def test_chop_one_spectrogram_file(self):
with tempfile.TemporaryDirectory(dir='/tmp',
prefix='chopping',
) as dir_nm:
chopper = SpectrogramChopper(
self.spectro_root,
dir_nm,
overwrite_policy=WhenAlreadyDone.OVERWRITE
)
species = Path(self.spectro_file).parent.stem
outdir = os.path.join(dir_nm, species)
true_snippet_time_width = chopper.chop_one_spectro_file(
self.spectro_file,
outdir,
'DOVE',
skip_size=self.skip_size
)
snippet_names = os.listdir(outdir)
num_expected_snippets = 0
cur_time = true_snippet_time_width
while cur_time < self.duration:
num_expected_snippets += 1
cur_time += self.skip_size
self.assertEqual(len(snippet_names), num_expected_snippets)
# Check embedded metadata of one snippet:
_spectro, metadata = SoundProcessor.load_spectrogram(Utils.listdir_abs(outdir)[0])
self.assertEqual(round(float(metadata['duration(secs)']), 3),
round(true_snippet_time_width, 3)
)
self.assertEqual(metadata['species'], 'DOVE')
def test_create_random_noise(self):
spectro, _metadata = SoundProcessor.load_spectrogram(
self.one_spectro_file)
new_spectro, _fname = SoundProcessor.random_noise(spectro,
noise_type='uniform')
self.assertTrue((new_spectro > spectro).any())
self.assertTrue((new_spectro <= 255).all())
def test_create_new_sample(self):
with tempfile.TemporaryDirectory(dir='/tmp',
prefix='test_spectro') as dst_dir:
# Time masking:
aug_spectro_path = self.spectro_augmenter_median.create_new_sample(
self.one_spectro_file, dst_dir, ImgAugMethod.TMASK)
# The two images shouldn't be the same:
orig, _metadata = SoundProcessor.load_spectrogram(
self.one_spectro_file)
aug, _metadata = SoundProcessor.load_spectrogram(aug_spectro_path)
self.assertFalse((orig == aug).all())
# Frequency masking:
aug_spectro_path = self.spectro_augmenter_median.create_new_sample(
self.one_spectro_file, dst_dir, ImgAugMethod.FMASK)
# The two images shouldn't be the same:
orig, _metadata = SoundProcessor.load_spectrogram(
self.one_spectro_file)
aug, _metadata = SoundProcessor.load_spectrogram(aug_spectro_path)
self.assertFalse((orig == aug).all())
def load_img(self, img_path):
'''
Returns a two-tuple: image tensor, img metadata
:param img_path: full path to image
:type img_path: str
:return Image loaded as a PIL, then downsized,
and transformed to a tensor. Plus any metadata
the image contains
:rtype (torch.Tensor, {str : str})
'''
img_obj_np, metadata = SoundProcessor.load_spectrogram(img_path, to_nparray=True)
img_obj_tns = torch.tensor(img_obj_np).unsqueeze(dim=0)
new_img_obj = self.transform_img(img_obj_tns)
print('bar')
def test_create_one_spectro(self):
# Test creating one spectrogram from an audio
# file. Ensure that sample rate, duration, and
# species are included int the destination spectrogram
# .png file:
audio_path = os.path.join(self.cur_dir,
'audio_aug_tst_data/DYSMEN_S/dys1.mp3')
(aud, sr) = SoundProcessor.load_audio(audio_path)
with tempfile.NamedTemporaryFile(suffix='.png',
prefix='spectro',
dir='/tmp',
delete=True) as fd:
SoundProcessor.create_spectrogram(aud,
sr,
fd.name,
info={'species': 'DYSMEN_C'})
_spectro, info = SoundProcessor.load_spectrogram(fd.name)
truth = {'sr': '22050', 'duration': '10.8', 'species': 'DYSMEN_C'}
self.assertDictEqual(info, truth)
def setUpClass(cls):
super(TestChopSpectrograms, cls).setUpClass()
cls.skip_size = 2 # sec
cls.cur_dir = os.path.dirname(__file__)
cls.spectro_root = os.path.join(cls.cur_dir,
'spectro_data_long')
cls.spectro_file = os.path.join(cls.spectro_root, 'DOVE/dove_long.png')
cls.num_spectro_files = len(Utils.find_in_dir_tree(
cls.spectro_root,
pattern='*.png',
entry_type='file'))
_spectro, metadata = SoundProcessor.load_spectrogram(cls.spectro_file)
try:
cls.duration = float(metadata['duration'])
except KeyError:
raise AssertionError(f"Spectrogram test file {os.path.basename(cls.spectro_file)} has no duration metadata")
cls.default_win_len = 5 # seconds
def create_one_saliency_map(self, model, img_path):
# We must run the model in evaluation mode
model.eval()
img_arr, metadata = SoundProcessor.load_spectrogram(img_path)
img.requires_grad_()
# Forward pass through the model to get the
# scores
scores = model(img)
