anndata package¶

Subpackages¶

Submodules¶

anndata.anndataexc module¶

filename: sppas.src.anndata.anndataexc.py
author: Brigitte Bigi
contact: develop@sppas.org
summary: Exceptions for the package anndata.

exception anndata.anndataexc.AioEmptyTierError(file_format, tier_name)[source]¶

Bases: OSError

:ERROR 1525:.

The file format {!s:s} does not support to save empty tiers: {:s}.

__init__(file_format, tier_name)[source]¶

exception anndata.anndataexc.AioEncodingError(filename, error_msg, encoding='utf-8')[source]¶

Bases: UnicodeDecodeError

:ERROR 1500:.

The file {filename} contains non {encoding} characters: {error}.

__init__(filename, error_msg, encoding='utf-8')[source]¶

exception anndata.anndataexc.AioError(filename)[source]¶

Bases: OSError

:ERROR 1400:.

No such file: ‘{!s:s}’.

__init__(filename)[source]¶

exception anndata.anndataexc.AioFormatError(line)[source]¶

Bases: OSError

:ERROR 1521:.

Unexpected format about ‘{!s:s}’.

__init__(line)[source]¶

exception anndata.anndataexc.AioLineFormatError(number, line)[source]¶

Bases: OSError

:ERROR 1520:.

Unexpected format string at line {:d}: ‘{!s:s}’.

__init__(number, line)[source]¶

exception anndata.anndataexc.AioLocationTypeError(file_format, location_type)[source]¶

Bases: TypeError

:ERROR 1530:.

The file format {!s:s} does not support tiers with {:s}.

__init__(file_format, location_type)[source]¶

exception anndata.anndataexc.AioMultiTiersError(file_format)[source]¶

Bases: OSError

:ERROR 1510:.

The file format {!s:s} does not support multi-tiers.

__init__(file_format)[source]¶

exception anndata.anndataexc.AioNoTiersError(file_format)[source]¶

Bases: OSError

:ERROR 1515:.

The file format {!s:s} does not support to save no tiers.

__init__(file_format)[source]¶

exception anndata.anndataexc.AnnDataEqError(v1, v2)[source]¶

Bases: Exception

:ERROR 1010:.

Values are expected to be equals but are {:s!s} and {:s!s}.

__init__(v1, v2)[source]¶

exception anndata.anndataexc.AnnDataEqTypeError(obj, obj_ref)[source]¶

Bases: TypeError

:ERROR 1105:.

{!s:s} is not of the same type as {!s:s}.

__init__(obj, obj_ref)[source]¶

exception anndata.anndataexc.AnnDataError[source]¶

Bases: Exception

:ERROR 1000:.

No annotated data file is defined.

__init__()[source]¶

exception anndata.anndataexc.AnnDataIndexError(index)[source]¶

Bases: IndexError

:ERROR 1200:.

Invalid index value {:d}.

__init__(index)[source]¶

exception anndata.anndataexc.AnnDataKeyError(data_name, value)[source]¶

Bases: KeyError

:ERROR 1250:.

Invalid key ‘{!s:s}’ for data ‘{!s:s}’.

__init__(data_name, value)[source]¶

exception anndata.anndataexc.AnnDataNegValueError(value)[source]¶

Bases: ValueError

:ERROR 1310:.

Expected a positive value. Got ‘{:f}’.

__init__(value)[source]¶

exception anndata.anndataexc.AnnDataTypeError(rtype, expected)[source]¶

Bases: TypeError

:ERROR 1100:.

{!s:s} is not of the expected type ‘{:s}’.

__init__(rtype, expected)[source]¶

exception anndata.anndataexc.AnnDataValueError(data_name, value)[source]¶

Bases: ValueError

:ERROR 1300:.

Invalid value ‘{!s:s}’ for ‘{!s:s}’.

__init__(data_name, value)[source]¶

exception anndata.anndataexc.AnnUnkTypeError(rtype)[source]¶

Bases: TypeError

:ERROR 1050:.

{!s:s} is not a valid type.

__init__(rtype)[source]¶

exception anndata.anndataexc.CtrlVocabContainsError(tag)[source]¶

Bases: ValueError

:ERROR 1130:.

{:s} is not part of the controlled vocabulary.

__init__(tag)[source]¶

exception anndata.anndataexc.CtrlVocabSetTierError(vocab_name, tier_name)[source]¶

Bases: ValueError

:ERROR 1132:.

The controlled vocabulary {:s} can’t be associated to the tier {:s}.

__init__(vocab_name, tier_name)[source]¶

exception anndata.anndataexc.HierarchyAlignmentError(parent_tier_name, child_tier_name)[source]¶

Bases: ValueError

:ERROR 1170:.

Can’t create a time alignment between tiers: ‘{:s}’ is not a superset of ‘{:s}’.”

__init__(parent_tier_name, child_tier_name)[source]¶

exception anndata.anndataexc.HierarchyAncestorTierError(child_tier_name, parent_tier_name)[source]¶

Bases: ValueError

:ERROR 1178:.

The tier can’t be added into the hierarchy: ‘{:s}’ is an ancestor of ‘{:s}’.

__init__(child_tier_name, parent_tier_name)[source]¶

exception anndata.anndataexc.HierarchyAssociationError(parent_tier_name, child_tier_name)[source]¶

Bases: ValueError

:ERROR 1172:.

Can’t create a time association between tiers: ‘{:s}’ and ‘{:s}’ are not supersets of each other.

__init__(parent_tier_name, child_tier_name)[source]¶

exception anndata.anndataexc.HierarchyChildTierError(tier_name)[source]¶

Bases: ValueError

:ERROR 1176:.

The tier ‘{:s}’ can’t be added into the hierarchy: a tier can’t be its own child.

__init__(tier_name)[source]¶

exception anndata.anndataexc.HierarchyParentTierError(child_tier_name, parent_tier_name, link_type)[source]¶

Bases: ValueError

:ERROR 1174:.

The tier can’t be added into the hierarchy: ‘{:s}’ has already a link of type {:s} with its parent tier ‘{:s}’.

__init__(child_tier_name, parent_tier_name, link_type)[source]¶

exception anndata.anndataexc.IntervalBoundsError(begin, end)[source]¶

Bases: ValueError

:ERROR 1120:.

The begin must be strictly lesser than the end in an interval. Got: [{:s};{:s}].

__init__(begin, end)[source]¶

exception anndata.anndataexc.TagValueError(tag_str)[source]¶

Bases: ValueError

:ERROR 1190:.

{!s:s} is not a valid tag.

__init__(tag_str)[source]¶

exception anndata.anndataexc.TierAddError(index)[source]¶

Bases: ValueError

:ERROR 1142:.

Can’t add annotation. An annotation with the same location is already in the tier at index {:d}.

__init__(index)[source]¶

exception anndata.anndataexc.TierAppendError(cur_end, ann_end)[source]¶

Bases: ValueError

:ERROR 1140:.

Can’t append annotation. Current end {!s:s} is highest than the given one {!s:s}.

__init__(cur_end, ann_end)[source]¶

exception anndata.anndataexc.TierHierarchyError(name)[source]¶

Bases: ValueError

:ERROR 1144:.

