     )
     logger.info("Partitioning...")
     partitions = runner.partition()
@@ -96,6 +92,7 @@ def esrun(config_path: Path, scratch_path: Path, checkpoint_path: str, num_worke
         runner.run_inference(partition_id)
         logger.info(f"Postprocessing for partition {partition_id}")
         runner.postprocess(partition_id)
+        break
 
     logger.info("Combining across partitions")
     runner.combine(partitions)
@@ -119,7 +116,6 @@ def one_stage(
     checkpoint_path: str,
     stage: EsrunStage,
     partition_id: str | None = None,
-    num_workers: int | None = None,
     inference_results_data_type: InferenceResultsDataType = InferenceResultsDataType.RASTER,
 ) -> None:
     """Run EsPredictRunner inference pipeline.
@@ -143,11 +139,6 @@ def one_stage(
         project_path=config_path,
         scratch_path=scratch_path,
         checkpoint_path=get_local_checkpoint(UPath(checkpoint_path)),
-        # only running one stage so we just override the workers for that stage
-        num_workers_partition=num_workers,
-        num_workers_inference=num_workers,
-        num_workers_postprocess=num_workers,
-        num_workers_combine=num_workers,
     )
     partitions = runner.partition()
 

From d5ba331ee5a950eb4cd161f0ea7fc4560a2867b7 Mon Sep 17 00:00:00 2001
From: hgherzog <henryh@allenai.org>
Date: Thu, 2 Oct 2025 18:11:02 +0000
Subject: [PATCH 08/11] inference config working locally

---
 esrun_data/mangrove/model.yaml                         |  4 ++--
 .../mangrove/prediction_request_geometry.geojson       | 10 +++++-----
 rslp/esrun/esrun.py                                    |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/esrun_data/mangrove/model.yaml b/esrun_data/mangrove/model.yaml
index d6c0ca10..ce579f8e 100644
--- a/esrun_data/mangrove/model.yaml
+++ b/esrun_data/mangrove/model.yaml
@@ -455,8 +455,8 @@ trainer:
   reload_dataloaders_every_n_epochs: 0
   default_root_dir: null
   model_registry: null
-rslp_project: ${WANDB_PROJECT}
-rslp_experiment: ${WANDB_NAME}
+# rslp_project: ${WANDB_PROJECT}
+# rslp_experiment: ${WANDB_NAME}
 # ${EXTRA_FILES_PATH}: Path to the extra pretrained model/data preprocessing config files
 # ${TRAINER_DATA_PATH}: Path to the rslearn trainer data directory. For intermediate checkpoints, trainer state, etc.
 # ${WANDB_ENTITY}: wandb entity for the trainer to log metrics to
\ No newline at end of file
diff --git a/esrun_data/mangrove/prediction_request_geometry.geojson b/esrun_data/mangrove/prediction_request_geometry.geojson
index 01e2faaf..cf94439d 100644
--- a/esrun_data/mangrove/prediction_request_geometry.geojson
+++ b/esrun_data/mangrove/prediction_request_geometry.geojson
@@ -19,7 +19,7 @@
           "tile_name": "N27E055",
           "gmw_tile_name": "GMW_N27E055",
           "es_start_time": "2018-01-01T00:00:00Z",
-          "es_end_time": "2019-12-31T23:59:59Z"
+          "es_end_time": "2018-03-01T23:59:59Z"
         },
         "geometry": {
           "type": "Polygon",
@@ -30,16 +30,16 @@
                 27.0
               ],
               [
-                56.0,
+                55.05,
                 27.0
               ],
               [
-                56.0,
-                26.0
+                55.05,
+                26.95
               ],
               [
                 55.0,
-                26.0
+                26.95
               ],
               [
                 55.0,
diff --git a/rslp/esrun/esrun.py b/rslp/esrun/esrun.py
index c068eb9c..e69e8f58 100644
--- a/rslp/esrun/esrun.py
+++ b/rslp/esrun/esrun.py
@@ -134,7 +134,7 @@ def one_stage(
         raise ValueError("partition_id cannot be set for COMBINE stage")
 
     # Configure esrun logging before creating the runner
-    configure_logging(log_level=logging.WARNING)
+    configure_logging(log_level=logging.INFO)
 
     runner = EsPredictRunner(
         # ESRun does not work with relative path, so make sure to convert to absolute here.

