Interoperability with netCDF-4 - Experience with NPP and HDF-EOS5 products
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This document discusses interoperability between HDF5 files and the netCDF-4 format. It begins with background on netCDF-3, netCDF-4, and the Climate and Forecast (CF) metadata conventions. It then demonstrates different use cases for accessing HDF5 data via netCDF-4, including when the HDF5 file follows the netCDF data model and CF conventions compared to when it does not. The document shares experiences working with HDF-EOS5 and JPSS data products in HDF5 format through this netCDF-4 interface. In particular, it finds that following the netCDF data model and CF conventions improves visualization of HDF5 data in tools like IDV that expect netCDF files.
![An example: Augment an HDF-EOS5 Grid
• The HDF-EOS5 saves the
coordinate information
XDim and YDim in an
equation
HDFEOS
GRIDS
• The tool retrieves the
CloudFractionAndPressure
values of XDim and YDim
Data Fields
CloudFraction[XDim][YDim]
• It creates coordinate
CloudPressure[XDim][YDim]
variables XDim and YDim
XDim
with the raw values
YDim
• Then it associates the
coordinate variables with
the data variables
• Then netCDF-4 can follow
the netCDF enhanced
model to access the HDFEOS5 data
www.hdfgroup.org](https://image.slidesharecdn.com/interoperability-netcdf-4-140113095547-phpapp02/85/Interoperability-with-netCDF-4-Experience-with-NPP-and-HDF-EOS5-products-37-320.jpg)
Interoperability with netCDF-4 - Experience with NPP and HDF-EOS5 products
- 1. The HDF Group Interoperability with netCDF-4 Kent Yang, Larry Knox, Elena Pourmal The HDF Group The 15th HDF and HDF-EOS Workshop April 17-19, 2012 Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 1 www.hdfgroup.org
- 2. Outline • Background • netCDF-4 • CF • Use cases • Experience with HDF-EOS5 products • Experience with JPSS products • Current Status and future directions Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 2 www.hdfgroup.org
- 3. Clarification –netCDF format • netCDF-3 format • Simple self-describing data format based on netCDF classic data model • netCDF-4 format • Uses HDF5 as a storage layer • Exploits • Compression, chunking, parallel-IO • Group hierarchy, user-defined data types, etc. • Supports both netCDF enhanced and netCDF classic data models • Interoperability with netCDF-4 format in this talk Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 3 www.hdfgroup.org
- 4. Clarification – netCDF packages • netCDF software packages • netCDF-C • Support both netCDF-3 and netCDF-4 formats • C++/Fortran Wrappers • netCDF-Java • Support both netCDF-3 and netCDF-4 formats • The implementation of the Common Data Model • netCDF version 4 • Generally mean the version 4 package of the netCDF-C library (Not only support netCDF-4 format) Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 4 www.hdfgroup.org
- 5. Why netCDF-4 • Big user community • User-friendly data models • Tools • Home-grown and third-party visualization and analysis tools - ncdump, ncgen, IDV, Panoply, Ferret etc. Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 5 www.hdfgroup.org
- 6. NetCDF Classic Model Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 6 www.hdfgroup.org
- 7. NetCDF enhanced model Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 7 www.hdfgroup.org
- 8. CF conventions • Metadata conventions for earth science data. • Sharing of files created with the NetCDF APIs, but not specifically to netCDF. • The CF conventions are now increasingly gaining acceptance. • URL: http://cf-pcmdi.llnl.gov/ Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 8 www.hdfgroup.org
- 9. • In this tutorial, we only review the key CF attributes that affect the access of NASA and other Earth Science HDF and HDF-EOS data via popular visualization tools. Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 9 www.hdfgroup.org
