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764 lines
31 KiB
Plaintext
/** @page ViewToolsJPSS Use Case: Examining a JPSS NPP File With HDF5 Tools
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Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand
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<hr>
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\section secViewToolsJPSSTOC Contents
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<ul>
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<li>\ref secViewToolsJPSSDeter</li>
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<li>\ref secViewToolsJPSSView</li>
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<li>\ref secViewToolsJPSSExam</li>
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</ul>
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This tutorial illustrates how to use the HDF5 tools to examine NPP files from the JPSS project. The following files are discussed:
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\code
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SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5 (<a href="https://\AEXURL/files/tutorial/SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5.gz">gzipped file</a>)
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SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5 (<a href="https://\AEXURL/files/tutorial/SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5.gz">gzipped file</a>)
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\endcode
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\section secViewToolsJPSSDeter Determining File Contents
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The first thing you may want to do is determine what is in your file. You can use the command-line tools or HDFView to do this:
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\li @ref subsecViewToolsJPSSDeter_h5dump
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\li @ref subsecViewToolsJPSSDeter_h5ls
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\li @ref subsecViewToolsJPSSDeter_HDFView
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JPSS NPP files all contain two root level groups:
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<table>
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<tr>
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<th>Group</th><th>Description</th>
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</tr>
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<tr>
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<td>/All_Data
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</td>
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<td>Contains the raw data and optional geo-location information.
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</td>
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</tr>
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<tr>
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<td>/Data_Products
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</td>
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<td>Contains a dataset ending in <code style="background-color:whitesmoke;">Aggr</code> with
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references to objects in the <code style="background-color:whitesmoke;">/All_Data</code> group.
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Contains granules (datasets with a name ending in <code style="background-color:whitesmoke;">Gran_#</code>)
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with references to selected regions in datasets under <code style="background-color:whitesmoke;">/All_Data</code>.
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</td>
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</tr>
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</table>
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\subsection subsecViewToolsJPSSDeter_h5dump h5dump
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With <code style="background-color:whitesmoke;">h5dump</code> you can see a list of the objects
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in the file using the <code style="background-color:whitesmoke;">-n</code> option:
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\code
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h5dump -n <file>
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\endcode
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For example:
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\code
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$ h5dump -n SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5
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HDF5 "SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5" {
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FILE_CONTENTS {
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group /
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group /All_Data
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group /All_Data/VIIRS-M9-SDR_All
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dataset /All_Data/VIIRS-M9-SDR_All/ModeGran
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dataset /All_Data/VIIRS-M9-SDR_All/ModeScan
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dataset /All_Data/VIIRS-M9-SDR_All/NumberOfBadChecksums
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dataset /All_Data/VIIRS-M9-SDR_All/NumberOfDiscardedPkts
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dataset /All_Data/VIIRS-M9-SDR_All/NumberOfMissingPkts
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dataset /All_Data/VIIRS-M9-SDR_All/NumberOfScans
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dataset /All_Data/VIIRS-M9-SDR_All/PadByte1
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dataset /All_Data/VIIRS-M9-SDR_All/QF1_VIIRSMBANDSDR
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dataset /All_Data/VIIRS-M9-SDR_All/QF2_SCAN_SDR
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dataset /All_Data/VIIRS-M9-SDR_All/QF3_SCAN_RDR
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dataset /All_Data/VIIRS-M9-SDR_All/QF4_SCAN_SDR
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dataset /All_Data/VIIRS-M9-SDR_All/QF5_GRAN_BADDETECTOR
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dataset /All_Data/VIIRS-M9-SDR_All/Radiance
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dataset /All_Data/VIIRS-M9-SDR_All/RadianceFactors
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dataset /All_Data/VIIRS-M9-SDR_All/Reflectance
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dataset /All_Data/VIIRS-M9-SDR_All/ReflectanceFactors
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group /Data_Products
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group /Data_Products/VIIRS-M9-SDR
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dataset /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Aggr
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dataset /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0
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dataset /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_1
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dataset /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_2
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dataset /Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_3
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}
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}
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\endcode
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In the output above you can see that there are four granules (ending in
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<code style="background-color:whitesmoke;">Gran_#</code>) in the
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<code style="background-color:whitesmoke;">/Data_Products/VIIRS-M9-SDR/</code> group.
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\subsection subsecViewToolsJPSSDeter_h5ls h5ls
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With <code style="background-color:whitesmoke;">h5ls</code> you can see a list of the objects in the
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file using the <code style="background-color:whitesmoke;">-lr</code>
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options. The <code style="background-color:whitesmoke;">h5ls</code> utility also shows shape and size
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(dataspace) information about datasets.
