HDF5 -- Hierarchical Data Format Release 5 (HDF5)

Driver short name

HDF5

Driver short name

HDF5Image

Build dependencies

libhdf5

This driver intended for HDF5 file formats importing.

Starting with GDAL 3.7, the driver can parse HDF-EOS5 encoded grid and swath metadata to establish projection and geotransform (for grids), and geolocation array (for swaths)

Driver capabilities

Supports Georeferencing

This driver supports georeferencing

Added in version 2.4:

Supports VirtualIO

This driver supports virtual I/O operations (/vsimem/, etc.)

Multiple Image Handling (Subdatasets)

Hierarchical Data Format is a container for several different datasets. For data storing. HDF contains multidimensional arrays filled by data. One HDF file may contain several arrays. They may differ in size, number of dimensions.

The first step is to get a report of the components images (arrays) in the file using gdalinfo, and then to import the desired images using gdal_translate. The gdalinfo utility lists all multidimensional subdatasets from the input HDF file. The name of individual images (subdatasets) are assigned to the SUBDATASET_n_NAME metadata item. The description for each image is found in the SUBDATASET_n_DESC metadata item. For HDF5 images the subdataset names will be formatted like this:

HDF5:file_name:subdataset

where:

file_name is the name of the input file, and

subdataset is the dataset name of the array to use (for internal use in GDAL).

Starting with GDAL 3.10, specifying the -if HDF5 option to command line utilities accepting it, or HDF5 as the only value of the papszAllowedDrivers of GDALOpenEx(), also forces the driver to recognize the passed filename, when it is not using subdataset syntax (it can typically be used to force open a netCDF file that would be nominally recognized by the netCDF driver).

On the second step you should provide this name for gdalinfo or gdal_translate for actual reading of the data.

For example, we want to read data from the OMI/Aura Ozone (O3) dataset:

$ gdalinfo OMI-Aura_L2-OMTO3_2005m0326t2307-o03709_v002-2005m0428t201311.he5
Driver: HDF5/Hierarchical Data Format Release 5
Size is 512, 512
Coordinate System is `'

Subdatasets:
  SUBDATASET_1_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/APrioriLayerO3
  SUBDATASET_1_DESC=[1496x60x11] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/APrioriLayerO3 (32-bit floating-point)
  SUBDATASET_2_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/AlgorithmFlags
  SUBDATASET_2_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/AlgorithmFlags (8-bit unsigned character)
  SUBDATASET_3_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/CloudFraction
  SUBDATASET_3_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/CloudFraction (32-bit floating-point)
  SUBDATASET_4_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/CloudTopPressure
  SUBDATASET_4_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/CloudTopPressure (32-bit floating-point)
  SUBDATASET_5_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/ColumnAmountO3
  SUBDATASET_5_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/ColumnAmountO3 (32-bit floating-point)
  SUBDATASET_6_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/LayerEfficiency
  SUBDATASET_6_DESC=[1496x60x11] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/LayerEfficiency (32-bit floating-point)
  SUBDATASET_7_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/NValue
  SUBDATASET_7_DESC=[1496x60x12] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/NValue (32-bit floating-point)
  SUBDATASET_8_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/O3BelowCloud
  SUBDATASET_8_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/O3BelowCloud (32-bit floating-point)
  SUBDATASET_9_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/QualityFlags
  SUBDATASET_9_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/QualityFlags (16-bit unsigned integer)
  SUBDATASET_10_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/Reflectivity331
  SUBDATASET_10_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/Reflectivity331 (32-bit floating-point)
  SUBDATASET_11_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/Reflectivity360
  SUBDATASET_11_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/Reflectivity360 (32-bit floating-point)
  SUBDATASET_12_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/Residual
  SUBDATASET_12_DESC=[1496x60x12] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/Residual (32-bit floating-point)
  SUBDATASET_13_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/ResidualStep1
  SUBDATASET_13_DESC=[1496x60x12] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/ResidualStep1 (32-bit floating-point)
  SUBDATASET_14_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/ResidualStep2
  SUBDATASET_14_DESC=[1496x60x12] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/ResidualStep2 (32-bit floating-point)
  SUBDATASET_15_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/SO2index
  SUBDATASET_15_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/SO2index (32-bit floating-point)
  SUBDATASET_16_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/Sensitivity
  SUBDATASET_16_DESC=[1496x60x12] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/Sensitivity (32-bit floating-point)
  SUBDATASET_17_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/StepOneO3
  SUBDATASET_17_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/StepOneO3 (32-bit floating-point)
  SUBDATASET_18_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/StepTwoO3
  SUBDATASET_18_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/StepTwoO3 (32-bit floating-point)
  SUBDATASET_19_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/TerrainPressure
  SUBDATASET_19_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/TerrainPressure (32-bit floating-point)
  SUBDATASET_20_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/UVAerosolIndex
  SUBDATASET_20_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/UVAerosolIndex (32-bit floating-point)
  SUBDATASET_21_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/dN_dR
  SUBDATASET_21_DESC=[1496x60x12] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/dN_dR (32-bit floating-point)
  SUBDATASET_22_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/dN_dT
  SUBDATASET_22_DESC=[1496x60x12] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Data_Fields/dN_dT (32-bit floating-point)
  SUBDATASET_23_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/GroundPixelQualityFlags
  SUBDATASET_23_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/GroundPixelQualityFlags (16-bit unsigned integer)
  SUBDATASET_24_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/Latitude
  SUBDATASET_24_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/Latitude (32-bit floating-point)
  SUBDATASET_25_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/Longitude
  SUBDATASET_25_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/Longitude (32-bit floating-point)
  SUBDATASET_26_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/RelativeAzimuthAngle
  SUBDATASET_26_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/RelativeAzimuthAngle (32-bit floating-point)
  SUBDATASET_27_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/SolarAzimuthAngle
  SUBDATASET_27_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/SolarAzimuthAngle (32-bit floating-point)
  SUBDATASET_28_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/SolarZenithAngle
  SUBDATASET_28_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/SolarZenithAngle (32-bit floating-point)
  SUBDATASET_29_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/TerrainHeight
  SUBDATASET_29_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/TerrainHeight (16-bit integer)
  SUBDATASET_30_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/ViewingAzimuthAngle
  SUBDATASET_30_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/ViewingAzimuthAngle (32-bit floating-point)
  SUBDATASET_31_NAME=HDF5:"OMI-Aura_L2-OMTO3_2005m0113t0224-o02648_v002-2005m0625t035355.he5"://HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/ViewingZenithAngle
  SUBDATASET_31_DESC=[1496x60] //HDFEOS/SWATHS/OMI_Column_Amount_O3/Geolocation_Fields/ViewingZenithAngle (32-bit floating-point)
Corner Coordinates:
Upper Left  (    0.0,    0.0)
Lower Left  (    0.0,  512.0)
Upper Right (  512.0,    0.0)
Lower Right (  512.0,  512.0)
Center      (  256.0,  256.0)