- 10. Key CF data description attributes Attribute Description Units A string that represents the quantity of measurement. A variable with no units attribute is assumed to be dimensionless. long_name A descriptive name that indicates a variable‟s content. standard_name A standard name that references a description of a variable‟s content in the standard name table of CF conventions. _FillValue A value used to represent missing or undefined data. valid_min Smallest valid value of a variable. valid_max Largest valid value of a variable. valid_range Smallest and largest valid values of a variable. Use these attributes if possible, especially use _FillValue, valid_min,valid_max if you have missing value(s). Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 10 www.hdfgroup.org
- 11. Reduction of dataset size Attribute Description scale_factor If present for a variable, the data are to be multiplied by this factor after the data are read by an application. add_offset If present for a variable, this number is to be added to the data after it is read by an application. If both scale_factor and add_offset attributes are present, the data are first scaled before the offset is added. The equation that describes the usage of scale_factor and add_offset is: Final_data_value = “scale_factor” * Raw_data_value + “add_offset”; Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 11 www.hdfgroup.org
- 12. “Units” for coordinate variables • Horizontal • Latitude – “degrees_north” • Longitude – “degrees_east” • Vertical • Pressure – “hPa” • Height(depth) – “Meter” (m) or “kilometer”(km) • Time • seconds(minutes etc.) since a time point • An example • “seconds since 1992-10-8 15:15:42.5 -6:00” Use these attributes with the CF values if possible, without following CF conventions for these attributes, some tools cannot properly visualize the data. Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 12 www.hdfgroup.org
- 13. “coordinates” attribute • List the associated coordinate variable names of the variable • An example • Variable: Temperature • • Associated Coordinate variables: “latitude”,“longitude”,”pressure” coordinates = “latitude longitude pressure” Include this attribute if possible. For some data products, this is the key attribute to specific the coordinates of a variable. Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 13 www.hdfgroup.org
- 14. The HDF Group Interoperability of HDF5 with netCDF-4 General Information Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 14 www.hdfgroup.org
- 15. Review Concepts • netCDF classic model • Shared dimension • netCDF enhanced model • Group hierarchy Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 15 www.hdfgroup.org
- 16. Use cases to access HDF5 via netCDF-4 1. General HDF5 • Follow neither netCDF data models nor CF conventions 2. netCDF-4 HDF5 • Follow netCDF enhanced data model 3. netCDF-4 CF HDF5 • Follow netCDF enhanced model and CF conventions 4. netCDF (classic) HDF5 • Follow netCDF classic model 5. netCDF (classic) CF HDF5 • Follow netCDF classic model and CF conventions Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 16 www.hdfgroup.org
- 17. How to demonstrate • Simple HDF5 files • netCDF tools • netCDF C • ncdump • netCDF Java • IDV Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 17 www.hdfgroup.org
- 18. • There are some limitations for netCDF4 to access HDF5 files Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 18 www.hdfgroup.org
- 19. General HDF5 • Add phony dimension names to variables • Generally cannot be opened by IDV Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 19 www.hdfgroup.org
- 20. netCDF-4 HDF5 • HDF5 that follows netCDF enhanced model • ncdump can pick up the dimension information • cannot be opened by IDV Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 20 www.hdfgroup.org
- 21. netCDF-4 CF HDF5 • HDF5 that follows netCDF enhanced model and CF conventions • cannot be opened by IDV Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 21 www.hdfgroup.org
- 22. • We will use several demos to show the differences for the last two cases • netCDF(classic) HDF5 • netCDF(classic) CF HDF5 • ncdump can dump all demo files Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 22 www.hdfgroup.org
- 23. Demo dataset Latitude/Longitude 10,12.5,15,17.5,20,22.5, …… 42.5, 45.0, 47.5 Data: 1,2,3,4,5,6,7,8,9,10, 11,12,13,14,15,16 Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 23 www.hdfgroup.org
- 24. Use case 4 and 5 IDV demo 1 CF category Units for latitude and longitude Apr. 17-19, 2012 netCDF classic ( Case 4) Units is “degrees” HDF/HDF-EOS Workshop XV netCDF classic CF (Case 5) Latitude: “degrees_north” Longitude: “degrees_east” 24 www.hdfgroup.org