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\code
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h5ls -lr <file>
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\endcode
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For example:
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\code
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$ h5ls -lr SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5
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/ Group
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/All_Data Group
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/All_Data/VIIRS-M9-SDR_All Group
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/All_Data/VIIRS-M9-SDR_All/ModeGran Dataset {4/Inf}
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/All_Data/VIIRS-M9-SDR_All/ModeScan Dataset {192/Inf}
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/All_Data/VIIRS-M9-SDR_All/NumberOfBadChecksums Dataset {192/Inf}
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/All_Data/VIIRS-M9-SDR_All/NumberOfDiscardedPkts Dataset {192/Inf}
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/All_Data/VIIRS-M9-SDR_All/NumberOfMissingPkts Dataset {192/Inf}
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/All_Data/VIIRS-M9-SDR_All/NumberOfScans Dataset {4/Inf}
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/All_Data/VIIRS-M9-SDR_All/PadByte1 Dataset {12/Inf}
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/All_Data/VIIRS-M9-SDR_All/QF1_VIIRSMBANDSDR Dataset {3072/Inf, 3200/Inf}
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/All_Data/VIIRS-M9-SDR_All/QF2_SCAN_SDR Dataset {192/Inf}
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/All_Data/VIIRS-M9-SDR_All/QF3_SCAN_RDR Dataset {192/Inf}
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/All_Data/VIIRS-M9-SDR_All/QF4_SCAN_SDR Dataset {3072/Inf}
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/All_Data/VIIRS-M9-SDR_All/QF5_GRAN_BADDETECTOR Dataset {64/Inf}
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/All_Data/VIIRS-M9-SDR_All/Radiance Dataset {3072/Inf, 3200/Inf}
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/All_Data/VIIRS-M9-SDR_All/RadianceFactors Dataset {8/Inf}
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/All_Data/VIIRS-M9-SDR_All/Reflectance Dataset {3072/Inf, 3200/Inf}
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/All_Data/VIIRS-M9-SDR_All/ReflectanceFactors Dataset {8/Inf}
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/Data_Products Group
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/Data_Products/VIIRS-M9-SDR Group
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/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Aggr Dataset {16/Inf}
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/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0 Dataset {16/Inf}
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/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_1 Dataset {16/Inf}
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/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_2 Dataset {16/Inf}
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/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_3 Dataset {16/Inf}
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\endcode
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Note that the <code style="background-color:whitesmoke;">Inf</code> indicates that those datasets are appendable or unlimited in size.
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\subsection subsecViewToolsJPSSDeter_HDFView HDFView
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If you open the file in HDFView, it will display the file and the root level groups within
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it in the TreeView on the left. An HDF5 file is a folder with a "5" in the middle, followed
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by the file name. There are two folders (groups) within the JPSS file
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(<code style="background-color:whitesmoke;">All_Data/</code> and <code style="background-color:whitesmoke;">Data Products/</code>),
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which you can select to see their contents:
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<table>
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<tr>
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<td>
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\image html hdfview-tree.png
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</td>
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</tr>
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</table>
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If you click twice with the left-mouse button on a folder or group in the TreeView, the contents
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of the folder will be listed. If you click twice on an object such as a dataset, a window with
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the object's values will be displayed.
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Underneath the <code style="background-color:whitesmoke;">VIIRS-M1-SDR</code> folder are what HDF5
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calls datasets. The scarlet letter <code style="background-color:whitesmoke;">"A"</code> attached
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to the group and datasets under <code style="background-color:whitesmoke;">Data_Products/</code>
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indicates that there are attributes associated with them.
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\section secViewToolsJPSSView Viewing the User Block
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All JPSS files contain a user block in XML with information about the file. The user block is an
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optional space allocated at the beginning of an HDF5 file that is not interpreted by the HDF5
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library. Its size is a multiple of 512.
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Since the user block in JPSS files is stored in ASCII and it is stored at the beginning of an
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HDF5 file, you could use a text editor or viewer to examine it. However, there are HDF5 utilities
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that can help with this:
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<table>
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<tr>
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<th>Utility</th><th>Description</th>
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</tr>
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<tr>
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<td>h5unjam
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</td>
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<td>Extracts a user block from an HDF5 file
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</td>
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</tr>
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<tr>
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<td>h5dump
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</td>
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<td>The -B (--superblock) option displays the size of the user block in an HDF5 file
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</td>
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</tr>
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</table>
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\subsection subsecViewToolsJPSSView_h5unjam h5unjam
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The \ref secViewToolsEditAdd tutorial topic discusses the use of the
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<code style="background-color:whitesmoke;">h5jam</code> and <code style="background-color:whitesmoke;">h5unjam</code>
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utilities for adding or removing a user block from a file. An input HDF5 file
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(<code style="background-color:whitesmoke;">-i</code>), output HDF5 file
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(<code style="background-color:whitesmoke;">-o</code>), and user block text file
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(<code style="background-color:whitesmoke;">-u</code>) can be specified with these tools. You can use the
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<code style="background-color:whitesmoke;">h5unjam</code> tool to extract and view the user block in a JPSS file:
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\code
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h5unjam -i <Input HDF5 File> -o <Output HDF5 File> -u <User Block File>
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\endcode
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For example this command will extract the user block into the file UB.xml:
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\code
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$ h5unjam -i SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5
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-o svm09-noUB.h5 -u UB.xml
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\endcode
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The input HDF5 file remains unchanged. The output HDF5 file will not contain the user block.
