Profile of HDF-EOS5 Files


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Profile of HDF-EOS5 Files

  1. 1. Profile of HDF-EOS5 Files Abe Taaheri, Raytheon Information Systems Larry Klein, RS Information Systems HDF-EOS Workshop X November 2006
  2. 2. General HDF-EOS5 File Structure • HDF-EOS5 file is any valid HDF5 file that contains: – a family of global attributes called: coremetadata.X Optional data objects:  family of global attributes called: archivemetadata.X  any number of Swath, Grid, Point, ZA, and Profile data structures.  another family of global attributes: StructMetadata.X • The global attributes provide information on the structure of HDF-EOS5 file or information on the data granule that file contains. • Other optional user-added global attributes such as “PGEVersion”, “OrbitNumber”, etc. are written as HDF5 attributes into a group called “FILE ATTRIBUTES” Page 2
  3. 3. General HDF-EOS5 File Structure • coremetadata.X Used to populate searchable database tables within the ECS archives. Data users use this information to locate particular HDF-EOS5 data granules. • archivemetadata.X Represents information that, by definition, will not be searchable. Contains whatever information the file creator considers useful to be in the file, but which will not be directly accessible by ECS databases. S • StructMetadata.X Describes contents and structure of HDF-EOS file. e.g. dimensions, compression methods, geolocation, projection information, etc. that are associated with the data itself. Page 3
  4. 4. General HDF-EOS5 File Structure • An HDF-EOS5 file – can contain any number of Grid, Point, Swath, Zonal Average, and Profile data structures – has no size limits.  A file containing 1000's of objects could cause program execution slow-downs – can be hybrid, containing plain HDF5 objects for special purposes.  HDF5 objects must be accessed by the HDF5 library and not by HDF-EOS5 extensions.  will require more knowledge of file contents on the part of an applications developer or data user. Page 4
  5. 5. Swath Structure P In st ru m en t Instrument Profiles instrument takes a series of scans perpendicular to the ground track of the satellite as it moves along that ground track at h • For a typical satellite swath, an Along Track • Or a sensor measures a vertical profile, instead of scanning across the ground track Page 5
  6. 6. Swath Structure “SWATHS” group • Swath_X groups are created when swaths are created Object Attribute <SwathName>: <AttrName> “Swath_1” • Swath attributes are set as Object Attributes. Group Attribute <DataFields>: <AttrName> Data Fields • Attributes for Data, Profile, or Gelocation Fields groups are set as Group Attributes Local Attribute <FieldName>: <AttrName> •Data/Geo fields’ parent group are created when fields are defined. • Dataset related attributes set for each data field or geolocation field are called Local Attributes. They may contain attributes such as fillvalue, units, etc. Data Field.1 Data Field.n “Swath_N” Profile Fields Profile Field.1 Profile Field.n Geolocation Fields Longitude Time Latitude Colatitude HDF5 Group HDF5 Attribute HDF5 Dataset Each Data Field object can have Attributes and/or Dimension Scales Page 6
  7. 7. Swath Structure • Geolocation Fields − Geolocation fields allow the Swath to be accurately tied to particular points on the Earth’s surface. − At least a time field (“Time”) or a latitude/longitude field pair (“Latitude” and “Longitude”). “Colatitude” may be substituted for “Latitude.” − Fields must be either one- or two-dimensional − The “Time” field is always in TAI format (International Atomic Time) Field Name Data Type Format Longitude float32 or float64 DD*, range [-180.0, 180.0] Latitude float32 or float64 DD*, range [-90.0, 90.0] Colatitude float32 or float64 DD*, range [0.0, 180.0] Time float64 TAI93 [seconds until(-) / since(+) midnight, 1/1/93] * DD = Decimal Degree Page 7
