From e0898c8c12df6fd6c9ddc6a4a7050998e42c0702 Mon Sep 17 00:00:00 2001
From: "Daniel.Frisinghelli" <daniel.frisinghelli@eurac.edu>
Date: Fri, 11 Dec 2020 15:07:14 +0100
Subject: [PATCH] Added support for hdf file format.
---
pysegcnn/core/utils.py | 174 +++++++++++++++++++++++++++++++++++++++--
1 file changed, 169 insertions(+), 5 deletions(-)
diff --git a/pysegcnn/core/utils.py b/pysegcnn/core/utils.py
index ba5f553..3a5ee0b 100644
--- a/pysegcnn/core/utils.py
+++ b/pysegcnn/core/utils.py
@@ -82,7 +82,7 @@ def img2np(path, tile_size=None, tile=None, pad=False, cval=0):
Parameters
----------
- path : `str` or `None` or :py:class:`numpy.ndarray`
+ path : `str` or :py:class:`pathlib.Path` or :py:class:`numpy.ndarray`
The image to read.
tile_size : `None` or `int`, optional
The size of a tile. The default is `None`.
@@ -113,11 +113,10 @@ def img2np(path, tile_size=None, tile=None, pad=False, cval=0):
"""
# check the type of path
- if isinstance(path, str):
- if not os.path.exists(path):
- raise FileNotFoundError('{} does not exist.'.format(path))
+ if isinstance(path, str) or isinstance(path, pathlib.Path):
+
# the image dataset as returned by gdal
- img = gdal.Open(path)
+ img = gdal.Open(str(path))
# number of bands
bands = img.RasterCount
@@ -252,6 +251,171 @@ def img2np(path, tile_size=None, tile=None, pad=False, cval=0):
return image
+def read_hdf(path, **kwargs):
+ """Read a file in Hierarchical Data Format (HDF) to a dictionary.
+
+ Parameters
+ ----------
+ path : `str` or py:class:`pathlib.Path`
+ The path to the hdf file to read.
+ **kwargs:
+ Additional keyword arguments passed to
+ :py:func:`pysegcnn.core.utils.img2np`.
+
+ Raises
+ ------
+ ValueError
+ Raised if ``path`` is not an hdf file.
+
+ Returns
+ -------
+ hdf_ds : `dict` [`str`, :py:class:`numpy.ndarray`]
+ The hdf file as a dictionary. The keys are the names of the
+ different datasets in the hdf file and the values are the corresponding
+ data as a :py:class:`numpy.ndarray`.
+
+ """
+ # check if the path points to an hdf file
+ if not str(path).endswith(('.h4', '.hdf', '.hdf4', '.hdf5', '.he2', '.h5',
+ '.he5')):
+ raise ValueError('{} is not an hdf file.'.format(path))
+
+ # read the hdf dataset
+ hdf = gdal.Open(str(path)).GetSubDatasets()
+
+ # iterate over the different subsets and store arrays in dictionary
+ hdf_ds = {}
+ for ds in hdf:
+ # name of the current dataset
+ name = ds[0].split(':')[-1]
+
+ # read the dataset to a numpy array
+ data = img2np(ds[0], **kwargs)
+
+ # store in dictionary
+ hdf_ds[name] = data
+
+ return hdf_ds
+
+
+def hdf2tifs(path, outpath=None, overwrite=False, create_stack=True, **kwargs):
+ """Convert a file in Hierarchical Data Format (HDF) to GeoTIFFs.
+
+ The GeoTIFFs share the same filename as ``path``, appended by the name of
+ the respective subdatasets.
+
+ The default (``outpath=None``) is to save the GeoTIFFs in a directory named
+ after the filename of ``path``, within the parent directory of ``path``.
+
+ Parameters
+ ----------
+ path : `str` or py:class:`pathlib.Path`
+ The path to the hdf file to convert.
+ outpath : `str` or py:class:`pathlib.Path`, optional
+ Path to save the GeoTIFF files. The default is `None`.
