AsdfFile

class asdf.AsdfFile(tree=None, uri=None, extensions=None, version=None, ignore_version_mismatch=True, ignore_unrecognized_tag=False, ignore_implicit_conversion=False, copy_arrays=False, lazy_load=True, custom_schema=None, _readonly=False)[source]

Bases: object

The main class that represents an ASDF file object.

Parameters
treedict or AsdfFile, optional

The main tree data in the ASDF file. Must conform to the ASDF schema.

uristr, optional

The URI for this ASDF file. Used to resolve relative references against. If not provided, will be automatically determined from the associated file object, if possible and if created from AsdfFile.open.

extensionsobject, optional

Additional extensions to use when reading and writing the file. May be any of the following: asdf.extension.AsdfExtension, asdf.extension.Extension, asdf.extension.AsdfExtensionList or a list of extensions.

versionstr, optional

The ASDF Standard version. If not provided, defaults to the configured default version. See asdf.config.AsdfConfig.default_version.

ignore_version_mismatchbool, optional

When True, do not raise warnings for mismatched schema versions. Set to True by default.

ignore_unrecognized_tagbool, optional

When True, do not raise warnings for unrecognized tags. Set to False by default.

ignore_implicit_conversionbool

When True, do not raise warnings when types in the tree are implicitly converted into a serializable object. The motivating case for this is currently namedtuple, which cannot be serialized as-is.

copy_arraysbool, optional

When False, when reading files, attempt to memmap underlying data arrays when possible.

lazy_loadbool, optional

When True and the underlying file handle is seekable, data arrays will only be loaded lazily: i.e. when they are accessed for the first time. In this case the underlying file must stay open during the lifetime of the tree. Setting to False causes all data arrays to be loaded up front, which means that they can be accessed even after the underlying file is closed. Note: even if lazy_load is False, copy_arrays is still taken into account.

custom_schemastr, optional

Path to a custom schema file that will be used for a secondary validation pass. This can be used to ensure that particular ASDF files follow custom conventions beyond those enforced by the standard.

Attributes Summary

blocks

Get the block manager associated with the AsdfFile.

comments

Get the comments after the header, before the tree.

extension_list

Get the AsdfExtensionList for this AsdfFile.

extension_manager

Get the ExtensionManager for this AsdfFile.

extensions

Get the list of user extensions that are enabled for use with this AsdfFile.

file_format_version

resolver

tag_mapping

tag_to_schema_resolver

tree

Get/set the tree of data in the ASDF file.

type_index

uri

Get the URI associated with the AsdfFile.

url_mapping

version

Get this AsdfFile’s ASDF Standard version.

version_map

version_string

Get this AsdfFile’s ASDF Standard version as a string.

Methods Summary

add_history_entry(description[, software])

Add an entry to the history list.

close()

Close the file handles associated with the AsdfFile.

copy()

fill_defaults()

Fill in any values that are missing in the tree using default values from the schema.

find_references()

Finds all external “JSON References” in the tree and converts them to reference.Reference objects.

get_array_compression(arr)

Get the compression type for the given array data.

get_array_storage(arr)

Get the block type for the given array data.

get_history_entries()

Get a list of history entries from the file object.

info([max_rows, max_cols, show_values])

Print a rendering of this file’s tree to stdout.

keys()

make_reference([path])

Make a new reference to a part of this file’s tree, that can be assigned as a reference to another tree.

open(fd[, uri, mode, validate_checksums, …])

Open an existing ASDF file.

open_external(uri, **kwargs)

Open an external ASDF file, from the given (possibly relative) URI.

remove_defaults()

Remove any values in the tree that are the same as the default values in the schema

resolve_and_inline()

Resolves all external references and inlines all data.

resolve_references(**kwargs)

Finds all external “JSON References” in the tree, loads the external content, and places it directly in the tree.

resolve_uri(uri)

Resolve a (possibly relative) URI against the URI of this ASDF file.

run_hook(hookname)

Run a “hook” for each custom type found in the tree.

run_modifying_hook(hookname[, validate])

Run a “hook” for each custom type found in the tree.

search([key, type, value, filter])

Search this file’s tree.

set_array_compression(arr, compression)

Set the compression to use for the given array data.

set_array_storage(arr, array_storage)

Set the block type to use for the given array data.

update([all_array_storage, …])

Update the file on disk in place.

validate()

Validate the current state of the tree against the ASDF schema.

write_to(fd[, all_array_storage, …])

Write the ASDF file to the given file-like object.

Attributes Documentation

blocks

Get the block manager associated with the AsdfFile.

comments

Get the comments after the header, before the tree.

extension_list

Get the AsdfExtensionList for this AsdfFile.

Returns
asdf.extension.AsdfExtensionList
extension_manager

Get the ExtensionManager for this AsdfFile.

Returns
asdf.extension.ExtensionManager
extensions

Get the list of user extensions that are enabled for use with this AsdfFile.

Returns
list of asdf.extension.ExtensionProxy
file_format_version
resolver
tag_mapping
tag_to_schema_resolver
tree

Get/set the tree of data in the ASDF file.

