617 questions
0
votes
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answers
81
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Python: Diagonalize a matrix of very high dimension?
Currently I am working on a problem which involves diagonalizing a matrix to get the eigen values and eigen vector. But now I want to expand the problem to a dimension of 200,000 x 200,000 in size.
I ...
0
votes
1
answer
138
views
Accessing hdf5 file datablock using tables rather than h5py
I had had some success reading hdf5 files generated from MSC/Nastran using both h5py and tables. Now I’m trying to do the same with a file generated by Simcenter/Nastran and I’m having trouble because ...
- 3
0
votes
1
answer
335
views
Add collect PyTables library to PyInstaller SPEC File
I am using PyInstaller to build an executable of a python script containing PyTables.
Since I've updated to the newest version, building the executable fails. The error reads:
Error: RuntimeError: ...
- 65
1
vote
1
answer
204
views
Filtering PyTables PerformanceWarning with warnings.filterwarnings() fails
There are a number of answers on this website detailing how one can ignore specific warnings in python (either by category or by providing a regex to match a warning message).
However, none of these ...
- 744
6
votes
1
answer
2k
views
PyTables install with python 3.11 fails on macOS M1
$ python -m pip install tables
stops with
Error: compiling Cython file
Environment
(I am within a virtual environment, created with pyenv. )
Only few packages installed atm
Package Version
------...
- 117
1
vote
0
answers
472
views
use Python to Read/Write a large HDF5 file in remote server
I am currently maintaining a large data file (over 10G) that is updated daily on a Linux server. The data is in HDF5 format with groups and datasets.
Now I have a local Windows client that needs to ...
- 11
1
vote
1
answer
79
views
How to resolve 'ValueError: invalid literal for int() with base 10: '5,3,2'' while reading hdf5 file using pandas?
I am trying to read a hdf5 file using Pandas, but getting this error:
ValueError: invalid literal for int() with base 10: '5,3,2'
I am only calling data = pd.read_hdf(path), so I have like no idea ...
- 374
1
vote
2
answers
191
views
How to choose whether to persist or discard changes in HDF5 file before closing
I'd like to manipulate a set of data in an hdf5 file and be able to decide, before closing the file, whether to discard every changes or not.
From the doc of File drivers:
HDF5 ships with a variety ...
- 1,412
-1
votes
2
answers
919
views
Pytables - simple h5 data
I'm finding it a lot harder to read in h5 data with pytables than I thought I would.
I can use the software hdfview to see indeed my h5 file is essentially a few 2d tables. This isn't useful to the ...
- 71
1
vote
2
answers
2k
views
Problems installing pytables on M1 Mac
I'm trying to install pytables on an M1 Mac (MacOS 12.6.1, python 3.11 and hdf5 1.12.2 installed using homebrew). Following the advice in https://stackoverflow.com/a/74276925 I did the following:
pip ...
- 438
1
vote
1
answer
76
views
Why cannot append rows to a non-chunked table
loadstep_row_data = loadsteps_table.row
for i in range(1, num_loadsteps_to_append):
loadstep_row_data ['loadStepID'] = i+1
loadstep_row_data ['profileID'] = i+1
...
- 37
2
votes
1
answer
720
views
How to save a list in a pandas dataframe cell to a HDF5 table format?
I have a dataframe that I want to save in the appendable format to a hdf5 file. The dataframe looks like this:
column1
0 [0, 1, 2, 3, 4]
And the code that replicates the issue is:
import pandas ...
- 993
0
votes
2
answers
347
views
What is the best way to query a pytable column with many values?
I have a 11 columns x 13,470,621 rows pytable. The first column of the table contains a unique identifier to each row (this identifier is always only present once in the table).
This is how I select ...
- 187
0
votes
1
answer
152
views
Pandas time series index attribute error when using TsTables & PyTables in creating a table class
I am trying to create a table structure through tb.IsDescription class, then create a .h5 file and populate it with a Pandas Dataframe with Datetime index, using TsTables package. I have already ...
- 1
0
votes
1
answer
487
views
HDF5 and PyTables: How to read data when the table or group name includes blank characters
How can I read a hdf5 table datablock as:
domains = h5.root.'a name with blanks'
If this is not possible, but maybe with special signs?
- 15