  8. 8. Swath Structure • Data Fields − Fields may have up to 8 dimensions. − An “unlimited” dimension must be the first dimension (in C-order). − For all multi-dimensional fields in scan- or profile-oriented Swaths, the dimension representing the “along track” dimension must precede the dimension representing the scan or profile dimension(s) (in C-order). − Compression is selectable at the field level within a Swath. All HDF5- supported compression methods are available through the HDF-EOS5 library. The compression method is stored within the file. Subsequent use of the library will un-compress the file. As in HDF5 the data needs to be chunked before the compression is applied. − Field names: * may be up to 64 characters in length. * Any character can be used with the exception of, ",", ";", " and "/". * are case sensitive. * must be unique within a particular Swath structure. Page 8
  9. 9. Compression Codes Compression Code HDFE_COMP_NONE Value Explanation 0 No Compression 1 Run Length Encoding Compression (not supported) HDFE_COMP_NBIT 2 NBIT Compression HDFE_COMP_SKPHUFF 3 Skipping Huffman (not supported) HDFE_COMP_DEFLATE 4 gzip Compression 5 szip Compression, Compression exactly as in hardware 6 szip Compression, allowing k split = 13 Compression 7 szip Compression, entropy coding method 8 szip Compression, nearest neighbor coding method 9 szip Compression, allowing k split = 13 Compression, or entropy coding method HDFE_COMP_RLE HDFE_COMP_SZIP_CHIP HDFE_COMP_SZIP_K13 HDFE_COMP_SZIP_EC HDFE_COMP_SZIP_NN HDFE_COMP_SZIP_K13orEC For Compression the data storage must be CHUNKED first Page 9
  10. 10. Compression Codes Compression Code Value HDFE_COMP_SZIP_K13orNN Explanation 10 11 shuffling + deflate(gzip) Compression 12 shuffling + Compression exactly as in hardware 13 shuffling + allowing k split = 13 Compression 14 shuffling + entropy coding method 15 shuffling + nearest neighbor coding method 16 shuffling + allowing k split = 13 Compression, or entropy coding method 17 HDFE_COMP_SHUF_DEFLATE szip Compression, allowing k split = 13 Compression, or nearest neighbor coding method shuffling + allowing k split = 13 Compression, or nearest neighbor coding method HDFE_COMP_SHUF_SZIP_CHIP HDFE_COMP_SHUF_SZIP_K13 HDFE_COMP_SHUF_SZIP_EC HDFE_COMP_SHUF_SZIP_NN HDFE_COMP_SHUF_SZIP_K13orEC HDFE_COMP_SHUF_SZIP_K13orNN For Compression the data storage must be CHUNKED first Page 10
  11. 11. Swath Structure • Dimension maps are the glue that holds the SWATH together. They define the relationship between data fields and geolocation fields by defining, one-by-one, the relationship of each dimension of each geolocation field with the corresponding dimension in each data field. Geolocation Dimension 0 1 2 3 4 5 6 7 8 9 Mapping Offset: 1 Increment: 2 11 13 15 0 1 2 3 4 5 6 7 8 9 10 12 14 1617 1819 Data Dimension A “Normal” Dimension Map Geolocation Dimension 0 1 2 3 4 5 6 7 8 910 1112 1314 151617 1819 0 1 2 3 4 5 6 7 8 9 Data Dimension Mapping Offset: -1 Increment: -2 A “Backwards” Dimension Map Page 11
  12. 12. Grid Structure • A grid contains grid corner locations and a set of projection equations (or references to them) along with their relevant parameters. • The equations and parameters can be used to compute the latitude and longitude for any point in the grid. A Data Field in a Mercator-Projected Grid • Important features of a Grid data set: the data fields, the dimensions, and the projection A Data Field in an Interrupted Goode’s Homolosine-Projected Grid Page 12
  13. 13. Grid Structure Data Field characteristics: −Fields may have up to 8 dims − An “unlimited” dimension must be the first dimension. − Dim order in field definitions: - C: “Band, YDim, XDim” - Fortran: “XDim, YDim, Band” − Compression is selectable at the field level within a Grid. Subsequent use of the library will un-compress the file. Data needs to be tiled before the compression is applied. − Field names must be unique within a particular Grid structure and are case sensitive. They may be up to 64 characters in length. − Any character can be used with the exception of, ",", ";", " and "/". Page 13
