rusterize 0.1.0__tar.gz → 0.1.1__tar.gz
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- {rusterize-0.1.0 → rusterize-0.1.1}/.github/workflows/CI.yml +0 -3
- rusterize-0.1.1/.github/workflows/test-compile.yml +148 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/Cargo.lock +90 -67
- {rusterize-0.1.0 → rusterize-0.1.1}/Cargo.toml +1 -1
- {rusterize-0.1.0 → rusterize-0.1.1}/PKG-INFO +38 -29
- {rusterize-0.1.0 → rusterize-0.1.1}/README.md +30 -21
- rusterize-0.1.1/img/plot.png +0 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/pyproject.toml +1 -1
- rusterize-0.1.1/python/rusterize/core.py +107 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/src/geo_validate.rs +8 -3
- {rusterize-0.1.0 → rusterize-0.1.1}/src/structs/raster.rs +33 -17
- rusterize-0.1.0/python/rusterize/core.py +0 -80
- {rusterize-0.1.0 → rusterize-0.1.1}/.gitignore +0 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/LICENSE +0 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/python/rusterize/__init__.py +0 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/rust-toolchain.toml +0 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/src/allocator.rs +0 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/src/edgelist.rs +0 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/src/lib.rs +0 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/src/pixel_functions.rs +0 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/src/rasterize_polygon.rs +0 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/src/structs/edge.rs +0 -0
- {rusterize-0.1.0 → rusterize-0.1.1}/src/structs/xarray.rs +0 -0
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Version: 0.1.
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Summary: High performance rasterization tool for Python
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Summary: High performance rasterization tool for Python built in Rust
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# rusterize
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High performance rasterization tool for
|
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for R. This version ports it to Python with a Rust backend.
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High performance rasterization tool for Python built in Rust. This
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repository is heavily based on the [fasterize](https://github.com/ecohealthalliance/fasterize.git) package built in C++
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for R. This version ports it to Python with a Rust backend, with some useful improvements.
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expr min lq mean median uq max neval
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|
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# Comparison with other tools
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While `rusterize` is fast, there are other very fast solutions out there, including
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1
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# rusterize
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2
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|
|
3
|
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High performance rasterization tool for
|
|
4
|
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repository is heavily based on the [
|
|
5
|
-
for R. This version ports it to Python with a Rust backend.
|
|
3
|
+
High performance rasterization tool for Python built in Rust. This
|
|
4
|
+
repository is heavily based on the [fasterize](https://github.com/ecohealthalliance/fasterize.git) package built in C++
|
|
5
|
+
for R. This version ports it to Python with a Rust backend, with some useful improvements.
|
|
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6
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Functionally, it takes an input [geopandas](https://geopandas.org/en/stable/)
|
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|
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|
|
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|
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|
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@@ -25,7 +25,7 @@ package. For this to work, you’ll need to have [Rust](https://www.rust-lang.or
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installed.
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# Clone repo
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30
|
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|
|
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|
|
@@ -44,22 +44,26 @@ maturin develop --profile dist-release
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|
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|
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``` python
|
|
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|
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# gdf = <import datasets as needed>
|
|
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51
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# rusterize
|
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53
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rusterize(gdf,
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(30, 30),
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|
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|
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|
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by="by",
|
|
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+
fun="sum",
|
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+
background=0)
|
|
59
61
|
```
|
|
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62
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|
|
61
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- `gdf`: geopandas dataframe to rasterize
|
|
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- `res`: tuple of (xres, yres) for
|
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- `res`: tuple of (xres, yres) for desired resolution
|
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- `out_shape`: tuple of (nrows, ncols) for desired output shape
|
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- `extent`: tuple of (xmin, ymin, xmax, ymax) for desired output extent
|
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- `field`: field to rasterize. Default is None (a value of `1` is rasterized).
|
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|
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|
|
@@ -67,10 +71,16 @@ rusterize(gdf,
|
|
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`last`. Available options are `sum`, `first`, `last`, `min`, `max`, `count`, or `any`
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from the polygons and is not modified, unless you specify a resolution value. If you only specify an output
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shape, the extent is maintained. This mimics the logics of `gdal_rasterize`.
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returns an array that is
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returns an array that is converted to a xarray on the Python side
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for simpliicty.
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**
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datasets.
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**rusterize** is fast! Let’s try it on small and large datasets.