- 25. Use case 4 and 5 IDV demo 1 CF category netCDF classic ( Case 4) netCDF classic CF (Case 5) Units for latitude and longitude Cannot open the file Correctly display the data Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 25 www.hdfgroup.org
- 26. Use case 4 and 5 IDV demo 2 CF category netCDF classic (Case 4) netCDF classic CF (Case 5) _FillValue No _FillValue attribute Have _FillValue Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 26 www.hdfgroup.org
- 27. Use case 4 and 5 IDV demo 2 CF category netCDF classic (Case 4) netCDF classic CF (Case 5) _FillValue Treat _FillValue as the real data Correctly filter out the _FillValue Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 27 www.hdfgroup.org
- 28. Use case 4 and 5 IDV demo 3 CF category scale_factor and add_offset scale_factor = 10.0 add_offset = 1000.0 netCDF classic(Case 4) Attribute names for scale_factor and add_offset don‟t follow CF conventions netCDF classic CF(Case 5) Have correct scale_factor and add_offset attribute names Attributes: Attributes: wrong_scale_name = 10.0 Wrong_offset_name = 1000.0 scale_factor = 10.0 add_offset = 1000.0 1,2,3,4,5,6,7,8,9,10, 11,12,13,14,15,16 Scale Offset 1010,1020,1030, …… Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 28 www.hdfgroup.org
- 29. Use case 4 and 5 IDV demo 3 CF category scale_factor and add_offset Apr. 17-19, 2012 netCDF classic(Case 4) Doesn‟t apply the scale_factor and add_offset HDF/HDF-EOS Workshop XV netCDF classic CF(Case 5) Correctly apply scale_factor and add_offset 29 www.hdfgroup.org
- 30. Use case 4 and 5 IDV demo 4 CF category coordinates Apr. 17-19, 2012 netCDF classic(Case 4) No „coordinates‟ attribute HDF/HDF-EOS Workshop XV netCDF classic CF(Case 5) Have „coordinates‟ 30 www.hdfgroup.org
- 31. Use case 4 and 5 IDV demo 4 CF category Coordinates Apr. 17-19, 2012 netCDF classic(Case 4) May not pick up the correct coordinate HDF/HDF-EOS Workshop XV netCDF classic CF(Case 5) Correctly pick up the right coordinate 31 www.hdfgroup.org
- 32. netCDF HDF5 vs netCDF CF HDF5 • CF attributes are key to make IDV correctly display the data Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 32 www.hdfgroup.org
- 33. Summary of use cases • There are some limitations for netCDF4 to access HDF5 files Use Cases ncdump IDV General HDF5 Can view (with phony dimensions) Generally cannot view netCDF-4 HDF5 Can view Generally cannot view netCDF-4 CF HDF5 Can view Generally cannot view netCDF Classic HDF5 Can view Can view some files but the visualization may not be right netCDF Classic CF HDF5 Can view Can view Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 33 www.hdfgroup.org
- 34. The HDF Group Interoperability of HDF5 with netCDF-4 Experience with HDF-EOS5 Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 34 www.hdfgroup.org
- 35. netCDF4 to access HDF-EOS5 files • Augmentation • One file can be accessed by both EOS5 and netCDF-4 • Accessed by netCDF4 • netCDF data model should be followed netCDF4 HDF-EOS5 HDF5 Augmentation HDF5 HDF-EOS5 file Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 35 www.hdfgroup.org
- 36. An HDF-EOS5 file structure HDFEOS GRIDS CloudFractionAndPressure Data Fields CloudFraction CloudPressure Because of the group hierarchy, we can only augment the HDF-EOS5 file by following the netCDF enhanced model Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 36 www.hdfgroup.org
- 37. An example: Augment an HDF-EOS5 Grid • The HDF-EOS5 saves the coordinate information XDim and YDim in an equation HDFEOS GRIDS • The tool retrieves the CloudFractionAndPressure values of XDim and YDim Data Fields CloudFraction[XDim][YDim] • It creates coordinate CloudPressure[XDim][YDim] variables XDim and YDim XDim with the raw values YDim • Then it associates the coordinate variables with the data variables • Then netCDF-4 can follow the netCDF enhanced model to access the HDFEOS5 data www.hdfgroup.org
- 38. • How does the augmented HDF-EOS5 file follow CF conventions? • The Aura teams(HIRDLS etc.) add key CF attributes when creating the original HDF-EOS5 file. Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 38 www.hdfgroup.org
