hdf5

Pytables h5py

由 天涯浪子 提交于 2020-03-01 12:22:17
Anthony Scopatz，南卡罗来纳大学助理教授，HDF客座博主 “Python 很棒，它的科学计算生态系统也是世界一流的。 HDF5 非常棒，是科学数据持久性的黄金标准。 许多人使用Python的HDF5，而这个数字只是由于 大熊猫的HDFStore 而增长 。 但是，使用Python的HDF5至少还有一个比它需要的结。 让我们改变它。“ 几乎在使用 Python的 HDF5时 ，您可以选择两个具有重叠功能的精彩软件包： h5py 和 PyTables 。 h5py使用自动生成的Cython更紧密地包装HDF5 API。 PyTables虽然也包装了HDF5，但更多地关注Table数据结构，并增加了复杂的索引和核心外查询。 您使用哪个包取决于您的使用案例 - 有时您真的需要两个！ 在 SciPy 2015上 ，来自PyTables，h5py，HDF Group，pandas以及社区成员的开发人员坐下来讨论了如何使Python和HDF5的故事更精简和更易于维护。 以下是我们提出的建议： 重构PyTables依赖于h5py与HDF5的结合。 更新h5py以支持PyTables重构（需要一些数据类型等）。 PyTables将保留其所有高级抽象。 使h5py - PyTables交互无缝。 确保API和HDF5文件向后兼容h5py和PyTable。 PyTables的主要版本号

h5py is running against HDF5 1.10.5 when it was built against 1.10.4

由 点点圈 提交于 2020-02-29 13:57:21
h5py is running against HDF5 1.10.5 when it was built against 1.10.4, this may cause problems '{0}.{1}.{2}'.format(*version.hdf5_built_version_tuple) conda安装的tensorflow报这个错误，安装更高版本的hdf5就行，然而conda目前最新就提供1.10.4版本哈哈哈a 找到一个简单的解决办法 pip uninstall h5py pip install h5py 可能是设置了某个变量吧，和conda默认的变量不一样 The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a

How to upload HDF5 file directly to S3 bucket in Python

由 蓝咒 提交于 2020-02-25 05:52:20
问题 I want to upload a HDF5 file created with h5py to S3 bucket without saving locally using boto3. This solution uses pickle.dumps and pickle.loads and other solutions I have found, store the file locally which I like to avoid. 回答1: You can use io.BytesIO() to and put_object as illustrated here 6. Hope this helps. Even in this case, you'd have to 'store' the data locally(though 'in memory'). You could also create a tempfile.TemporaryFile and then upload your file with put_object. I don't think

How to upload HDF5 file directly to S3 bucket in Python

由 牧云@^-^@ 提交于 2020-02-25 05:50:19
问题 I want to upload a HDF5 file created with h5py to S3 bucket without saving locally using boto3. This solution uses pickle.dumps and pickle.loads and other solutions I have found, store the file locally which I like to avoid. 回答1: You can use io.BytesIO() to and put_object as illustrated here 6. Hope this helps. Even in this case, you'd have to 'store' the data locally(though 'in memory'). You could also create a tempfile.TemporaryFile and then upload your file with put_object. I don't think

Creating HDF5 compound attributes using h5py

由 最后都变了- 提交于 2020-02-23 07:06:41
问题 I'm trying to create some simple HDF5 datasets that contain attributes with a compound datatype using h5py. The goal is an attribute that has two integers. Here are two example of attributes I'd like to create. My attempts end up with an array of two values such as How can I code this using h5py and get a single value that contains two integers? Current code looks something like dt_type = np.dtype({"names": ["val1"],"formats": [('<i4', 2)]}) # also tried np.dtype({"names": ["val1", "val2"],

Compressing HDF5 files with H5Py

由 送分小仙女□ 提交于 2020-02-05 03:48:32
问题 I'm passing thousands of .csv containing time and amplitude to a .hdf5 file. To give an example I used a small amount of .csv files which correspond to a total of ~11MB. After passing all the .csv to hdf5, the latter has a size of ~36MB (without using compression="gzip" ). By using compression="gzip" the file size is around 38MB. I understand that hdf5 is compressing the dataset only, that is, the numpy array in my case (~500 rows with float number). To make a comparison, I was saving all the

Matlab创建HDF5数据集-压缩

由 扶醉桌前 提交于 2020-01-27 09:16:01
概述 创建HDF5数据集必须先后使用h5create h5write命令 h5create官方链接 h5write官方链接 我创造的数据集大小是256x256x3x50000 每个256x256x3是RGB图片样本。 问题 如果在matlab里将RGB三维矩阵存成JPG，大小只有6KB 但是我把三维矩阵存入到HDF5中，大小竟达到200+KB 全部存取完大小达到200x50000=10GB，这对于我成万计的样本量是万万不能接受的。 解决 感谢 链接 的启发。 可以在h5create中加入压缩等级（0~9），采用gzip压缩。 h5create(filename,'/X',[3 256 256 Inf],'ChunkSize',[3 256 256 1],'Deflate',8); 这样单样本（算上其他附加标签）的大小就被压缩至9KB，达到期望大小。 解决完问题后才想起来，其实jpg也是采用了压缩算法才会把数据量变小的。如果h5create中未压缩，将会把样本中大量255值原封不动存入，自然会导致HDF5文件大小增大。 来源： CSDN 作者： pu扑朔迷离 链接： https://blog.csdn.net/bluehatihati/article/details/103767511

Inserting Many HDF5 Datasets Very Slow

由 折月煮酒 提交于 2020-01-24 20:30:28
问题 There is a dramatic slowdown when inserting many datasets into a group. I have found that the slowdown point is proportional to the length of the name and number of datasets. A larger dataset does take a bit longer to insert but it didn't affect when the slowdown occurred. The following example exaggerates the length of the name just to illustrate the point without waiting a long time. Python 3 HDF5 Version 1.8.15 (1.10.1 gets even slower) h5py version: 2.6.0 Example: import numpy as np

Determining signed state for HDF5 variables in NetCDF

由 点点圈 提交于 2020-01-24 12:55:19
问题 My team has been given HDF5 files to read. They contain structured data with unsigned variables. I and my team were overjoyed to find the NetCDF library, which allows pure-Java reading of HDF5 files, albeit using the NetCDF data model. No problem---we thought we'd just translate from the NetCDF data model to whatever model we wanted. As long as we get the data out. Then we tried to read an unsigned 32-bit integer from the HDF5 file. We can load up HDFView 2.9 and see that the variable is an

How can I write a large multidimensional array to an HDF5 file in parts?

由 旧时模样 提交于 2020-01-24 09:18:25
问题 I'm using HDF5DotNet in C# and I have a very large array (several GB) that I want to write to an HDF5 file. It's too big to store the whole thing in memory, so I'm generating regions of it at a time and want to write them out, but still have it look like one big array when it's read back out. I know this is possible with HDF5 but the documentation for the .NET API is somewhat sparse. I wrote some short example code with a 5 x 3 array filled with values 1..15: const int ROWS = 5; const int
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