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Contract: pyramids

Version 1. Multi resolution copies of rasters and point clouds made by the ras-pyramid and pc-pyramid commands, read by moraine.cli.view, moraine info and moraine quicklook (decision 0007).

Marker

0.zarr carries the attribute moraine_pyramid = {"version": 1, "kind": "raster" | "point cloud", "method": ..., "stats": {...}}. Readers reject versions newer than they support. Pyramids made before the marker existed are recognized by level 1 being half the size of level 0.

method (optional, absent in pyramids made before it existed) says how each level is made from the finer one: "decimate" (the default of rasters: every 2nd pixel) or "mean" (the mean of the 2 x 2 blocks over the finite pixels) for rasters, "first" (the default: the first cell with a point of each 2 x 2 block) or "mean" (the mean of the cells with points) for point clouds. A pyramid without method is decimate / first.

stats (optional, written since the statistics are computed when the pyramid is built) are the statistics of all the data (the points of a point cloud pyramid): nan_fraction, min, max, mean, std (exact), p01, p50, p99 (of a regular sample of at most 2**23 finite values) and warnings; for complex data the value fields describe the amplitude and are named amplitude_min, ...; for boolean data only true_fraction. The optional stats.zarr, shape (*channels, 8) float64 with the attribute columns (nan_fraction, min, max, mean, std, p01, p50, p99), has the same statistics of every channel (image, pair) of a stack, nan where a channel has no finite value.

Raster pyramid (ras-pyramid)

<dir>/
├── 0.zarr        the raster itself, shape (nlines, width[, n])
├── 1.zarr        every 2nd pixel of 0
├── ...
├── L.zarr        L = floor(log2(min(nlines, width))), at least 2 pixels per side
└── stats.zarr    per channel statistics (see the marker above)
  • Level l has shape (ceil(nlines / 2**l), ceil(width / 2**l)[, n]). With method decimate it is ras[::2**l, ::2**l], same dtype; with method mean every cell is the mean of its 2**l x 2**l block of the data over the finite pixels (nan where all are nan; complex data averaged as complex numbers), same dtype for floating point and complex data, float32 for integer and boolean data.
  • Chunks are (chunks[0], chunks[1], 1, ...) (default (256, 256)).

Point cloud pyramid (pc-pyramid)

<dir>/
├── bounds.toml   bounds = [x0, y0, xm, ym] of the rendered grid
├── x.zarr, y.zarr   coordinates of the points, (n_points,)
├── pc.zarr       the point cloud data, (n_points[, n])
├── 0.zarr ...    the points rasterized on a grid of `ras_resolution`, level l with cell size ras_resolution * 2**l
├── idx_0.zarr ...   per level, the index of the point shown in each cell, -1 for empty cells
├── rtree.zarr    bounding box tree of the points (`HilbertRtree`): (n_nodes, 4) float64, [x0, y0, xm, ym] of
│                 each node, `page_size` (points per leaf) and `n_points` in its attributes; optional, readers
│                 build it from x.zarr / y.zarr when a pyramid has none
└── stats.zarr    per channel statistics of the points (see the marker above)
  • Rows of the grid are y, columns x, like the rasters.
  • Cell (i, j) of level 0 is centred at (x0 + j * ras_resolution, y0 + i * ras_resolution) of bounds; every point is in the cell of its nearest centre and the grid reaches the cells of the largest coordinates, so bounds = [min x, min y, x0 + (width - 1) * ras_resolution, y0 + (nlines - 1) * ras_resolution] and points in different cells never share one. Pyramids made before this was fixed may have the points of the last line or column merged into the previous one.
  • Cells without points are nan in l.zarr and -1 in idx_l.zarr; the cells have the dtype of the points for floating point and complex data and are float32 for integer and boolean data.
  • idx_l keeps the first non empty cell of each 2 x 2 block for the next level. With method first, l.zarr is the value of that cell; with method mean, the mean of the non empty cells of the block (over the points of the finer levels: the mean of the points of the 2**l x 2**l block of level 0 cells).