gdal-summarize

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Summarization of rasters across bands in Python with GDAL

gdal-summarize 최신버젼 다운로드

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# gdal-summarize

The goal of `gdal-summarize.py` is to summarize raster data across
layers. There are two common use cases for this tool. The first is
calculating a cell-wise summary across the bands of a raster file
(e.g. a GeoTIFF). For example, given a multi-band input GeoTIFF file
`input.tif`, to calculate the cell-wise mean of the first three bands
use:

``` bash
gdal-summarize.py input.tif --bands 1 2 3 --outfile output.tif
```

Alternatively, to compute the cell-wise mean across multiple GeoTIFF
files (`input1.tif`, `input2.tif`, and `input3.tif`) use:

``` bash
gdal-summarize.py input1.tif input2.tif input3.tif --outfile output.tif
```

If these input files have multiple bands, the default behavior is to
summarize them across the **first** band of each file; however, the
`--bands` argument can override this behavior:

``` bash
# summarize across the second band of each file
gdal-summarize.py input1.tif input2.tif input3.tif --bands 2 --outfile output.tif
# summarize across band 1 of input1.tif and band 2 of input2.tif
gdal-summarize.py input1.tif input2.tif --bands 1 2 --outfile output.tif
```

For usage examples of `gdal-summarize.py` and a comparison with R, look
at [this
document](https://github.com/mstrimas/gdal-summarize/blob/master/raster-summarize.md)
on the GitHub repo. The code for the excellent
[`gdal_calc.py`](https://gdal.org/programs/gdal_calc.html) served as the
starting point for `gdal-summarize.py`.

## Summary Functions

The default behavior is to perform a cell-wise mean; however, other
summary functions are available via the `--function` argument:

-   `mean`: cell-wise mean across layers.
-   `median`: cell-wise median across layers.
-   `max`: cell-wise max across layers.
-   `sum`: cell-wise sum across layers.
-   `meannz`: cell-wise mean across layers after removing zeros.
-   `count`: count the number layers with non-negative value for each
    cell.
-   `richness`: count the number of layers with positive values for each
    cell.

In all cases, these functions remove missing values (i.e. NoData or NA)
prior to calculating the summary statistic. For example, the mean of the
numners, 1, 2, and NoData is 1.5. This is similar to the way
`na.rm = TRUE` works in R. I’d be happy to add additional summary
functions, just [open an
issue](https://github.com/mstrimas/gdal-summarize/issues/new/choose) or
[submit a pull
request](https://github.com/mstrimas/gdal-summarize/compare).

## Example dataset

This repository contains two example datasets for testing
`gdal-summarize.py`. The **small example**, consists of two GeoTIFF
files (`data/small1.tif` and `data/small2.tif`) each of which has two
bands with dimensions 3x3. The files are filled with count data
(i.e. non-negative integers) and contain both zeros and missing values.
These files are meant to be small enough that the correct results can be
manually calculated to help understand how the functions are working.
The data in the first file looks like this:

The **large example**, consists of two GeoTIFF files (`data/large1.tif`
and `data/large2.tif`) each of which has 9 bands with dimensions
250x250. The files are filled with simulated species occupancy
(i.e. real numbers between 0 and 1) and contain both zeros and missing
values. These files were generated using the `simulate_species()`
function from the [`prioritizr` R package](https://prioritizr.net/). The
data in the first file looks like this:

## Dependencies

`gdal-summarize.py` uses the GDAL Python 3 bindings and therefore
requires [GDAL](https://gdal.org/) be installed on your system. On Mac
OS, this can be accomplished using [homebrew](https://brew.sh/) with:

``` bash
brew install gdal
```

## Getting Help

Use `gdal-summarize.py -h` to get help and usage guidelines for this
tool:

``` bash
usage: gdal-summarize.py [-h] --outfile OUTFILE [--bands BANDS [BANDS ...]] [--function {mean,median,max,sum,meannz,count,richness}]
                         [--block_size BLOCK_SIZE BLOCK_SIZE] [--nrows NROWS] [--quiet] [--overwrite]
                         files [files ...]

Summarize a set of rasters layers.

positional arguments:
  files                 input raster file(s)

optional arguments:
  -h, --help            show this help message and exit
  --outfile OUTFILE, -o OUTFILE
                        output raster
  --bands BANDS [BANDS ...], -b BANDS [BANDS ...]
                        bands to summarize. single file: bands in this file to
                        summarize (default all bands); multiple files: bands
                        in corresponding files to summarize (default = 1)
  --function {mean,median,max,sum,meannz,count,richness}, -f {mean,median,max,sum,meannz,count,richness}
                        summarization function (default = 'mean')
  --block_size BLOCK_SIZE BLOCK_SIZE, -s BLOCK_SIZE BLOCK_SIZE
                        x and y dimensions of blocks to process (default based
                        on input)
  --nrows NROWS, -n NROWS
                        number of rows to process in a single block
                        (block_size ignored if provided)
  --overwrite, -w       overwrite existing file
  --creation-option CREATION_OPTIONS, --co CREATION_OPTIONS
                        passes one or more creation options to the output
                        format driver multiple
  --quiet, -q           supress messages
```

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