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> User's Guide: Hierarchical datasets in Python - Release 1.3.2</TH
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>Appendix C. Utilities</TD
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>This utility is a very powerful one and lets you copy any
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leaf, group or complete subtree into another file. During
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the copy process you are allowed to change the filter
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properties if you want so. Also, in the case of duplicated
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pathnames, you can decide if you want to overwrite already
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existing nodes on the destination file. Generally
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> can be useful in may
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situations, like replicating a subtree in another file,
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change the filters in objects and see how affect this to
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the compression degree or I/O performance, consolidating
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specific data in repositories or even <SPAN
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> files and create true
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NAME="subsectionC.2.1"
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>For instructions on how to use it, just pass the
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> flag to the command:
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to see the message usage:
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> usage: ptrepack [-h] [-v] [-o] [-R start,stop,step] [--non-recursive]
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[--dest-title=title] [--dont-copyuser-attrs] [--overwrite-nodes]
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[--complevel=(0-9)] [--complib=lib] [--shuffle=(0|1)]
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[--fletcher32=(0|1)] [--keep-source-filters]
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sourcefile:sourcegroup destfile:destgroup
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-h -- Print usage message.
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-v -- Show more information.
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-o -- Overwite destination file.
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-R RANGE -- Select a RANGE of rows (in the form "start,stop,step")
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during the copy of *all* the leaves.
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--non-recursive -- Do not do a recursive copy. Default is to do it.
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--dest-title=title -- Title for the new file (if not specified,
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the source is copied).
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--dont-copy-userattrs -- Do not copy the user attrs (default is to do it)
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--overwrite-nodes -- Overwrite destination nodes if they exist. Default is
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to not overwrite them.
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--complevel=(0-9) -- Set a compression level (0 for no compression, which
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--complib=lib -- Set the compression library to be used during the copy.
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lib can be set to "zlib", "lzo", "ucl" or "bzip2". Defaults to "zlib".
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--shuffle=(0|1) -- Activate or not the shuffling filter (default is active
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--fletcher32=(0|1) -- Whether to activate or not the fletcher32 filter (not
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--keep-source-filters -- Use the original filters in source files. The
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default is not doing that if any of --complevel, --complib, --shuffle
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or --fletcher32 option is specified.
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NAME="subsectionC.2.2"
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>C.2.2. A small tutorial on <SPAN
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>Imagine that we have ended the tutorial 1 (see the
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>examples/tutorial1-1.py</SAMP
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want to copy our reduced data (i.e. those datasets that
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file. First, let's remember the content of the
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>examples/tutorial1.h5</SAMP
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> $ ptdump tutorial1.h5
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Filename: 'tutorial1.h5' Title: 'Test file' , Last modif.: 'Fri Feb 6
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19:33:28 2004' , rootUEP='/', filters=Filters(), Format version: 1.2
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/ (Group) 'Test file'
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/columns (Group) 'Pressure and Name'
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/columns/name (Array(3,)) 'Name column selection'
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/columns/pressure (Array(3,)) 'Pressure column selection'
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/detector (Group) 'Detector information'
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/detector/readout (Table(10L,)) 'Readout example'
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non-existing file. That's easy:
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> $ ptrepack tutorial1.h5:/columns reduced.h5
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That's all. Let's see the contents of the newly created
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> $ ptdump reduced.h5
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Filename: 'reduced.h5' Title: '' , Last modif.: 'Fri Feb 20 15:26:47 2004' ,
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rootUEP='/', filters=Filters(), Format version: 1.2
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/name (Array(3,)) 'Name column selection'
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/pressure (Array(3,)) 'Pressure column selection'
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so, you have copied the children of
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> group into the <SPAN
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>Now, you suddenly realized that what you intended to do
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was to copy all the hierarchy, the group
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> itself included. You can do that
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by just specifying the destination group:
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> $ ptrepack tutorial1.h5:/columns reduced.h5:/columns
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Filename: 'reduced.h5' Title: '' , Last modif.: 'Fri Feb 20 15:39:15 2004' ,
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rootUEP='/', filters=Filters(), Format version: 1.2
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/name (Array(3,)) 'Name column selection'
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/pressure (Array(3,)) 'Pressure column selection'
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/columns/name (Array(3,)) 'Name column selection'
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/columns/pressure (Array(3,)) 'Pressure column selection'
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OK. Much better. But you want to get rid of the existing
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nodes on the new file. You can achieve this by adding
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> $ ptrepack -o tutorial1.h5:/columns reduced.h5:/columns
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Filename: 'reduced.h5' Title: '' , Last modif.: 'Fri Feb 20 15:41:57 2004' ,
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rootUEP='/', filters=Filters(), Format version: 1.2
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/columns/name (Array(3,)) 'Name column selection'
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/columns/pressure (Array(3,)) 'Pressure column selection'
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where you can see how the old contents of the
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> file has been overwritten.
