# -*- coding: utf-8 -*-
"""
python -c "import utool as ut; ut.write_modscript_alias('Tgen.sh', 'wbia.templates.template_generator')"
sh Tgen.sh --key species --invert --Tcfg with_getters=True with_setters=False --modfname manual_species_funcs
# TODO: Fix this name it is too special case
"""
import logging
import uuid
import functools
# import numpy as np
# import vtool as vt
import numpy as np
from wbia import constants as const
from wbia.control import accessor_decors, controller_inject # NOQA
import utool as ut
from wbia.control.controller_inject import make_ibs_register_decorator
print, rrr, profile = ut.inject2(__name__)
logger = logging.getLogger('wbia')
CLASS_INJECT_KEY, register_ibs_method = make_ibs_register_decorator(__name__)
register_api = controller_inject.get_wbia_flask_api(__name__)
SPECIES_ROWID = 'species_rowid'
SPECIES_UUID = 'species_uuid'
SPECIES_TEXT = 'species_text'
SPECIES_NICE = 'species_nice'
SPECIES_CODE = 'species_code'
SPECIES_NOTE = 'species_note'
SPECIES_ENABLED = 'species_toggle_enabled'
@register_ibs_method
@accessor_decors.ider
@register_api('/api/species/', methods=['GET'], __api_plural_check__=False)
def _get_all_species_rowids(ibs):
r"""
Returns:
list_ (list): all nids of known animals
(does not include unknown names)
"""
# all_known_species_rowids = ibs._get_all_known_lblannot_rowids(const.SPECIES_KEY)
all_known_species_rowids = ibs.db.get_all_rowids(const.SPECIES_TABLE)
return all_known_species_rowids
[docs]@register_ibs_method
@accessor_decors.ider
def get_all_species_texts(ibs):
r"""
Returns:
list_ (list): all nids of known animals
(does not include unknown names)
"""
species_rowid_list = ibs._get_all_species_rowids()
species_text_list = ibs.get_species_texts(species_rowid_list)
return species_text_list
[docs]@register_ibs_method
@accessor_decors.ider
def get_all_species_nice(ibs):
r"""
Returns:
list_ (list): all nids of known animals
(does not include unknown names)
"""
species_rowid_list = ibs._get_all_species_rowids()
species_nice_list = ibs.get_species_nice(species_rowid_list)
return species_nice_list
[docs]@register_ibs_method
# @register_api('/api/species/sanitize/', methods=['PUT'])
def sanitize_species_texts(ibs, species_text_list):
r"""
changes unknown species to the unknown value
Args:
ibs (IBEISController): wbia controller object
species_text_list (list):
Returns:
list: species_text_list_
CommandLine:
python -m wbia.control.manual_species_funcs --test-sanitize_species_texts
RESTful:
Method: POST
URL: /api/species/sanitize
Example:
>>> # ENABLE_DOCTEST
>>> from wbia.control.manual_species_funcs import * # NOQA
>>> import wbia
>>> # build test data
>>> ibs = wbia.opendb('testdb1')
>>> species_text_list = ['foo', 'bar', 'zebra_plains']
>>> # execute function
>>> species_text_list_ = sanitize_species_texts(ibs, species_text_list)
>>> # verify results
>>> result = ut.repr2(species_text_list_, nl=False)
>>> print(result)
['foo', 'bar', 'zebra_plains']
"""
# valid_species = ibs.get_all_species_texts()
# ibsfuncs.assert_valid_species_texts(ibs, species_text_list, iswarning=True)
# def _sanitize_species_text(species_text):
# if species_text is None:
# return None
# elif species_text in valid_species:
# return species_text
# else:
# return const.UNKNOWN
# species_text_list_ = [_sanitize_species_text(species_text)
# for species_text in species_text_list]
# # old but same logic
# #species_text_list_ = [None if species_text is None else
# # species_text if species_text in valid_species else
# # const.UNKNOWN
# # for species_text in species_text_list]
# # oldest different logic
# #species_text_list_ = [None
# # if species_text is None or species_text == const.UNKNOWN
# # else species_text.lower()
# # for species_text in species_text_list]
# #species_text_list_ = [species_text if species_text in valid_species else None
# # for species_text in species_text_list_]
# return species_text_list_
return species_text_list
def _convert_species_nice_to_text(species_nice_list):
import re
def _convert(nice):
nice = re.sub(r'[ ]+', '_', nice)
nice = re.sub(r'[^a-zA-Z0-9_\+]+', '', nice)
nice = re.sub(r'[_]+', '_', nice)
nice = nice.lower()
return nice
return [_convert(species_nice) for species_nice in species_nice_list]
def _convert_species_nice_to_code(species_nice_list):
import re
def _convert(text):
text = re.sub(r'[_]+', ' ', text)
text = text.title()
text = re.sub(r'[^A-Z0-9\+]+', '', text)
return text
species_text_list = _convert_species_nice_to_text(species_nice_list)
return [_convert(species_text) for species_text in species_text_list]
[docs]@register_ibs_method
@accessor_decors.adder
@register_api('/api/species/', methods=['POST'], __api_plural_check__=False)
def add_species(
ibs,
species_nice_list,
species_text_list=None,
species_code_list=None,
species_uuid_list=None,
species_note_list=None,
skip_cleaning=False,
):
r"""
Adds a list of species.
