Merge branch 'labs-mosaic'

.github/actions/python_build/action.yml

@@ -16,6 +16,11 @@ runs:
         pip install build wheel pyspark==${{ matrix.spark }} numpy==${{ matrix.numpy }}
         pip install --no-build-isolation --no-cache-dir --force-reinstall gdal==${{ matrix.gdal }}
         pip install .
+    - name: Give Python interpreter write access to checkpointing / raster write location
+      shell: bash
+      run: |
+        sudo mkdir -p /mnt/mosaic_tmp
+        sudo chmod -R 777 /mnt/mosaic_tmp
     - name: Test and build python package
       shell: bash
       run: |

.github/workflows/build_main.yml

@@ -11,7 +11,7 @@ on:
       - "**"
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: larger
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     strategy:

.github/workflows/build_python.yml

@@ -7,7 +7,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: larger
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     strategy:

.github/workflows/build_r.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: larger
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     strategy:

.github/workflows/build_scala.yml

@@ -6,7 +6,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: larger
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     strategy:

CHANGELOG.md

@@ -1,11 +1,58 @@
 ## v0.4.3 [DBR 13.3 LTS]
+
+This is the final mainline release of Mosaic. Future development will be focused on the planned spatial-utils library, which will be a successor to Mosaic and will include new features and improvements. The first release of spatial-utils is expected in the coming months.
+
+We will continue to maintain Mosaic for the foreseeable future, including bug fixes and security updates. However, we recommend that users start transitioning to spatial-utils as soon as possible to take advantage of the new features and improvements that will be available in that library.
+
+This release includes a number of enhancements and fixes, detailed below.
+
+### Raster checkpointing functions
+Fuse-based checkpointing for raster operations is disabled by default but can be enabled and managed through:
+- spark configs `spark.databricks.labs.mosaic.raster.use.checkpoint` and `spark.databricks.labs.mosaic.raster.checkpoint`.
+- python: `mos.enable_gdal(spark, with_checkpoint_path=path)`.
+- scala: `MosaicGDAL.enableGDALWithCheckpoint(spark, path)`.
+
+This feature is designed to improve performance and reduce memory usage for raster operations by writing intermediate data to a fuse directory. This is particularly useful for large rasters or when working with many rasters in a single operation. 
+
+We plan further enhancements to this feature (including automatic cleanup of checkpoint locations) as part of the first release of spatial-utils.
+
+### Enhancements and fixes to the raster processing APIs
+  - Added `RST_Write`, a function that permits writing each raster 'tile' in a DataFrame to a specified location (e.g. fuse directory) using the appropriate GDAL driver and tile data / path. This is useful for formalizing the path when writing a Lakehouse table and allows removal of interim checkpointed data.
+  - Python bindings added for `RST_Avg`, `RST_Max`, `RST_Median`, `RST_Min`, and `RST_PixelCount`.
+  - `RST_PixelCount` now supports optional 'countNoData' and 'countMask' parameters (defaults are false, can now be true) to optionally get full pixel counts where mask is 0.0 and noData is what is configured in the tile.
+  - `RST_Clip` now exposes the GDAL Warp option `CUTLINE_ALL_TOUCHED` which determines whether or not any given pixel is included whether the clipping geometry crosses the centre point of the pixel (false) or any part of the pixel (true). The default is true but this is now configurable.
+  - Within clipping operations such as `RST_Clip` we now correctly set the CRS in the generated Shapefile Feature Layer used for clipping. This means that the CRS of the input geometry will be respected when clipping rasters.
+  - Added two new functions for getting and upcasting the datatype of a raster band: `RST_Type` and `RST_UpdateType`. Use these for ensuring that the datatype of a raster is appropriate for the operations being performed, e.g. upcasting the types of integer-typed input rasters before performing raster algebra like NDVI calculations where the result needs to be a float.
+  - Added `RST_AsFormat`, a function that translates rasters between formats e.g. from NetCDF to GeoTIFF.
+  - The logic underpinning `RST_MemSize` (and related operations) has been updated to fall back to estimating based on the raster dimensions and data types of each band if the raster is held in-memory.
+  - `RST_To_Overlapping_Tiles` is renamed `RST_ToOverlappingTiles`. The original expression remains but is marked as deprecated.
+  - `RST_WorldToRasterCoordY` now returns the correct `y` value (was returning `x`)
+  - Docs added for expression `RST_SetSRID`.
+  - Docs updated for `RST_FromContent` to capture the optional 'driver' parameter.
+
+### Dependency management
+Updates to and pinning of Python language and dependency versions:
 - Pyspark requirement removed from python setup.cfg as it is supplied by DBR
 - Python version limited to "<3.11,>=3.10" for DBR
-- iPython dependency limited to "<8.11,>=7.4.2" for both DBR and keplergl-jupyter 
-- Expanded support for fuse-based checkpointing (persisted raster storage), managed through:
-  - spark config 'spark.databricks.labs.mosaic.raster.use.checkpoint' in addition to 'spark.databricks.labs.mosaic.raster.checkpoint'.
-  - python: `mos.enable_gdal(spark, with_checkpoint_path=path)`.
-  - scala: `MosaicGDAL.enableGDALWithCheckpoint(spark, path)`.
+- iPython dependency limited to "<8.11,>=7.4.2" for both DBR and keplergl-jupyter
+- numpy now limited to "<2.0,>=1.21.5" to match DBR minimum
+
+### Surface mesh APIs
+A set of experimental APIs for for creating and working with surface meshes (i.e. triangulated irregular networks) have been added to Mosaic. Users can now generate a conforming Delaunay triangulation over point data (optionally including 'break' lines as hard constraints), interpolate elevation over a regular grid and rasterize the results to produce terrain models.
+  - `ST_Triangulate` performs a conforming Delaunay triangulation using a set of mass points and break lines. 
+  - `ST_InterpolateElevation` computes the interpolated elevations of a grid of points.
+  - `RST_DTMFromGeoms` burns the interpolated elevations into a raster.
+
+### British National Grid
+Two fixes have been made to the British National Grid indexing system:
+- Corrected a typo in the grid letter array used to perform lookups.
+- Updated the logic used for identifying quadrants when these are specified in a grid reference
+
+### Documentation
+A few updates to our documentation and examples library:
+- An example walkthrough has been added for arbitrary GDAL Warp and Transform operations using a pyspark UDF (see the section "API Documentation / Rasterio + GDAL UDFs")
+- The Python "Quickstart Notebook" has been updated to use the `MosaicAnalyzer` class (added after `MosaicFrame` was deprecated)
+
 