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The <code style="background-color:whitesmoke;">UB.xml</code> file contains the user block
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which can be viewed with a browser.
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\subsection subsecViewToolsJPSSView_h5dump h5dump
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The h5dump utility has the <code style="background-color:whitesmoke;">-B (--superblock)</code> option for displaying the superblock in an HDF5 file.
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The superblock contains information about the file such as the file signature, file consistency flags,
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the number of bytes to store addresses and size of an object, as well as the size of the user block:
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\code
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h5dump -B (--superblock)
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\endcode
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Below is an example (Unix):
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\code
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$ h5dump -B -H SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5 | more
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HDF5 "SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5" {
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SUPER_BLOCK {
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SUPERBLOCK_VERSION 0
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FREELIST_VERSION 0
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SYMBOLTABLE_VERSION 0
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OBJECTHEADER_VERSION 0
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OFFSET_SIZE 8
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LENGTH_SIZE 8
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BTREE_RANK 16
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BTREE_LEAF 4
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ISTORE_K 32
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USER_BLOCK {
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USERBLOCK_SIZE 1024
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}
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}
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\endcode
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Once you have the size of the user block, you can extract it from the file using system commands.
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For example, on Unix platforms you can use the head command-line tool:
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\code
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head -c <USERBLOCK_SIZE> <JPSS File> >& USERBLOCK.xml
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\endcode
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There are Unix tools for Windows that may work, such as <a href="http://gnuwin32.sourceforge.net/packages/coreutils.htm">CoreUtils for Windows</a>.
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\section secViewToolsJPSSExam Examining a Granule
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<ul>
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<li>@ref subsecViewToolsJPSSExam_h5dump<br />
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<ul>
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<li>@ref subsubsecViewToolsJPSSExam_h5dumpRegRef</li>
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<li>@ref subsubsecViewToolsJPSSExam_h5dumpQuality</li>
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<li>@ref subsubsecViewToolsJPSSExam_h5dumpProps</li>
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</ul></li>
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<li>@ref subsecViewToolsJPSSExamr_HDFView</li>
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</ul>
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\subsection subsecViewToolsJPSSExam_h5dump h5dump
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There are several options that you may first want to use when examining a granule with h5dump:
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<table>
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<tr>
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<th>Option</th><th>Description</th>
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</tr>
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<tr>
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<td>-H, --header
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</td>
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<td>Prints header (metadata) information only
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</td>
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</tr>
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<tr>
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<td>-d D, --dataset=D
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</td>
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<td>Specifies the granule dataset
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</td>
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</tr>
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<tr>
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<td>-A 0, --onlyattr=0
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</td>
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<td>Suppresses attributes
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</td>
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</tr>
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<tr>
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<td>-p, --properties
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</td>
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<td>Show properties of datasets
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(See Properties)
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</td>
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</tr>
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</table>
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You would specify the dataset (<code style="background-color:whitesmoke;">-d D</code>) and the
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<code style="background-color:whitesmoke;">-H</code> options to view the metadata associated with
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a specific granule. There are many attributes associated with a granule and
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<code style="background-color:whitesmoke;">-A 0</code> can be used to suppress those.
