read_vrt: SrcRect/DstRect scaling not applied to source array placement

[brendancol]

read_vrt did not resample source pixel data when a source band's <SrcRect> size differed from its <DstRect> size. The decoded source array was assigned directly into the destination buffer with no resample step, so downsampling raised ValueError: could not broadcast input array from shape (S,S) into shape (D,D) and upsampling left holes -- only the top-left sr.x_size/sr.y_size pixels of each destination cell were written.

When sr.size != dr.size, the fix reads the full source rect, applies nodata masking, nearest-neighbour resamples to (dr.y_size, dr.x_size), then clips into the window. Matches GDAL SimpleSource semantics. <ComplexSource><ResampleAlg> is parsed off the XML so a follow-up can add bilinear / cubic, but nearest is used regardless for now.

What was broken

xrspatial/geotiff/_vrt.py:464-472 computed a source-coordinate window from scale_x = sr.x_size / dr.x_size and scale_y = sr.y_size / dr.y_size. It then called read_to_array(window=...), which returned an array sized to the source window, and copied it directly into the destination slice at L577-583 with no resample step. The "size mismatch" guard at L573-575 compared src_arr.shape against out_r1 - out_r0 where out_r1 = out_r0 + src_arr.shape[0], so the guard never tripped.

Reproducer:

import numpy as np, tempfile, os
from xrspatial.geotiff._writer import write
from xrspatial.geotiff._vrt import read_vrt

with tempfile.TemporaryDirectory() as tmp:
    arr = np.arange(16, dtype=np.uint16).reshape(4, 4)
    src_path = os.path.join(tmp, 'src.tif')
    write(arr, src_path, compression='none', tiled=False)

    vrt_path = os.path.join(tmp, 'down.vrt')
    with open(vrt_path, 'w') as f:
        f.write(f'''<VRTDataset rasterXSize="2" rasterYSize="2">
  <GeoTransform>0.0, 2.0, 0.0, 0.0, 0.0, -2.0</GeoTransform>
  <VRTRasterBand dataType="UInt16" band="1">
    <SimpleSource>
      <SourceFilename relativeToVRT="0">{src_path}</SourceFilename>
      <SourceBand>1</SourceBand>
      <SrcRect xOff="0" yOff="0" xSize="4" ySize="4"/>
      <DstRect xOff="0" yOff="0" xSize="2" ySize="2"/>
    </SimpleSource>
  </VRTRasterBand>
</VRTDataset>''')

    read_vrt(vrt_path)
    # ValueError: could not broadcast input array from shape (4,4) into shape (2,2)

What's fixed

A new _resample_nearest helper. Integer-ratio paths short-circuit to np.repeat (upsample) or strided slicing (downsample); non-integer ratios use a per-axis nearest-index gather. The centre-of-output-pixel rule (floor((out_idx + 0.5) * src_size / out_size)) matches GDAL's nearest-neighbour rounding.

read_vrt now reads the full source rect when sr.size != dr.size, runs nodata masking, resamples to (dr.y_size, dr.x_size), then clips to the window subregion. Same-size sources still use windowed reads as before -- the windowed path is cheaper and the resample is only invoked when the source rect actually needs scaling.

Nodata masking runs before the resample so the sentinel survives nearest sampling. NaN flows through the float-masking branch; the integer-into-float promotion runs against the source-shaped array and the resulting NaN propagates through the resample.

Test plan

• pytest xrspatial/geotiff/tests/test_vrt_scaled_rects_1694.py -- 7 new tests pass
• All 7 new tests fail before the fix (verified by stash-and-rerun)
• pytest xrspatial/geotiff/tests/test_vrt_*.py -- 96 passed, no VRT regressions
• pytest xrspatial/geotiff/tests/ -- 1696 passed, 3 failures are a pre-existing matplotlib/palette RecursionError unrelated to VRT

New tests cover downsample 4x4 -> 2x2 (no broadcast error, nearest-neighbour values match), upsample 2x2 -> 4x4 (each source pixel repeated 2x2, no holes), non-integer scale 3x3 -> 2x2 (general index-mapping path), per-band scale mix (band 1 downsampled, band 2 native), window=(0,0,1,1) on a downsampled source (returns the right pixel), nodata preservation across a 4x4 -> 2x2 resample with all-sentinel samples (all NaN), and a mixed sentinel / valid source -> mixed NaN / valid destination case.

Fixes #1694

[Copilot]

Pull request overview

This PR fixes xrspatial.geotiff._vrt.read_vrt so VRT sources with differing <SrcRect> and <DstRect> sizes are properly nearest-neighbour resampled before being placed into the destination buffer, matching GDAL SimpleSource semantics and avoiding broadcast errors / “holes”.

Changes:

• Add _resample_nearest helper and update read_vrt to resample when SrcRect and DstRect sizes differ.
• Parse and record <ComplexSource><ResampleAlg> in the VRT parser (informational for now; still uses nearest).
• Add regression tests covering downsample/upsample/non-integer scaling, windowed reads, band mixes, and nodata behavior (issue #1694).

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.

File	Description
xrspatial/geotiff/_vrt.py	Implements SrcRect/DstRect-aware resampling (nearest) during source placement; parses ResampleAlg.
xrspatial/geotiff/tests/test_vrt_scaled_rects_1694.py	New regression tests validating scaled-rect placement, window behavior, and nodata preservation.

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