# Get the index corresponding to the maximum score and the maximum score itself.
score_max_index = scores.argmax()
score_max = scores[0,score_max_index]
# Backward function on score_max performs
# the backward pass in the computation graph and
# calculates the gradient of score_max with respect
# to nodes in the computation graph:
score_max.backward()
# Saliency would be the gradient with respect to the input image now. But note that the input image has 3 channels,
# R, G and B. To derive a single class saliency value for each pixel (i, j), we take the maximum magnitude
# across all colour channels.
saliency, _ = torch.max(img.grad.data.abs(),dim=1)
# code to plot the saliency map as a heatmap
plt.imshow(saliency[0], cmap=plt.cm.hot)
plt.axis('off')
plt.show()
def set_metadata(cls, png_fpath, info_to_set, outfile=None, setting=False):
'''
Modify metadata in a .png file. Distinguishes between
replacing existing metadata (setting == True), and adding
to the existing info (set == False). Either way, takes
a dict of metadata in info_to_set.
If outfile is None (or same as the input file png_fpath),
the modification is in-place.
:param png_fpath: input png file
:type png_fpath: str
:param info_to_set: dict of metadata information
:type info_to_set: {str : str}
:param outfile: if provided, create a new png file with the
provided metadata
:type outfile: {None | str}
:param setting: whether or not to replace existing metadata
with info_to_set, or to add. Replacing only for common
keys
:type setting: bool
'''
if type(info_to_set) != dict:
raise TypeError(f"info_to_set must be a dict, not {type(dict)}")
img, metadata = SoundProcessor.load_spectrogram(png_fpath)
if outfile is None:
outfile = png_fpath
if setting:
metadata = info_to_set
else:
metadata.update(info_to_set)
SoundProcessor.save_image(img, outfile, metadata)
def snips_iterator(self, root=None):
'''
If root is a generator or iterable, we assume that it
will yield absolute paths to snippets. If root
is None, we set root to self.snip_dir.
Else, assume root is a directory below which snippets
are found.
In the latter case: recursively find snippet files,
starting with root. Yield one snippet file after
the other, if its recording ID matches this
instance's Raven selection table's ID.
:param root: file or directory with snippet files
:type root: {root | str | types.GeneratorTypes}
:return a series of full snippet file paths whose
file names indicate that the snippets are covered
in this instance's Raven table.
:rtype str
:raise StopIteration
'''
if root is None:
root = self.snip_dir
metadata_list = []
if type(root) != str and \
(isinstance(root, types.GeneratorType) or \
isinstance(root, Iterable)
):
# Root is a ready made generator.
snip_gen = root
else:
# Make a generator of snippets that originate
# from the given recording (id):
snip_gen = self.dir_tree_snip_gen(root)
# Create the time sorted list of snippet
# metadata:
for snip_path in snip_gen:
_img_arr, metadata = SoundProcessor.load_spectrogram(
snip_path, to_nparray=False)
metadata['snip_path'] = snip_path
metadata_list.append(metadata)
time_sorted_metadata = sorted(metadata_list,
key=lambda md: md['start_time(secs)'])
# Now keep feeding the list of sorted
# metadata:
# Since Python 3.7 generators raising
# StopIteration is no longer silently
# discarded; so need to catch it ourselves:
try:
for metadata in time_sorted_metadata:
yield metadata
return
except StopIteration:
return
def match_snippet(self, selections, snip_metadata, outdir):
'''
Workhorse:
For each snippet_path S, examines the time span covered by S.