- 39. Use cases to access HDF5 via netCDF-4 1. General HDF5 • Follow neither netCDF data models nor CF conventions 2. netCDF-4 HDF5 • Follow netCDF enhanced data model 3. netCDF-4 CF HDF5 • Follow netCDF enhanced model and CF conventions 4. netCDF (classic) HDF5 • Follow netCDF classic model 5. netCDF (classic) CF HDF5 • Follow netCDF classic model and CF conventions Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 39 www.hdfgroup.org
- 40. The HDF Group Interoperability of HDF5 with netCDF-4 Experience with JPSS Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 40 www.hdfgroup.org
- 41. Applications for JPSS files • Many potentially useful applications are netCDF based • Structure of JPSS files allows for effective modification – data is separated from objects that are unknown to netCDF-4 Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 41 www.hdfgroup.org
- 42. JPSS obstacles to using netCDF-4 tools 1. Limitations of netCDF-4 – HDF5 may have objects unknown to netCDF-4 (Use case 1) • References • Multi-dimensional attributes • Chunked datasets (variables) with unlimited maximum size Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 42 www.hdfgroup.org
- 43. JPSS obstacles to using netCDF-4 tools 1. Limitations of netCDF-4 - objects unknown to netCDF-4 2. Files are not netCDF Classic Model conformant (Use case 4) a) Group structure b) Important information including dimensions in separate xml file c) Geolocation data in separate file or group Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 43 www.hdfgroup.org
- 44. JPSS obstacles to using netCDF-4 tools 1. Limitations of netCDF-4 - objects unknown to netCDF-4 2. Not netCDF Classic Model conformant 3. Key CF Attributes (Use Case 5) • Latitude Longitude • Measurement units • Valid_min valid_max (determined by data type and fill values) • Scale factors Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 44 www.hdfgroup.org
- 45. Modification of JPSS files to overcome obstacles Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 45 www.hdfgroup.org
- 46. JPSS file structure / /All_Data VIIRS-M3-SDR_All Raw data /Data_Products VIIRS-M3-SDR References to raw data Groups Apr. 17-19, 2012 Datasets HDF/HDF-EOS Workshop XV 46 www.hdfgroup.org
- 47. JPSS file structure 1. Hide problem objects / /All_Data VIIRS-M3-SDR_All Raw data /Data_Products VIIRS-M3-SDR References to raw data Groups Apr. 17-19, 2012 Datasets HDF/HDF-EOS Workshop XV 47 www.hdfgroup.org
- 48. JPSS file structure 2. Hide structure that does not conform to Classic Model / /All_Data VIIRS-M3-SDR_All Raw data /Data_Products VIIRS-M3-SDR References to raw data Groups Apr. 17-19, 2012 Datasets HDF/HDF-EOS Workshop XV 48 www.hdfgroup.org
- 49. JPSS file structure 3. Import external information from product profiles / /All_Data VIIRS-M3-SDR_All Group Raw data datasets Geolocation datasets Dimension name and length and other attributes from product profiles /Data_Products VIIRS-M3-SDR Reference datasets Groups Apr. 17-19, 2012 Datasets XV HDF/HDF-EOS Workshop attributes 49 www.hdfgroup.org
- 50. Tool for obstacles 1 – 3: H5augjpss 1. Hides problem objects 2. Makes structure conform to Classic Model 3. Imports external information Files are modified! Copy to preserve original • Final obstacle: CF compliance Manual additions with HDFView or h5edit Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 50 www.hdfgroup.org
- 51. Key CF data description attributes Variable Latitude Longitude Radiance Apr. 17-19, 2012 Required Attribute Units Units Coordinates add_offset scale_factor valid_min valid_max Type string string string float float ushort ushort HDF/HDF-EOS Workshop XV Value degrees_north degrees_east Latitude Longitude -0.08 2.8339462E-4 0 65527 51 www.hdfgroup.org
- 52. Summary Obstacles to making JPSS files readable by netCDF-4 can be addressed by: • hiding file structure and objects unknown to netCDF-4. • importing information to interpret the data from external files. Product specific information for CF compliance is currently added with HDFView or h5edit. Unknown objects that are hidden can be unhidden with saved object address. No tool is planned to remove imported data. Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 52 www.hdfgroup.org
- 53. The HDF Group Interoperability of HDF5 with netCDF-4 Current Status and Future Directions Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 53 www.hdfgroup.org