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For example:
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\code
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h5dump -H -A 0 -d "/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0"
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SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5
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\endcode
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This command displays:
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\code
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HDF5 "SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5" {
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DATASET "/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0" {
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DATATYPE H5T_REFERENCE { H5T_STD_REF_DSETREG }
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DATASPACE SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
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}
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}
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\endcode
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To see the actual contents of the granule remove the <code style="background-color:whitesmoke;">-H</code> option:
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\code
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h5dump -A 0 -d "/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0"
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SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5
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\endcode
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The above command displays:
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\code
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HDF5 "SVM09_npp_d20120229_t0849107_e0854511_b01759_c20120229145452682127_noaa_ops.h5" {
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DATASET "/Data_Products/VIIRS-M9-SDR/VIIRS-M9-SDR_Gran_0" {
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DATATYPE H5T_REFERENCE { H5T_STD_REF_DSETREG }
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DATASPACE SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
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DATA {
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DATASET /All_Data/VIIRS-M9-SDR_All/Radiance {(0,0)-(767,3199)},
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DATASET /All_Data/VIIRS-M9-SDR_All/Reflectance {(0,0)-(767,3199)},
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DATASET /All_Data/VIIRS-M9-SDR_All/ModeScan {(0)-(47)},
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DATASET /All_Data/VIIRS-M9-SDR_All/ModeGran {(0)-(0)},
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DATASET /All_Data/VIIRS-M9-SDR_All/PadByte1 {(0)-(2)},
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DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfScans {(0)-(0)},
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DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfMissingPkts {(0)-(47)},
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DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfBadChecksums {(0)-(47)},
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DATASET /All_Data/VIIRS-M9-SDR_All/NumberOfDiscardedPkts {(0)-(47)},
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DATASET /All_Data/VIIRS-M9-SDR_All/QF1_VIIRSMBANDSDR {(0,0)-(767,3199)},
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DATASET /All_Data/VIIRS-M9-SDR_All/QF2_SCAN_SDR {(0)-(47)},
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DATASET /All_Data/VIIRS-M9-SDR_All/QF3_SCAN_RDR {(0)-(47)},
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DATASET /All_Data/VIIRS-M9-SDR_All/QF4_SCAN_SDR {(0)-(767)},
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DATASET /All_Data/VIIRS-M9-SDR_All/QF5_GRAN_BADDETECTOR {(0)-(15)},
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DATASET /All_Data/VIIRS-M9-SDR_All/RadianceFactors {(0)-(1)},
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DATASET /All_Data/VIIRS-M9-SDR_All/ReflectanceFactors {(0)-(1)}
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}
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}
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}
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\endcode
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As you can see in the output above, the datatype for this dataset is:
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\code
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DATATYPE H5T_REFERENCE { H5T_STD_REF_DSETREG }
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\endcode
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This indicates that it is a dataset specifically for storing references to regions (or subsets)
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in other datasets. The dataset contains 16 such references, and more can be added to it, as
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indicated by the dataspace (in other words it is unlimited):
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\code
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DATASPACE SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
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\endcode
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\subsubsection subsubsecViewToolsJPSSExam_h5dumpRegRef Viewing a Region Reference
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What if we wanted to look at the <code style="background-color:whitesmoke;">NumberOfScans</code> data for a specific granule in a file?
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First, we may be interested in determining whether the scans were done at night or in the day. If a scan was at night, there will be no data.
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|
|
The attribute <code style="background-color:whitesmoke;">N_Day_Night_Flag</code> is used to determine when the scan was done. If you don't know where this attribute is located, you can use the <code style="background-color:whitesmoke;">-N</code> option to search for it in the file. If you were to run this command on the <code style="background-color:whitesmoke;">SVM09</code> file used above, you would see that the <code style="background-color:whitesmoke;">N_Day_Night_Flag</code> attribute has a value of <code style="background-color:whitesmoke;">Night</code> for the four granules in the file. Indeed, if you actually examine the <code style="background-color:whitesmoke;">NumberOfScans</code> data, you will see that only fill values are written.