  14. 14. Grid Structure Dimensions: • Two predefined dimensions for Data Fields: “XDim” and “YDim”. - defined when the grid is created - stored in the structure metadata. - relate data fields to each other and to the geolocation information • Fields are Two - eight dimensional many fields will need not more than three: the predefined dimensions “XDim” and “YDim” and a third dimension for depth, height, or band. Page 14
  15. 15. Grid Structure • Projection: − Is the heart of the Grid structure. − Provides a convenient way to encode geolocation information as a set of mathematical equations, capable of transforming Earth coordinates (lat/long) to X-Y coordinates on a sheet of paper − General Coordinate Transformation Package (GCTP) library contains all projection related conversions and calculations. − Supported projections: Geographic Mercator Cylindrical Equal area Transverse Mercator Hotin Oblique Mercator Sinusoidal Integerized Sinusoidal Polar Stereographic Albers Conical Equal Area Interrupted Goode’s Homolosine Lambert Azimuthal Equal Area Polyconic Universal Transverse Mercator Space Oblique Mercator Lambert Conformal Conic Page 15
  16. 16. Point Structure Lat 61.12 45.31 38.50 38.39 30.00 37.45 18.00 43.40 34.03 32.45 33.30 42.15 35.05 34.12 46.32 47.36 39.44 21.25 44.58 41.49 25.45 • Made up of a series of data records taken at [possibly] irregular time intervals and at scattered geographic locations • Loosely organized form of geolocated data supported by HDF-EOS • Level are linked by a common field name called LinkField • Usually shared info is stored in Parent level, while data values stored in Child level • The values for the LinkFiled in the Parent level must be unique Sain tto Ciao hcg LsAgls o nee Wsigo ahntn Mai im Lt a Ln o 4.9 -73 14 8.7 3.3-1.4 40 181 3.0 -70 85 7.0 2.5 -01 54 8.1 Lon -149.48 -122.41 -77.00 -90.15 -90.05 -122.26 -76.45 -79.23 -118.14 -96.48 -112.00 -71.07 -106.40 -77.56 -87.25 -122.20 -104.59 -78.00 -93.15 -87.37 -80.11 Temp(C) 15.00 17.00 24.00 27.00 22.00 25.00 27.00 30.00 25.00 32.00 30.00 28.00 30.00 28.00 30.00 32.00 31.00 28.00 32.00 28.00 19.00 Dewpt(C) 5.00 5.00 7.00 11.00 7.00 10.00 4.00 14.00 4.00 8.00 10.00 7.00 9.00 9.00 8.00 15.00 16.00 7.00 13.00 9.00 3.00 Tm Tm() ie epC 00 80 3 00 90 2 10 00 1 00 80 2 0 00 90 2 1 10 00 2 2 10 10 2 4 10 00 6 10 10 8 10 20 9 10 30 1 1 10 40 1 2 00 60 1 5 00 70 1 6 Page 16
  17. 17. Point Structure • Point structure groups are created when user creates “Point_1”, ….. • Data and Linkage groups are created automatically when the level is defined “POINTS” Group Object Attribute <SwathName>: <AttrName> “Point_1” are defined determines the (0based) level index Group Attribute <SwathName>: <AttrName> Data • FWDPOINTER Linkage will Local Attribute <SwathName>: <AttrName> • The order in which the levels not be set (acutally first one is set to (-1,-1)) if the records in Child level is not monotonic in LinkFiekd • A level can contain any number of fields and records Level 1 “Point_n” Linkag Level n FWD BCK POINTER POINTER HDF5 Group Level Data Page 17
  18. 18. ZA Structure “ZAS” group • “Zonal Average” structure is basically a swath like structure without geolocation. • The interface is designed to support data that has not associated with specific geolocation information. Object Attribute <SwathName>: <AttrName> Group Attribute <DataFields>: <AttrName> Local Attribute <FieldName>: <AttrName> “Za_1” “Za_n” Data Fields Data Field.n HDF5 Group Page 18
  19. 19. “h5dump” output of a simple HDF-EOS5 file HDF5 "Grid.he5" { GROUP "/" { GROUP "HDFEOS" { GROUP "ADDITIONAL" { GROUP "FILE_ATTRIBUTES" { } } GROUP "GRIDS" { GROUP "TMGrid" { GROUP "Data Fields" { DATASET "Voltage" { DATATYPE H5T_IEEE_F32BE DATASPACE SIMPLE { ( 5, 7 ) / ( 5, 7 ) } DATA { (0,0): -1.11111,-1.11111,-1.11111,-1.11111,-1.11111, (0,5): -1.11111,-1.11111, ……………………………….. (4,0): -1.11111,-1.11111,-1.11111,-1.11111,-1.11111, (4,5): -1.11111,-1.11111 } Page 19