Returns:
list: speciesid_list - species rowids
RESTful:
Method: POST
URL: /api/species/
CommandLine:
python -m wbia.control.manual_species_funcs --test-add_species
Example:
>>> # ENABLE_DOCTEST
>>> from wbia.control.manual_species_funcs import * # NOQA
>>> import wbia
>>> import utool as ut
>>> ibs = wbia.opendb('testdb1')
>>> species_text_list = [
... 'jaguar', 'zebra_plains', 'zebra_plains', '____', 'TYPO',
... '____', 'zebra_grevys', 'bear_polar+head']
>>> species_rowid_list = ibs.add_species(species_text_list)
>>> print(ut.repr2(list(zip(species_text_list, species_rowid_list))))
>>> ibs.print_species_table()
>>> species_text = ibs.get_species_texts(species_rowid_list)
>>> # Ensure we leave testdb1 in a clean state
>>> ibs.delete_species(ibs.get_species_rowids_from_text(['jaguar', 'TYPO']))
>>> all_species_rowids = ibs._get_all_species_rowids()
>>> result = ut.repr2(species_text, nl=False) + '\n'
>>> result += ut.repr2(all_species_rowids, nl=False) + '\n'
>>> result += ut.repr2(ibs.get_species_texts(all_species_rowids), nl=False) + '\n'
>>> result += ut.repr2(ibs.get_species_codes(all_species_rowids), nl=False)
>>> print(result)
['jaguar', 'zebra_plains', 'zebra_plains', '____', 'typo', '____', 'zebra_grevys', 'bear_polar+head']
[1, 2, 3, 6]
['zebra_plains', 'zebra_grevys', 'bear_polar', 'bear_polar+head']
['PZ', 'GZ', 'PB', 'BP+H']
"""
# Strip all spaces
species_nice_list = [
const.UNKNOWN if _ is None else _.strip() for _ in species_nice_list
]
if species_text_list is None:
species_text_list = _convert_species_nice_to_text(species_nice_list)
if species_code_list is None:
species_code_list = _convert_species_nice_to_code(species_nice_list)
if species_note_list is None:
species_note_list = [''] * len(species_text_list)
if species_uuid_list is None:
species_uuid_list = [uuid.uuid4() for _ in range(len(species_text_list))]
# Sanatize to remove invalid names
flag_list = np.array(
[
species_nice is None
or species_nice.strip() in ['_', const.UNKNOWN, 'none', 'None', '']
for species_nice in species_nice_list
]
)
species_uuid_list = ut.filterfalse_items(species_uuid_list, flag_list)
species_nice_list = ut.filterfalse_items(species_nice_list, flag_list)
species_text_list = ut.filterfalse_items(species_text_list, flag_list)
species_code_list = ut.filterfalse_items(species_code_list, flag_list)
species_note_list = ut.filterfalse_items(species_note_list, flag_list)
superkey_paramx = (1,)
# TODO Allow for better ensure=False without using partial
# Just autogenerate these functions
get_rowid_from_superkey = functools.partial(
ibs.get_species_rowids_from_text, ensure=False
)
colnames = [SPECIES_UUID, SPECIES_TEXT, SPECIES_NICE, SPECIES_CODE, SPECIES_NOTE]
params_iter = list(
zip(
species_uuid_list,
species_text_list,
species_nice_list,
species_code_list,
species_note_list,
)
)
species_rowid_list = ibs.db.add_cleanly(
const.SPECIES_TABLE,
colnames,
params_iter,
get_rowid_from_superkey,
superkey_paramx,
)
temp_list = np.array([-1] * len(flag_list))
temp_list[flag_list == False] = np.array(species_rowid_list) # NOQA
temp_list[flag_list == True] = const.UNKNOWN_SPECIES_ROWID # NOQA
species_rowid_list = list(temp_list)
assert -1 not in species_rowid_list
# Clean species
if not skip_cleaning:
species_mapping_dict = ibs._clean_species()
if species_mapping_dict is not None:
species_rowid_list = [
species_mapping_dict.get(species_rowid, species_rowid)
for species_rowid in species_rowid_list
]
return species_rowid_list
# value_list = ibs.sanitize_species_texts(species_text_list)
# lbltype_rowid = ibs.lbltype_ids[const.SPECIES_KEY]
# lbltype_rowid_list = [lbltype_rowid] * len(species_text_list)
# species_rowid_list = ibs.add_lblannots(lbltype_rowid_list, value_list, species_note_list)
# # species_rowid_list = [const.UNKNOWN_SPECIES_ROWID if rowid is None else
# rowid for rowid in species_rowid_list]
# return species_rowid_list
[docs]@register_ibs_method