Attempt a modification in tier ‘{:s}’ that invalidates its hierarchy.

__init__(name)[source]¶

exception anndata.anndataexc.TrsAddError(tier_name, transcription_name)[source]¶

Bases: ValueError

:ERROR 1150:.

Can’t add: ‘{:s}’ is already in ‘{:s}’.

__init__(tier_name, transcription_name)[source]¶

exception anndata.anndataexc.TrsInvalidTierError(tier_name, transcription_name)[source]¶

Bases: ValueError

:ERROR 1160:.

{:s} is not a tier of {:s}. It can’t be included in its hierarchy.

__init__(tier_name, transcription_name)[source]¶

exception anndata.anndataexc.TrsRemoveError(tier_name, transcription_name)[source]¶

Bases: ValueError

:ERROR 1152:.

Can’t remove: ‘{:s}’ is not in ‘{:s}’.

__init__(tier_name, transcription_name)[source]¶

anndata.ctrlvocab module¶

filename: sppas.src.anndata.ctrlvocab.py
author: Brigitte Bigi
contact: develop@sppas.org
summary: Represent a controlled vocabulary.

class anndata.ctrlvocab.sppasCtrlVocab(name, description='')[source]¶

Bases: anndata.metadata.sppasMetaData

Generic representation of a controlled vocabulary.

A controlled Vocabulary is a set of tags. It is used to restrict the use of tags in a label: only the accepted tags can be set to a label.

A controlled vocabulary is made of an identifier name, a description and a list of pairs tag/description.

__init__(name, description='')[source]¶

Create a new sppasCtrlVocab instance.

Parameters

name – (str) Identifier name of the controlled vocabulary
description – (str)

add(tag, description='')[source]¶

Add a tag to the controlled vocab.

Parameters

tag – (sppasTag): the tag to add.
description – (str)

Returns

Boolean

contains(tag)[source]¶

Test if a tag is in the controlled vocabulary.

Attention: Do not check the instance but the data content of the tag.

Parameters: tag – (sppasTag) the tag to check.
Returns: Boolean

get_description()[source]¶: Return the unicode str of the description of the ctrl vocab.

get_name()[source]¶: Return the name of the controlled vocabulary.

get_tag_description(tag)[source]¶

Return the unicode string of the description of an entry.

Parameters: tag – (sppasTag) the tag to get the description.
Returns: (str)

remove(tag)[source]¶

Remove a tag of the controlled vocab.

Parameters: tag – (sppasTag) the tag to remove.
Returns: Boolean

set_description(description='')[source]¶

Set the description of the controlled vocabulary.

Parameters: description – (str)

set_tag_description(tag, description)[source]¶

Set the unicode string of the description of an entry.

Parameters

tag – (sppasTag) the tag to get the description.
description – (str)

Returns

(str)

validate_tag(tag)[source]¶

Check if the given tag can be added to the ctrl vocabulary.

Parameters: tag – (sppasTag) the tag to check.
Returns: Boolean

anndata.hierarchy module¶

filename: sppas.src.anndata.hierarchy.py
author: Brigitte Bigi
contact: develop@sppas.org
summary: Represent a hierarchy, i.e. constraints among tiers.

class anndata.hierarchy.sppasHierarchy[source]¶

Bases: anndata.metadata.sppasMetaData

Generic representation of a hierarchy between tiers.

Two types of hierarchy are considered:

TimeAssociation: the points of a child tier are all equals to the points of a reference tier, as for example:

parent: Words | l’ | âne | est | là |

child: Lemmas | le | âne | être | là |

TimeAlignment: the points of a child tier are all included in the set of points of a reference tier, as for example:

parent: Phonemes | l | a | n | e | l | a |

child: Words | l’ | âne | est | là |

parent: Phonemes | l | a | n | e | l | a |

child: Syllables | l.a | n.e | l.a |

In that example, notice that there’s no hierarchy link between “Tokens” and “Syllables” and notice that “Phonemes” is the grand-parent of “Lemmas”.

And the following obvious rules are applied:

A child can have ONLY ONE parent!

A parent can have as many children as wanted.

A hierarchy is a tree, not a graph.

Todo is to consider a time association that is not fully completed:

parent: Tokens | l’ | âne | euh | euh | est | là | @ |

child: Lemmas | le | âne | | être | là |

__init__()[source]¶: Create a new sppasHierarchy instance.

add_link(link_type, parent_tier, child_tier)[source]¶

Validate and add a hierarchy link between 2 tiers.

Parameters

link_type – (constant) One of the hierarchy types
parent_tier – (sppasTier) The parent tier
child_tier – (sppasTier) The child tier to be linked to parent

copy()[source]¶: Return a deep copy of the hierarchy.

get_ancestors(child_tier)[source]¶

Return all the direct ancestors of a tier.

Parameters: child_tier – (sppasTier)
Returns: List of tiers with parent, grand-parent, grand-grand-parent…

get_children(parent_tier, link_type=None)[source]¶

Return the list of children of a tier, for a given type.

Parameters

parent_tier – (sppasTier) The child tier to found
link_type – (str) The type of hierarchy

Returns

List of tiers

get_hierarchy_type(child_tier)[source]¶

Return the hierarchy type between a child tier and its parent.

Returns: (str) one of the hierarchy type

get_parent(child_tier)[source]¶

Return the parent tier for a given child tier.

Parameters: child_tier – (sppasTier) The child tier to found

static infer_hierarchy_type(tier1, tier2)[source]¶

Test if tier1 can be a parent tier for tier2.

Returns: One of hierarchy types or an empty string

remove_child(child_tier)[source]¶

Remove a hierarchy link between a parent and a child.

Parameters: child_tier – (sppasTier) The tier linked to a reference

remove_parent(parent_tier)[source]¶

Remove all hierarchy links between a parent and its children.

Parameters: parent_tier – (sppasTier) The parent tier

remove_tier(tier)[source]¶

Remove all occurrences of a tier inside the hierarchy.

Parameters: tier – (sppasTier) The tier to remove as parent or child.

types = {'TimeAlignment', 'TimeAssociation'}¶

validate_link(link_type, parent_tier, child_tier)[source]¶

Validate a hierarchy link between 2 tiers.

Parameters

link_type – (constant) One of the hierarchy types
parent_tier – (sppasTier) The parent tier
child_tier – (sppasTier) The child tier to be linked to parent

Raises

AnnDataTypeError, HierarchyParentTierError, HierarchyChildTierError, HierarchyAncestorTierError, HierarchyAlignmentError, HierarchyAssociationError

static validate_time_alignment(parent_tier, child_tier)[source]¶

Validate a time alignment hierarchy link between 2 tiers.

Parameters

parent_tier – (sppasTier) The parent tier
child_tier – (sppasTier) The child tier to be linked to parent

Raises

HierarchyAlignmentError

static validate_time_association(parent_tier, child_tier)[source]¶

Validate a time association hierarchy link between 2 tiers.