When set, the tree will be validated against the ASDF schema.

type_index
uri

Get the URI associated with the AsdfFile.

In many cases, it is automatically determined from the file handle used to read or write the file.

url_mapping
version

Get this AsdfFile’s ASDF Standard version.

Returns
asdf.versioning.AsdfVersion
version_map
version_string

Get this AsdfFile’s ASDF Standard version as a string.

Returns
str

Methods Documentation

add_history_entry(description, software=None)[source]

Add an entry to the history list.

Parameters
descriptionstr

A description of the change.

softwaredict or list of dict

A description of the software used. It should not include asdf itself, as that is automatically notated in the asdf_library entry.

Each dict must have the following keys:

  • name: The name of the software

  • author: The author or institution that produced the software

  • homepage: A URI to the homepage of the software

  • version: The version of the software

close()[source]

Close the file handles associated with the AsdfFile.

copy()[source]
fill_defaults()[source]

Fill in any values that are missing in the tree using default values from the schema.

find_references()[source]

Finds all external “JSON References” in the tree and converts them to reference.Reference objects.

get_array_compression(arr)[source]

Get the compression type for the given array data.

Parameters
arrnumpy.ndarray
Returns
compressionstr or None
get_array_storage(arr)[source]

Get the block type for the given array data.

Parameters
arrnumpy.ndarray
get_history_entries()[source]

Get a list of history entries from the file object.

Returns
entrieslist

A list of history entries.

info(max_rows=24, max_cols=120, show_values=True)[source]

Print a rendering of this file’s tree to stdout.

Parameters
max_rowsint, tuple, or None, optional

Maximum number of lines to print. Nodes that cannot be displayed will be elided with a message. If int, constrain total number of displayed lines. If tuple, constrain lines per node at the depth corresponding to the tuple index. If None, display all lines.

max_colsint or None, optional

Maximum length of line to print. Nodes that cannot be fully displayed will be truncated with a message. If int, constrain length of displayed lines. If None, line length is unconstrained.

show_valuesbool, optional

Set to False to disable display of primitive values in the rendered tree.

keys() → a set-like object providing a view on D’s keys[source]
make_reference(path=[])[source]

Make a new reference to a part of this file’s tree, that can be assigned as a reference to another tree.

Parameters
pathlist of str and int, optional

The parts of the path pointing to an item in this tree. If omitted, points to the root of the tree.

Returns
referencereference.Reference

A reference object.

Examples

For the given AsdfFile ff, add an external reference to the data in an external file:

>>> import asdf
>>> flat = asdf.open("http://stsci.edu/reference_files/flat.asdf")  
>>> ff.tree['flat_field'] = flat.make_reference(['data'])  
classmethod open(fd, uri=None, mode='r', validate_checksums=False, extensions=None, ignore_version_mismatch=True, ignore_unrecognized_tag=False, _force_raw_types=False, copy_arrays=False, lazy_load=True, custom_schema=None, strict_extension_check=False, ignore_missing_extensions=False, **kwargs)[source]

Open an existing ASDF file.

Deprecated since version 2.2: Use asdf.open instead.

open_external(uri, **kwargs)[source]

Open an external ASDF file, from the given (possibly relative) URI. There is a cache (internal to this ASDF file) that ensures each external ASDF file is loaded only once.

Parameters
uristr

An absolute or relative URI to resolve against the URI of this ASDF file.

Returns
asdffileAsdfFile

The external ASDF file.

remove_defaults()[source]

Remove any values in the tree that are the same as the default values in the schema

resolve_and_inline()[source]

Resolves all external references and inlines all data. This produces something that, when saved, is a 100% valid YAML file.

resolve_references(**kwargs)[source]

Finds all external “JSON References” in the tree, loads the external content, and places it directly in the tree. Saving a ASDF file after this operation means it will have no external references, and will be completely self-contained.

resolve_uri(uri)[source]

Resolve a (possibly relative) URI against the URI of this ASDF file. May be overridden by base classes to change how URIs are resolved. This does not apply any uri_mapping that was passed to the constructor.

Parameters
uristr

An absolute or relative URI to resolve against the URI of this ASDF file.

Returns
uristr

The resolved URI.

run_hook(hookname)[source]

Run a “hook” for each custom type found in the tree.

Parameters
hooknamestr

The name of the hook. If a AsdfType is found with a method with this name, it will be called for every instance of the corresponding custom type in the tree.

run_modifying_hook(hookname, validate=True)[source]

Run a “hook” for each custom type found in the tree. The hook is free to return a different object in order to modify the tree.

Parameters
hooknamestr

The name of the hook. If a AsdfType is found with a method with this name, it will be called for every instance of the corresponding custom type in the tree.

validatebool

When True (default) validate the resulting tree.

search(key=NotSet, type=NotSet, value=NotSet, filter=None)[source]

Search this file’s tree.