|
|
|
|
For that reason we will examine the <code style="background-color:whitesmoke;">NumberOfScans</code> data for the <code style="background-color:whitesmoke;">SVMO1</code> file below, as it was obtained during the day:
|
|
\code
|
|
h5dump -N N_Day_Night_Flag SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
|
|
\endcode
|
|
|
|
It displays:
|
|
\code
|
|
HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
|
|
ATTRIBUTE "N_Day_Night_Flag" {
|
|
DATATYPE H5T_STRING {
|
|
STRSIZE 4;
|
|
STRPAD H5T_STR_NULLTERM;
|
|
CSET H5T_CSET_ASCII;
|
|
CTYPE H5T_C_S1;
|
|
}
|
|
DATASPACE SIMPLE { ( 1, 1 ) / ( 1, 1 ) }
|
|
DATA {
|
|
(0,0): "Day"
|
|
}
|
|
}
|
|
}
|
|
\endcode
|
|
|
|
There is just one granule in this <code style="background-color:whitesmoke;">SVM01</code> file, as shown below:
|
|
\code
|
|
$ h5dump -n SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
|
|
HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
|
|
FILE_CONTENTS {
|
|
group /
|
|
group /All_Data
|
|
group /All_Data/VIIRS-M1-SDR_All
|
|
dataset /All_Data/VIIRS-M1-SDR_All/ModeGran
|
|
dataset /All_Data/VIIRS-M1-SDR_All/ModeScan
|
|
dataset /All_Data/VIIRS-M1-SDR_All/NumberOfBadChecksums
|
|
dataset /All_Data/VIIRS-M1-SDR_All/NumberOfDiscardedPkts
|
|
dataset /All_Data/VIIRS-M1-SDR_All/NumberOfMissingPkts
|
|
dataset /All_Data/VIIRS-M1-SDR_All/NumberOfScans
|
|
dataset /All_Data/VIIRS-M1-SDR_All/PadByte1
|
|
dataset /All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR
|
|
dataset /All_Data/VIIRS-M1-SDR_All/QF2_SCAN_SDR
|
|
dataset /All_Data/VIIRS-M1-SDR_All/QF3_SCAN_RDR
|
|
dataset /All_Data/VIIRS-M1-SDR_All/QF4_SCAN_SDR
|
|
dataset /All_Data/VIIRS-M1-SDR_All/QF5_GRAN_BADDETECTOR
|
|
dataset /All_Data/VIIRS-M1-SDR_All/Radiance
|
|
dataset /All_Data/VIIRS-M1-SDR_All/RadianceFactors
|
|
dataset /All_Data/VIIRS-M1-SDR_All/Reflectance
|
|
dataset /All_Data/VIIRS-M1-SDR_All/ReflectanceFactors
|
|
group /Data_Products
|
|
group /Data_Products/VIIRS-M1-SDR
|
|
dataset /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Aggr
|
|
dataset /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0
|
|
}
|
|
}
|
|
\endcode
|
|
|
|
Now examine the references in the <code style="background-color:whitesmoke;">VIIRS-M1-SDR_Gran_0</code> granule
|
|
\code
|
|
$ h5dump -A 0 -d "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0"
|
|
SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
|
|
HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
|
|
DATASET "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0" {
|
|
DATATYPE H5T_REFERENCE { H5T_STD_REF_DSETREG }
|
|
DATASPACE SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
|
|
DATA {
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/Radiance {(0,0)-(767,3199)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/Reflectance {(0,0)-(767,3199)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/ModeScan {(0)-(47)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/ModeGran {(0)-(0)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/PadByte1 {(0)-(2)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfScans {(0)-(0)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfMissingPkts {(0)-(47)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfBadChecksums {(0)-(47)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfDiscardedPkts {(0)-(47)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR {(0,0)-(767,3199)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/QF2_SCAN_SDR {(0)-(47)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/QF3_SCAN_RDR {(0)-(47)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/QF4_SCAN_SDR {(0)-(767)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/QF5_GRAN_BADDETECTOR {(0)-(15)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/RadianceFactors {(0)-(1)},
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/ReflectanceFactors {(0)-(1)}
|
|
}
|
|
}
|
|
}
|
|
\endcode
|
|
|
|
In the output above, you can see that the <code style="background-color:whitesmoke;">NumberOfScans</code>
|
|
reference is the sixth reference in the granule counting from the top.
|
|
|
|
The list of references shown above is a 0-based index to the dataset. Therefore, to specify
|
|
<code style="background-color:whitesmoke;">NumberOfScans</code>, enter a start offset of
|
|
<code style="background-color:whitesmoke;">5</code> for the <code style="background-color:whitesmoke;">-s</code>
|
|
option (the sixth reference minus 1). To see the region reference data, use the <code style="background-color:whitesmoke;">-R</code> option.
|
|
|
|
This command will display the data in the <code style="background-color:whitesmoke;">NumberOfScans</code> region reference:
|
|
\code
|
|
h5dump -A 0 -d "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0" -s 5 -R
|
|
SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
|
|
\endcode
|
|
|
|
It displays the number of scans (48):
|
|
\code
|
|
HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
|
|
DATASET "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0" {
|
|
DATATYPE H5T_REFERENCE { H5T_STD_REF_DSETREG }
|
|
DATASPACE SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
|
|
SUBSET {
|
|
START ( 5 );
|
|
STRIDE ( 1 );
|
|
COUNT ( 1 );
|
|
BLOCK ( 1 );
|
|
DATA {
|
|
(5): DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfScans {
|
|
(5): REGION_TYPE BLOCK (0)-(0)
|
|
(5): DATATYPE H5T_STD_I32BE
|
|
(5): DATASPACE SIMPLE { ( 1 ) / ( H5S_UNLIMITED ) }
|
|
(5): DATA {
|
|
(0): 48
|
|
(5): }
|
|
(5): }
|
|
}
|
|
}
|
|
}
|
|
}
|
|
\endcode
|
|
|
|
The <code style="background-color:whitesmoke;">-s</code> option may be familiar as one of the options
|
|
that was described in the \ref secViewToolsViewSub tutorial topic. The other subsetting options are not included,
|
|
indicating that the default values are used.