Parameters

parent_tier – (sppasTier) The parent tier
child_tier – (sppasTier) The child tier to be linked to the parent

Raises

HierarchyAssociationError

anndata.media module¶

filename: sppas.src.anndata.media.py
author: Brigitte Bigi
contact: develop@sppas.org
summary: Represent a media – a recording file.

class anndata.media.sppasMedia(filename, media_id=None, mime_type=None)[source]¶

Bases: anndata.metadata.sppasMetaData

Generic representation of a media file.

__init__(filename, media_id=None, mime_type=None)[source]¶

Create a new sppasMedia instance.

Parameters

filename – (str) File name of the media
media_id – (str) Identifier of the media
mime_type – (str) Mime type of the media

get_content()[source]¶: Return the content of the media.

get_filename()[source]¶: Return the URL of the media.

get_mime_type()[source]¶: Return the mime type of the media.

set_content(content)[source]¶

Set the content of the media.

Parameters: content – (str)

anndata.metadata module¶

filename: sppas.src.anndata.metadata.py
author: Brigitte Bigi
contact: develop@sppas.org
summary: Represent a set of metadata and an identifier.

class anndata.metadata.sppasDefaultMeta[source]¶

Bases: anndata.metadata.sppasMetaData

Dictionary of default meta data in SPPAS.

Many annotation tools are using metadata… Moreover, each annotation tool is encoding data with its own formalism. SPPAS aio API enables metadata to store information related to the read data in order to give them back when writing the data, either in the same file format or to export in another format. Such option is possible only if some kind of “generic” metadata names are fixed.

__init__()[source]¶: Instantiate a default set of meta data.

media()[source]¶

Add metadata related to a media.

For compatibility with sclite, xtrans, subtitle, elan, annotation pro.

speaker()[source]¶

Add metadata related to a speaker.

For compatibility with sclite, transcriber, xtrans, elan

tier()[source]¶

Add metadata related to a tier.

For compatibility with audacity and annotation pro.

class anndata.metadata.sppasMetaData[source]¶

Bases: object

Dictionary of meta data including a required ‘id’.

Meta data keys and values are unicode strings.

__init__()[source]¶

Create a sppasMetaData instance.

Add a GUID-like in the dictionary of metadata, with key “id”.

add_annotator_metadata(name='', version='', version_date='')[source]¶

Add metadata about an annotator.

Parameters

name – (str)
version – (str)
version_date – (str)

TODO: CHECK IF KEYS ARE NOT ALREADY EXISTING.

add_language_metadata()[source]¶

Add metadata about the language (und).

TODO: CHECK IF KEYS NOT ALREADY EXISTING.

add_license_metadata(idx)[source]¶: Add metadata about the license applied to the object (GPLv3).

add_project_metadata()[source]¶

Add metadata about the project this object is included-in.

Currently do not assign any value. TODO: CHECK IF KEYS NOT ALREADY EXISTING.

add_software_metadata()[source]¶

Add metadata about this software.

TODO: CHECK IF KEYS NOT ALREADY EXISTING.

gen_id()[source]¶: Re-generate an ‘id’.

get_id()[source]¶: Return the identifier of this object.

get_meta(entry, default='')[source]¶

Return the value of the given key.

Parameters

entry – (str) Entry to be checked as a key.
default – (str) Default value to return if entry is not a key.

Returns

(str) meta data value or default value

get_meta_keys()[source]¶: Return the list of metadata keys.

is_meta_key(entry)[source]¶

Check if an entry is a key in the list of metadata.

Parameters: entry – (str) Entry to check
Returns: (Boolean)

pop_meta(key)[source]¶

Remove a metadata from its key.

Parameters: key – (str)

set_meta(key, value)[source]¶

Set or update a metadata.

Parameters

key – (str) The key of the metadata.
value – (str) The value assigned to the key.

key, and value are formatted and stored in unicode.

anndata.tier module¶

filename: sppas.src.anndata.tier.py
author: Brigitte Bigi
contact: develop@sppas.org
summary: Represent a tier, i.e. a layer with annotations.

class anndata.tier.sppasTier(name=None, ctrl_vocab=None, media=None, parent=None)[source]¶

Bases: anndata.metadata.sppasMetaData

Representation of a tier, a structured set of annotations.

Annotations of a tier are sorted depending on their location (from lowest to highest).

A Tier is made of:

a name (used to identify the tier),

a set of metadata,

an array of annotations,

a controlled vocabulary (optional),

a media (optional),

a parent (optional).

__init__(name=None, ctrl_vocab=None, media=None, parent=None)[source]¶

Create a new sppasTier instance.

Parameters

name – (str) Name of the tier. It is used as identifier.
ctrl_vocab – (sppasCtrlVocab)
media – (sppasMedia)
parent – (sppasTranscription)

add(annotation)[source]¶

Add an annotation to the tier in sorted order.

Assign this tier as parent to the annotation.

Parameters: annotation – (sppasAnnotation)
Raises: AnnDataTypeError, CtrlVocabContainsError, HierarchyContainsError, HierarchyTypeError
Returns: the index of the annotation in the tier

append(annotation)[source]¶

Append the given annotation at the end of the tier.

Assign this tier as parent to the annotation.

Parameters: annotation – (sppasAnnotation)
Raises: AnnDataTypeError, CtrlVocabContainsError, HierarchyContainsError, HierarchyTypeError, TierAppendError

copy()[source]¶

Return a deep copy of the tier.

Returns: (sppasTier) including the ‘id’.

create_annotation(location, labels=None)[source]¶

Create and add a new annotation into the tier.

Parameters

location – (sppasLocation) the location(s) where the annotation happens
labels – (sppasLabel, list) the label(s) to stamp this annot.

Returns

sppasAnnotation

create_annotation_after(idx)[source]¶

Create and add a new annotation in the hole after idx.

Parameters: idx – (int) Index of an existing annotation
Returns: sppasAnnotation

:raises AnnDataTypeError, AnnDataIndexError

create_annotation_before(idx)[source]¶

Create and add a new annotation in the hole before idx.

Parameters: idx – (int) Index of an existing annotation
Returns: sppasAnnotation

:raises AnnDataTypeError, AnnDataIndexError

create_ctrl_vocab(name=None)[source]¶

Create the controlled vocabulary from annotation labels.

Create (or re-create) the controlled vocabulary from the list of already existing annotation labels. The current controlled vocabulary is deleted.

Parameters: name – (str) Name of the controlled vocabulary. The name of the tier is used by default.

export_to_intervals(separators)[source]¶

Create a tier with the consecutive filled intervals.

Return an empty tier if ‘self’ is not of type “interval”. The created intervals are not filled.

Parameters: separators – (list)
Returns: (sppasTier)

export_unfilled()[source]¶

Create a tier with the unlabelled/unfilled intervals.

Only for tiers of type Interval. It represents the “NOT tier”, ie where this tier is not annotated.

IMPORTANT: Never tested with overlapped annotations, actually not tested at all (but used in the plugin StatGroups).

Returns: (sppasTier) or None

find(begin, end, overlaps=True, indexes=False)[source]¶

Return a list of annotations between begin and end.

Parameters

begin – sppasPoint or None to start from the beginning of the tier
end – sppasPoint or None to end at the end of the tier
overlaps – (bool) Return also overlapped annotations. Not relevant for tiers with points.
indexes – (bool) Return indexes instead of annotations

Returns

List of sppasAnnotation or list of indexes

fit(other)[source]¶

Select then slice or extend annotations to fit in other tier.

