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Questions tagged [hdf]

Hierarchical Data Format (HDF, HDF4, or HDF5) is a set of file formats and libraries designed to store and organize large amounts of numerical data.

Hierarchical Data Format (HDF, HDF4, or HDF5) is a set of file formats and libraries designed to store and organize large amounts of numerical data.

Originally developed at the National Center for Supercomputing Applications, it is supported by the non-profit HDF Group, whose mission is to ensure continued development of HDF5 technologies, and the continued accessibility of data stored in HDF.

In keeping with this goal, the HDF format, libraries and associated tools are available under a liberal, BSD-like license for general use. HDF is supported by many commercial and non-commercial software platforms, including Java, MATLAB/Scilab, Octave, IDL, Python, and R. The freely available HDF distribution consists of the library, command-line utilities, test suite source, Java interface, and the Java-based HDF Viewer (HDFView).

There are two major versions of HDF; HDF4 and HDF5, which differ significantly in design and API.

Wikipedia: http://en.wikipedia.org/wiki/Hierarchical_Data_Format

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How to filter for specific objects in a HDF5 file

Learning the ILNumerics HDF5 API. I really like the option to setup a complex HDF5 file in one expression using C# object initializers. I created the following file: using (var f = new H5File("myFile.h5")) { f.Add(new H5Group("myTopNode") { …
user492238
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How to use HDF to store a very large matrix

I am planning to use HDF to store a very large matrix, something like 1e6 x 1e6 of floats. I would need to read the matrix in batches of consecutive rows or columns. My question is, what would be the optimal way to structure/tweak the HDF file to…
Bitwise
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How do I represent a multi-block cylindrical system in XDMF v2?

I can represent my HDF5 files using XDMF (specific type XMF used in CFD). But it is recognizing my R-Z coordinates and X-Y coordinates. It thinks I am working in 2D Cartesian X-Y. In other words, the variable X is actually Radius, R and Y is…
wander95
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HDF5/NetCDF: Reading a Java array in parallel using Scala

I have a code as shown below. The HDF5 dataset/NetCDF variable is an array of size k*N where k is the number of sets and N is the number of elements (3-D points). Currently, I am reading it as a 1-D array and then splitting it into arrays to create…
Quiescent
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Is not an HDF5 file error when iterating over multi-resolution HDF5 files

I want to run cooler balance (from cooler) on each resolution of each file with .mcool extension. for mcool_file in input/*.mcool; do while IFS= read -r id; do # id=./../input/A001C007.hg38.nodups.pairs.mcool::/resolutions/200 cooler…
melolili
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How do I make GDAL use HDF4 formats?

After manually installing the HDF4 library (it is not available with Homebrew), my GDAL (installed via Homebrew) does not support HDF4 file formats (gdalinfo --formats). How can I solve this problem?
LiWa
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Why is GDAL on Mac terminal not opening my .hdf-files from MODIS Terra/Aqua?

I try to get one variable raster data set from a multidimensional .hdf file using gdal_translate. The type of file I try to open is from: https://e4ftl01.cr.usgs.gov/MOTA/MCD12C1.061/2021.01.01/ Why is GDAL on Mac Terminal providing me with the…
LiWa
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Unable to get data from hdf file in python

I have two hdf files, hdf4 and hdf5. In both cases, I am able to load the files in python using respective libraries (pyhdf and h5py). But inside the files, I can only read the data fields' name, size, and other parameters. The datasets are coming…
Sky
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create hdf5 compound dataset with field/column labels

I have a problem creating the hdf5 file schema like the image below. I can make the first level grouping without a problem. And I can make the traces and rge labels datasets but I have a really hard time recreating the metadata because it contains…
nAo
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Converting HDF files to GeoTiff files using Python's GDAL

I want, convert the file named "MAM35S0.A2008010.0000.002.2008010173218.hdf"(MODIS Aqua product) to GTiff format. The datasheet is "HDF4_EOS:EOS_SWATH:"MAM35S0.A2008010.0000.002.2008010173218.hdf":mod35:Cloud_Mask", but normal conversion was not…
ZEESEN
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I get error when I install hdf5 with Cmake

I get error when I install hdf5 with CMake. When I run the build-VS2019-64.bat file built with VSCode on cmd, I get the error below: No tests were found!!! When I run cmake in the command, it worked fine, so it doesn't seem to be a problem with…
Jay Kim
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h5py problem - driver lock request failed - how to fix? (under WSL Ubuntu)

I am trying to use the h5py (https://pypi.org/project/h5py/) package to handle the data of datasets in that format. I am using a side library to write datasets in that format, it uses the h5py. I got the following error when I tried to use their…
twistfire
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HDF5 Extend 1-D Dataset (C++)

I am trying to create a dataset in a HDF5 file and then extend it. I have a toy example, based largely on this demo. Here is my code: #include #include using namespace H5; int main(int argc, char* argv[]) { const int DIM0 =…
Mr Squid
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Split 1 HDF file into 2 HDF files at the ratio of 90:10

I am trying to process data to train a model. I have a dataset processed and saved in a HDF5 file (original HDF file) to separate into two unoverlapping HDF files at the ratio 90:10. I would like to separate data stored in that HDF file into two…
christine
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Make hdf5-1.14.0 on Debian: conflicting types for ‘ssize_t’

I have tried building HDF5 from source, on a virtual machine Linux #1 SMP Debian 5.10.140-1 (2022-09-02). I followed the basic instructions: gunzip < hdf5-1.14.0.tar.gz | tar xf - cd hdf5-1.14.0 ./configure…
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