Fix data dimension swapping and axis errors

src/deepforest/datasets/prediction.py

@@ -444,8 +444,8 @@ def __init__(self, path, patch_size, patch_overlap):
     def prepare_items(self):
         # Get raster shape without keeping file open
         with rio.open(self.path) as src:
-            width = src.shape[0]
-            height = src.shape[1]
+            height = src.shape[0]
+            width = src.shape[1]
 
             # Check is tiled
             if not src.is_tiled:
@@ -460,8 +460,8 @@ def prepare_items(self):
 
         # Generate sliding windows
         self.windows = slidingwindow.generateForSize(
-            height,
             width,
+            height,
             dimOrder=slidingwindow.DimOrder.ChannelHeightWidth,
             maxWindowSize=self.patch_size,
             overlapPercent=self.patch_overlap,

src/deepforest/preprocess.py

@@ -206,8 +206,8 @@ def split_raster(
         )
         numpy_image = numpy_image.transpose(2, 0, 1)
 
-    # Check that it's 3 bands
-    bands = numpy_image.shape[2]
+    # Check that it's 3 bands (image is now channels-first: C x H x W)
+    bands = numpy_image.shape[0]
     if not bands == 3:
         warnings.warn(
             f"Input image had non-3 band shape of {numpy_image.shape}, selecting first 3 bands",

tests/test_datasets_prediction.py

@@ -2,60 +2,99 @@
 import os
 
 import numpy as np
-from PIL import Image
 import pytest
+from PIL import Image
 
 from deepforest import get_data
-from deepforest.datasets.prediction import TiledRaster, SingleImage, MultiImage, FromCSVFile, PredictionDataset
+from deepforest.datasets.prediction import (
+    FromCSVFile,
+    MultiImage,
+    SingleImage,
+    TiledRaster,
+)
 
 
 def test_TiledRaster():
     tile_path = get_data("test_tiled.tif")
-    ds = TiledRaster(path=tile_path,
-                             patch_size=300,
-                             patch_overlap=0)
+    ds = TiledRaster(path=tile_path, patch_size=300, patch_overlap=0)
     assert len(ds) == 16
 
     # assert crop shape
     assert ds[1].shape == (3, 300, 300)
 
+
+def test_TiledRaster_non_square(tmp_path):
+    import rasterio as rio
+    from rasterio.transform import from_origin
+
+    transform = from_origin(0, 0, 1, 1)
+    raster_path = str(tmp_path / "non_square.tif")
+    # create a 3 band, 500 height, 800 width raster
+    with rio.open(
+        raster_path,
+        "w",
+        driver="GTiff",
+        height=500,
+        width=800,
+        count=3,
+        dtype=np.uint8,
+        crs="+proj=latlong",
+        transform=transform,
+        tiled=True,
+        blockxsize=256,
+        blockysize=256,
+    ) as dst:
+        dst.write(np.zeros((3, 500, 800), dtype=np.uint8))
+
+    ds = TiledRaster(path=raster_path, patch_size=400, patch_overlap=0)
+
+    # width 800 -> 2 patches. height 500 -> 2 patches. Total = 4 patches
+    assert len(ds) == 4
+
+
 def test_SingleImage_path():
-    ds = SingleImage(
-        path=get_data("OSBS_029.png"),
-        patch_size=300,
-        patch_overlap=0)
+    ds = SingleImage(path=get_data("OSBS_029.png"), patch_size=300, patch_overlap=0)
 
     assert len(ds) == 4
     assert ds[0].shape == (3, 300, 300)
 
     for i in range(len(ds)):
         assert ds.get_crop(i).shape == (3, 300, 300)
 
+
 def test_invalid_image_shape():
     # Not 3 channels
     test_data = (np.random.rand(300, 300, 4) * 255).astype(np.uint8)
     with pytest.raises(ValueError):
         SingleImage(image=Image.fromarray(test_data))
 
+
 def test_valid_image():
     # 8-bit, HWC
-    test_data = np.random.randint(0, 256, (300,300,3)).astype(np.uint8)
+    test_data = np.random.randint(0, 256, (300, 300, 3)).astype(np.uint8)
     SingleImage(image=Image.fromarray(test_data))
 
+
 def test_valid_array():
     # 8-bit, HWC
-    test_data = np.random.randint(0, 256, (300,300,3)).astype(np.uint8)
+    test_data = np.random.randint(0, 256, (300, 300, 3)).astype(np.uint8)
     SingleImage(image=test_data)
 
+
 def test_MultiImage():
-    ds = MultiImage(paths=[get_data("OSBS_029.png"), get_data("OSBS_029.png")],
-                    patch_size=300,
-                    patch_overlap=0)
+    ds = MultiImage(
+        paths=[get_data("OSBS_029.png"), get_data("OSBS_029.png")],
+        patch_size=300,
+        patch_overlap=0,
+    )
     # 2 windows each image 2 * 2 = 4
     assert len(ds) == 2
     assert ds[0][0].shape == (3, 300, 300)
 
+
 def test_FromCSVFile():
-    ds = FromCSVFile(csv_file=get_data("example.csv"),
-                     root_dir=os.path.dirname(get_data("example.csv")))
+    ds = FromCSVFile(
+        csv_file=get_data("example.csv"),
+        root_dir=os.path.dirname(get_data("example.csv")),
+    )
     assert len(ds) == 1