|
|
|
|
If you leave off the <code style="background-color:whitesmoke;">-R</code> option, you will see the subset selection, but not the data:
|
|
\code
|
|
$ h5dump -A 0 -d "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0" -s 5
|
|
SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
|
|
HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
|
|
DATASET "/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0" {
|
|
DATATYPE H5T_REFERENCE { H5T_STD_REF_DSETREG }
|
|
DATASPACE SIMPLE { ( 16 ) / ( H5S_UNLIMITED ) }
|
|
SUBSET {
|
|
START ( 5 );
|
|
STRIDE ( 1 );
|
|
COUNT ( 1 );
|
|
BLOCK ( 1 );
|
|
DATA {
|
|
DATASET /All_Data/VIIRS-M1-SDR_All/NumberOfScans {(0)-(0)}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
\endcode
|
|
|
|
\subsubsection subsubsecViewToolsJPSSExam_h5dumpQuality Viewing a Quality Flag
|
|
The quality flags in an NPP file can be viewed with h5dump using the <code style="background-color:whitesmoke;">-M</code>
|
|
option. Quality flags are packed into each integer value in a quality flag dataset. Quality flag datasets in NPP
|
|
files begin with the letters <code style="background-color:whitesmoke;">QF</code>.
|
|
|
|
In the following NPP file, there are five Quality Flag datasets
|
|
(<code style="background-color:whitesmoke;">/All_Data/VIIRS-M1-SDR_All/QF*</code>):
|
|
\code
|
|
$ h5dump -n SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
|
|
HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
|
|
FILE_CONTENTS {
|
|
group /
|
|
group /All_Data
|
|
group /All_Data/VIIRS-M1-SDR_All
|
|
dataset /All_Data/VIIRS-M1-SDR_All/ModeGran
|
|
dataset /All_Data/VIIRS-M1-SDR_All/ModeScan
|
|
dataset /All_Data/VIIRS-M1-SDR_All/NumberOfBadChecksums
|
|
dataset /All_Data/VIIRS-M1-SDR_All/NumberOfDiscardedPkts
|
|
dataset /All_Data/VIIRS-M1-SDR_All/NumberOfMissingPkts
|
|
dataset /All_Data/VIIRS-M1-SDR_All/NumberOfScans
|
|
dataset /All_Data/VIIRS-M1-SDR_All/PadByte1
|
|
dataset /All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR
|
|
dataset /All_Data/VIIRS-M1-SDR_All/QF2_SCAN_SDR
|
|
dataset /All_Data/VIIRS-M1-SDR_All/QF3_SCAN_RDR
|
|
dataset /All_Data/VIIRS-M1-SDR_All/QF4_SCAN_SDR
|
|
dataset /All_Data/VIIRS-M1-SDR_All/QF5_GRAN_BADDETECTOR
|
|
dataset /All_Data/VIIRS-M1-SDR_All/Radiance
|
|
dataset /All_Data/VIIRS-M1-SDR_All/RadianceFactors
|
|
dataset /All_Data/VIIRS-M1-SDR_All/Reflectance
|
|
dataset /All_Data/VIIRS-M1-SDR_All/ReflectanceFactors
|
|
group /Data_Products
|
|
group /Data_Products/VIIRS-M1-SDR
|
|
dataset /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Aggr
|
|
dataset /Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0
|
|
}
|
|
}
|
|
\endcode
|
|
|
|
The flags in this particular dataset happen to be stored in every two bits of each quality flag dataset
|
|
element, and the values range from 0 to 2. In other words, to see the quality flag values for this
|
|
dataset, these bits would be examined: 0 and 1, 2 and 3, 4 and 5, or 6 and 7 (This information was
|
|
obtained from the Product Profile XML File.)
|
|
|
|
For example, bits 0 and 1 in the <code style="background-color:whitesmoke;">VQF1_VIIRSMBANDSDR</code> dataset specify the flag that
|
|
"Indicates calibration quality due to bad space view offsets, OBC view offsets, etc or use of a
|
|
previous calibration view". It has 3 values: Good (0), Poor (1), or No Calibration (2).