@accessor_decors.deleter
# @cache_invalidator(const.SPECIES_TABLE)
@register_api('/api/species/', methods=['DELETE'], __api_plural_check__=False)
def delete_species(ibs, species_rowid_list):
r"""
deletes species from the database
CAREFUL. YOU PROBABLY DO NOT WANT TO USE THIS
at least ensure that no annot is associated with any of these species rowids
RESTful:
Method: DELETE
URL: /api/species/
"""
if ut.VERBOSE:
logger.info('[ibs] deleting %d speciess' % len(species_rowid_list))
ibs.db.delete_rowids(const.SPECIES_TABLE, species_rowid_list)
# ibs.delete_lblannots(species_rowid_list)
[docs]@register_ibs_method
# @accessor_decors.deleter
def delete_empty_species(ibs):
r"""
deletes empty species from the database
"""
species_text_set = set(ibs.get_all_species_texts())
aid_list = ibs.get_valid_aids()
used_species_text_set = set(ibs.get_annot_species_texts(aid_list))
unused_species_text_set = species_text_set - used_species_text_set
unused_species_text_list = list(unused_species_text_set)
unused_species_rowid_list = ibs.get_species_rowids_from_text(unused_species_text_list)
logger.info('Deleting unused species: %r' % (unused_species_text_list,))
ibs.delete_species(unused_species_rowid_list)
[docs]@register_ibs_method
@accessor_decors.getter_1to1
@register_api('/api/species/rowid/text/', methods=['GET'], __api_plural_check__=False)
def get_species_rowids_from_text(ibs, species_text_list, ensure=True, **kwargs):
r"""
Returns:
species_rowid_list (list): Creates one if it doesnt exist
CommandLine:
python -m wbia.control.manual_species_funcs --test-get_species_rowids_from_text:0
python -m wbia.control.manual_species_funcs --test-get_species_rowids_from_text:1
RESTful:
Method: GET
URL: /api/species/rowid/text/
Example:
>>> # ENABLE_DOCTEST
>>> from wbia.control.manual_species_funcs import * # NOQA
>>> import wbia
>>> import utool as ut
>>> ibs = wbia.opendb('testdb1')
>>> species_text_list = [
... u'jaguar', u'zebra_plains', u'zebra_plains', '____', 'TYPO',
... '____', u'zebra_grevys', u'bear_polar']
>>> ensure = False
>>> species_rowid_list = ibs.get_species_rowids_from_text(species_text_list, ensure)
>>> # print(ut.repr2(list(zip(species_text_list, species_rowid_list))))
>>> ensure = True
>>> species_rowid_list = ibs.get_species_rowids_from_text(species_text_list, ensure)
>>> # print(ut.repr2(list(zip(species_text_list, species_rowid_list))))
>>> ibs.print_species_table()
>>> species_text = ibs.get_species_texts(species_rowid_list)
>>> # Ensure we leave testdb1 in a clean state
>>> ibs.delete_species(ibs.get_species_rowids_from_text(['jaguar', 'TYPO']))
>>> all_species_rowids = ibs._get_all_species_rowids()
>>> assert ut.repr2(species_text, nl=False) == ['jaguar', 'zebra_plains', 'zebra_plains', '____', 'typo', '____', 'zebra_grevys', 'bear_polar']
>>> assert ut.repr2(all_species_rowids, nl=False) == [1, 2, 3, 6]
>>> assert ut.repr2(ibs.get_species_texts(all_species_rowids), nl=False) == ['zebra_plains', 'zebra_grevys', 'bear_polar', 'bear_polar+head']
Example:
>>> # ENABLE_DOCTEST
>>> from wbia.control.manual_species_funcs import * # NOQA
>>> import wbia
>>> import utool as ut # NOQA
>>> ibs = wbia.opendb('testdb1')
>>> species_text_list = [
... u'jaguar', u'zebra_plains', u'zebra_plains', '____', 'TYPO',
... '____', u'zebra_grevys', u'bear_polar']
>>> ensure = False
>>> species_rowid_list = ibs.get_species_rowids_from_text(species_text_list, ensure)
"""
if ensure:
species_rowid_list = ibs.add_species(species_text_list, **kwargs)
else:
species_text_list_ = ibs.sanitize_species_texts(species_text_list)
# lbltype_rowid = ibs.lbltype_ids[const.SPECIES_KEY]
# lbltype_rowid_list = [lbltype_rowid] * len(species_text_list_)
# species_rowid_list = ibs.get_lblannot_rowid_from_superkey(lbltype_rowid_list, species_text_list_)
# Ugg species and names need their own table
# species_rowid_list = [const.UNKNOWN_SPECIES_ROWID if rowid is None else
# rowid for rowid in species_rowid_list]
species_rowid_list = ibs.db.get(
const.SPECIES_TABLE,
(SPECIES_ROWID,),
species_text_list_,
id_colname=SPECIES_TEXT,
)
# BIG HACK FOR ENFORCING UNKNOWN SPECIESS HAVE ROWID 0
species_rowid_list = [
const.UNKNOWN_SPECIES_ROWID
if text is None or text == const.UNKNOWN
else rowid
for rowid, text in zip(species_rowid_list, species_text_list_)
]
return species_rowid_list
[docs]@register_ibs_method
@accessor_decors.getter_1to1
@register_api('/api/species/rowid/uuid/', methods=['GET'], __api_plural_check__=False)
def get_species_rowids_from_uuids(ibs, species_uuid_list):
r"""
Returns:
species_rowid_list (list): Creates one if it doesnt exist
CommandLine:
python -m wbia.control.manual_species_funcs --test-get_species_rowids_from_text:0
python -m wbia.control.manual_species_funcs --test-get_species_rowids_from_text:1
RESTful:
Method: GET
URL: /api/species/rowid/uuid/
"""
species_rowid_list = ibs.db.get(
const.SPECIES_TABLE, (SPECIES_ROWID,), species_uuid_list, id_colname=SPECIES_UUID
)
species_rowid_list = [
const.UNKNOWN_SPECIES_ROWID if text is None or text == const.UNKNOWN else rowid
for rowid, text in zip(species_rowid_list, species_uuid_list)
]
return species_rowid_list
[docs]@register_ibs_method
@accessor_decors.getter_1to1
@register_api('/api/species/uuid/', methods=['GET'], __api_plural_check__=False)
def get_species_uuids(ibs, species_rowid_list):
r"""
Returns:
list_ (list): uuids_list - species uuids
RESTful:
Method: GET
URL: /api/species/uuid/
"""
uuids_list = ibs.db.get(const.SPECIES_TABLE, (SPECIES_UUID,), species_rowid_list)
# notes_list = ibs.get_lblannot_notes(nid_list)
return uuids_list
[docs]@register_ibs_method
@accessor_decors.getter_1to1
@accessor_decors.cache_getter(const.SPECIES_TABLE, SPECIES_TEXT)
@register_api('/api/species/text/', methods=['GET'], __api_plural_check__=False)
def get_species_texts(ibs, species_rowid_list):
r"""
Returns:
list: species_text_list text names
CommandLine:
python -m wbia.control.manual_species_funcs --test-get_species_texts --enableall
RESTful:
Method: GET
URL: /api/species/text/
Example:
>>> # ENABLE_DOCTEST
>>> from wbia.control.manual_species_funcs import * # NOQA
>>> import wbia
>>> ibs = wbia.opendb('testdb1')
>>> species_rowid_list = ibs._get_all_species_rowids()
>>> result = get_species_texts(ibs, species_rowid_list)
>>> result = ut.repr2(result)
>>> print(result)
['zebra_plains', 'zebra_grevys', 'bear_polar', 'bear_polar+head']
"""
# FIXME: use standalone species table
# species_text_list = ibs.get_lblannot_values(species_rowid_list, const.SPECIES_KEY)
species_text_list = ibs.db.get(
const.SPECIES_TABLE, (SPECIES_TEXT,), species_rowid_list
)
species_text_list = [
const.UNKNOWN if rowid == const.UNKNOWN_SPECIES_ROWID else species_text
for species_text, rowid in zip(species_text_list, species_rowid_list)
]
species_text_list = [
const.UNKNOWN if code is None else code for code in species_text_list
]
return species_text_list
[docs]@register_ibs_method
@accessor_decors.getter_1to1
@accessor_decors.cache_getter(const.SPECIES_TABLE, SPECIES_NICE)
@register_api('/api/species/nice/', methods=['GET'], __api_plural_check__=False)
def get_species_nice(ibs, species_rowid_list):
r"""
Returns:
list: species_text_list nice names
CommandLine:
python -m wbia.control.manual_species_funcs --test-get_species_nice --enableall