  20. 20. “h5dump” output of a simple HDF-EOS5 file (cont.) ATTRIBUTE "_FillValue" { DATATYPE H5T_IEEE_F32BE DATASPACE SIMPLE { ( 1 ) / ( 1 ) } DATA { (0): -1.11111 } } } } } } } GROUP "HDFEOS INFORMATION" { ATTRIBUTE "HDFEOSVersion" { DATATYPE H5T_STRING { STRSIZE 32; STRPAD H5T_STR_NULLTERM; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; } Page 20
  21. 21. “h5dump” output of a simple HDF-EOS5 file (cont.) DATASPACE SCALAR DATA { (0): "HDFEOS_5.1.10" } } DATASET "StructMetadata.0" { DATATYPE H5T_STRING { STRSIZE 32000; STRPAD H5T_STR_NULLTERM; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; } DATASPACE SCALAR DATA { (0): "GROUP=SwathStructure END_GROUP=SwathStructure GROUP=GridStructure GROUP=GRID_1 GridName="TMGrid" XDim=5 YDim=7 Page 21
  22. 22. “h5dump” output of a simple HDF-EOS5 file (cont.) UpperLeftPointMtrs=(4855670.775390,9458558.924830) LowerRightMtrs=(5201746.439830,-10466077.249420) Projection=HE5_GCTP_TM ProjParams=(0,0,0.999600,0,-75000000,0,5000000, 0,0,0,0,0,0) SphereCode=0 GROUP=Dimension OBJECT=Dimension_1 DimensionName="Time" Size=10 END_OBJECT=Dimension_1 OBJECT=Dimension_2 DimensionName="Unlim" Size=-1 END_OBJECT=Dimension_2 END_GROUP=Dimension Page 22
  23. 23. “h5dump” output of a simple HDF-EOS5 file (cont.) GROUP=DataField OBJECT=DataField_1 DataFieldName="Voltage" DataType=H5T_NATIVE_FLOAT DimList=("XDim","YDim") MaxdimList=("XDim","YDim") END_OBJECT=DataField_1 END_GROUP=DataField GROUP=MergedFields END_GROUP=MergedFields END_GROUP=GRID_1 END_GROUP=GridStructure GROUP=PointStructure END_GROUP=PointStructure GROUP=ZaStructure END_GROUP=ZaStructure END " } } } } } Page 23
  24. 24. RFC Comments Draft Community Standard (ESE-RFC-008) 1. "For all multi-dimension fields in scan- or profile-oriented Swaths, the dimension representing the "along track" dimension must precede the dimension representing the scan or profile dimension(s)." This is incorrect in Fortran. - This can be clarified 2. A reserved field name is called "Latitude", but there is no software check for this. Users can inadvertently create fields called "latitude" or "LATITUDE" as there is no feedback from the library that this is incorrect. - This can be implemented easily on reserved field names 3. Also HDF allows parallel I/O while HDF-EOS does not. This may become even more problematic as HDF-EOS is entering maintenance phase and active development on it may be curtailed. - This cannot be done at this time (Labor intensive). 4. HDF-EOS adds another layer of complexity to an already complex system. When a bug occurs in the HDF-EOS or HDF libraries, it is not always apparent which library is the culprit. - What can be done? Page 24
  25. 25. RFC Comments Draft Community Standard (ESE-RFC-008) 5. HDF-EOS is a complicated library which requires support. With the release of HDF-EOS5 in Toolkit 5.2.14, the Swath, Grid and EH support libraries total over 60,000 lines of code. 6. We must be confident that the original HDF5 and HDF-EOS5 developers, or qualified successors, continue to support these formats. - If we also consider TOOLKIT, HDF(EOS)View, etc total should more than 2,000,000 lines of code, that needs support. 7. If a file contains 2 or more grids, and the grids each contain identically named fields then everything is fine when data is accessed via the HDF-EOS interface, but users of tools which in turn use the basic HDF4 interface are not able to distinguish between them. These tools reportedly include GRADS, HDFLook, and Giovanni. - One should access HDF_EOS objects only using HDF-EOS interfaces. 8. I did not see anything on the Point and Zonal Average APIs in the specification. I don's see anything on datatypes, but that is probably covered in the HDF5 Specification. I'm assuming a reference guide would have more detail. - Zonal Average is like Swath without geolocation field. As far as we know Point has not been used in any product. Page 25