|
|
|
|
The <code style="background-color:whitesmoke;">-M</code> option is used to specify the quality
|
|
flag bit offset (<code style="background-color:whitesmoke;">O</code>) and length (<code style="background-color:whitesmoke;">L</code>):
|
|
\code
|
|
h5dump -d DATASET -M O,L FILE
|
|
\endcode
|
|
|
|
To view the first quality flag (0-1) in a 5 x 6 subset of the <code style="background-color:whitesmoke;">QF1_VIIRSMBANDSDR</code> dataset, specify:
|
|
\code
|
|
h5dump -d "/All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR[0,0;;5,6;]"
|
|
-M 0,2 SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
|
|
\endcode
|
|
|
|
This outputs:
|
|
\code
|
|
HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
|
|
DATASET "/All_Data/VIIRS-M1-SDR_All/QF1_VIIRSMBANDSDR" {
|
|
DATATYPE H5T_STD_U8BE
|
|
DATASPACE SIMPLE { ( 768, 3200 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
|
|
PACKED_BITS OFFSET=0 LENGTH=2
|
|
SUBSET {
|
|
START ( 0, 0 );
|
|
STRIDE ( 1, 1 );
|
|
COUNT ( 5, 6 );
|
|
BLOCK ( 1, 1 );
|
|
DATA {
|
|
(0,0): 2, 2, 2, 2, 2, 2,
|
|
(1,0): 2, 2, 2, 2, 2, 2,
|
|
(2,0): 0, 0, 0, 0, 0, 0,
|
|
(3,0): 0, 0, 0, 0, 0, 0,
|
|
(4,0): 0, 0, 0, 0, 0, 0
|
|
}
|
|
}
|
|
}
|
|
}
|
|
\endcode
|
|
|
|
To view more than one quality flag at a time simply add the bit offset and length values to
|
|
<code style="background-color:whitesmoke;">-M</code>, separated by commas. For example, this
|
|
<code style="background-color:whitesmoke;">-M</code> option specifies bits 0-1 and 2-3:
|
|
\code
|
|
h5dump -d DATASET -M 0,2,2,2 FILE
|
|
\endcode
|
|
|
|
\subsubsection subsubsecViewToolsJPSSExam_h5dumpProps Properties
|
|
To view properties of a specific dataset with <code style="background-color:whitesmoke;">h5dump</code>
|
|
use the <code style="background-color:whitesmoke;">-p</code> option along with the
|
|
<code style="background-color:whitesmoke;">-d</code> option. Depending on the number of attributes
|
|
and the amount of data, the <code style="background-color:whitesmoke;">-A 0</code> and
|
|
<code style="background-color:whitesmoke;">-H</code> options can also be specified to suppress
|
|
printing of attributes and data values:
|
|
\code
|
|
h5dump -p -H -A 0 -d DATASET
|
|
\endcode
|
|
|
|
The <code style="background-color:whitesmoke;">-p</code> option shows any compression filters
|
|
associated with a dataset, as well as layout and fill value information. This option can be helpful
|
|
in diagnosing performance and other issues.
|
|
|
|
As an example, examine the <code style="background-color:whitesmoke;">/All_Data/VIIRS-M1-SDR_All/Radiance</code>
|
|
dataset in the <code style="background-color:whitesmoke;">SVM01</code> file:
|
|
\code
|
|
$ h5dump -p -H -A 0 -d "/All_Data/VIIRS-M1-SDR_All/Radiance"
|
|
SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
|
|
HDF5 "SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5" {
|
|
DATASET "/All_Data/VIIRS-M1-SDR_All/Radiance" {
|
|
DATATYPE H5T_STD_U16BE
|
|
DATASPACE SIMPLE { ( 768, 3200 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
|
|
STORAGE_LAYOUT {
|
|
CHUNKED ( 768, 3200 )
|
|
SIZE 4915200
|
|
}
|
|
FILTERS {
|
|
NONE
|
|
}
|
|
FILLVALUE {
|
|
FILL_TIME H5D_FILL_TIME_IFSET
|
|
VALUE 65529
|
|
}
|
|
ALLOCATION_TIME {
|
|
H5D_ALLOC_TIME_INCR
|
|
}
|
|
}
|
|
}
|
|
\endcode
|
|
|
|
We can see that the chunk size for this dataset is 768 x 3200, and the storage size is 4915200.
|
|
|
|
What if the chunk size were smaller?
|
|
|
|
The dataset was modified to have a chunk size of 1 x 10, using the
|
|
<code style="background-color:whitesmoke;">h5repack</code> utility, as shown below.