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>You can copy just one single node in the repacking
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operation and change its name in destination:
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> $ ptrepack tutorial1.h5:/detector/readout reduced.h5:/rawdata
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Filename: 'reduced.h5' Title: '' , Last modif.: 'Fri Feb 20 15:52:22 2004',
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rootUEP='/', filters=Filters(), Format version: 1.2
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/rawdata (Table(10L,)) 'Readout example'
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/columns/name (Array(3,)) 'Name column selection'
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/columns/pressure (Array(3,)) 'Pressure column selection'
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>/detector/readout</SAMP
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>We can change the filter properties as well:
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> $ ptrepack --complevel=1 tutorial1.h5:/detector/readout reduced.h5:/rawdata
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Problems doing the copy from 'tutorial1.h5:/detector/readout' to
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'reduced.h5:/rawdata'
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The error was --> exceptions.ValueError: The destination
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(/rawdata (Table(10L,)) 'Readout example') already exists.
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Assert the overwrite parameter if you really want to overwrite it.
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The destination file looks like:
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Filename: 'reduced.h5' Title: ''; Last modif.: 'Fri Feb 20 15:52:22 2004';
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rootUEP='/'; filters=Filters(), Format version: 1.2
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/rawdata (Table(10L,)) 'Readout example'
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/columns/name (Array(3,)) 'Name column selection'
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/columns/pressure (Array(3,)) 'Pressure column selection'
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Traceback (most recent call last):
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File "../utils/ptrepack", line 358, in ?
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start=start, stop=stop, step=step)
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File "../utils/ptrepack", line 111, in copyLeaf
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raise RuntimeError, "Please, check that the node names are not
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duplicated in destination, and if so, add the --overwrite-nodes flag
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RuntimeError: Please, check that the node names are not duplicated in
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destination, and if so, add the --overwrite-nodes flag if desired.
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ooops!. We ran into problems: we forgot that
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> pathname already existed
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in destination file. Let's add the
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>--overwrite-nodes</SAMP
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> $ ptrepack --overwrite-nodes --complevel=1 tutorial1.h5:/detector/readout
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Filename: 'reduced.h5' Title: ''; Last modif.: 'Fri Feb 20 16:02:20 2004';
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rootUEP='/'; filters=Filters(), Format version: 1.2
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/rawdata (Table(10L,), shuffle, zlib(1)) 'Readout example'
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/columns/name (Array(3,)) 'Name column selection'
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/columns/pressure (Array(3,)) 'Pressure column selection'
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you can check how the filter properties has been changed
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> table. Check as the other
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>Finally, let's copy a <SPAN
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> table in origin to destination,
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under a new group called <SAMP
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the name, for example, <SAMP
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> $ ptrepack -R1,8,3 tutorial1.h5:/detector/readout reduced.h5:/slices/aslice
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Filename: 'reduced.h5' Title: ''; Last modif.: 'Fri Feb 20 16:17:13 2004';
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rootUEP='/'; filters=Filters(); Format version: 1.2
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/rawdata (Table(10L,), shuffle, zlib(1)) 'Readout example'
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/columns/name (Array(3,)) 'Name column selection'
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/columns/pressure (Array(3,)) 'Pressure column selection'
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/slices/aslice (Table(3L,)) 'Readout example'
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note how only 3 rows of the original
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> table has been copied to the new
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> destination. Note as well how the
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previously inexistent <SAMP
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created in the same operation.
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