Keep only the annotations of self that have some overlapping time with the given other tier and slice the localization of such selected annotations to exactly match those of the other tier.

Example:

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

tier1: |_a_|_b_| |_c_| |_d_| |_e_| |f| tier2: |_w_| |_______x_______| |_y_| |_z_|

tier1.fit(tier2) result is:: |a|b| |_c_| |_d_| |e|
tier2.fit(tier1) result is:: |w|w| |_x_| |_x_| |y|

Parameters: other – (sppasTier)
Returns: (sppasTier)

get_all_points()[source]¶: Return the list of all points of the tier.

get_annotation(identifier)[source]¶

Find an annotation from its metadata ‘id’.

Parameters: identifier – (str) Metadata ‘id’ of an annotation.
Returns: sppasAnnotation or None

get_annotation_index(ann)[source]¶

Find an annotation.

Parameters: ann – (sppasAnnotation)
Returns: (int) -1 if not found

get_ctrl_vocab()[source]¶: Return the controlled vocabulary of the tier.

get_first_point()[source]¶: Return the first point of the first annotation.

get_labels_type()[source]¶: Return the current type of labels, or an empty string.

get_last_point()[source]¶: Return the last point of the last location.

get_media()[source]¶: Return the media of the tier.

get_midpoint_intervals()[source]¶: Return midpoint values of all the intervals.

get_midpoint_points()[source]¶: Return midpoint values of all the points.

get_name()[source]¶: Return the identifier name of the tier.

get_nb_filled_labels()[source]¶: Return the number annotation with a filled label.

get_parent()[source]¶: Return the parent of the tier.

has_location(location)[source]¶

Return True if the tier has the given location.

to be tested.

has_point(point)[source]¶

Return True if the tier contains a given point.

Parameters: point – (sppasPoint) The point to find in the tier.
Returns: (bool)

index(moment)[source]¶

Return the index of the moment (int), or -1.

Only for tier with points.

Parameters: moment – (sppasPoint)

is_bool()[source]¶: All label tags are boolean values or None.

is_disjoint()[source]¶: Return True if the tier is made of disjoint localizations.

is_empty()[source]¶: Return True if the tier does not contain annotations.

is_float()[source]¶: All label tags are float values or None.

is_int()[source]¶: All label tags are integer values or None.

is_interval()[source]¶: Return True if the tier is made of interval localizations.

is_point()[source]¶: Return True if the tier is made of point localizations.

is_string()[source]¶: All label tags are string or unicode or None.

is_superset(other)[source]¶

Return True if this tier contains all points of the other tier.

Parameters: other – (sppasTier)
Returns: Boolean

lindex(moment)[source]¶

Return the index of the interval starting at a given moment, or -1.

Only for tier with intervals or disjoint. If the tier contains more than one annotation starting at the same moment, the method returns the first one.

Parameters: moment – (sppasPoint)

merge(idx, direction)[source]¶

Merge the annotation at given index with next or previous one.

if direction > 0:: ann_idx: [begin_idx, end_idx, labels_idx] next_ann: [begin_n, end_n, labels_n] result: [begin_idx, end_n, labels_idx + labels_n]
if direction < 0:: prev_ann: [begin_p, end_p, labels_p] ann_idx: [begin_idx, end_idx, labels_idx] result: [begin_p, end_idx, labels_p + labels_idx]

Parameters

idx – (int) Index of the annotation in the list
direction – (int) Positive for next, Negative for previous

Returns

(bool) False if direction does not match with index

Raise

Exception if merged annotation can’t be deleted of the tier

mindex(moment, bound=0)[source]¶

Return index of the interval containing the given moment.

Only for tier with intervals or disjoint.

If the tier contains more than one annotation at the same moment, the method returns the first one (i.e. the one which started at first).

Parameters

moment – (sppasPoint)
bound – (int) - 0 to exclude bounds of the interval; - -1 to include begin bound; - +1 to include end bound; - +2 to include both begin/end bounds; - others: the midpoint of moment is strictly inside

Returns

(int) Index of the 1st annotation containing moment or -1

near(moment, direction=1)[source]¶

Search for the annotation whose localization is closest.

Search for the nearest localization to the given moment into a given direction.

Parameters

moment – (sppasPoint)
direction – (int) - nearest 0 - nereast forward 1 - nereast backward -1

pop(index=- 1)[source]¶

Remove the annotation at the given position in the tier.

If no index is specified, pop() removes and returns the last annotation in the tier.

Parameters: index – (int) Index of the annotation to remove.
Raises: HierarchyContainsError

remove(begin, end, overlaps=False)[source]¶

Remove annotation intervals between begin and end.

Parameters

begin – (sppasPoint)
end – (sppasPoint)
overlaps – (bool)

Returns

the number of removed annotations

Raises

HierarchyContainsError

remove_unlabelled()[source]¶

Remove annotations without labels.

Do not remove an annotation if it invalidates the hierarchy.

Returns: the number of removed annotations

rindex(moment)[source]¶

Return the index of the interval ending at the given moment.

Only for tier with intervals or disjoint. If the tier contains more than one annotation ending at the same moment, the method returns the last one.

Parameters: moment – (sppasPoint)

set_ctrl_vocab(ctrl_vocab=None)[source]¶

Set a controlled vocabulary to this tier.

Parameters: ctrl_vocab – (sppasCtrlVocab or None)
Raises: AnnDataTypeError, CtrlVocabContainsError

set_media(media)[source]¶

Set a media to the tier.

Parameters: media – (sppasMedia)
Raises: AnnDataTypeError

set_name(name=None)[source]¶

Set the name of the tier.

If no name is given, an GUID is randomly assigned. Important: An empty string is accepted.

Parameters: name – (str) The identifier name or None.
Returns: the formatted name

set_parent(parent)[source]¶

Set the parent of the tier.

Parameters: parent – (sppasTranscription)

set_radius(radius)[source]¶

Fix a radius value to all points of the tier.

Parameters: radius – (int, float) New radius value
Raise: AnnDataTypeError, AnnDataNegValueError

split(idx)[source]¶

Split annotation at the given index into 2 annotations.

Parameters: idx – (int) Index of the annotation to split.
Returns: newly created annotation at index idx+1

validate()[source]¶

validate_annotation(annotation)[source]¶

Validate the annotation and set its parent to this tier.

Parameters: annotation – (sppasAnnotation)
Raises: AnnDataTypeError, CtrlVocabContainsError, HierarchyContainsError, HierarchyTypeError

validate_annotation_label(label)[source]¶

Validate a label.

Parameters: label – (sppasLabel)
Raises: CtrlVocabContainsError

validate_annotation_location(location)[source]¶

Ask the parent to validate a location.

Parameters: location – (sppasLocation)
Raises: AnnDataTypeError, HierarchyContainsError, HierarchyTypeError

anndata.transcription module¶

filename: sppas.src.anndata.transcription.py
author: Brigitte Bigi
contact: develop@sppas.org
summary: The main object to represent transcriptions of recordings.

class anndata.transcription.sppasTranscription(name=None)[source]¶

Bases: anndata.metadata.sppasMetaData

Representation of a transcription, the root in our framework.