 ## v0.4.2 [DBR 13.3 LTS]
 - Geopandas now fixed to "<0.14.4,>=0.14" due to conflict with minimum numpy version in geopandas 0.14.4.

CONTRIBUTING.md

@@ -102,7 +102,7 @@ The python bindings can be tested using [unittest](https://docs.python.org/3/lib
 - Move to the `python/` directory and install the project and its dependencies:
     `pip install . && pip install pyspark==<project_spark_version>`
   (where 'project_spark_version' corresponds to the version of Spark 
-  used for the target Databricks Runtime, e.g. `3.2.1`.
+  used for the target Databricks Runtime, e.g. `3.4.1` for DBR 13.3 LTS.
 - Run the tests using `unittest`: `python -m unittest`
 
 The project wheel file can be built with [build](https://pypa-build.readthedocs.io/en/stable/).

R/.gitignore

@@ -1,3 +1,9 @@
 **/.Rhistory
 **/*.tar.gz
+**/*.Rproj
 /sparklyr-mosaic/metastore_db/
+/sparklyr-mosaic/mosaic_checkpoint/
+/sparklyr-mosaic/mosaic_tmp/
+/sparkr-mosaic/metastore_db/
+/sparkr-mosaic/mosaic_checkpoint/
+/sparkr-mosaic/mosaic_tmp/

R/sparkR-mosaic/sparkrMosaic/DESCRIPTION

@@ -8,7 +8,7 @@ Description: This package extends SparkR to bring the Databricks Mosaic for geos
 License: Databricks
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Collate:
     'enableGDAL.R'
     'enableMosaic.R'