- 54. Current Status • Opportunities for interoperability primarily involve reading HDF5 produced files using netCDF-4 and netCDF-4 based tools. • Issues are periodically identified and some have been solved. Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 54 www.hdfgroup.org
- 55. Future Directions Continue working with Unidata to reduce obstacles to HDF5/netCDF-4 interoperability Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 55 www.hdfgroup.org
- 56. The HDF Group Thank You! Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 56 www.hdfgroup.org
- 57. Acknowledgements This work was supported by Subcontract number 114820 under Raytheon Contract number NNG10HP02C, funded by the National Aeronautics and Space Administration (NASA) and by cooperative agreement number NNX08AO77A from the NASA. Any opinions, findings, conclusions, or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of Raytheon or the National Aeronautics and Space Administration. Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 57 www.hdfgroup.org
- 58. The HDF Group Questions/comments? Apr. 17-19, 2012 HDF/HDF-EOS Workshop XV 58 www.hdfgroup.org
Editor's Notes
- #5: At the end of the slide, how many people are familiar with netCDF-4?
- #6: May skip this slide quickly: not mention data model.Several popular tools that are used widely by Earth Science community.
- #7: The shared dimensions can be easily used by Earth Science applications to specify the coordinate variables.
- #8: Group hierarchy and User-defined datatypes are key concepts to addTo the enhanced model.After this slide, ask the audiences how many people heard of CF conventions, how many people would like to know how CF attributes can affectthe visualization results.
- #11: May quickly go through this slide if audiences know CF attributes._FillVaule only specifies one distinct missing or undefined value. Using valid_min, valid_max or valid_range multiple distinct missing or undefined values can be filtered out
- #12: Be careful when using these two attributes. Joe will share with you MODIS examples.
- #13: Also make sure to use the exact format. Some tools are picky.
- #14: At the end of slides, just mention other CF requirement: The variable and attribute names can only have number, letter and underscore. No other characters are allowed.
- #20: HDFView: t_int.h5ncdump –h t_int.h5 Not workingTdset.h5 ncdump –h tdset.h5 working
- #25: Demos:Lat/Lon: screenshots and IDV demoUnits that don’t follow CF, IDV cannot open the file.Units that follow CF, IDV can.
- #26: Demos:Lat/Lon: screenshots and IDV demoUnits that don’t follow CF, IDV cannot open the file.Units that follow CF, IDV can.
- #27: Demos:_FillValue: 1) Use HDFView to show the data, 2) IDV first shows the data without the fillvalue attribute 3) Add _FillValue attribute at HDFView. Change the HDF5 dataset name to another name.4) Save the file(not to another HDF5 file) 5) Open with the IDV again, this time the _FillValue is not printed.
- #28: Demos:_FillValue: 1) Use HDFView to show the data, 2) IDV first shows the data without the fillvalue attribute 3) Add _FillValue attribute at HDFView. Change the HDF5 dataset name to another name.4) Save the file(not to another HDF5 file) 5) Open with the IDV again, this time the _FillValue is not printed.
- #29: Demos:Show the scale factor and add_offset. The initial value and the final value.2.Show the wrong attribute name and the right attribute name3.. Demo:file with the wrong attribute names(1,2,3…)file with the right attribute names(1010,1020, etc.)
- #30: Demos:Show the scale factor and add_offset. The initial value and the final value.2.Show the wrong attribute name and the right attribute name3.. Demo:file with the wrong attribute names(1,2,3…)file with the right attribute names(1010,1020, etc.)
- #31: Demos:Screenshots:Let the audience note the “coordinates” attribute.4. Show IDV, don’t display the value plot(IDV has a bug), just show the vertical coordinate
- #32: Demos:Screenshots:Let the audience note the “coordinates” attribute.4. Show IDV, don’t display the value plot(IDV has a bug), just show the vertical coordinate
- #37: The netCDF-4 requires the association of dimensions with coordinate variables.