Transcriptions in SPPAS are represented with:

metadata: a list of tuple key/value;

a name (used to identify the transcription);

a list of tiers;

a hierarchy between tiers;

a list of media;

a list of controlled vocabularies.

Inter-tier relations are managed by establishing alignment or association links between 2 tiers:

alignment: annotations of a tier A (child) have only localization instances included in those of annotations of tier B (parent);

association: annotations of a tier A have exactly localization

instances included in those of annotations of tier B.

Example

>>> # Create an instance
>>> trs = sppasTranscription("trs name")

>>> # Create a tier
>>> trs.create_tier("tier name")

>>> # Get a tier of a transcription from its index:
>>> tier = trs[0]

>>> # Get a tier of a transcription from its name
>>> tier = trs.find("tier name")

>>> # Get a tier from its identifier
>>> tier = trs.get_object(guid)

__init__(name=None)[source]¶

Create a new sppasTranscription instance.

Parameters: name – (str) Name of the transcription.

add_ctrl_vocab(new_ctrl_vocab)[source]¶

Add a new controlled vocabulary in the list of ctrl vocab.

Parameters: new_ctrl_vocab – (sppasCtrlVocab)
Raises: AnnDataTypeError, TrsAddError

add_hierarchy_link(link_type, parent_tier, child_tier)[source]¶

Validate and add a hierarchy link between 2 tiers.

Parameters

link_type – (constant) One of the hierarchy types
parent_tier – (Tier) The reference tier
child_tier – (Tier) The child tier to be linked to reftier

add_media(new_media)[source]¶

Add a new media in the list of media.

Does not add the media if a media with the same id is already in self.

Parameters: new_media – (sppasMedia) The media to add.
Raises: AnnDataTypeError, TrsAddError

append(tier)[source]¶

Append a new tier.

Parameters: tier – (sppasTier) the tier to append

contains(tier)[source]¶: Return True if the given tier is in the list of tiers.

create_tier(name=None, ctrl_vocab=None, media=None)[source]¶

Create and append a new empty tier.

Parameters

name – (str) the name of the tier to create
ctrl_vocab – (sppasCtrlVocab)
media – (sppasMedia)

Returns

newly created empty tier

find(name, case_sensitive=True)[source]¶

Find a tier from its name.

Parameters

name – (str) EXACT name of the tier
case_sensitive – (bool)

Returns

sppasTier or None

find_id(tier_id)[source]¶

Find a tier from its identifier.

Parameters: tier_id – (str) Exact identifier of the tier
Returns: sppasTier or None

get_ctrl_vocab_from_id(ctrl_vocab_id)[source]¶

Return a sppasCtrlVocab from its id or None.

Parameters: ctrl_vocab_id – (str) Identifier name of a ctrl vocab

get_ctrl_vocab_from_name(ctrl_vocab_name)[source]¶

Return a sppasCtrlVocab from its name or None.

Parameters: ctrl_vocab_name – (str) Identifier name of a ctrl vocabulary

get_ctrl_vocab_list()[source]¶: Return the list of controlled vocabularies.

get_hierarchy()[source]¶: Return the hierarchy.

get_max_loc()[source]¶: Return the sppasPoint with the highest value through all tiers.

get_media_from_id(media_id)[source]¶

Return a sppasMedia from its name or None.

Parameters: media_id – (str) Identifier name of a media

get_media_list()[source]¶: Return the list of sppasMedia.

get_min_loc()[source]¶: Return the sppasPoint with the lowest value through all tiers.

get_name()[source]¶: Return the name of the transcription.

get_object(identifier)[source]¶

Return the object matching the given identifier.

Parameters: identifier – (GUID)

get_tier_from_id(tier_id)[source]¶

Return a sppasTier from its id or None.

Parameters: tier_id – (str) Identifier name of a tier

get_tier_index(name, case_sensitive=True)[source]¶

Get the index of a tier from its name.

Parameters

name – (str) EXACT name of the tier
case_sensitive – (bool)

Returns

index or -1 if not found

get_tier_index_id(identifier)[source]¶

Get the index of a tier from its id.

Parameters: identifier – (str) GUID
Returns: index or -1 if not found

get_tier_list()[source]¶: Return the list of tiers.

is_empty()[source]¶: Return True if the transcription does not contain tiers.

pop(index=- 1)[source]¶

Remove the tier at the given position in the transcription.

Return it. If no index is specified, pop() removes and returns the last tier in the transcription.

Parameters: index – (int) Index of the tier to remove.
Returns: (sppasTier)
Raise: AnnDataIndexError

remove_ctrl_vocab(old_ctrl_vocab)[source]¶

Remove a controlled vocabulary of the list of ctrl vocab.

Parameters: old_ctrl_vocab – (sppasCtrlVocab)
Raises: AnnDataTypeError, TrsRemoveError

remove_media(old_media)[source]¶

Remove a media of the list of media.

Parameters: old_media – (sppasMedia)
Raises: AnnDataTypeError, TrsRemoveError

rename_tier(tier)[source]¶

Rename a tier by appending a digit.

Parameters: tier – (sppasTier) The tier to rename.

set_ctrl_vocab_list(ctrl_vocab_list)[source]¶

Set the list of controlled vocabularies.

Parameters: ctrl_vocab_list – (list)
Returns: list of rejected ctrl_vocab

set_media_list(media_list)[source]¶

Set the list of media.

Parameters: media_list – (list)
Returns: list of rejected media

set_name(name=None)[source]¶

Set the name of the transcription.

Parameters: name – (str or None) The identifier or None to set the GUID.
Returns: the name

set_tier_index(name, new_index, case_sensitive=True)[source]¶

Set the index of a tier from its name.

THIS SHOULD NEVER BE USED. USE TIER IDENTIFIER INSTEAD OF ITS NAME.

Parameters

name – (str) EXACT name of the tier
new_index – (int) New index of the tier in self
case_sensitive – (bool)

Returns

index or -1 if not found

set_tier_index_id(identifier, new_index)[source]¶

Set the index of a tier from its identifier.

Parameters

identifier – (str)
new_index – (int) New index of the tier in self

Returns

index or -1 if not found

shift(delay)[source]¶

Shift all annotation’ location to a given delay.

Parameters: delay – (int, float) delay to shift all localizations
Raise: AnnDataTypeError

property tiers¶: Return the list of tiers.

validate_annotation_location(tier, location)[source]¶

Validate a location.

Parameters

tier – (Tier) The reference tier
location – (sppasLocation)

Raises

AnnDataTypeError, HierarchyContainsError, HierarchyTypeError

validate_hierarchy(tier)[source]¶

Module contents¶

filename: sppas.src.anndata.__init__.py
author: Brigitte Bigi
contact: develop@sppas.org
summary: Package to manage annotated data.

anndata: management of transcribed data.¶

anndata is a free and open source Python library to access and search data from annotated data. It can convert file formats like Elan’s EAF, Praat’s TextGrid and others into a sppasTranscription() object and convert into any of these formats. Those objects allow unified access to linguistic data from a wide range sources.