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``` python
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[pytest-benchmark](https://pytest-benchmark.readthedocs.io/en/stable/):
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```
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``` r
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```
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```
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```
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expr min lq mean median uq max neval
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datasets? This is a benchmark with 350K+ geometries rasterized at 30
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meters (20 rounds) with no field value and pixel function `sum`.
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```
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```
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# rusterize
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--------------------------------------------- benchmark: 1 tests --------------------------------------------
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Name (time in s) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations
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# Comparison with other tools
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While `rusterize` is fast, there are other very fast solutions out there, including
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While `rusterize` is fast, there are other very fast solutions out there, including:
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Binary file
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[project]
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name = "rusterize"
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-
description = "High performance rasterization tool for Python
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+
description = "High performance rasterization tool for Python built in Rust"
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readme = "README.md"
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requires-python = ">=3.10"
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license = {file = "LICENSE"}
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@@ -0,0 +1,107 @@
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from __future__ import annotations
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+
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from types import NoneType
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from typing import Any, Dict, Optional, Tuple, Union
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import polars as pl
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from pandas import DataFrame
|
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import rioxarray
|
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from xarray import DataArray
|
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from .rusterize import _rusterize
|
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+
|
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+
def rusterize(gdf: DataFrame,
|
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+
res: Optional[Union[Tuple[int, ...], Tuple[float, ...]]] = None,
|
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|
+
out_shape: Optional[Union[Tuple[int, ...]]] = None,
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extent: Optional[Union[Tuple[int, ...], Tuple[float, ...]]] = None,
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field: Optional[str] = None,
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by: Optional[str] = None,
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fun: str = "last",
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background: Optional[Union[int, float]] = None,
|
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) -> Dict[str, Any]:
|
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"""
|
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Fast geopandas rasterization into xarray.DataArray
|
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+
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+
Args:
|
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+
:param gdf: geopandas dataframe to rasterize.
|
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+
:param res: tuple of (xres, yres) for rasterized data.
|
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|
+
:param out_shape: tuple of (nrows, ncols) for regularized output shape.
|
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+
:param extent: tuple of (xmin, xmax, ymin, ymax) for regularized extent.
|
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|
+
:param field: field to rasterize. Default is None.
|
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|
+
:param by: column to rasterize, assigns each unique value to a layer in the stack based on field. Default is None.
|
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|
+
:param fun: pixel function to use, see fasterize for options. Default is `last`.
|
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|
+
:param background: background value in final raster. Default is None.
|
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|
+
|
|
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|
+
Returns:
|
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|
+
Rasterized xarray.DataArray.
|
|
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|
+
|
|
38
|
+
Note:
|
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|
+
When any of `res`, `out_shape`, or `extent` is not provided, it is inferred from the other arguments when applicable.
|
|
40
|
+
Unless `extent` is specified, a half-pixel buffer is applied to avoid missing points on the border.
|
|
41
|
+
The logics dictating the final spatial properties of the rasterized geometries follow those of GDAL.
|
|
42
|
+
"""
|
|
43
|
+
# type checks
|
|
44
|
+
if not isinstance(gdf, DataFrame):
|
|
45
|
+
raise TypeError("Must pass a valid geopandas dataframe.")
|
|
46
|
+
if not isinstance(res, (tuple, NoneType)):
|
|
47
|
+
raise TypeError("Must pass a valid resolution tuple (x, y).")
|
|
48
|
+
if not isinstance(out_shape, (tuple, NoneType)):
|
|
49
|
+
raise TypeError("Must pass a valid output shape tuple (nrows, ncols).")
|
|
50
|
+
if not isinstance(extent, (tuple, NoneType)):
|
|
51
|
+
raise TypeError("Must pass a valid extent tuple (xmin, ymin, xmax, ymax).")
|
|
52
|
+
if not isinstance(field, (str, NoneType)):
|
|
53
|
+
raise TypeError("Must pass a valid string to field.")
|
|
54
|
+
if not isinstance(by, (str, NoneType)):
|
|
55
|
+
raise TypeError("Must pass a valid string to by.")
|
|
56
|
+
if not isinstance(fun, str):
|
|
57
|
+
raise TypeError("Must pass a valid string to pixel_fn. Select only of sum, first, last, min, max, count, or any.")