Finds the selection table row (if any) whose begin/end
times overlap with S's time span.
Modifies the snippet's metadata by adding:
'low_freq' : <low bound of frequency involved in vocalization
'high_freq' : <high bound of frequency involved in vocalization
'multiple_species' : <list of species heard simultaneously>
'type' : <whether Song/Call/Call-1/Call-Trill...>
The selections are expected to be a list of dicts as
produced by Utils.read_raven_selection_table(). This
means:
o Dicts are sorted by selection start time
o the d['mix'] is a possibly empty list of species
names.
:param selections: list of dicts, each containing the
information of one selection table row.
:type selections: {str : str}
:param snip_metadata: metadata of one snippet, with 'snip_path'
entry added
:type snip_metadata: {str : Any}
:param outdir: directory where to write the updated
snippets. Value is allowed to be same as snippet_path,
but then the snippets will be updated in place
:type outdir: str
'''
snippet_path = snip_metadata['snip_path']
# This is the second time the snippet is loaded!!!!
# First time was in method snips_iterator() of
# class SelTblSnipsAssoc. See TODO at top for need
# to avoid this time consuming operation:
spectro_arr, metadata = SoundProcessor.load_spectrogram(snippet_path)
# Sanity check:
try:
snippet_tstart = float(metadata['start_time(secs)'])
except Exception as e:
print(e)
# End time of snippet:
snippet_tend = float(metadata['end_time(secs)'])
# Find the index of the select table row (dict)
# whose time interval overlaps:
snippet_interval = Interval(snippet_tstart, snippet_tend)
# The returned selection dict *may* be a
# 'phantom' selection, which is created in
# find_covering_sel() when a snippet straddles
# multiple selection rows:
sel_dict = self.find_covering_sel(selections, snippet_interval)
if sel_dict is None:
# This snippet_path was not involved in
# any of the human-created selection
# rectangles. ******* JUST RETURN IF MIX IS NON-EMPTY?
metadata['species'] = 'noise'
self.save_updated_snippet(
outdir,
'noise',
Path(snippet_path).name, # without parents
spectro_arr,
metadata)
return
low_f = sel_dict['Low Freq (Hz)']
high_f = sel_dict['High Freq (Hz)']
species = sel_dict['species']
voc_type = sel_dict['type'] # Song/Call/Song-Trill, etc.
# Get possibly empty list of species
# names that also occur in the selection:
multiple_species = sel_dict['mix']
# The species, and entries in the mix field
# will be used as part of file names.
# So ensure that they have no spaces.
# Also: convert the "no bird" entries to
# 'noise':
if species == 'no bird':
species = 'noise'
else:
species = species.replace(' ', '_')
new_multiple_species = []
for entry in multiple_species:
if entry == 'no bird' or entry == 'noise':
# Don't add noise as "also-present":
continue
else:
new_multiple_species.append(entry.replace(' ', '_'))
metadata['species'] = species
metadata['low_freq'] = low_f
metadata['high_freq'] = high_f
metadata['type'] = voc_type
metadata['multiple_species'] = new_multiple_species
# If this snippet is marked as noise,
# but the multiple_species field indicates
# that the snippet juts into non-noise
# selections, don't save this snippet as noise
# right here, but allow the loop over the
# muiltiple_species below to save it as a
# non-noise snippet; the second clause of the
# 'or' says: this snippet truly is noise:
if species != 'noise' or \
(species == 'noise' and len(new_multiple_species) == 0):
self.save_updated_snippet(
outdir,
species,
Path(snippet_path).name, # without parents
spectro_arr,
metadata)
# If the snippet_path matched, and contained multiple
# overlapping calls, create a copy of the snippet_path
# for each species:
if len(new_multiple_species) > 0:
# Ensure the human coder did not include
# the primary species in the list of overlaps:
try:
del new_multiple_species[new_multiple_species.index(species)]
except (IndexError, ValueError):
# All good, species wasn't in the list of additionals
pass
for overlap_species in new_multiple_species:
# If this snippet reaches into a selection
# that simply records "no bird" or "noise",
# no need to create a phantom, b/c noise
# is everywhere anyway:
if overlap_species == 'no bird' or \
overlap_species == 'noise':
continue
metadata['species'] = overlap_species
# New name for a copy of this snippet_path:
p = Path(snippet_path)
new_fname = f"{p.stem}_{overlap_species}{p.suffix}"
self.save_updated_snippet(outdir, overlap_species, new_fname,
spectro_arr, metadata)
def extract_metadata(cls, png_src, show=False, printout=False):
'''
Given a .png file path, or a directory:
o extract metadata
o print the metadata if requested (printout == True)
o show the .png file if requested (show == True)
o return: if png_src is a dir: a list of metadata dicts
else just one metadata dict
If png_src is a directory, all .png files below the
directory will be found recursively, and printed/shown/returned
as requested.