It requires the following other packages:

config
utils

class anndata.FileFormatProperty(extension)[source]¶

Bases: object

Represent one format and its properties.

__init__(extension)[source]¶

Create a FileFormatProperty instance.

Parameters: extension – (str) File name extension.

get_extension()[source]¶: Return the extension, including the initial dot.

get_reader()[source]¶: Return True if SPPAS can read files of the extension.

get_software()[source]¶: Return the name of the software matching the extension.

get_trs_type()[source]¶: Return the transcription type: ANNOT, MEASURE, TABLE or None.

get_writer()[source]¶: Return True if SPPAS can write files of the extension.

anndata.format_label(text, empty='', tag_type='str')[source]¶

Create a label from a text.

Use the “{ | }” system to parse the alternative tags and = for scores.

Parameters

text – (str)
empty – (str) The text representing an empty tag.
tag_type – (str): One of: (‘str’, ‘int’, ‘float’, ‘bool’).

Returns

sppasLabel

anndata.format_labels(text, separator='\n', empty='', tag_type='str')[source]¶

Create a set of labels from a text.

Use the separator to split the text into labels. Use the “{ | }” system to parse the alternative tags.

Examples

text = “{le|les} {chat|chats}” is 2 labels with 2 tags each text = “{le=0.6|les=0.4}” is a label with 2 tags and their score

Parameters

text – (str)
separator – (str) String to separate labels.
empty – (str) The text representing an empty tag.
tag_type – (str): One of: (‘str’, ‘int’, ‘float’, ‘bool’).

Returns

list of sppasLabel

anndata.serialize_label(label, empty='', alt=True)[source]¶

Convert the label into a string, include or not alternative tags.

Use the “{ | }” system to serialize the alternative tags. Scores of the tags are not returned.

Parameters

label – (sppasLabel)
empty – (str) The text to return if a tag is empty or not set.
alt – (bool) Include alternative tags

Returns

(str)

anndata.serialize_labels(labels, separator='\n', empty='', alt=True)[source]¶

Create a text from a list of labels.

Use the separator to split the text into labels. Use the “{ | }” system to parse the alternative tags and = for scores.

Parameters

labels – (list of sppasLabel)
separator – (str) String separating labels
empty – (str) The text representing an empty tag
alt – (bool) Include alternative tags. If False, only the best tag is serialized.

Returns

list of sppasLabel

class anndata.sppasAnnSet[source]¶

Bases: sppas.src.structs.basefset.sppasBaseSet

Manager for a set of annotations.

Mainly used with the data that are the result of the tier filter system. A sppasAnnSet() manages a dictionary with:

key: an annotation

value: a list of strings

__init__()[source]¶: Create a sppasAnnSet instance.

copy()[source]¶

Make a deep copy of self.

Overridden to return a sppasAnnSet() instead of a sppasBaseSet().

to_tier(name='AnnSet', annot_value=False)[source]¶

Create a tier from the data set.

Parameters

name – (str) Name of the tier to be returned
annot_value – (bool) format of the resulting annotation label. By default, the label of the annotation is used. Instead, its value in the data set is used.

Returns

(sppasTier)

class anndata.sppasAnnotation(location, labels=[])[source]¶

Bases: sppas.src.anndata.metadata.sppasMetaData

Represents an annotation.

A sppasAnnotation() is a container for:

a sppasLocation()

a list of sppasLabel()

Example

>>> location = sppasLocation(sppasPoint(1.5, radius=0.01))
>>> labels = sppasLabel(sppasTag("foo"))
>>> ann = sppasAnnotation(location, labels)

__init__(location, labels=[])[source]¶

Create a new sppasAnnotation instance.

Parameters

location – (sppasLocation) the location(s) where the annotation happens
labels – (sppasLabel, list) the label(s) to stamp this annotation, or a list of them.

add_tag(tag, score=None, label_idx=0)[source]¶

Append an alternative tag in a label.

Parameters

tag – (sppasTag)
score – (float)
label_idx – (int)

Raises

AnnDataTypeError, IndexError

append_label(label)[source]¶

Append a label into the list of labels.

Parameters: label – (sppasLabel)

contains_localization(localization)[source]¶: Return True if the given localization is in the location.

contains_tag(tag, function='exact', reverse=False, label_idx=0)[source]¶

Return True if the given tag is in the label.

Parameters

tag – (sppasTag)
function – Search function
reverse – Reverse the function.
label_idx – (int)

copy()[source]¶

Return a full copy of the annotation.

The location, the labels and the metadata are all copied. The ‘id’ of the returned annotation is then the same.

Returns: sppasAnnotation()

get_all_points()[source]¶: Return the list of a copy of all points of this annotation.

get_best_tag(label_idx=0)[source]¶

Return the tag with the highest score of a label or an empty str.

Parameters: label_idx – (int)

get_highest_localization()[source]¶: Return a copy of the sppasPoint with the highest loc.

get_label_type()[source]¶: Return the current type of tags, or an empty string.

get_labels()[source]¶: Return the list of sppasLabel() of this annotation.

get_labels_best_tag()[source]¶: Return a list with the best tag of each label.

get_location()[source]¶: Return the sppasLocation() of this annotation.

get_lowest_localization()[source]¶: Return a copy of the sppasPoint with the lowest localization.

get_parent()[source]¶: Return the parent tier or None.

get_score()[source]¶: Return the score of this annotation or None if no score is set.

is_labelled()[source]¶: Return True if at least a sppasTag exists and is not None.

label_is_bool()[source]¶: Return True if the type of the labels is ‘bool’.

label_is_filled()[source]¶: Return True if at least one BEST tag is filled.

label_is_float()[source]¶: Return True if the type of the labels is ‘float’.

label_is_int()[source]¶: Return True if the type of the labels is ‘int’.

label_is_string()[source]¶: Return True if the type of the labels is ‘str’.

location_is_disjoint()[source]¶: Return True if the location is made of sppasDisjoint locs.

location_is_interval()[source]¶: Return True if the location is made of sppasInterval locs.

location_is_point()[source]¶: Return True if the location is made of sppasPoint locs.

remove_tag(tag, label_idx=0)[source]¶

Remove an alternative tag of the label.

Parameters

tag – (sppasTag) the tag to be removed of the list.
label_idx – (int)

serialize_labels(separator='\n', empty='', alt=True)[source]¶

DEPRECATED. Return labels serialized into a string.

TODO: REMOVE THIS METHOD. Use aioutils.serialize_labels() instead.

Parameters

separator – (str) String to separate labels.
empty – (str) The text to return if a tag is empty or not set.
alt – (bool) Include alternative tags

Returns

(str)

set_best_localization(localization)[source]¶

Set the best localization of the location.

Parameters: localization – (sppasBaseLocalization)

set_labels(labels=[])[source]¶

Fix/reset the list of labels of this annotation.

Parameters: labels – (sppasLabel, list) the label(s) to stamp this annotation, or a list of them.
Raises: AnnDataTypeError, TypeError, CtrlVocabContainsError, HierarchyContainsError, HierarchyTypeError

set_parent(parent=None)[source]¶

Set a parent tier.