+ overwrite : `bool`, optional
+ Whether to overwrite existing GeoTIFF files in ``outpath``. The default
+ is `False`.
+ create_stack : `bool`, optional
+ Whether to create a GeoTIFF stack of all the subdatasets in ``path``.
+ The default is `True`.
+ **kwargs :
+ Additional keyword arguments passed to :py:func:`gdal.Translate`.
+
+ """
+ # check if the path points to an hdf file
+ path = pathlib.Path(path)
+ if not str(path).endswith(('.h4', '.hdf', '.hdf4', '.hdf5', '.he2', '.h5',
+ '.he5')):
+ raise ValueError('{} is not an hdf file.'.format(path))
+
+ # check whether an output path is defined
+ if outpath is None:
+ outpath = path.parent
+ else:
+ outpath = pathlib.Path(outpath)
+
+ # create the output directory
+ outpath = outpath.joinpath(path.stem.replace('.', '_'))
+
+ # check whether the output path exists
+ if not outpath.exists():
+ LOGGER.info('mkdir {}'.format(str(outpath)))
+ outpath.mkdir(parents=True, exist_ok=True)
+
+ # check whether the output path contains GeoTIFF files
+ tifs = [f for f in outpath.iterdir() if f.suffix in ['.tif', '.TIF']]
+
+ # check whether to overwrite existing files
+ if tifs:
+ LOGGER.info('The following files already exist in {}'
+ .format(str(outpath)))
+ LOGGER.info('\n'.join(['{}'.format(str(tif.name)) for tif in tifs])
+ )
+ if not overwrite:
+ # return if not overwriting
+ LOGGER.info('Aborting...')
+ return
+
+ # remove existing files and prepare to overwrite
+ LOGGER.info('Overwrite {}'.format(str(outpath)))
+ for tif in tifs:
+ tif.unlink()
+
+ # read the hdf dataset
+ hdf = gdal.Open(str(path)).GetSubDatasets()
+
+ # iterate over the different subdatasets in the hdf
+ for ds in hdf:
+
+ # name of the current subdataset
+ name = ds[0].split(':')[-1]
+
+ # filename of the GeoTIFF
+ tif_name = outpath.joinpath(path.name.replace(path.suffix,
+ '_{}.tif'.format(name)))
+
+ # convert hdf subdataset to GeoTIFF
+ gdal.Translate(str(tif_name), gdal.Open(ds[0]), **kwargs)
+
+ # check whether to create a GeoTIFF stack
+ if create_stack:
+ # filename for the GeoTIFF stack
+ stk = tif_name.parent.joinpath(path.name.replace(path.suffix, '.tif'))
+ LOGGER.info('Creating GeoTIFF stack: {}'.format(stk))
+
+ # generated GeoTIFF files
+ tifs = [str(f) for f in outpath.iterdir() if f.suffix in
+ ['.tif', '.TIF']]
+
+ # create stacked GeoTIFF
+ stack_tifs(str(stk), tifs)
+
+ return
+
+
+def stack_tifs(filename, tifs, **kwargs):
+ """Create a stacked GeoTIFF from a list of single-band GeoTIFFs.
+
+ Parameters
+ ----------
+ filename : `str` or py:class:`pathlib.Path`
+ The filename of the stacked GeoTIFF ending with `.tif`.
+ tifs : `list` [`str`]
+ The list of the paths to the GeoTIFF files to stack.
+ **kwargs :
+ Additional keyword arguments passed to :py:func:`gdal.Translate`.
+
+ """
+ # build virtual raster dataset
+ vrt = str(filename).replace('.tif', '.vrt')
+ vrt_ds = gdal.BuildVRT(str(vrt), tifs, separate=True)
+
+ # create GeoTIFF stack
+ gdal.Translate(str(filename), vrt_ds, **kwargs)
+
+ return
+
def is_divisible(img_size, tile_size, pad=False):
"""Check whether an image is evenly divisible into square tiles.
--
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