Modern IDL by Michael Galloy

API documentation for example code

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fileio/

mg_h5_getdata.pro

file i/o, hdf5, sdf

includes main-level program

Routine for extracting datasets, slices of datasets, or attributes from an HDF 5 file with simple notation.

Examples

An example file is provided with the IDL distribution: IDL> f = filepath('hdf5_test.h5', subdir=['examples', 'data']) A full dataset can be easily extracted: IDL> fullResult = mg_h5_getdata(f, '/arrays/3D int array') Slices can also be pulled out: IDL> bounds = [[3, 3, 1], [5, 49, 2], [0, 49, 3]] IDL> res1 = mg_h5_getdata(f, '/arrays/3D int array', bounds=bounds) IDL> help, res1 RESULT1 LONG = Array[1, 23, 17] Verify that the slice is the same as the slice pulled out of the fullResult: IDL> same = array_equal(fullResult[3, 5:*:2, 0:49:3], res1) IDL> print, same ? 'equal' : 'error' equal Normal IDL array indexing notation can be used as well: IDL> bounds = '3, 5:*:2, 0:49:3' IDL> res2 = mg_h5_getdata(f, '/arrays/3D int array', bounds=bounds) IDL> print, array_equal(res1, res2) ? 'equal' : 'error' equal The variable location and bounds can be combined to slice a variable: IDL> res3 = mg_h5_getdata(f, '/arrays/3D int array[3, 5:*:2, 0:49:3]') IDL> print, array_equal(res1, res3) ? 'equal' : 'error' equal Attributes can be accessed as well: IDL> print, mg_h5_getdata(f, '/images/Eskimo.CLASS') IMAGE This example is available as a main-level program included in this file: IDL> .run mg_h5_getdata

Author information

Author

Michael Galloy

Copyright

This library is released under a BSD-type license.

Copyright (c) 2007-2010, Michael Galloy <mgalloy@idldev.com>

All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

a. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. b. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. c. Neither the name of Michael Galloy nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Other file information

Todo:

better error messages when items not found

Routines

result = mg_h5_getdata_convertbounds(sbounds [, dimensions=lonarr(ndims)] [, /single])

Converts normal IDL indexing notation (represented as a string) into a lonarr(ndims, 3) where the first row is start values, the second row is the end values, and the last row is the stride value.

mg_h5_getdata_computeslab, bounds [, start=lonarr(ndims)] [, count=lonarr(ndims)] [, block=lonarr(ndims)] [, stride=lonarr(ndims)]

Compute the H5D_SELECT_HYPERSLAB arguments from the bounds.

result = mg_h5_getdata_getvariable(fileId, variable [, bounds=lonarr(3, ndims) or string] [, error=long])

Reads data in a dataset.

result = mg_h5_getdata_getattributedata(loc, attname)

Get the value of the attribute from its group, dataset, or type.

result = mg_h5_getdata_getattribute(fileId, variable [, error=long])

Get the value of an attribute in a file.

result = mg_h5_getdata(filename, variable [, bounds=lonarr(3, ndims) or string] [, error=long])

Pulls out a section of a HDF5 variable.

Routine details

top source mg_h5_getdata_convertboundsprivate

result = mg_h5_getdata_convertbounds(sbounds [, dimensions=lonarr(ndims)] [, /single])

Converts normal IDL indexing notation (represented as a string) into a lonarr(ndims, 3) where the first row is start values, the second row is the end values, and the last row is the stride value.

Return value

lonarr(ndims, 3)

Parameters

sbounds in required type=string

bounds specified as a string using IDL's normal indexing notation

Keywords

dimensions in optional type=lonarr(ndims)

dimensions of the full array; required if a '*' is used in sbounds

single out optional type=boolean

set to a named variable to determine if the bounds expression was specified in single-index dimensioning

top source mg_h5_getdata_computeslabprivate

mg_h5_getdata_computeslab, bounds [, start=lonarr(ndims)] [, count=lonarr(ndims)] [, block=lonarr(ndims)] [, stride=lonarr(ndims)]

Compute the H5D_SELECT_HYPERSLAB arguments from the bounds.

Parameters

bounds in required type=lonarr(ndims, 3)

bounds

Keywords

start out optional type=lonarr(ndims)

input for start argument to H5S_SELECT_HYPERSLAB

count out optional type=lonarr(ndims)

input for count argument to H5S_SELECT_HYPERSLAB

block out optional type=lonarr(ndims)

input for block keyword to H5S_SELECT_HYPERSLAB

stride out optional type=lonarr(ndims)

input for stride keyword to H5S_SELECT_HYPERSLAB

top source mg_h5_getdata_getvariableprivate

result = mg_h5_getdata_getvariable(fileId, variable [, bounds=lonarr(3, ndims) or string] [, error=long])

Reads data in a dataset.

Return value

value of data read from dataset

Parameters

fileId in required type=long

HDF 5 indentifier of the file

variable in required type=string

string navigating the path to the dataset

Keywords

bounds in optional type=lonarr(3, ndims) or string

gives start value, end value, and stride for each dimension of the variable

error out optional type=long

error value

top source mg_h5_getdata_getattributedataprivate

result = mg_h5_getdata_getattributedata(loc, attname)

Get the value of the attribute from its group, dataset, or type.

Return value

attribute data

Parameters

loc in required type=long

identifier of group, dataset, or type that contains the attribute

attname in required type=string

attribute name

top source mg_h5_getdata_getattributeprivate

result = mg_h5_getdata_getattribute(fileId, variable [, error=long])

Get the value of an attribute in a file.

Return value

attribute value

Parameters

fileId in required type=long

HDF 5 file identifier of the file to read

variable in required type=string

path to attribute using "/" to navigate groups/datasets and "." to indicate the attribute name

Keywords

error out optional type=long

error value

top source mg_h5_getdata

result = mg_h5_getdata(filename, variable [, bounds=lonarr(3, ndims) or string] [, error=long])

Pulls out a section of a HDF5 variable.

Return value

data array

Parameters

filename in required type=string

filename of the HDF5 file

variable in required type=string

variable name (with path if inside a group)

Keywords

bounds in optional type=lonarr(3, ndims) or string

gives start value, end value, and stride for each dimension of the variable

error out optional type=long

error value

File attributes

Modification date: Mon Mar 21 13:25:40 2011
Lines: 446
Docformat: rst rst