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Questions tagged [hdf5]

The Hierarchical Data Format (HDF5) is a binary file format designed to store large amount of numerical data.

HDF5 refers to:

  • A binary file format designed to store efficiently large amount of numerical data
  • Libraries of function to create and manipulate these files

Main features

  • Free
  • Completely portable
  • Very mature
  • No limit on the number and size of the datasets
  • Flexible in the kind and structure of the data and meta-data
  • Complete library in C and Fortran well documented
  • A lot of wrappers and tools are available (Python, Matlab, Java, …)

Some links to get started

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HDF5 hid_t obj_id? Difference between HDF5 API and other hdf5-functions

I'm trying to work with HDF5-Files (in C++). Therefor I work with the Examples from the HDF5-API: http://www.hdfgroup.org/HDF5/doc/cpplus_RM/namespaceH5.html There are a lot of useful examples but I have trouble when I try to "mix" it with other…
smaica
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lxml.etree.parse segfaults when h5py has been imported

I am having difficulty using lxml and h5py together in the same package. When they have both been imported, even if they are not imported in the same file, calling lxml.etree.parse() always segfaults. In [1]: from lxml import etree In [2]: parser =…
Vorticity
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hdf5 example code h5_rdwt.c does not work

I have a problem running an example code from hdf5 called h5_rdwt.c (in eclipse). You can find this here: http://www.hdfgroup.org/HDF5/Tutor/rdwt.html#rdwr The code is: /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * …
smaica
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Pandas not modifying default hdf format

I'm trying to store data to hdf format and want to set the default data type to table so I can query it later. I am using the basic code: import pandas as pd from numpy import random as R pd.set_option('io.hdf.default_format','table') s =…
Lucidnonsense
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Python 2.7: Appending Data to Table in Pandas

I am reading data from image files and I want to append this data into a single HDF file. Here is my code: datafile = pd.HDFStore(os.path.join(path,'imageData.h5')) for file in fileList: data = {'X Position' : pd.Series(xpos, index=index1), …
salamander
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Android NDK: compile HDF5 library with source code

Now I have a 3rd party library (HDF5)in source code. But this library is written in C++. Is it possible to use android NDK to compile it? How? Do I need to write own makefile to configure it OR use android.mk to configure? And I found this library…
Saddy
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R reading HDF5 data from a specific subset

At this point i am working on a project where i have to use large HDF5 files in R. I have a HDF5 file which consists of 4 subsets. the structure is as followed: MeansSIS.HDF5 Quality (32-bit floating-point,735 x 1980) TOA (32-bit floating-point,735…
Jurgen1213
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HDF5 Read Dataset in Thread Error

I write Server Application which will send extracted data from HDF5 files to many clients simultaneously There is a code (run in separate thread): var _fileID = H5F.open("C:\\Temp\\MLS-Aura_L2GP-Temperature_v03-33-c01_2012d347.he5",…
woken
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Vitables or other HDF5 viewers on Windows?

I was looking for a hdf5 viewer for windows and came across vitables. However, vitables requires sip, which has all kinds of install problems under Anaconda... another alternative would be HDFview, but that requires a full Java installation (I use…
H. Arponen
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Difficulty parsing hdf5 compound data type

Using h5dump on the .h5 file, I see the following dataset: GROUP "T" { DATASET "CON" { DATATYPE H5T_COMPOUND { H5T_IEEE_F32LE "price"; H5T_STRING { STRSIZE 1; STRPAD H5T_STR_NULLTERM; CSET…
user3135658
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packet table with heterogeneous rows

I'm trying to store some data in HDF5 using the C++ API, with several requirements: an arbitrary number of entries can be stored, each entry has the same number of rows (of types int and double), the number and type of the rows should be…
Shep
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Open hdf5 string dataset

I am just wondering why I am getting these errors.I already included H5cpp.h.Here I am just trying to read a string from existing hdf5 database.Also I am not sure how I would define memspace. Thank you Reader.cpp: In member function ‘void…
tryu hjkl
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HDF5 Fortran90 append data as hyperslabs - only first column working

I have a Fortran 90 program that creates a large column of integers at the end of each loop. I would like to write this column into an HDF5 file with each new integer column being written as a new column in the HDF5 file. That is, at the end of the…
EP_Guy
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Pandas and HDF5 aggregate performance

I'm trying to understand the ideal way to organise data within Pandas to achieve the best aggregating performance. The data I am dealing with is of the form yyyy-mm.csv which I just read_csv in and then to_hdf out. It generally looks something a bit…
user3043451
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compressing HDF5 files in Mathematica

I am working with Mathematica 9 and exporting huge lists (a typical list will have dimensions of 182500,4,8,42). Each file has about 6 lists of this size (all integers, not sure if this makes a difference in lists, I know it do in other array types,…
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