def test_find_in_tree_gen(self):
res = list(Utils.find_in_tree_gen(self.spectros_dir, pattern='*.png'))
expected = [
f"{self.spectros_dir}/AMADEC/Amaziliadecora1061880.png",
f"{self.spectros_dir}/FORANA/SONG_XC609364-41759.png",
f"{self.spectros_dir}/FORANA/SONG_XC253440-FORANA04.png",
f"{self.spectros_dir}/FORANA/SONG_XC520628-passarochao.png",
f"{self.spectros_dir}/FORANA/SONG_XC360575-BFAN.png",
f"{self.spectros_dir}/FORANA/SONG_XC171241-Formicarius_analis.png"
]
self.assertSetEqual(set(res), set(expected))
def img_generator(self, in_img_or_dir):
if os.path.isfile(in_img_or_dir):
return iter([in_img_or_dir])
return Utils.find_in_tree_gen(in_img_or_dir, '*.png')
def __init__(self,
selection_tbl_loc,
spectrogram_locs,
out_dir,
unittesting=False):
'''
Create snippet copies into out_dir
for all snippets that are covered
by any of the given selection tables.
:param selection_tbl_loc: path to individual selection
table or a directory containing selection tables.
Each tbl is a tsv file with extension .txt
:type selection_tbl_loc: str
:param spectrogram_locs: individual or directory of
spectrogram snippets.
:type spectrogram_locs: str
:param out_dir: destination of snippet copies
:type out_dir: src
:param unittesting: if True, does not initialize
the instance, or run any operations
:type unittesting: bool
'''
if unittesting:
return
if not os.path.exists(selection_tbl_loc):
print(f"Cannot open {selection_tbl_loc}")
sys.exit(1)
if not os.path.exists(spectrogram_locs):
print(f"Spectrogram snippets {spectrogram_locs} not found")
sys.exit(1)
# Is path to sel tbl an individual tsv file?
if os.path.isfile(selection_tbl_loc):
table_paths = iter([selection_tbl_loc])
else:
# Caller gave directory of .csv files.
# Get them all recursively:
table_paths = Utils.find_in_tree_gen(selection_tbl_loc,
pattern="*.txt")
# Is snippets path to an individual .png snippet file?
if os.path.isfile(spectrogram_locs):
snippet_paths = iter([spectrogram_locs])
else:
# Caller gave directory of .png files.
# Get them all recursively:
snippet_paths = Utils.find_in_tree_gen(spectrogram_locs,
pattern="*.png")
# If out_dir does not exist, create it,
# and all dirs along the path:
if not os.path.exists(out_dir):
os.makedirs(out_dir)
# Get dict:
# {<recording-id> : SelTblSnipsAssoc-instance}
# where each SelTblSnipsAssoc instance is a generator
# of snippet metadata from snippet that are covered in
# the selection table that is associated with the instance.
# In addition the absolute snippet path is added as
# entry of key 'snip_path'.
#
# The generator feeds out the snippet metadata in order of
# start time.
#
# For brevity, call each instance of SelTblSnipsAssoc
# an 'assoc'
rec_id_assocs = self.create_snips_gen_for_sel_tbls(
snippet_paths, table_paths)
for assoc in rec_id_assocs.values():
# The assoc focuses on a single selection
# table, and the snippets it covers.
# Get the info contained in each row of
# the sel tb. This will be a list of dicts, each with
# the information from one selection tbl row:
selections = Utils.read_raven_selection_table(
assoc.raven_sel_tbl_path)
# Go through each snippet in the association, enrich its
# metadata with species info. Then copy the enriched
# snippet to the target dir:
for snip_metadata in iter(assoc):
self.match_snippet(selections, snip_metadata, out_dir)