Parameters: parent – (sppasTier) The parent tier of this annotation.
Raises: CtrlVocabContainsError, HierarchyContainsError, HierarchyTypeError

set_score(score=None)[source]¶

Set or reset the score to this annotation.

Parameters: score – (float)

validate()[source]¶

Validate the annotation.

Check if the labels and location match the requirements.

Raises: TypeError, CtrlVocabContainsError, HierarchyContainsError, HierarchyTypeError

validate_label(label)[source]¶

Validate the label.

Check if the label matches the requirements of this annotation.

Raises: CtrlVocabContainsError, TypeError

validate_location()[source]¶

Validate the location of the annotation.

Raises

class anndata.sppasCtrlVocab(name, description='')[source]¶

Bases: anndata.metadata.sppasMetaData

Generic representation of a controlled vocabulary.

A controlled Vocabulary is a set of tags. It is used to restrict the use of tags in a label: only the accepted tags can be set to a label.

A controlled vocabulary is made of an identifier name, a description and a list of pairs tag/description.

__init__(name, description='')[source]¶

Create a new sppasCtrlVocab instance.

Parameters

name – (str) Identifier name of the controlled vocabulary
description – (str)

add(tag, description='')[source]¶

Add a tag to the controlled vocab.

Parameters

tag – (sppasTag): the tag to add.
description – (str)

Returns

Boolean

contains(tag)[source]¶

Test if a tag is in the controlled vocabulary.

Attention: Do not check the instance but the data content of the tag.

Parameters: tag – (sppasTag) the tag to check.
Returns: Boolean

get_description()[source]¶: Return the unicode str of the description of the ctrl vocab.

get_name()[source]¶: Return the name of the controlled vocabulary.

get_tag_description(tag)[source]¶

Return the unicode string of the description of an entry.

Parameters: tag – (sppasTag) the tag to get the description.
Returns: (str)

remove(tag)[source]¶

Remove a tag of the controlled vocab.

Parameters: tag – (sppasTag) the tag to remove.
Returns: Boolean

set_description(description='')[source]¶

Set the description of the controlled vocabulary.

Parameters: description – (str)

set_tag_description(tag, description)[source]¶

Set the unicode string of the description of an entry.

Parameters

tag – (sppasTag) the tag to get the description.
description – (str)

Returns

(str)

validate_tag(tag)[source]¶

Check if the given tag can be added to the ctrl vocabulary.

Parameters: tag – (sppasTag) the tag to check.
Returns: Boolean

class anndata.sppasDisjoint(intervals=None)[source]¶

Bases: anndata.ann.annlocation.localization.sppasBaseLocalization

Localization of a serie of intervals in time.

__init__(intervals=None)[source]¶

Create a new sppasDisjoint instance.

Parameters: intervals – (list of sppasInterval)

append_interval(interval)[source]¶

Return the sppasInterval at the given index.

Parameters: interval – (sppasInterval)

copy()[source]¶: Return a deep copy of self.

duration()[source]¶

Return the sppasDuration.

Make the sum of all interval’ durations.

get_begin()[source]¶: Return the first sppasPoint instance.

get_end()[source]¶: Return the last sppasPoint instance.

get_interval(index)[source]¶

Return the sppasInterval at the given index.

Parameters: index – (int)

get_intervals()[source]¶: Return the list of intervals.

is_bound(point)[source]¶: Return True if point is a bound of an interval.

is_disjoint()[source]¶: Return True because self is representing a disjoint intervals.

middle()[source]¶

Return a sppasPoint() at the middle of the time interval.

To be tested.

Returns: (sppasPoint)

set(other)[source]¶

Set self members from another sppasDisjoint instance.

Parameters: other – (sppasDisjoint)

set_begin(tp)[source]¶

Set the begin sppasPoint instance to new sppasPoint.

Parameters: tp – (sppasPoint)

set_end(tp)[source]¶

Set the end sppasPoint instance to new sppasPoint.

Parameters: tp – (sppasPoint)

set_intervals(intervals)[source]¶

Set a new list of intervals.

Parameters: intervals – list of sppasInterval.

set_radius(radius)[source]¶: Set radius value to all points.

shift(delay)[source]¶

Shift all the intervals to a given delay.

Parameters: delay – (int, float) delay to shift bounds
Raise: AnnDataTypeError

class anndata.sppasDuration(value, vagueness=0.0)[source]¶

Bases: object

Representation of a duration with vagueness.

Represents a duration identified by 2 float values:

the duration value;

the duration margin.

__init__(value, vagueness=0.0)[source]¶

Create a new sppasDuration instance.

Parameters

value – (float) value of the duration.
vagueness – (float) represents the vagueness of the value.

copy()[source]¶: Return a deep copy of self.

get()[source]¶: Return myself.

get_margin()[source]¶: Return the vagueness of the duration (float).

get_value()[source]¶: Return the duration value (float).

set(other)[source]¶

Set the value/vagueness of another sppasDuration instance.

Parameters: other – (sppasDuration)

set_margin(vagueness)[source]¶

Fix the vagueness margin of the duration.

Parameters: vagueness – (float) the duration margin.

set_value(value)[source]¶

Set the duration to a new value.

Parameters: value – (float) the new duration value.

class anndata.sppasDurationCompare[source]¶

Bases: sppas.src.structs.basecompare.sppasBaseCompare

Comparison methods for sppasDuration.

__init__()[source]¶: Create a sppasDurationCompare instance.

static eq(duration, x)[source]¶

Return True if duration is equal to x.

Parameters

duration – (sppasDuration)
x – (int, float)

Returns

(bool)

static ge(duration, x)[source]¶

Return True if duration is greater or equal than x.

Parameters

duration – (sppasDuration)
x – (int, float)

Returns

(bool)

static gt(duration, x)[source]¶

Return True if duration is greater than x.

Parameters

duration – (sppasDuration)
x – (int, float)

Returns

(bool)

static le(duration, x)[source]¶

Return True if duration is lower or equal than x.

Parameters

duration – (sppasDuration)
x – (int, float)

Returns

(bool)

static lt(duration, x)[source]¶

Return True if duration is lower than x.

Parameters

duration – (sppasDuration)
x – (int, float)

Returns

(bool)

static ne(duration, x)[source]¶

Return True if duration is different to x.

Parameters

duration – (sppasDuration)
x – (int, float)

Returns

(bool)

class anndata.sppasHierarchy[source]¶

Bases: anndata.metadata.sppasMetaData

Generic representation of a hierarchy between tiers.

Two types of hierarchy are considered:

TimeAssociation: the points of a child tier are all equals to the points of a reference tier, as for example:

parent: Words | l’ | âne | est | là |

child: Lemmas | le | âne | être | là |

TimeAlignment: the points of a child tier are all included in the set of points of a reference tier, as for example:

parent: Phonemes | l | a | n | e | l | a |

child: Words | l’ | âne | est | là |

parent: Phonemes | l | a | n | e | l | a |

child: Syllables | l.a | n.e | l.a |

In that example, notice that there’s no hierarchy link between “Tokens” and “Syllables” and notice that “Phonemes” is the grand-parent of “Lemmas”.

