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Datasets are very similar to NumPy arrays. They are homogeneous collections of data elements, with an immutable datatype and hyper rectangular shape. They are represented in h5py by a thin proxy class which supports familiar NumPy operations like slicing, along with a variety of descriptive attributes:. See FAQ for the list of dtypes h5py supports. New datasets are created using either Group.
To make an empty dataset, all you have to do is specify a name, shape, and optionally the data type defaults to 'f':. Keywords shape and dtype may be specified along with data ; if so, they will override data. An HDF5 dataset created with the default settings will be contiguous ; in other words, laid out on disk in traditional C order. This means the dataset is divided up into regularly-sized pieces which are stored haphazardly on disk, and indexed using a B-tree.
Chunked storage makes it possible to resize datasets, and because the data is how to enable show translucent selection rectangle option trading in fixed-size chunks, to use compression filters. To enable chunked storage, how to enable show translucent selection rectangle option trading the keyword chunks to a tuple indicating the chunk shape:. Data will be read and written in blocks with shape; for example, the data in dset[0: Chunking has performance implications.
Also keep in mind that when any element in a chunk is accessed, the entire chunk is read from disk. Auto-chunking is also enabled when using compression or maxshapeetc. In HDF5, datasets can be resized once created up to a maximum size, by calling Dataset.
You specify this maximum size when creating the dataset, via the keyword maxshape:. Indicate these axes how to enable show translucent selection rectangle option trading None:. Resizing an array with existing data works differently than in NumPy; if any axis shrinks, the data in the missing region is discarded.
Chunked data may be transformed by the HDF5 filter pipeline. The most common use is applying transparent compression. Data is compressed on the way to disk, and automatically decompressed when read. Once the dataset is created with a particular compression filter applied, data may be read and written as normal with no special steps required.
Enable compression with the compression keyword to Group. In addition to the compression filters listed above, compression filters can be dynamically loaded by the underlying HDF5 library. This is done by passing a filter number to Group. The filter will then be skipped when subsequently reading the block.
HDF5 also includes a lossy filter which trades precision for storage space. Works with integer how to enable show translucent selection rectangle option trading floating-point data only. Enable the scale-offset filter by setting Group. For integer data, this specifies the number of bits to retain.
Set to 0 to have HDF5 automatically compute the number of bits required for lossless compression of the chunk. For floating-point data, indicates the number of digits after the decimal point to retain. Currently the scale-offset filter does not preserve special float values i.
NaN, infsee https: Enabling the shuffle filter rearranges the bytes in the chunk and may improve how to enable show translucent selection rectangle option trading ratio. No significant speed penalty, lossless. Enable by setting Group. Adds a checksum to each chunk to detect data corruption. Attempts to read corrupted chunks will fail with an error.
No significant speed penalty. HDF5 datasets re-use the NumPy slicing syntax to read and write to the file. The following slicing arguments are recognized:. To retrieve the contents of a scalar dataset, you can use the same syntax as in NumPy: In other words, index into the dataset using an empty tuple.
Broadcasting is implemented using repeated hyperslab selections, and is safe to use with very large target selections. A subset of the NumPy fancy-indexing syntax is supported. Use this with caution, as the underlying HDF5 mechanisms may have different performance than you expect. For any axis, you can provide an explicit list of points you want; how to enable show translucent selection rectangle option trading a dataset with shape 10, The result of this operation is a 1-D array with elements arranged in the standard NumPy C-style order.
Behind the scenes, this generates a laundry list of points to select, so be careful when using it with large masks:. As with NumPy arrays, the len of a dataset is the length of the first axis, and iterating over a dataset iterates over the first axis. However, modifications to the yielded data are not recorded in the file. Resizing a dataset while iterating has undefined results. HDF5 has the concept of Empty or Null datasets and attributes. These are not the same as an array with a shape ofor a scalar dataspace in HDF5 terms.
Instead, it is a dataset with an associated type, no data, and no shape. In h5py, we represent this as either a dataset with shape Noneor an instance of h5py.
Empty datasets and attributes cannot be sliced. To create an empty attribute, use how to enable show translucent selection rectangle option trading. Empty as per Attributes:. Similarly, reading an empty attribute returns h5py. An empty dataset has shape defined as Nonewhich is the best way of determining whether a dataset is empty or not. Dataset objects are typically created via Group. Call this constructor to create a new Dataset bound to an existing DatasetID identifier.
NumPy-style slicing to retrieve data. NumPy-style slicing to write data. Read from an HDF5 dataset directly into a NumPy array, which can avoid making an intermediate copy as happens with slicing. The destination array must be C-contiguous and writable, and must have a datatype to which the source data may be cast. Data type conversion will be carried out on the fly by HDF5. Use the output of numpy.
Return a context manager allowing you to read data as a particular type. Conversion is handled by HDF5 directly, on the fly:. Change the shape of a dataset. Datasets may be resized only up to Dataset. NumPy-style shape tuple indicating the maxiumum dimensions up to which the dataset may be resized. Axes with None are unlimited. Tuple giving the chunk shape, or None if chunked storage is not used. String with the currently applied compression filter, or None if compression is not enabled for this dataset.
Options for the compression filter. Setting for the HDF5 scale-offset filter integeror None if scale-offset compression is not used for this dataset. Value used when reading uninitialized portions of the dataset, or None if no fill value has been defined, in which case HDF5 will use a type-appropriate default value. Access to Dimension Scales. Attributes for this dataset. An HDF5 object reference pointing to this dataset. See Using object references. Proxy object for creating HDF5 region references.
See Using region references. File instance in which this dataset resides. Group instance containing this dataset. How to enable show translucent selection rectangle option trading are represented in h5py by a thin proxy class which supports familiar NumPy operations like slicing, along with a variety of descriptive attributes: To make an empty dataset, all you have to do is specify a name, shape, and optionally the data type defaults to 'f': To enable chunked storage, set the keyword chunks to a tuple indicating the chunk shape: You specify this maximum size when creating the dataset, via the keyword maxshape: Note Resizing an array with existing data works differently than in NumPy; if any axis shrinks, the data in the missing region is discarded.
Good compression, moderate speed. LZF filter "lzf" Available with every installation of h5py C source code also available. Low to moderate compression, very fast. Not available with all installations of HDF5 due to legal reasons.