Parameters
keyNotSet, str, or any other object

Search query that selects nodes by dict key or list index. If NotSet, the node key is unconstrained. If str, the input is searched among keys/indexes as a regular expression pattern. If any other object, node’s key or index must equal the queried key.

typeNotSet, str, or builtins.type

Search query that selects nodes by type. If NotSet, the node type is unconstrained. If str, the input is searched among (fully qualified) node type names as a regular expression pattern. If builtins.type, the node must be an instance of the input.

valueNotSet, str, or any other object

Search query that selects nodes by value. If NotSet, the node value is unconstrained. If str, the input is searched among values as a regular expression pattern. If any other object, node’s value must equal the queried value.

filtercallable

Callable that filters nodes by arbitrary criteria. The callable accepts one or two arguments:

  • the node

  • the node’s list index or dict key (optional)

and returns True to retain the node, or False to remove it from the search results.

Returns
asdf.search.AsdfSearchResult

the result of the search

set_array_compression(arr, compression)[source]

Set the compression to use for the given array data.

Parameters
arrnumpy.ndarray

The array to set. If multiple views of the array are in the tree, only the most recent compression setting will be used, since all views share a single block.

compressionstr or None

Must be one of:

  • '' or None: no compression

  • zlib: Use zlib compression

  • bzp2: Use bzip2 compression

  • lz4: Use lz4 compression

  • input: Use the same compression as in the file read. If there is no prior file, acts as None.

set_array_storage(arr, array_storage)[source]

Set the block type to use for the given array data.

Parameters
arrnumpy.ndarray

The array to set. If multiple views of the array are in the tree, only the most recent block type setting will be used, since all views share a single block.

array_storagestr

Must be one of:

  • internal: The default. The array data will be stored in a binary block in the same ASDF file.

  • external: Store the data in a binary block in a separate ASDF file.

  • inline: Store the data as YAML inline in the tree.

update(all_array_storage=None, all_array_compression='input', auto_inline=None, pad_blocks=False, include_block_index=True, version=None)[source]

Update the file on disk in place.

Parameters
all_array_storagestring, optional

If provided, override the array storage type of all blocks in the file immediately before writing. Must be one of:

  • internal: The default. The array data will be stored in a binary block in the same ASDF file.

  • external: Store the data in a binary block in a separate ASDF file.

  • inline: Store the data as YAML inline in the tree.

all_array_compressionstring, optional

If provided, set the compression type on all binary blocks in the file. Must be one of:

  • '' or None: No compression.

  • zlib: Use zlib compression.

  • bzp2: Use bzip2 compression.

  • lz4: Use lz4 compression.

  • input: Use the same compression as in the file read. If there is no prior file, acts as None

auto_inlineint, optional

When the number of elements in an array is less than this threshold, store the array as inline YAML, rather than a binary block. This only works on arrays that do not share data with other arrays. Default is 0.

pad_blocksfloat or bool, optional

Add extra space between blocks to allow for updating of the file. If False (default), add no padding (always return 0). If True, add a default amount of padding of 10% If a float, it is a factor to multiple content_size by to get the new total size.

include_block_indexbool, optional

If False, don’t include a block index at the end of the file. (Default: True) A block index is never written if the file has a streamed block.

versionstr, optional

Update the ASDF Standard version of this AsdfFile before writing.

validate()[source]

Validate the current state of the tree against the ASDF schema.

write_to(fd, all_array_storage=None, all_array_compression='input', auto_inline=100, pad_blocks=False, include_block_index=True, version=None)[source]

Write the ASDF file to the given file-like object.

write_to does not change the underlying file descriptor in the AsdfFile object, but merely copies the content to a new file.

Parameters
fdstring or file-like object

May be a string path to a file, or a Python file-like object. If a string path, the file is automatically closed after writing. If not a string path, it is the caller’s responsibility to close the object.

all_array_storagestring, optional

If provided, override the array storage type of all blocks in the file immediately before writing. Must be one of:

  • internal: The default. The array data will be stored in a binary block in the same ASDF file.

  • external: Store the data in a binary block in a separate ASDF file.

  • inline: Store the data as YAML inline in the tree.

all_array_compressionstring, optional

If provided, set the compression type on all binary blocks in the file. Must be one of:

  • '' or None: No compression.

  • zlib: Use zlib compression.

  • bzp2: Use bzip2 compression.

  • lz4: Use lz4 compression.

  • input: Use the same compression as in the file read. If there is no prior file, acts as None.

auto_inlineint, optional

When the number of elements in an array is less than this threshold, store the array as inline YAML, rather than a binary block. This only works on arrays that do not share data with other arrays. Default is 100. Care needs to be taken when modifying files not written with default. Storage type is not preserved. For example, reading an array of length ten stored in a binary block, then writing it out using the default auto_inline will cause that array’s storage to change to inline.

pad_blocksfloat or bool, optional

Add extra space between blocks to allow for updating of the file. If False (default), add no padding (always return 0). If True, add a default amount of padding of 10% If a float, it is a factor to multiple content_size by to get the new total size.

include_block_indexbool, optional

If False, don’t include a block index at the end of the file. (Default: True) A block index is never written if the file has a streamed block.

versionstr, optional

Update the ASDF Standard version of this AsdfFile before writing.