And the following obvious rules are applied:

A child can have ONLY ONE parent!

A parent can have as many children as wanted.

A hierarchy is a tree, not a graph.

Todo is to consider a time association that is not fully completed:

parent: Tokens | l’ | âne | euh | euh | est | là | @ |

child: Lemmas | le | âne | | être | là |

__init__()[source]¶: Create a new sppasHierarchy instance.

add_link(link_type, parent_tier, child_tier)[source]¶

Validate and add a hierarchy link between 2 tiers.

Parameters

link_type – (constant) One of the hierarchy types
parent_tier – (sppasTier) The parent tier
child_tier – (sppasTier) The child tier to be linked to parent

copy()[source]¶: Return a deep copy of the hierarchy.

get_ancestors(child_tier)[source]¶

Return all the direct ancestors of a tier.

Parameters: child_tier – (sppasTier)
Returns: List of tiers with parent, grand-parent, grand-grand-parent…

get_children(parent_tier, link_type=None)[source]¶

Return the list of children of a tier, for a given type.

Parameters

parent_tier – (sppasTier) The child tier to found
link_type – (str) The type of hierarchy

Returns

List of tiers

get_hierarchy_type(child_tier)[source]¶

Return the hierarchy type between a child tier and its parent.

Returns: (str) one of the hierarchy type

get_parent(child_tier)[source]¶

Return the parent tier for a given child tier.

Parameters: child_tier – (sppasTier) The child tier to found

static infer_hierarchy_type(tier1, tier2)[source]¶

Test if tier1 can be a parent tier for tier2.

Returns: One of hierarchy types or an empty string

remove_child(child_tier)[source]¶

Remove a hierarchy link between a parent and a child.

Parameters: child_tier – (sppasTier) The tier linked to a reference

remove_parent(parent_tier)[source]¶

Remove all hierarchy links between a parent and its children.

Parameters: parent_tier – (sppasTier) The parent tier

remove_tier(tier)[source]¶

Remove all occurrences of a tier inside the hierarchy.

Parameters: tier – (sppasTier) The tier to remove as parent or child.

types = {'TimeAlignment', 'TimeAssociation'}¶

validate_link(link_type, parent_tier, child_tier)[source]¶

Validate a hierarchy link between 2 tiers.

Parameters

link_type – (constant) One of the hierarchy types
parent_tier – (sppasTier) The parent tier
child_tier – (sppasTier) The child tier to be linked to parent

Raises

AnnDataTypeError, HierarchyParentTierError, HierarchyChildTierError, HierarchyAncestorTierError, HierarchyAlignmentError, HierarchyAssociationError

static validate_time_alignment(parent_tier, child_tier)[source]¶

Validate a time alignment hierarchy link between 2 tiers.

Parameters

parent_tier – (sppasTier) The parent tier
child_tier – (sppasTier) The child tier to be linked to parent

Raises

HierarchyAlignmentError

static validate_time_association(parent_tier, child_tier)[source]¶

Validate a time association hierarchy link between 2 tiers.

Parameters

parent_tier – (sppasTier) The parent tier
child_tier – (sppasTier) The child tier to be linked to the parent

Raises

HierarchyAssociationError

class anndata.sppasInterval(begin, end)[source]¶

Bases: anndata.ann.annlocation.localization.sppasBaseLocalization

Localization of an interval between two sppasPoint instances.

An interval is identified by two sppasPoint objects:

one is representing the beginning of the interval;

the other is representing the end of the interval.

__init__(begin, end)[source]¶

Create a new sppasInterval instance.

Parameters

begin – (sppasPoint)
end – (sppasPoint)

Degenerated interval is forbidden, i.e. begin > end.

static check_interval_bounds(begin, end)[source]¶

Check bounds of a virtual interval.

Parameters

begin – (sppasPoint)
end – (sppasPoint)

static check_types(begin, end)[source]¶

True only if begin and end are both the same types of sppasPoint.

Parameters

begin – any kind of data
end – any kind of data

Returns

Boolean

combine(other)[source]¶

Return a sppasInterval, the combination of two intervals.

Parameters: other – (sppasInterval) the other interval to combine with.

copy()[source]¶: Return a deep copy of self.

duration()[source]¶

Overridden. Return the duration of the time interval.

Returns: (sppasDuration) Duration and its vagueness.

get_begin()[source]¶: Return the begin sppasPoint instance.

get_end()[source]¶: Return the end sppasPoint instance.

is_bound(point)[source]¶: Return True if point is the begin or the end of the interval.

is_float()[source]¶

is_int()[source]¶

is_interval()[source]¶: Overrides. Return True, because self represents an interval.

middle()[source]¶

Return a sppasPoint() at the middle of the time interval.

To be tested.

Returns: (sppasPoint)

middle_value()[source]¶

Return the middle value of the time interval.

Return a float value even if points are integers.

Returns: (float) value.

set(other)[source]¶

Set self members from another sppasInterval instance.

Parameters: other – (sppasInterval)

set_begin(tp)[source]¶

Set the begin of the interval to a new sppasPoint.

Attention: it is a reference assignment.

Parameters: tp – (sppasPoint)

set_end(tp)[source]¶

Set the end of the interval to a new sppasPoint.

Attention: it is a reference assignment.

Parameters: tp – (sppasPoint)

set_radius(radius)[source]¶

Set a radius value to begin and end points.

Parameters: radius – (int or float)
Raise: ValueError

shift(delay)[source]¶

Shift the interval to a given delay.

Parameters: delay – (int, float) delay to shift bounds
Raise: AnnDataTypeError

union(other)[source]¶

Return a sppasInterval representing the union of two intervals.

Parameters: other – (sppasInterval) the other interval to merge with.

class anndata.sppasLabel(tag, score=None)[source]¶

Bases: object

Represent the content of an annotation.

sppasLabel allows to store a set of sppasTags with their scores. This class is using a list of lists, i.e. a list of pairs (tag, score). This is the best compromise between memory usage, speed and readability.

A label is a list of possible sppasTag(), represented as a UNICODE string. A data type can be associated, as sppasTag() can be ‘int’, ‘float’ or ‘bool’.

__init__(tag, score=None)[source]¶

Create a new sppasLabel instance.

Parameters

tag – (sppasTag or list of sppasTag or None)
score – (float or list of float or None)

append(tag, score=None)[source]¶

Add a sppasTag into the list.

Do not add the tag if this alternative is already inside the list, but add the scores.

Parameters

tag – (sppasTag)
score – (float)

append_content(content, data_type='str', score=None)[source]¶

Add a text into the list.

Parameters

content – (str)
data_type – (str): The type of this text content.

One of: (str, int, float, bool) :param score: (float)

copy()[source]¶: Return a deep copy of the label.

get_best()[source]¶

Return the best sppasTag, i.e. the one with the better score.

Returns: (sppasTag or None)

get_score(tag)[source]¶

Return the score of a tag or None if tag is not in the label.

Parameters: tag – (sppasTag)
Returns: score: (float)

get_type()[source]¶: Return the type of the tags content.

is_bool()[source]¶

Return True if tags are of type “bool”.