R/sparkR-mosaic/sparkrMosaic/tests/testthat/testRasterFunctions.R

@@ -8,6 +8,7 @@ generate_singleband_raster_df <- function() {
 
 test_that("mosaic can read single-band GeoTiff", {
   sdf <- generate_singleband_raster_df()
+
   row <- first(sdf)
   expect_equal(row$length, 1067862L)
   expect_equal(row$x_size, 2400)
@@ -34,12 +35,15 @@ test_that("scalar raster functions behave as intended", {
   sdf <- withColumn(sdf, "rst_scaley", rst_scaley(column("tile")))
   sdf <- withColumn(sdf, "rst_srid", rst_srid(column("tile")))
   sdf <- withColumn(sdf, "rst_summary", rst_summary(column("tile")))
+  sdf <- withColumn(sdf, "rst_type", rst_type(column("tile")))
+  sdf <- withColumn(sdf, "rst_updatetype", rst_updatetype(column("tile"), lit("Float32")))
   sdf <- withColumn(sdf, "rst_upperleftx", rst_upperleftx(column("tile")))
   sdf <- withColumn(sdf, "rst_upperlefty", rst_upperlefty(column("tile")))
   sdf <- withColumn(sdf, "rst_width", rst_width(column("tile")))
   sdf <- withColumn(sdf, "rst_worldtorastercoordx", rst_worldtorastercoordx(column("tile"), lit(0.0), lit(0.0)))
   sdf <- withColumn(sdf, "rst_worldtorastercoordy", rst_worldtorastercoordy(column("tile"), lit(0.0), lit(0.0)))
   sdf <- withColumn(sdf, "rst_worldtorastercoord", rst_worldtorastercoord(column("tile"), lit(0.0), lit(0.0)))
+  sdf <- withColumn(sdf, "rst_write", rst_write(column("tile"), lit("/mnt/mosaic_tmp/write-raster")))
 
   expect_no_error(write.df(sdf, source = "noop", mode = "overwrite"))
 })
@@ -64,7 +68,7 @@ test_that("raster flatmap functions behave as intended", {
   expect_equal(nrow(tessellate_sdf), 63)
 
   overlap_sdf <- generate_singleband_raster_df()
-  overlap_sdf <- withColumn(overlap_sdf, "rst_to_overlapping_tiles", rst_to_overlapping_tiles(column("tile"), lit(200L), lit(200L), lit(10L)))
+  overlap_sdf <- withColumn(overlap_sdf, "rst_tooverlappingtiles", rst_tooverlappingtiles(column("tile"), lit(200L), lit(200L), lit(10L)))
 
   expect_no_error(write.df(overlap_sdf, source = "noop", mode = "overwrite"))
   expect_equal(nrow(overlap_sdf), 87)
@@ -73,7 +77,7 @@ test_that("raster flatmap functions behave as intended", {
 test_that("raster aggregation functions behave as intended", {
   collection_sdf <- generate_singleband_raster_df()
   collection_sdf <- withColumn(collection_sdf, "extent", st_astext(rst_boundingbox(column("tile"))))
-  collection_sdf <- withColumn(collection_sdf, "tile", rst_to_overlapping_tiles(column("tile"), lit(200L), lit(200L), lit(10L)))
+  collection_sdf <- withColumn(collection_sdf, "tile", rst_tooverlappingtiles(column("tile"), lit(200L), lit(200L), lit(10L)))
 
   merge_sdf <- summarize(
     groupBy(collection_sdf, "path"),
@@ -124,7 +128,7 @@ test_that("the tessellate-join-clip-merge flow works on NetCDF files", {
   raster_sdf <- withColumn(raster_sdf, "timestep", element_at(rst_metadata(column("tile")), "NC_GLOBAL#GDAL_MOSAIC_BAND_INDEX"))
   raster_sdf <- where(raster_sdf, "timestep = 21")
   raster_sdf <- withColumn(raster_sdf, "tile", rst_setsrid(column("tile"), lit(4326L)))
-  raster_sdf <- withColumn(raster_sdf, "tile", rst_to_overlapping_tiles(column("tile"), lit(20L), lit(20L), lit(10L)))
+  raster_sdf <- withColumn(raster_sdf, "tile", rst_tooverlappingtiles(column("tile"), lit(20L), lit(20L), lit(10L)))
   raster_sdf <- withColumn(raster_sdf, "tile", rst_tessellate(column("tile"), lit(target_resolution)))
 
   clipped_sdf <- join(raster_sdf, census_sdf, raster_sdf$tile.index_id == census_sdf$index_id)
@@ -137,4 +141,33 @@ test_that("the tessellate-join-clip-merge flow works on NetCDF files", {
 
   expect_equal(nrow(merged_precipitation), 1)
 