Now select one of the subdatasets, described as [1645x60] CloudFraction (32-bit floating-point):

$ gdalinfo HDF5:"OMI-Aura_L2-OMTO3_2005m0326t2307-o03709_v002-2005m0428t201311.he5":CloudFraction
Driver: HDF5Image/HDF5 Dataset
Size is 60, 1645
Coordinate System is:
GEOGCS["WGS 84",
    DATUM["WGS_1984",
        SPHEROID["WGS 84",6378137,298.257223563,
            AUTHORITY["EPSG","7030"]],
        TOWGS84[0,0,0,0,0,0,0],
        AUTHORITY["EPSG","6326"]],
    PRIMEM["Greenwich",0,
        AUTHORITY["EPSG","8901"]],
    UNIT["degree",0.0174532925199433,
        AUTHORITY["EPSG","9108"]],
    AXIS["Lat",NORTH],
    AXIS["Long",EAST],
    AUTHORITY["EPSG","4326"]]
GCP Projection = GEOGCS["WGS 84",DATUM["WGS_1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],TOWGS84[0,0,0,0,0,0,0],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9108"]],AXIS["Lat",NORTH],AXIS["Long",EAST],AUTHORITY["EPSG","4326"]]
GCP[  0]: Id=, Info=
          (0.5,0.5) -> (261.575,-84.3495,0)
GCP[  1]: Id=, Info=
          (2.5,0.5) -> (240.826,-85.9928,0)
GCP[  2]: Id=, Info=
          (4.5,0.5) -> (216.754,-86.5932,0)
GCP[  3]: Id=, Info=
          (6.5,0.5) -> (195.5,-86.5541,0)
GCP[  4]: Id=, Info=
          (8.5,0.5) -> (180.265,-86.2009,0)
GCP[  5]: Id=, Info=
          (10.5,0.5) -> (170.011,-85.7315,0)
GCP[  6]: Id=, Info=
          (12.5,0.5) -> (162.987,-85.2337,0)
... 3000 GCPs are read from the file if Latitude and Longitude arrays are presents

Corner Coordinates: Upper Left ( 0.0, 0.0) Lower Left ( 0.0, 1645.0) Upper Right ( 60.0, 0.0) Lower Right ( 60.0, 1645.0) Center ( 30.0, 822.5) Band 1 Block=60x1 Type=Float32, ColorInterp=Undefined Open GDAL Datasets: 1 N DriverIsNULL 512x512x0

You may use gdal_translate for reading image bands from this dataset.

Note that you should provide exactly the contents of the line marked SUBDATASET_n_NAME to GDAL, including the HDF5: prefix.

This driver is intended only for importing remote sensing and geospatial datasets in form of raster images(2D or 3D arrays). If you want explore all data contained in HDF file you should use another tools (you can find information about different HDF tools using links at end of this page).

Georeference

There is no universal way of storing georeferencing in HDF files. However, some product types have mechanisms for saving georeferencing, and some of these are supported by GDAL. Currently supported are (subdataset_type shown in parenthesis):

• HDF5 OMI/Aura Ozone (O3) Total Column 1-Orbit L2 Swath 13x24km (Level-2 OMTO3)

• HDF-EOS5 grids (starting with GDAL 3.7)

• HDF-EOS5 swaths (starting with GDAL 3.7)

Multi-file support

Starting with GDAL 3.1, the driver supports opening datasets split over several files using the 'family' HDF5 file driver. For that, GDAL must be provided with the filename of the first part, containing in it a single '0' (zero) character, or ending with 0.h5 or 0.hdf5

Multidimensional API support

Added in version 3.1.

The HDF5 driver supports the 多次元ラスターデータモデル for reading operations.

Driver building

This driver built on top of NCSA HDF5 library, so you need to download prebuild HDF5 libraries: HDF5-1.6.4 library or higher. You also need zlib 1.2 and szlib 2.0. For windows user be sure to set the attributes writable (especially if you are using Cygwin) and that the DLLs can be located somewhere by your PATH environment variable. You may also download source code NCSA HDF Home Page (see links below).

See Also

Implemented as hdf5dataset.cpp and hdf5imagedataset.cpp.

The NCSA HDF5 Download Page at the National Center for Supercomputing Applications

The HDFView is a visual tool for browsing and editing NCSA HDF4 and HDF5 files.

Documentation to individual products, supported by this driver:

• OMTO3: OMI/Aura Ozone (O3) Total Column 1-Orbit L2 Swath 13x24km V003

• HDF-EOS5 Data Model, File Format and Library