Questions tagged [hdf5-format]
The hdf5-format tag has no usage guidance.
30 questions
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Splitting HDF5 file
Below I am attaching the h5 file that I want to analyze.
There are two branches "S_F_VAL_0", "S_F_VAL_1"
Each branch has 10 branches, which then have a dataset that is a 3D array ...
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1
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Strange behavior exporting UnsignedInteger64 in HDF5 format
The UnsignedInteger64 data format should be able to encode correctly any integer in $[0,2^{64}-1]$. When using this data format with ...
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Handling Missing Values in HDF5
Suppose you have a dataset with missing or "bad" values e.g.
X = RandomReal[{0, 1}, {10000000}];
X = If[# < 0.1, "Bad", #] & /@ X;
...
- 1,334
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1
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Some problems importing *.hdf5 files in MA12.2
I'm attempting to Import datasets from a *.hdf5 file into Mathematica 12.2 in Win 7.
After looking at the syntax in the Wolfram Documentation Center and displaying the StructureGraph, I had no problem ...
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Export high precision data to HDF5
Recently, I would like to use HDF5 instead of CSV because of times Import taking.
Especially, I have to manage large data with high precision (about 50 degits) and ...
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Delete dataset from hdf5 file
Is there any way to remove a dataset from an hdf5 file using mathematica? Or, alternatively, is it possible to overwrite a dataset while keeping the other datasets intact?
I've tried the following
<...
- 369
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2
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308
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Where is HDF5Tools documentation?
MMA 12 apparently has a new package, HDF5Tools, which includes desperately needed functions that allow one to open an HDF5 file, get data from it, then close it ...
- 1,352
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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 ...
- 31.8k
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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 ...
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143
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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 ...
- 133
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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 ...
- 133
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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
...
- 5,026
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102
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HDF5 does not support string?
I did a simulation for Baccarat.
So some results are saved like this.
...
- 5,026
3
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0
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61
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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,
...
- 5,026
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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.
- 2,493
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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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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
...
- 8,529
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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 ...
- 31.8k
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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 ...
9
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2
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996
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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 ...
- 1,048
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3
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499
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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 ...
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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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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 ...
user16306
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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 ...
- 1,800
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4
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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 ...
- 181
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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:
...
- 1,364
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1
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291
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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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1
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783
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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 ...
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4
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2k
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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 ...
- 13.8k
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4
answers
2k
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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 ...
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