anypytools.h5py_wrapper¶
Created on Mon Jan 16 11:40:42 2012.
@author: mel
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class
anypytools.h5py_wrapper.File(*args, **kwargs)[source]¶ Represents an HDF5 file.
Create a new file object.
See the h5py user guide for a detailed explanation of the options.
- name
Name of the file on disk, or file-like object. Note: for files created with the ‘core’ driver, HDF5 still requires this be non-empty.
- mode
r Readonly, file must exist (default) r+ Read/write, file must exist w Create file, truncate if exists w- or x Create file, fail if exists a Read/write if exists, create otherwise
- driver
Name of the driver to use. Legal values are None (default, recommended), ‘core’, ‘sec2’, ‘direct’, ‘stdio’, ‘mpio’, ‘ros3’.
- libver
Library version bounds. Supported values: ‘earliest’, ‘v108’, ‘v110’, ‘v112’ and ‘latest’. The ‘v108’, ‘v110’ and ‘v112’ options can only be specified with the HDF5 1.10.2 library or later.
- userblock_size
Desired size of user block. Only allowed when creating a new file (mode w, w- or x).
- swmr
Open the file in SWMR read mode. Only used when mode = ‘r’.
- rdcc_nbytes
Total size of the dataset chunk cache in bytes. The default size is 1024**2 (1 MiB) per dataset. Applies to all datasets unless individually changed.
- rdcc_w0
The chunk preemption policy for all datasets. This must be between 0 and 1 inclusive and indicates the weighting according to which chunks which have been fully read or written are penalized when determining which chunks to flush from cache. A value of 0 means fully read or written chunks are treated no differently than other chunks (the preemption is strictly LRU) while a value of 1 means fully read or written chunks are always preempted before other chunks. If your application only reads or writes data once, this can be safely set to 1. Otherwise, this should be set lower depending on how often you re-read or re-write the same data. The default value is 0.75. Applies to all datasets unless individually changed.
- rdcc_nslots
The number of chunk slots in the raw data chunk cache for this file. Increasing this value reduces the number of cache collisions, but slightly increases the memory used. Due to the hashing strategy, this value should ideally be a prime number. As a rule of thumb, this value should be at least 10 times the number of chunks that can fit in rdcc_nbytes bytes. For maximum performance, this value should be set approximately 100 times that number of chunks. The default value is 521. Applies to all datasets unless individually changed.
- track_order
Track dataset/group/attribute creation order under root group if True. If None use global default h5.get_config().track_order.
- fs_strategy
The file space handling strategy to be used. Only allowed when creating a new file (mode w, w- or x). Defined as: “fsm” FSM, Aggregators, VFD “page” Paged FSM, VFD “aggregate” Aggregators, VFD “none” VFD If None use HDF5 defaults.
- fs_page_size
File space page size in bytes. Only used when fs_strategy=”page”. If None use the HDF5 default (4096 bytes).
- fs_persist
A boolean value to indicate whether free space should be persistent or not. Only allowed when creating a new file. The default value is False.
- fs_threshold
The smallest free-space section size that the free space manager will track. Only allowed when creating a new file. The default value is 1.
- page_buf_size
Page buffer size in bytes. Only allowed for HDF5 files created with fs_strategy=”page”. Must be a power of two value and greater or equal than the file space page size when creating the file. It is not used by default.
- min_meta_keep
Minimum percentage of metadata to keep in the page buffer before allowing pages containing metadata to be evicted. Applicable only if page_buf_size is set. Default value is zero.
- min_raw_keep
Minimum percentage of raw data to keep in the page buffer before allowing pages containing raw data to be evicted. Applicable only if page_buf_size is set. Default value is zero.
- locking
The file locking behavior. Defined as:
False (or “false”) – Disable file locking
True (or “true”) – Enable file locking
“best-effort” – Enable file locking but ignore some errors
None – Use HDF5 defaults
Warning
The HDF5_USE_FILE_LOCKING environment variable can override this parameter.
Only available with HDF5 >= 1.12.1 or 1.10.x >= 1.10.7.
- alignment_threshold
Together with
alignment_interval, this property ensures that any file object greater than or equal in size to the alignement threshold (in bytes) will be aligned on an address which is a multiple of alignment interval.- alignment_interval
This property should be used in conjunction with
alignment_threshold. See the description above. For more details, see https://portal.hdfgroup.org/display/HDF5/H5P_SET_ALIGNMENT- meta_block_size
Set the current minimum size, in bytes, of new metadata block allocations. See https://portal.hdfgroup.org/display/HDF5/H5P_SET_META_BLOCK_SIZE
- Additional keywords
Passed on to the selected file driver.
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get(path, *args)[source]¶ Retrieve an item or other information.
- “name” given only:
Return the item, or “default” if it doesn’t exist
- “getclass” is True:
Return the class of object (Group, Dataset, etc.), or “default” if nothing with that name exists
- “getlink” is True:
Return HardLink, SoftLink or ExternalLink instances. Return “default” if nothing with that name exists.
- “getlink” and “getclass” are True:
Return HardLink, SoftLink and ExternalLink classes. Return “default” if nothing with that name exists.
Example:
>>> cls = group.get('foo', getclass=True) >>> if cls == SoftLink:
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property
file¶ Return a File instance associated with this object
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property
parent¶ Return the parent group of this object.
This is always equivalent to obj.file[posixpath.dirname(obj.name)]. ValueError if this object is anonymous.
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class
anypytools.h5py_wrapper.Group(arg)[source]¶ Represents an HDF5 group.
Create a new Group object by binding to a low-level GroupID.
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get(path, *args)[source]¶ Retrieve an item or other information.
- “name” given only:
Return the item, or “default” if it doesn’t exist
- “getclass” is True:
Return the class of object (Group, Dataset, etc.), or “default” if nothing with that name exists
- “getlink” is True:
Return HardLink, SoftLink or ExternalLink instances. Return “default” if nothing with that name exists.
- “getlink” and “getclass” are True:
Return HardLink, SoftLink and ExternalLink classes. Return “default” if nothing with that name exists.
Example:
>>> cls = group.get('foo', getclass=True) >>> if cls == SoftLink:
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property
file¶ Return a File instance associated with this object
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property
parent¶ Return the parent group of this object.
This is always equivalent to obj.file[posixpath.dirname(obj.name)]. ValueError if this object is anonymous.
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