|
|
58
|
+
if not isinstance(background, (int, float, NoneType)):
|
|
59
|
+
raise TypeError("Must pass a valid background type.")
|
|
60
|
+
|
|
61
|
+
# value check
|
|
62
|
+
if not res and not out_shape and not extent:
|
|
63
|
+
raise ValueError("One of `res`, `out_shape`, or `extent` must be provided.")
|
|
64
|
+
if extent and not res and not out_shape:
|
|
65
|
+
raise ValueError("Must also specify `res` or `out_shape` with extent.")
|
|
66
|
+
if res and (len(res) != 2 or any(r <= 0 for r in res) or any(not isinstance(r, (int, float)) for r in res)):
|
|
67
|
+
raise ValueError("Resolution must be 2 positive numbers.")
|
|
68
|
+
if out_shape and (len(out_shape) != 2 or any(s <= 0 for s in out_shape) or any(not isinstance(s, int) for s in out_shape)):
|
|
69
|
+
raise ValueError("Output shape must be 2 positive integers.")
|
|
70
|
+
if extent and len(extent) != 4:
|
|
71
|
+
raise ValueError("Extent must be 4 numbers (xmin, ymin, xmax, ymax).")
|
|
72
|
+
if by and not field:
|
|
73
|
+
raise ValueError("If by is specified, field must also be specified.")
|
|
74
|
+
|
|
75
|
+
# defaults
|
|
76
|
+
_res = res if res else (0, 0)
|
|
77
|
+
_shape = out_shape if out_shape else (0, 0)
|
|
78
|
+
(_bounds, has_extent) = (extent, True) if extent else (gdf.total_bounds, False)
|
|
79
|
+
|
|
80
|
+
# RasterInfo
|
|
81
|
+
raster_info = {
|
|
82
|
+
"xmin": _bounds[0],
|
|
83
|
+
"ymin": _bounds[1],
|
|
84
|
+
"xmax": _bounds[2],
|
|
85
|
+
"ymax": _bounds[3],
|
|
86
|
+
"xres": _res[0],
|
|
87
|
+
"yres": _res[1],
|
|
88
|
+
"nrows": _shape[0],
|
|
89
|
+
"ncols": _shape[1],
|
|
90
|
+
"has_extent": has_extent
|
|
91
|
+
}
|
|
92
|
+
|
|
93
|
+
# extract columns of interest and convert to polars
|
|
94
|
+
cols = list(set([col for col in (field, by) if col]))
|
|
95
|
+
df = pl.from_pandas(gdf[cols]) if cols else None
|
|
96
|
+
|
|
97
|
+
# rusterize
|
|
98
|
+
r = _rusterize(
|
|
99
|
+
gdf.geometry,
|
|
100
|
+
raster_info,
|
|
101
|
+
fun,
|
|
102
|
+
df,
|
|
103
|
+
field,
|
|
104
|
+
by,
|
|
105
|
+
background
|
|
106
|
+
)
|
|
107
|
+
return DataArray.from_dict(r).rio.write_crs(gdf.crs, inplace=True)
|
|
@@ -79,10 +79,15 @@ pub fn validate_geometries(
|
|
|
79
79
|
.ok();
|
|
80
80
|
}
|
|
81
81
|
|
|
82
|
-
// update
|
|
83
|
-
|
|
84
|
-
|
|
82
|
+
// update RasterInfo spatial properties
|
|
83
|
+
if !raster_info.has_extent {
|
|
84
|
+
let bbox = bounding_rect(&geometry).unwrap();
|
|
85
|
+
println!("{:?}", bbox);
|
|
86
|
+
raster_info.update_bounds(bbox);
|
|
87
|
+
}
|
|
85
88
|
}
|
|
86
89
|
|
|
90
|
+
// update RasterInfo spatial properties
|
|
91
|
+
raster_info.update_dims();
|
|
87
92
|
(geometry, df)
|
|
88
93
|
}
|
|
@@ -20,26 +20,47 @@ pub struct RasterInfo {
|
|
|
20
20
|
pub ymax: f64,
|
|
21
21
|
pub xres: f64,
|
|
22
22
|
pub yres: f64,
|
|
23
|
+
pub has_extent: bool,
|
|
23
24
|
}
|
|
24
25
|
|
|
25
26
|
impl RasterInfo {
|
|
26
|
-
// map PyAny to RasterInfo
|
|
27
27
|
pub fn from(pyinfo: &Bound<PyAny>) -> Self {
|
|
28
|
+
// map PyAny to RasterInfo
|
|
28
29
|
let raster_info: RasterInfo = pyinfo
|
|
29
30
|
.extract()
|
|
30
31
|
.expect("Wrong mapping passed to RasterInfo struct");