  26. 26. RFC Comments Draft Community Standard (ESE-RFC-008) 9. I have never tried to develop an implementation of HDF-EOS5. However, the standard doesn't provide sufficient information to either reproduce or parse a correct coremetadata string. The standard stipulates the syntax of the structural metadata string description language (ODL), but contains no discussion of the lexicon or semantics to be used when creating these strings. - This is in SDP Toolkit and too much to bring it up in the HDF-EOS Standards. 10. The description of the standard should be completed so that all components of the metadata are well defined. - Metadata is in SDP TOOLKIT with ample examples. It was left out to concentrate on Swath and Grid structures in the Draft Community Standard (ESE-RFC-008) 11. Additionally the Draft Community Standard (ESE-RFC-008) states in section 7.2.3 that SDP toolkit contains the tools for parsing the coremetadata strings. Thus, the HDF-EOS(5) format is based not only upon HDF(5) but also put the SDP toolkit library. In this way the claim that HDF-EOS(5) is based upon HDF(5) is incomplete - it is also based on SDP toolkit, or a library of similar functionality - HDF-EOS Objects depend only on HDF5 library. Only ECS metadata is handled using Toolkit. Page 26
  27. 27. RFC Comments Draft Community Standard (ESE-RFC-008) 12. Handing HDF-EOS in a high level language without HDF-EOS support would be difficult. This is because the standard relies on an obscure, obsolete syntax (Jet Propulsion Laboratory's ODL syntax) for its data serialization. Parsers for ODL are rare and not widely supported in different programming languages. The metadata stored with a dataset is effectively dumped into a metaphorical "black hole". - XML implementation was abandoned because of high cost. 13. The API documentation describes input variables to functions as being either IN or OUT (or perhaps both). In the case of variables which are passed IN type parameters it has never been clear if the functions will modify the referent or not. Are IN type parameter referents constants? - IN type parameters are not modified in functions (if that is the case, then it is explained in the Users Guide). 14. The primary failing of HDF-EOS as a useful product was made clear by an participant in the 2004 HDF/HDF-EOS meeting in Aurora, CO. The participate pointed out that HDF-EOS was not a standard but an implementation effectively "locked" to the particular programming languages which have been supported by the HDF-EOS(5) developers. This inhibits use of HDF-EOS(5) format data in other programming languages than C or Fortran. - We can support any language HDF can, but it would be labor intensive to do so. Page 27
  28. 28. RFC Comments Draft Community Standard (ESE-RFC-008) 15. For all practical purposes it is impossible to read or write HDF-EOS5 datasets completely without using the existing libraries. Much of the high level software used for scientific data analysis doesn't support HDF-EOS5 libraries completely or in a timely fashion. This lack support (in contrast to HDF) makes it a less than desirable form in which to store data. - What can be done? 16. SDP Toolkit which contains the recommended ODL parser is not supported under Mac OS X or Windows. - SDP Toolkit parser is supported under Mac OS X. A shorter version of SDP TOOLKIT, called MTD Toolkit, supports metadata handling tools in Windows. 17. ODL should be abandoned as a data serialization syntax. Indeed, the need for data serialization should be reconsidered altogether as the underlying HDF(5) data structure contains the necessary components to maintain structured data. - Too much work for redesigning HDf_EOS5 18. A set of Quality Assurance (QA) tools should be developed which analyze a target dataset to verify that it is a lexically and syntactically correct HDF-EOS formatted dataset. The QA tools should be both distributed as open source and made available as a Web based service. Page 28 - Good idea, but very labor intensive.
  29. 29. RFC Comments Draft Community Standard (ESE-RFC-008) 19. Example codes should be provided in different programming languages which produce and read the most commonly used HDF-EOS data structures. - Requires more work than can be done in the maintenance phase Page 29