From f3aaba7b96e2d84ffbd73a28aaa181fe486b7917 Mon Sep 17 00:00:00 2001
From: hgherzog <henryh@allenai.org>
Date: Thu, 2 Oct 2025 18:44:33 +0000
Subject: [PATCH 09/11] add extra fiels path

---
 esrun_data/mangrove/model.yaml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/esrun_data/mangrove/model.yaml b/esrun_data/mangrove/model.yaml
index ce579f8e..ec4a4332 100644
--- a/esrun_data/mangrove/model.yaml
+++ b/esrun_data/mangrove/model.yaml
@@ -9,14 +9,12 @@ model:
         encoder:
         - class_path: rslp.helios.model.Helios
           init_args:
-            checkpoint_path: /weka/dfive-default/helios/checkpoints/yawenzzzz/latent_mim_cross_random_per_modality_patchdisc_add_contrastive_0.1_1/step300000
+            checkpoint_path: ${EXTRA_FILES_PATH}/step300000
             selector:
             - encoder
             forward_kwargs:
               patch_size: 2
-            random_initialization: false
-            embedding_size: null
-            patch_size: null
+            random_initialization: true
             autocast_dtype: bfloat16
         decoders:
           mangrove_classification:

From 6c890b3e949fdee65ff7d2144f0e3d1f014e53e5 Mon Sep 17 00:00:00 2001
From: hgherzog <henryh@allenai.org>
Date: Mon, 6 Oct 2025 17:55:14 +0000
Subject: [PATCH 10/11] try updating raster merger

---
 esrun_data/mangrove/model.yaml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/esrun_data/mangrove/model.yaml b/esrun_data/mangrove/model.yaml
index ec4a4332..eff0e079 100644
--- a/esrun_data/mangrove/model.yaml
+++ b/esrun_data/mangrove/model.yaml
@@ -343,7 +343,7 @@ data:
         skip_targets: null
     predict_config:
       patch_size: 2 #I think this is actually the window size for inference processing
-      overlap_ratio: 0.5
+      overlap_ratio: null
       load_all_patches: true
       skip_targets: true
       transforms:
@@ -391,10 +391,7 @@ trainer:
       path: ${DATASET_PATH}
       output_layer: ${PREDICTION_OUTPUT_LAYER}
       selector: ["mangrove_classification"]
-      merger:
-        class_path: rslearn.train.prediction_writer.RasterMerger
-        init_args:
-          padding: 2
+      merger: null
   - class_path: lightning.pytorch.callbacks.ModelCheckpoint
     init_args:
       dirpath: gs://rslearn-eai/projects/2025_09_15_mangrove_classification/mangrove_classification_segment_helios_base_S2_ts_ws2_ps2/checkpoints

From 38e11f54fdeb573688b859cfd5ee43f7ca903df0 Mon Sep 17 00:00:00 2001
From: hgherzog <henryh@allenai.org>
Date: Mon, 6 Oct 2025 19:37:11 +0000
Subject: [PATCH 11/11] remove inference writer

---
 esrun_data/mangrove/esrun.yaml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/esrun_data/mangrove/esrun.yaml b/esrun_data/mangrove/esrun.yaml
index 4112ffc4..d744280a 100644
--- a/esrun_data/mangrove/esrun.yaml
+++ b/esrun_data/mangrove/esrun.yaml
@@ -36,11 +36,3 @@ postprocessing_strategies:
 
 inference_results_config:
   data_type: RASTER
-
-
-inference_writer:
-  selector: ["mangrove_classification"]
-  merger:
-    class_path: rslearn.train.prediction_writer.RasterMerger
-    init_args:
-      padding: 2
\ No newline at end of file