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
35
|
-
|
|
32
|
+
|
|
33
|
+
raster_info
|
|
34
|
+
}
|
|
35
|
+
|
|
36
|
+
pub fn update_dims(&mut self) {
|
|
37
|
+
// extend bounds by half pixel to avoid missing points on the border
|
|
38
|
+
if !self.has_extent && self.xres != 0.0 {
|
|
39
|
+
self.xmin -= self.xres / 2.0;
|
|
40
|
+
self.xmax += self.xres / 2.0;
|
|
41
|
+
self.ymin -= self.yres / 2.0;
|
|
42
|
+
self.ymax += self.yres / 2.0;
|
|
43
|
+
}
|
|
44
|
+
|
|
45
|
+
// calculate resolution
|
|
46
|
+
if self.xres == 0.0 {
|
|
47
|
+
self.resolution();
|
|
48
|
+
}
|
|
49
|
+
|
|
50
|
+
// calculate shape
|
|
51
|
+
if self.nrows == 0 {
|
|
52
|
+
self.shape();
|
|
36
53
|
}
|
|
37
54
|
}
|
|
38
55
|
|
|
39
|
-
fn shape(&self)
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
|
|
56
|
+
fn shape(&mut self) {
|
|
57
|
+
self.nrows = ((self.ymax - self.ymin) / self.yres).round() as usize;
|
|
58
|
+
self.ncols = ((self.xmax - self.xmin) / self.xres).round() as usize;
|
|
59
|
+
}
|
|
60
|
+
|
|
61
|
+
fn resolution(&mut self) {
|
|
62
|
+
self.xres = (self.xmax - self.xmin) / self.ncols as f64;
|
|
63
|
+
self.yres = (self.ymax - self.ymin) / self.nrows as f64;
|
|
43
64
|
}
|
|
44
65
|
|
|
45
66
|
pub fn update_bounds(&mut self, rect: Rect) {
|
|
@@ -48,11 +69,6 @@ impl RasterInfo {
|
|
|
48
69
|
self.xmax = rect.max().x;
|
|
49
70
|
self.ymin = rect.min().y;
|
|
50
71
|
self.ymax = rect.max().y;
|
|
51
|
-
|
|
52
|
-
// recalculate shape
|
|
53
|
-
let (nrows, ncols) = self.shape();
|
|
54
|
-
self.nrows = nrows;
|
|
55
|
-
self.ncols = ncols;
|
|
56
72
|
}
|
|
57
73
|
|
|
58
74
|
pub fn build_raster(&self, bands: usize, background: f64) -> Array3<f64> {
|
|
@@ -66,13 +82,13 @@ impl RasterInfo {
|
|
|
66
82
|
) -> (Bound<'py, PyArray1<f64>>, Bound<'py, PyArray1<f64>>) {
|
|
67
83
|
let y_coords = Array::range(
|
|
68
84
|
self.ymax - self.yres / 2.0,
|
|
69
|
-
self.ymax - self.nrows as f64 * self.yres
|
|
85
|
+
self.ymax - self.nrows as f64 * self.yres,
|
|
70
86
|
-self.yres,
|
|
71
87
|
)
|
|
72
88
|
.into_pyarray_bound(py);
|
|
73
89
|
let x_coords = Array::range(
|
|
74
90
|
self.xmin + self.xres / 2.0,
|
|
75
|
-
self.xmin + self.ncols as f64 * self.xres
|
|
91
|
+
self.xmin + self.ncols as f64 * self.xres,
|
|
76
92
|
self.xres,
|
|
77
93
|
)
|
|
78
94
|
.into_pyarray_bound(py);
|
|
@@ -1,80 +0,0 @@
|
|
|
1
|
-
from __future__ import annotations
|
|
2
|
-
|
|
3
|
-
from typing import Any, Dict, Optional, Tuple, Union
|
|
4
|
-
|
|
5
|
-
import polars as pl
|
|
6
|
-
from pandas import DataFrame
|
|
7
|
-
import rioxarray
|
|
8
|
-
from xarray import DataArray
|
|
9
|
-
from .rusterize import _rusterize
|
|
10
|
-
|
|
11
|
-
|
|
12
|
-
def rusterize(gdf: DataFrame,
|
|
13
|
-
res: Union[Tuple[int, ...], Tuple[float, ...]],
|
|
14
|
-
field: Optional[str] = None,
|
|
15
|
-
by: Optional[str] = None,
|
|
16
|
-
fun: str = "last",
|
|
17
|
-
background: Optional[Union[int, float]] = None,
|
|
18
|
-
) -> Dict[str, Any]:
|
|
19
|
-
"""
|
|
20
|
-
Fast geopandas rasterization into xarray.DataArray
|
|
21
|
-
|
|
22
|
-
Args:
|
|
23
|
-
:param gdf: geopandas dataframe to rasterize.
