288 lines
12 KiB
Python
288 lines
12 KiB
Python
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#!/usr/bin/env python3
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###############################################################################
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# $Id: gdal2xyz.py 2be8649aadb3f869590306cd5a18a3387a650581 2021-04-23 12:08:46 +0300 Idan Miara $
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#
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# Project: GDAL
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# Purpose: Script to translate GDAL supported raster into XYZ ASCII
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# point stream.
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# Author: Frank Warmerdam, warmerdam@pobox.com
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#
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###############################################################################
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# Copyright (c) 2002, Frank Warmerdam <warmerdam@pobox.com>
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# Copyright (c) 2020-2021, Idan Miara <idan@miara.com>
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#
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# Permission is hereby granted, free of charge, to any person obtaining a
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# copy of this software and associated documentation files (the "Software"),
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# to deal in the Software without restriction, including without limitation
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# the rights to use, copy, modify, merge, publish, distribute, sublicense,
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# and/or sell copies of the Software, and to permit persons to whom the
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# Software is furnished to do so, subject to the following conditions:
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#
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# The above copyright notice and this permission notice shall be included
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# in all copies or substantial portions of the Software.
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#
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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# DEALINGS IN THE SOFTWARE.
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###############################################################################
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import sys
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import textwrap
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from argparse import RawDescriptionHelpFormatter
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from numbers import Number, Real
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from typing import Optional, Union, Sequence, Tuple
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import numpy as np
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from osgeo import gdal
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from osgeo_utils.auxiliary.base import PathLikeOrStr
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from osgeo_utils.auxiliary.progress import get_progress_callback, OptionalProgressCallback
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from osgeo_utils.auxiliary.util import PathOrDS, get_bands, open_ds
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from osgeo_utils.auxiliary.numpy_util import GDALTypeCodeAndNumericTypeCodeFromDataSet
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from osgeo_utils.auxiliary.gdal_argparse import GDALArgumentParser
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def gdal2xyz(srcfile: PathOrDS, dstfile: PathLikeOrStr = None,
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srcwin: Optional[Sequence[int]] = None,
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skip: Union[int, Sequence[int]] = 1,
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band_nums: Optional[Sequence[int]] = None, delim: str = ' ',
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skip_nodata: bool = False,
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src_nodata: Optional[Union[Sequence, Number]] = None, dst_nodata: Optional[Union[Sequence, Number]] = None,
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return_np_arrays: bool = False, pre_allocate_np_arrays: bool = True,
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progress_callback: OptionalProgressCallback = ...) -> Optional[Tuple]:
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"""
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translates a raster file (or dataset) into xyz format
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skip - how many rows/cols to skip each iteration
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srcwin (xoff, yoff, xsize, ysize) - Selects a subwindow from the source image for copying based on pixel/line location.
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band_nums - selected input bands to process, None to process all.
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delim - the delimiter to use between values in a line
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skip_nodata - Exclude the output lines with nodata value (as determined by srcnodata)
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src_nodata - The nodata value of the dataset (for skipping or replacing)
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default (`None`) - Use the dataset NoDataValue;
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`Sequence`/`Number` - use the given nodata value (per band or per dataset).
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dst_nodata - Replace source nodata with a given nodata. Has an effect only if not setting `-skipnodata`
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default(`None`) - use srcnodata, no replacement;
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`Sequence`/`Number` - replace the `srcnodata` with the given nodata value (per band or per dataset).
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srcfile - The source dataset filename or dataset object
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dstfile - The output dataset filename; for dstfile=None - if return_np_arrays=False then output will be printed to stdout
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return_np_arrays - return numpy arrays of the result, otherwise returns None
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pre_allocate_np_arrays - pre-allocated result arrays.
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Should be faster unless skip_nodata and the input is very sparse thus most data points will be skipped.
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progress_callback - progress callback function. use None for quiet or Ellipsis for using the default callback
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"""
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result = None
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progress_callback = get_progress_callback(progress_callback)
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# Open source file.
