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Questions tagged [hdf5-format]

The tag has no usage guidance.

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1answer
87 views

Problem importing from HDF5

I'm trying to import an item from a valid HDF5 file, but I get this error: I can read the metadata, but cannot import the actual tensor dataset: And yet it's not an issue with the file's data - as ...
2
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0answers
43 views

Structured HDF5 Export doesn't create any output

I tried to use this example to organize my data, but ExportStructuredHDF5[file,data] just doesn't create or override a file in the specified folder... Minimal ...
2
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1answer
60 views

How to write both Attributes and DataFormat to an HDF5 file?

I can't figure out the command to Export an HDF5 file from Mathematica that includes both an Attribute and a DataFormat. I can do one or the other, but not both. Related questions: How to export ...
3
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1answer
311 views

How can I work with larger-than-memory hdf5 files

I am using Mathematica 11.0 and am trying to work with large .h5 files. Does anyone know if it's possible to work with files that are larger than the amount of available memory? I'm hoping that ...
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0answers
58 views

How to export this data/string more efficiently if possible at all? [duplicate]

Previously I asked a related question about my test data. Looking at the size of the data ans // ByteCount 9602605504 ...
3
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0answers
61 views

HDF5 does not support string?

I did a simulation for Baccarat. So some results are saved like this. ...
3
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0answers
37 views

Possible to add a “Heading” for the columns in HDF5 format?

A similar post was found here, but it's not using MMA. A small test to export HDF5 file, ...
1
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1answer
233 views

Mathematica + HDF5 basic examples

How to export/import basic Mathematica types using HDF5 file format? I find that the official Mathematica doc is missing some examples.
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0answers
120 views

Open a hdf5 file in SWMR (single writer multiple reader) mode in Mathematica 9.0?

I'm running an experiment where I want to be able to save my data to HDF5 on a shared network drive on one computer (using python and h5py), and be able to read it and do analysis while it's running (...
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2answers
406 views

Exporting structured data to HDF5

Sadly the documentation is lacking any useful examples on how to Export more complex data in HDF5. There is only ...
8
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1answer
222 views

How to export nontrivial data to h5?

Version 11.1.1 comes with improved support for the HDFv5 (HDF is an acronym for Hierarchical Data Format) file format. How can I export (and import) the following data into h5 format? The data I ...
1
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1answer
704 views

How to append new data to an already existed hdf5 file?

Assume I export some data into a file like: data = {{1, 2, 3}, {4, 5, 6}}; Export["test.h5",data,{"Datasets","/h1"}]; How can I append ...
8
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2answers
553 views

Extracting and displaying data from GW150914 hdf5 files

Has anyone looked at the LIGO data using Mathematica or know how to do this? I'm not familiar with the hdf5 format but I've been able to import the data, consisting primarily of 131,072 floating ...
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2answers
189 views

How can I export to HDF5 with a specific Datatype (“DataFormat”)

I am trying to export some largish integer arrays to HDF5 and know that every entry in them would fit into an unsigned 8 bit integer array. As the default "DataFormat" for export that Mathematica is ...
1
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3answers
831 views

HDF5 file managing for dummies

I am new to HDF5 format and I am also not hundred percent confident with Mathematica. I have googled to find out examples to deal with HDF5 files in Mathematica but couldn't find one that work out for ...
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0answers
173 views

File Formats for Scientific Data [duplicate]

I have a simulation written in another language which currently just dumps all its data (doubles, lists of doubles, lists of lists of doubles) in lines in ASCII, and then I read it into Mathematica by ...
6
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1answer
627 views

Best practices with HDF5 and Datasets

I work with colleagues who rely on HDF5 as their data interchange format (largely exported from Python's Pandas). Of course we ...
18
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4answers
751 views

HDF5 importing large arrays

I have some computations that output a 300,000,000 element array of long unsigned ints, so about 2.4GB, in an h5 file. Mathematica handles files south of 2GB fine, albeit taking very long to import ...
7
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2answers
660 views

HDF5 and complex numbers

I'm exporting an array with complex numbers with HDF5 format. When I'm import it, I only get the real part. Simple example: ...
0
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1answer
221 views

Importing and manipulating data in HDF format

I have two matrices A1 and A2 in HDF format. I use the following code to import them. ...
6
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1answer
552 views

Exporting multiple arrays in a single HDF5 file in Mathematica 7

Bug introduced in 7.0 and fixed in 8.0 I am using Mathematica 7 and I need to export a table of data and the corresponding x and ...
10
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3answers
1k views

How to export attributes or annotations to an HDF5 file?

I'm trying to export attributes and annotations to an HDF5 file. But the documentation here is horrible and there are no examples of this. I spent some time playing, but I can't get it to work. Here ...
14
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4answers
990 views

DataEncoding and compression in HDF5 format

I would like to export data in HDF5 format with Mathematica 9. The Mathematica manual about Import and Export of this format can be read here. As I'm dealing with large arrays, export often lead to ...