+})
+
+test_that("a terrain model can be produced from point geometries", {
+
+sdf <- createDataFrame(
+  data.frame(
+    wkt = c(
+      "POINT Z (3 2 1)",
+      "POINT Z (2 1 0)",
+      "POINT Z (1 3 3)",
+      "POINT Z (0 2 2)"
+    )
+  )
+)
+
+sdf <- agg(groupBy(sdf), masspoints = collect_list(column("wkt")))
+sdf <- withColumn(sdf, "breaklines", expr("array('LINESTRING EMPTY')"))
+sdf <- withColumn(sdf, "splitPointFinder", lit("NONENCROACHING"))
+sdf <- withColumn(sdf, "origin", st_geomfromwkt(lit("POINT (0.6 1.8)")))
+sdf <- withColumn(sdf, "xWidth", lit(12L))
+sdf <- withColumn(sdf, "yWidth", lit(6L))
+sdf <- withColumn(sdf, "xSize", lit(0.1))
+sdf <- withColumn(sdf, "ySize", lit(0.1))
+sdf <- withColumn(sdf, "noData", lit(-9999.0))
+sdf <- withColumn(sdf, "tile", rst_dtmfromgeoms(
+column("masspoints"), column("breaklines"), lit(0.0), lit(0.01), column("splitPointFinder"),
+column("origin"), column("xWidth"), column("yWidth"), column("xSize"), column("ySize"), column("noData")
+))
+expect_equal(SparkR::count(sdf), 1)
 })

R/sparkR-mosaic/sparkrMosaic/tests/testthat/testVectorFunctions.R

@@ -93,4 +93,47 @@ test_that("aggregate vector functions behave as intended", {
   expect_true(first(sdf.intersection)$comparison_intersects)
   expect_true(first(sdf.intersection)$comparison_intersection)
 
-})
+})
+
+test_that("triangulation / interpolation functions behave as intended", {
+sdf <- createDataFrame(
+  data.frame(
+    wkt = c(
+      "POINT Z (3 2 1)",
+      "POINT Z (2 1 0)",
+      "POINT Z (1 3 3)",
+      "POINT Z (0 2 2)"
+    )
+  )
+)
+
+sdf <- agg(groupBy(sdf), masspoints = collect_list(column("wkt")))
+sdf <- withColumn(sdf, "breaklines", expr("array('LINESTRING EMPTY')"))
+triangulation_sdf <- withColumn(sdf, "triangles", st_triangulate(column("masspoints"), column("breaklines"), lit(0.0), lit(0.01), lit("NONENCROACHING")))
+cache(triangulation_sdf)
+expect_equal(SparkR::count(triangulation_sdf), 2)
+expected <- c("POLYGON Z((0 2 2, 2 1 0, 1 3 3, 0 2 2))", "POLYGON Z((1 3 3, 2 1 0, 3 2 1, 1 3 3))")
+expect_contains(expected, first(triangulation_sdf)$triangles)
+
+interpolation_sdf <- sdf
+interpolation_sdf <- withColumn(interpolation_sdf, "origin", st_geomfromwkt(lit("POINT (0.55 1.75)")))
+interpolation_sdf <- withColumn(interpolation_sdf, "xWidth", lit(12L))
+interpolation_sdf <- withColumn(interpolation_sdf, "yWidth", lit(6L))
+interpolation_sdf <- withColumn(interpolation_sdf, "xSize", lit(0.1))
+interpolation_sdf <- withColumn(interpolation_sdf, "ySize", lit(0.1))
+interpolation_sdf <- withColumn(interpolation_sdf, "interpolated", st_interpolateelevation(
+  column("masspoints"),
+  column("breaklines"),
+  lit(0.01),
+  lit(0.01),
+  lit("NONENCROACHING"),
+  column("origin"),
+  column("xWidth"),
+  column("yWidth"),
+  column("xSize"),
+  column("ySize")
+))
+cache(interpolation_sdf)
+expect_equal(SparkR::count(interpolation_sdf), 6 * 12)
+expect_contains(collect(interpolation_sdf)$interpolated, "POINT Z(1.6 1.8 1.2)")
+})

R/sparklyr-mosaic/sparklyrMosaic/DESCRIPTION

@@ -8,7 +8,7 @@ Description: This package extends sparklyr to bring the Databricks Mosaic for ge
 License: Databricks
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Collate:
     'enableGDAL.R'
     'enableMosaic.R'