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ds = open_ds(srcfile, access_mode=gdal.GA_ReadOnly)
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if ds is None:
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raise Exception(f'Could not open {srcfile}.')
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bands = get_bands(ds, band_nums)
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band_count = len(bands)
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gt = ds.GetGeoTransform()
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# Collect information on all the source files.
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if srcwin is None:
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srcwin = (0, 0, ds.RasterXSize, ds.RasterYSize)
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dt, np_dt = GDALTypeCodeAndNumericTypeCodeFromDataSet(ds)
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# Open the output file.
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if dstfile is not None:
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dst_fh = open(dstfile, 'wt')
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elif return_np_arrays:
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dst_fh = None
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else:
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dst_fh = sys.stdout
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if dst_fh:
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if dt == gdal.GDT_Int32 or dt == gdal.GDT_UInt32:
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band_format = (("%d" + delim) * len(bands)).rstrip(delim) + '\n'
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else:
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band_format = (("%g" + delim) * len(bands)).rstrip(delim) + '\n'
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# Setup an appropriate print format.
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if abs(gt[0]) < 180 and abs(gt[3]) < 180 \
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and abs(ds.RasterXSize * gt[1]) < 180 \
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and abs(ds.RasterYSize * gt[5]) < 180:
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frmt = '%.10g' + delim + '%.10g' + delim + '%s'
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else:
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frmt = '%.3f' + delim + '%.3f' + delim + '%s'
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if isinstance(src_nodata, Number):
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src_nodata = [src_nodata] * band_count
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elif src_nodata is None:
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src_nodata = list(band.GetNoDataValue() for band in bands)
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if None in src_nodata:
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src_nodata = None
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if src_nodata is not None:
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src_nodata = np.asarray(src_nodata, dtype=np_dt)
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if isinstance(dst_nodata, Number):
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dst_nodata = [dst_nodata] * band_count
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if (dst_nodata is None) or (None in dst_nodata) or (src_nodata is None):
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dst_nodata = None
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if dst_nodata is not None:
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dst_nodata = np.asarray(dst_nodata, dtype=np_dt)
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skip_nodata = skip_nodata and (src_nodata is not None)
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replace_nodata = (not skip_nodata) and (dst_nodata is not None)
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process_nodata = skip_nodata or replace_nodata
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if isinstance(skip, Sequence):
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x_skip, y_skip = skip
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else:
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x_skip = y_skip = skip
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x_off, y_off, x_size, y_size = srcwin
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bands_count = len(bands)
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nXBlocks = (x_size - x_off) // x_skip
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nYBlocks = (y_size - y_off) // y_skip
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progress_end = nXBlocks * nYBlocks
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progress_curr = 0
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progress_prev = -1
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progress_parts = 100
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if return_np_arrays:
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size = progress_end if pre_allocate_np_arrays else 0
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all_geo_x = np.empty(size)
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all_geo_y = np.empty(size)
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all_data = np.empty((size, band_count), dtype=np_dt)
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# Loop emitting data.