|
|
24
|
-
:param res: tuple of (xres, yres) for rasterized data.
|
|
25
|
-
:param field: field to rasterize. Default is None.
|
|
26
|
-
:param by: column to rasterize, assigns each unique value to a layer in the stack based on field. Default is None.
|
|
27
|
-
:param fun: pixel function to use, see fasterize for options. Default is `last`.
|
|
28
|
-
:param background: background value in final raster. Default is None.
|
|
29
|
-
|
|
30
|
-
Returns:
|
|
31
|
-
Dictionary containing rasterized geometries and spatial attributes to build a xarray.DataArray.
|
|
32
|
-
"""
|
|
33
|
-
# type checks
|
|
34
|
-
if not isinstance(gdf, DataFrame):
|
|
35
|
-
raise TypeError("Must pass a valid geopandas dataframe.")
|
|
36
|
-
if not isinstance(field, (str, type(None))):
|
|
37
|
-
raise TypeError("Must pass a valid string to field.")
|
|
38
|
-
if not isinstance(by, (str, type(None))):
|
|
39
|
-
raise TypeError("Must pass a valid string to by.")
|
|
40
|
-
if not isinstance(res, tuple):
|
|
41
|
-
raise TypeError("Must pass a valid resolution tuple (x, y).")
|
|
42
|
-
if not isinstance(fun, str):
|
|
43
|
-
raise TypeError("Must pass a valid string to pixel_fn. Select only of sum, first, last, min, max, count, or any.")
|
|
44
|
-
if not isinstance(background, (int, float, type(None))):
|
|
45
|
-
raise TypeError("Must pass a valid background type.")
|
|
46
|
-
|
|
47
|
-
# value check
|
|
48
|
-
if by and not field:
|
|
49
|
-
raise ValueError("If by is specified, field must also be specified.")
|
|
50
|
-
if len(res) != 2 or any((res[0], res[1])) <= 0 or not isinstance(res[0], type(res[1])):
|
|
51
|
-
raise ValueError("Must pass valid resolution tuple of values of consistent dtype.")
|
|
52
|
-
|
|
53
|
-
# RasterInfo
|
|
54
|
-
bounds = gdf.total_bounds
|
|
55
|
-
raster_info = {
|
|
56
|
-
"xmin": bounds[0],
|
|
57
|
-
"ymin": bounds[1],
|
|
58
|
-
"xmax": bounds[2],
|
|
59
|
-
"ymax": bounds[3],
|
|
60
|
-
"xres": res[0],
|
|
61
|
-
"yres": res[1],
|
|
62
|
-
"nrows": 0,
|
|
63
|
-
"ncols": 0
|
|
64
|
-
}
|
|
65
|
-
|
|
66
|
-
# extract columns of interest and convert to polars
|
|
67
|
-
cols = list(set([col for col in (field, by) if col]))
|
|
68
|
-
df = pl.from_pandas(gdf[cols]) if cols else None
|
|
69
|
-
|
|
70
|
-
# rusterize
|
|
71
|
-
r = _rusterize(
|
|
72
|
-
gdf.geometry,
|
|
73
|
-
raster_info,
|
|
74
|
-
fun,
|
|
75
|
-
df,
|
|
76
|
-
field,
|
|
77
|
-
by,
|
|
78
|
-
background
|
|
79
|
-
)
|
|
80
|
-
return DataArray.from_dict(r).rio.write_crs(gdf.crs, inplace=True)
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|