RESTful:
Method: GET
URL: /api/species/nice/
Example:
>>> # ENABLE_DOCTEST
>>> from wbia.control.manual_species_funcs import * # NOQA
>>> import wbia
>>> ibs = wbia.opendb('testdb1')
>>> ibs._clean_species()
>>> species_rowid_list = ibs._get_all_species_rowids()
>>> result = get_species_nice(ibs, species_rowid_list)
>>> result = ut.repr2(result)
>>> print(result)
['Zebra (Plains)', "Zebra (Grevy's)", 'Polar Bear', 'bear_polar+head']
"""
# FIXME: use standalone species table
# species_nice_list = ibs.get_lblannot_values(species_rowid_list, const.SPECIES_KEY)
species_nice_list = ibs.db.get(
const.SPECIES_TABLE, (SPECIES_NICE,), species_rowid_list
)
species_nice_list = [
const.UNKNOWN if rowid == const.UNKNOWN_SPECIES_ROWID else species_nice
for species_nice, rowid in zip(species_nice_list, species_rowid_list)
]
species_nice_list = [
'Unknown' if code is None else code for code in species_nice_list
]
return species_nice_list
[docs]@register_ibs_method
@accessor_decors.getter_1to1
@register_api('/api/species/code/', methods=['GET'], __api_plural_check__=False)
def get_species_codes(ibs, species_rowid_list):
r"""
Returns:
list_ (list): code_list - species codes
RESTful:
Method: GET
URL: /api/species/code/
"""
species_code_list = ibs.db.get(
const.SPECIES_TABLE, (SPECIES_CODE,), species_rowid_list
)
species_code_list = [
'UNKNOWN' if code is None else code for code in species_code_list
]
return species_code_list
[docs]@register_ibs_method
@accessor_decors.getter_1to1
@register_api('/api/species/note/', methods=['GET'], __api_plural_check__=False)
def get_species_notes(ibs, species_rowid_list):
r"""
Returns:
list_ (list): notes_list - species notes
RESTful:
Method: GET
URL: /api/species/note/
"""
notes_list = ibs.db.get(const.SPECIES_TABLE, (SPECIES_NOTE,), species_rowid_list)
# notes_list = ibs.get_lblannot_notes(nid_list)
return notes_list
[docs]@register_ibs_method
@accessor_decors.getter_1to1
# @register_api('/api/species/enabled/', methods=['GET'])
def get_species_enabled(ibs, species_rowid_list):
r"""
Returns:
list_ (list): "Species Enabled" flag, true if the species is enabled
"""
enabled_list = ibs.db.get(const.SPECIES_TABLE, (SPECIES_ENABLED,), species_rowid_list)
return enabled_list
@register_ibs_method
@accessor_decors.setter
def _set_species_texts(ibs, species_rowid_list, species_text_list):
r"""
Sets the species nice names
"""
id_iter = ((species_rowid,) for species_rowid in species_rowid_list)
val_list = ((enabled,) for enabled in species_text_list)
ibs.db.set(const.SPECIES_TABLE, (SPECIES_TEXT,), val_list, id_iter)
@register_ibs_method
@accessor_decors.setter
def _set_species_nice(ibs, species_rowid_list, species_nice_list):
r"""
Sets the species nice names
"""
id_iter = ((species_rowid,) for species_rowid in species_rowid_list)
val_list = ((enabled,) for enabled in species_nice_list)
ibs.db.set(const.SPECIES_TABLE, (SPECIES_NICE,), val_list, id_iter)
@register_ibs_method
@accessor_decors.setter
def _set_species_code(ibs, species_rowid_list, species_code_list):
r"""
Sets the species nice names
"""
id_iter = ((species_rowid,) for species_rowid in species_rowid_list)
val_list = ((enabled,) for enabled in species_code_list)
ibs.db.set(const.SPECIES_TABLE, (SPECIES_CODE,), val_list, id_iter)
[docs]@register_ibs_method
@accessor_decors.setter
# @register_api('/api/species/enabled/', methods=['PUT'])
def set_species_enabled(ibs, species_rowid_list, enabled_list):
r"""
Sets the species all instances enabled bit
"""
id_iter = ((species_rowid,) for species_rowid in species_rowid_list)
val_list = ((enabled,) for enabled in enabled_list)
ibs.db.set(const.SPECIES_TABLE, (SPECIES_ENABLED,), val_list, id_iter)