hdf5 | Official HDF5® Library Repository

 by   HDFGroup C Version: snapshot License: Non-SPDX

kandi X-RAY | hdf5 Summary

kandi X-RAY | hdf5 Summary

hdf5 is a C library. hdf5 has no bugs and it has low support. However hdf5 has 18 vulnerabilities and it has a Non-SPDX License. You can download it from GitHub.

HDF5 version 1.13.1-1 currently under development.
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              hdf5 has a low active ecosystem.
              It has 365 star(s) with 191 fork(s). There are 25 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 167 open issues and 271 have been closed. On average issues are closed in 198 days. There are 17 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of hdf5 is snapshot

            kandi-Quality Quality

              hdf5 has no bugs reported.

            kandi-Security Security

              hdf5 has 18 vulnerability issues reported (4 critical, 5 high, 9 medium, 0 low).

            kandi-License License

              hdf5 has a Non-SPDX License.
              Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

            kandi-Reuse Reuse

              hdf5 releases are available to install and integrate.
              Installation instructions are not available. Examples and code snippets are available.

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            hdf5 Key Features

            No Key Features are available at this moment for hdf5.

            hdf5 Examples and Code Snippets

            Load a model from an hdf5 file .
            pythondot img1Lines of Code : 90dot img1License : Non-SPDX (Apache License 2.0)
            copy iconCopy
            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
              
            Load weights from a hdf5 group .
            pythondot img2Lines of Code : 84dot img2License : Non-SPDX (Apache License 2.0)
            copy iconCopy
            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  
            Save a model to an hdf5 file .
            pythondot img3Lines of Code : 80dot img3License : Non-SPDX (Apache License 2.0)
            copy iconCopy
            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

            QUESTION

            Unable to install hdf5 library from homebrew
            Asked 2021-Jun-07 at 21:57

            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 21:53

            It 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.

            Source https://stackoverflow.com/questions/67876124

            QUESTION

            Dataloader worker exited unexpectedly while running on Visual Studio. But runs okay on Google Colab
            Asked 2021-Jun-05 at 07:59

            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 07:59

            Windows 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:

            Source https://stackoverflow.com/questions/67258047

            QUESTION

            How to plot accuracy with a trained model
            Asked 2021-May-31 at 18:59

            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 18:58

            QUESTION

            How to supress b'' character when accessing HDF5 file in Python?
            Asked 2021-May-30 at 16:41

            So I'm trying to access entries in subdirectories in a HDF5 file. Below is my code

            ...

            ANSWER

            Answered 2021-May-30 at 16:41

            I 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.

            Source https://stackoverflow.com/questions/67763506

            QUESTION

            Plotting astronomical scatter plot - mean vs longitude (galactic)
            Asked 2021-May-24 at 17:29

            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 17:29

            I 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 of HEALPix)
            • Changed matplot type (removeprojection=)
            • Changes y-variable from b_rad to faraday_sky_mean on scatter plot.
            • Deleted c=faraday_sky_mean from plt.scatter() so data points are not color coded.

            See code below.

            Source https://stackoverflow.com/questions/67666918

            QUESTION

            Writing Data to an HDF5 File Using H5Py Results in an Empty File
            Asked 2021-May-22 at 17:44

            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 17:44

            Per 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.

            Source https://stackoverflow.com/questions/67551184

            QUESTION

            IndexError: list index out of range, NLP BERT Tensorflow
            Asked 2021-May-19 at 18:39

            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 01:44

            As 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:

            Source https://stackoverflow.com/questions/67577227

            QUESTION

            How to keep hdf5 binary of a pandas dataframe in-memory?
            Asked 2021-May-18 at 12:59

            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 12:59

            The 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.

            Source https://stackoverflow.com/questions/67488733

            QUESTION

            Plotting images from array containing datatype UInt8
            Asked 2021-May-14 at 16:23

            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 16:23

            First, I'd be careful about how you're reshapeing; 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:

            Source https://stackoverflow.com/questions/67455116

            QUESTION

            How be sure on_epoch_end triggers
            Asked 2021-May-14 at 07:24

            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 07:24

            Since seems to be a TF bug, I found a workaround to trigger on_epoch_end() of my generator.

            Source https://stackoverflow.com/questions/67182474

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install hdf5

            You can download it from GitHub.

            Support

            This release is fully functional for the API described in the documentation. Full Documentation and Programming Resources for this release can be found at. See the RELEASE.txt file in the release_docs/ directory for information specific to the features and updates included in this release of the library. Several more files are located within the release_docs/ directory with specific details for several common platforms and configurations.
            Find more information at:

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            https://github.com/HDFGroup/hdf5.git

          • CLI

            gh repo clone HDFGroup/hdf5

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            git@github.com:HDFGroup/hdf5.git

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