hdf5 | Official HDF5® Library Repository
kandi X-RAY | hdf5 Summary
kandi X-RAY | hdf5 Summary
HDF5 version 1.13.1-1 currently under development.
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hdf5 Key Features
hdf5 Examples and Code Snippets
def load_model_from_hdf5(filepath, custom_objects=None, compile=True): # pylint: disable=redefined-builtin
"""Loads a model saved via `save_model_to_hdf5`.
Args:
filepath: One of the following:
- String, path to the saved model
def load_weights_from_hdf5_group_by_name(
f, layers, skip_mismatch=False):
"""Implements name-based weight loading.
(instead of topological weight loading).
Layers that have no matching name are skipped.
Args:
f: A pointer to a H
def save_model_to_hdf5(model, filepath, overwrite=True, include_optimizer=True):
"""Saves a model to a HDF5 file.
The saved model contains:
- the model's configuration (topology)
- the model's weights
- the model's optimizer's
Community Discussions
Trending Discussions on hdf5
QUESTION
I am trying to install the hdf5 library from Homebrew. Running brew install hdf5
in the terminal returns the following error message:
==> Searching for similarly named formulae...
Error: No similarly named formulae found.
Error: No available formula or cask with the name "hdf5".
==> Searching for a previously deleted formula (in the last month)...
Error: No previously deleted formula found.
==> Searching taps on GitHub...
Error: No formulae found in taps.
I am running this on a mac with Mojave version 10.14.6. What next steps should I try to download the hdf5 library?
...ANSWER
Answered 2021-Jun-07 at 21:53It seems that at least part of my Homebrew download was in the wrong location. Running brew doctor
, I got Warning: Homebrew/homebrew-core was not tapped properly!
. This was fixed by running rm -rf "/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core"
and then brew tap homebrew/core
.
QUESTION
So I have this dataloader that loads data from hdf5 but exits unexpectedly when I am using num_workers>0 (it works ok when 0). More strangely, it works okay with more workers on google colab, but not on my computer. On my computer I have the following error:
Traceback (most recent call last): File "C:\Users\Flavio Maia\AppData\Roaming\Python\Python37\site-packages\torch\utils\data\dataloader.py", line 986, in _try_get_data data = self._data_queue.get(timeout=timeout) File "C:\Program Files (x86)\Microsoft Visual Studio\Shared\Python37_64\lib\multiprocessing\queues.py", line 105, in get raise Empty _queue.Empty
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "", line 2, in File "C:\Users\Flavio Maia\AppData\Roaming\Python\Python37\site-packages\torch\utils\data\dataloader.py", line 517, in next data = self._next_data() File "C:\Users\Flavio Maia\AppData\Roaming\Python\Python37\site-packages\torch\utils\data\dataloader.py", line 1182, in _next_data idx, data = self._get_data() File "C:\Users\Flavio Maia\AppData\Roaming\Python\Python37\site-packages\torch\utils\data\dataloader.py", line 1148, in _get_data success, data = self._try_get_data() File "C:\Users\Flavio Maia\AppData\Roaming\Python\Python37\site-packages\torch\utils\data\dataloader.py", line 999, in _try_get_data raise RuntimeError('DataLoader worker (pid(s) {}) exited unexpectedly'.format(pids_str)) from e RuntimeError: DataLoader worker (pid(s) 12332) exited unexpectedly
Also, my getitem function is:
...ANSWER
Answered 2021-Jun-05 at 07:59Windows can't handle num_workers > 0
. You can just set it to 0 which is fine. What also should work: Put all your train / test script in a train/test()
function and call it under if __name__ == "__main__":
For example like this:
QUESTION
I have a Tensorflow
model already trained in my notebook, and I want to plot accuracy and loss after that.