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idx = 0
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for y in range(y_off, y_off + y_size, y_skip):
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size = bands_count if pre_allocate_np_arrays else 0
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data = np.empty((size, x_size), dtype=np_dt) # dims: (bands_count, x_size)
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for i_bnd, band in enumerate(bands):
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band_data = band.ReadAsArray(x_off, y, x_size, 1) # read one band line
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if pre_allocate_np_arrays:
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data[i_bnd] = band_data[0]
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else:
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data = np.append(data, band_data, axis=0)
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for x_i in range(0, x_size, x_skip):
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progress_curr += 1
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if progress_callback:
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progress_frac = progress_curr / progress_end
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progress = int(progress_frac * progress_parts)
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if progress > progress_prev:
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progress_prev = progress
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progress_callback(progress_frac)
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x_i_data = data[:, x_i] # single pixel, dims: (bands)
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if process_nodata and np.array_equal(src_nodata, x_i_data):
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if skip_nodata:
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continue
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elif replace_nodata:
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x_i_data = dst_nodata
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x = x_i + x_off
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geo_x = gt[0] + (x + 0.5) * gt[1] + (y + 0.5) * gt[2]
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geo_y = gt[3] + (x + 0.5) * gt[4] + (y + 0.5) * gt[5]
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if dst_fh:
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band_str = band_format % tuple(x_i_data)
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line = frmt % (float(geo_x), float(geo_y), band_str)
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dst_fh.write(line)
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if return_np_arrays:
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if pre_allocate_np_arrays:
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all_geo_x[idx] = geo_x
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all_geo_y[idx] = geo_y
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all_data[idx] = x_i_data
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else:
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all_geo_x = np.append(all_geo_x, geo_x)
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all_geo_y = np.append(all_geo_y, geo_y)
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all_data = np.append(all_data, [x_i_data], axis=0)
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idx += 1
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if return_np_arrays:
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nodata = None if skip_nodata else dst_nodata if replace_nodata else src_nodata
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if idx != progress_curr:
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all_geo_x = all_geo_x[:idx]
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all_geo_y = all_geo_y[:idx]
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all_data = all_data[:idx, :]
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result = all_geo_x, all_geo_y, all_data.transpose(), nodata
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return result
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def main(argv):
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parser = GDALArgumentParser(
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formatter_class=RawDescriptionHelpFormatter,
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description=textwrap.dedent('''\
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The gdal2xyz utility can be used to translate a raster file into xyz format.
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It can be used as an alternative to gdal_translate of=xyz,
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But supporting other options, for example:
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* Select more then one band;
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* Skip or replace nodata value;
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* Return the output as numpy arrays.'''))
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parser.add_argument("-skip", dest="skip", action="store_true", default=1,
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help="How many rows/cols to skip in each iteration.")
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parser.add_argument("-srcwin", metavar=('xoff', 'yoff', 'xsize', 'ysize'), dest="srcwin", type=float, nargs=4,
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help="Selects a subwindow from the source image for copying based on pixel/line location")
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parser.add_argument("-b", "-band", "--band", dest="band_nums", metavar="band", type=int, nargs='+',
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help="Select bands from the input spectral bands for output. "
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"Bands are numbered from 1 in the order spectral bands are specified. "
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"Multiple -b switches may be used. When no -b switch is used, the first band will be used."
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"In order to use all input bands set -allbands or -b 0..")
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parser.add_argument("-allbands", "--allbands", dest="allbands", action="store_true",
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help="Select all input bands.")
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parser.add_argument("-csv", dest="delim", const=',', default=' ', action="store_const",
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help="Use comma instead of space as a delimiter.")
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parser.add_argument("-skipnodata", "--skipnodata", "-skip_nodata", dest="skip_nodata", action="store_true",
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help="Exclude the output lines with nodata value (as determined by srcnodata).")
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parser.add_argument("-srcnodata", '-nodatavalue', dest="src_nodata", type=Real, nargs='*',
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help="The nodata value of the dataset (for skipping or replacing) "
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"Default (None) - Use the dataset nodata value; "
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"Sequence/Number - Use the given nodata value (per band or per dataset).")
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parser.add_argument("-dstnodata", dest="dst_nodata", type=Real, nargs='*',
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help="Replace source nodata with a given nodata. "
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"Has an effect only if not setting -skipnodata. "
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"Default(None) - Use srcnodata, no replacement; "
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"Sequence/Number - Replace the srcnodata with the given nodata value "
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"(per band or per dataset).")
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parser.add_argument("srcfile", metavar="src_dataset", type=str,
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help="The source dataset name. It can be either file name, "
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"URL of data source or subdataset name for multi-dataset files.")
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parser.add_argument("dstfile", metavar="dst_dataset", type=str,
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help="The destination file name.")
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args = parser.parse_args(argv[1:])
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if args.allbands:
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args.band_nums = None
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elif not args.band_nums:
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args.band_nums = 1
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kwargs = vars(args)
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del kwargs["allbands"]
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try:
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return gdal2xyz(**kwargs)
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except IOError as e:
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print(e)
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return 1
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if __name__ == '__main__':
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sys.exit(main(sys.argv))
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