|
|
\code
|
|
$ h5repack -l /All_Data/VIIRS-M1-SDR_All/Radiance:CHUNK=1x10
|
|
SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5 SVM01repack.h5
|
|
|
|
$ h5dump -p -H -A 0 -d "/All_Data/VIIRS-M1-SDR_All/Radiance" SVM01repack.h5
|
|
HDF5 "SVM01repack.h5" {
|
|
DATASET "/All_Data/VIIRS-M1-SDR_All/Radiance" {
|
|
DATATYPE H5T_STD_U16BE
|
|
DATASPACE SIMPLE { ( 768, 3200 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) }
|
|
STORAGE_LAYOUT {
|
|
CHUNKED ( 1, 10 )
|
|
SIZE 4915200
|
|
}
|
|
FILTERS {
|
|
NONE
|
|
}
|
|
FILLVALUE {
|
|
FILL_TIME H5D_FILL_TIME_IFSET
|
|
VALUE 65529
|
|
}
|
|
ALLOCATION_TIME {
|
|
H5D_ALLOC_TIME_INCR
|
|
}
|
|
}
|
|
}
|
|
\endcode
|
|
|
|
In this case, the storage size of the dataset is the same, but the size of the file almost doubled!:
|
|
\code
|
|
$ ls -1sh
|
|
total 35M
|
|
12M SVM01_npp_d20130524_t1255132_e1256374_b08146_c20130524192048864992_noaa_ops.h5
|
|
23M SVM01repack.h5
|
|
\endcode
|
|
|
|
In general, the smaller the chunk size, the more chunks that HDF5 has to keep track of, which increases
|
|
the size of the file and can affect performance.
|
|
|
|
\subsection subsecViewToolsJPSSExamr_HDFView HDFView
|
|
As mentioned previously, the structure of an HDF5 file is displayed in the TreeView on the left side of the HDFView screen,
|
|
and you can click on objects and have metadata information displayed on the right side.
|
|
|
|
To discover more about the granule <code style="background-color:whitesmoke;">/Data_Products/VIIRS-M1-SDR/VIIRS-M1-SDR_Gran_0</code>
|
|
in the <code style="background-color:whitesmoke;">SVM01</code> file shown below in the TreeView, position
|
|
the mouse over the granule and click to select. Properties for the object is displayed on the right side of the HDFView screen.
|
|
You can see Datatype and Dataspace information on the <code style="background-color:whitesmoke;">General Object Info</code>
|
|
tab, any Attributes associated with the granulewill be on the
|
|
<code style="background-color:whitesmoke;">Object Attribute Info</code> tab. In the
|
|
<code style="background-color:whitesmoke;">General Object Info</code>, you can see that the dataset is a
|
|
Region Reference dataset, and that there are sixteen Region References in this dataset:
|
|
<table>
|
|
<tr>
|
|
<td>
|
|
\image html hdfview-prop.png
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|
</td>
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|
</tr>
|
|
</table>
|
|
|
|
To examine the data in the granule, click twice on it with the left mouse button in the TreeView,
|
|
and it will open in a new window.:
|
|
<table>
|
|
<tr>
|
|
<td>
|
|
\image html hdfview-regref.png
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
|
|
If you click twice with the left mouse button on the fifth Region Reference
|
|
<code style="background-color:whitesmoke;">/All_Data/VIIRS-M1-SDR_All/NumberOfScans</code> a window
|
|
will pop up with the value(s) of the reference:
|
|
<table>
|
|
<tr>
|
|
<td>
|
|
\image html hdfview-regref2.png
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
|
|
You can also set a user option to automatically show the value(s) in a Region Reference. Under the
|
|
<code style="background-color:whitesmoke;">Tools</code> pull-down menu, select
|
|
<code style="background-color:whitesmoke;">User Options</code> and then select
|
|
<code style="background-color:whitesmoke;">HDF Settings</code> and then select
|
|
<code style="background-color:whitesmoke;">Show RegRef Values</code> in the
|
|
<code style="background-color:whitesmoke;">Data</code> section (see the middle of the image below):
|
|
<table>
|
|
<tr>
|
|
<td>
|
|
\image html hdfview-regrefval.png
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
|
|
Then you will automatically see the values of the Region Reference when you open it and select an entry:
|
|
<table>
|
|
<tr>
|
|
<td>
|
|
\image html hdfview-regref1.png
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
|
|
You can view and set quality flags by clicking the right mouse button over a quality flags dataset under
|
|
<code style="background-color:whitesmoke;">All_Data</code> and selecting
|
|
<code style="background-color:whitesmoke;">Open As</code> from the pop-up menu. In the middle of
|
|
the window that pops up, you will see where you can specify <code style="background-color:whitesmoke;">Bitmask</code> options.
|
|
<table>
|
|
<tr>
|
|
<td>
|
|
\image html hdfview-qf.png
|
|
</td>
|
|
</tr>
|
|
</table>
|
|
|
|
<hr>
|
|
Navigate back: \ref index "Main" / \ref GettingStarted / \ref ViewToolsCommand
|
|
|
|
*/
|