Here is my code:
...ANSWER
Answered 2021-May-31 at 18:58Try this:
QUESTION
So I'm trying to access entries in subdirectories in a HDF5 file. Below is my code
...ANSWER
Answered 2021-May-30 at 16:41I think the problem is that you actually have a bytes
object being returned (I can't be sure without reproducing it with your data). The problem is you don't want to use str()
to decode the bytes, because that's what's giving you the 'b' in the first place. Instead use entry.decode()
to convert the bytes
to a str
.
QUESTION
I want to create a scatter plot with the X-Axis as the longitude coordinates in the healpix file https://wwwmpa.mpa-garching.mpg.de/~ensslin/research/data/faraday2020.html (Healpix)
and the Y-Axis as the mean values in hdf5 file https://wwwmpa.mpa-garching.mpg.de/~ensslin/research/data/faraday2020.html (Faraday sky 2020)
Code until now:
...ANSWER
Answered 2021-May-24 at 17:29I think you're close. IMHO, this scatter plot is easier than plotting with both skyplot coordinates (projection="aitoff"
). The process is similar to the answers I posted on your earlier question: Plot mean and standard dev values on skyplot using astropy from hdf5 file. You just need some minor teaks to the function parameters.
I modified your code to create a 2D scatter plot. Here's a quick summary of the differences:
- Changed
from astropy.coordinates import SkyCoord
(instead ofHEALPix
) - Changed matplot type (remove
projection=
) - Changes y-variable from
b_rad
tofaraday_sky_mean
on scatter plot. - Deleted
c=faraday_sky_mean
fromplt.scatter()
so data points are not color coded.
See code below.
QUESTION
I'm working on converting a large database for storage in an HDF5 file. To get familiar with H5Py (version 3.2.1) and HDF5, I read the docs for H5Py and wrote a small script that stores random data in an HDF5 file, shown below.
...ANSWER
Answered 2021-May-22 at 17:44Per the comments by @hpaulj, I investigated the different versions. The version of HDFView in the Ubuntu repository is so old that it isn't able to open the generated HDF5 file. Switching to h5dump, I was able to verify the structure of my file was written correctly.
QUESTION
So I used Bert model trained it and saved it as hdf5 file, but when I try to predict , it shows this error :
IndexError: list index out of range
here is the code
...ANSWER
Answered 2021-May-18 at 01:44As shown in the ktrain tutorials and example notebooks like this one, you need to use the Predictor
instance to make predictions on raw text inputs:
QUESTION
I would like to get the byte contents of a pandas dataframe exported as hdf5, ideally without actually saving the file (i.e., in-memory).
On python>=3.6, < 3.9
(and pandas==1.2.4
, pytables==3.6.1
) the following used to work:
ANSWER
Answered 2021-May-18 at 12:59The fix was to do conda install -c conda-forge pytables
instead of pip install pytables
. I still don't understand the ultimate reason behind the error, though.
QUESTION
I have a bunch of images (of cats) and want to plot one of them. The values image are in the format UInt8
and contain 3 bands. When I try to plot using plots I get the following error, ERROR: StackOverflowError
.
ANSWER
Answered 2021-May-14 at 16:23First, I'd be careful about how you're reshape
ing; I think this will merely rearrange the pixels in your images instead of swapping the dimensions, which it seems like you want to do. You may want train_data_rsp = permutedims(train_data_x, (4, 2, 3, 1))
which will actually swap the dimensions around and give you a 209×64×64×3
array with the semantics of which pixels belong to which images preserved.
Then, Julia's Images
package has a colorview
function that lets you combine the separate R,G,B channels into a single image. You'll first need to convert your array element type into N0f8
(a single-byte format where 0 corresponds to 0 and 255 to 1) so that Images
can work with it. It would look something like this:
QUESTION
I made a simple HDF5 reader class to avoid loading entire dataset in memory. I used sequence class to do so, but I'm not sure if on_epoch_end() function will trigger correctly.
I put a single print inside it, but it never appear! So I think there is something wrong in my code:
...ANSWER
Answered 2021-May-14 at 07:24Since seems to be a TF bug, I found a workaround to trigger on_epoch_end()
of my generator.
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