:param png_src: .png file or directory tree root containing
.png file
:type png_src: src
:param show: whether or not to display the .png file
:type show: bool
:param printout: whether or not to print metadata
to stdout
:type printout: bool
:return: list of metadata dicts, if png_src is a dir,
else one metadata dict
:rtype {{src : src} | [{src : src}]}
'''
if show:
# To save startup time, only load
# matplotlib if needed:
import matplotlib.pyplot as plt
if os.path.isfile(png_src):
img, metadata = SoundProcessor.load_spectrogram(png_src)
snip_path_md_gen = iter([(png_src, metadata)])
else:
snip_path_md_gen = cls.metadata_list(png_src)
md_list = []
for snippet_path, metadata in snip_path_md_gen:
md_list.append(metadata)
if printout:
try:
print(f"{Path(snippet_path).name}---", end='')
# Very inefficient: if using metadata_list()
# above, we lost the img array. Could fix,
# but not worth it for now:
try:
print(f"Shape: {img.shape}")
except UnboundLocalError:
img, metadata = SoundProcessor.load_spectrogram(
snippet_path)
print(f"Shape: {img.shape}")
if len(metadata) == 0:
print("No metadata")
pprint.pprint(metadata, sort_dicts=False, indent=4)
#for key, val in metadata.items():
# print(f"{key} : {val}")
except Exception as _e:
print("No metadata available")
if show:
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
ax.set_title(os.path.basename(snippet_path))
ax.set_axis_off()
plt.imshow(img, cmap='gray')
plt.show()
return md_list[0] if os.path.isfile(png_src) else md_list
def chop_one_spectro_file(
cls,
spectro_fname,
out_dir,
species_name,
window_len=5,
skip_size=2,
original_duration=None,
overwrite_policy=WhenAlreadyDone.ASK,
):
"""
Generates window_len second spectrogram snippets
from spectrograms files of arbitrary length.
To compute the number of time slices to extract
for each snippet, the time_slices of the spectrogram time
slices in fractional seconds must be known. The time_slices
can be approximated if the play length of the underlying
audio is known (even if the precise fft settings are unavailable).
If the given .png file contains metadata with a 'duration'
key, then the corresponding value is used as the duration of
the original audio file in fractional seconds. This metadata
will be present if the .png file was created with the
SoundProcessor.create_spectrogram().
To enable use of spectrogram images created elsewhere, callers
can instead supply original_duration in fractional seconds.
For now, if neither the embedded metadata, nor the original_duration
is supplied, a ValueError is raised.
:param spectro_fname: full path to spectrogram file to chop
:type spectro_fname: str
:param out_dir: root directory under which spectrogram
snippets will be saved (in different subdirs)
:type out_dir: str
:param species_name: name of species to embed in the
metadata of this snippet, and use for determining
subdirectory where to place the snippet
:type species_name: str
:param window_len: number of seconds to be covered by each snippet
:type window_len: int
:param skip_size: number of seconds to shift right in
time for the start of each chop
:type skip_size: int
:param original_duration:
:raise ValueError: if neither embedded duration metadata is found
in the given file, nor original_duration is provided
"""
# Read the spectrogram, getting an np array:
spectro_arr, metadata = SoundProcessor.load_spectrogram(spectro_fname)
duration = metadata.get('duration', None)
if duration is None:
if original_duration is None:
raise ValueError(
f"Time duration of original recording cannot be determined for {spectro_fname}"
)
else:
duration = float(original_duration)
else:
duration = float(duration)
# If original file is already at or below
# the single window length, it's a snippet
# in itself. Copy it to the output with an
# appropriate snippet name to match the other
# snippets: wall start time is zero:
if duration < window_len:
# No partial snippets
return
# Note: Also have sample rate ('sr') and species ('label')
# in the metadata, but don't need those here.
_freq_bands, time_slices = spectro_arr.shape
# Time in fractions of second
# per spectrogram column:
twidth = duration / time_slices
# Integer of duration (which is in seconds):
time_dur_int = int(np.ceil(duration))
time_upper_bound = 1 + time_dur_int - skip_size
# Caller specifies skip_size and window
# length in *seconds*. Convert to spectrogram
# time slices (with rounding error):
samples_win_len = int(window_len // twidth)
# Does samples_win_len satisfy the
# minimum spectrogram snippet width for
# pretrained models?
samples_win_len = max(cls.MIN_SNIPPET_WIDTH, samples_win_len)
time_true_each_snippet = samples_win_len * twidth
samples_skip_size = int(skip_size // twidth)
samples_upper_bound = int(time_upper_bound // twidth)
assert (samples_upper_bound <= time_slices)
for _snip_num, samples_start_idx in enumerate(
range(0, samples_upper_bound, samples_skip_size)):
# Absolute start time of this snippet
# within the entire spectrogram:
wall_start_time = samples_start_idx * twidth
# Create a name for the snippet file:
snippet_path = cls.create_snippet_fpath(spectro_fname,
round(wall_start_time),
out_dir)
spectro_done = os.path.exists(snippet_path)
if spectro_done:
if overwrite_policy == WhenAlreadyDone.SKIP:
# Next snippet:
continue
elif overwrite_policy == WhenAlreadyDone.ASK:
if not Utils.user_confirm(
f"Snippet {Path(snippet_path).stem} exists, overwrite?",
default='N'):
continue
# Chop: All rows, columns from current
# window start for window lenth samples:
snippet_data = spectro_arr[:, samples_start_idx:samples_start_idx +
samples_win_len]
_num_rows, num_cols = snippet_data.shape
if num_cols < samples_win_len:
# Leave that little spectrogram
# snippet leftover for Elijah:
break
snippet_info = metadata.copy()
# Add the
snippet_info['duration(secs)'] = samples_win_len * twidth
snippet_info['start_time(secs)'] = wall_start_time
snippet_info['end_time(secs)'] = wall_start_time + (
samples_win_len * twidth)
snippet_info['species'] = species_name
SoundProcessor.save_image(snippet_data, snippet_path, snippet_info)
return time_true_each_snippet
def create_new_sample(self, sample_path, out_dir, method):
'''
Given one spectrogram file, and an image augmentation
method name, compute that augmentation, create a file name
that gives insight into the aug applied, and write that
new spectrogram file to out_dir.
Currently available types of image augmentation technique:
o adding random or uniform sounds
o frequency masking
o time masking
Returns the full path of the newly created spectrogram file:
:param sample_path: absolute path to spectrogram
:type sample_path: str
:param out_dir: destination of resulting new spectros
:type out_dir: src
:param method: the (spectrogram) image augmentation method to apply
:type method: ImgAugMethod
:return: Newly created spectro file (full path) or None,
if a failure occurred.
:rtype: {str | None|
'''
success = False
spectro, metadata = SoundProcessor.load_spectrogram(sample_path)
if method == ImgAugMethod.NOISE:
try:
# Default is uniform noise:
new_spectro, out_fname = SoundProcessor.random_noise(spectro)
metadata['augmentation'] = 'noise'
success = True
except Exception as e:
sample_fname = Path(sample_path).stem
self.log.err(
f"Failed to add noise to {sample_fname} ({repr(e)})")
elif method == ImgAugMethod.FMASK:
try:
# Horizontal bands:
new_spectro, out_fname = SoundProcessor.freq_mask(
spectro,
max_height=15 # num freq bands
)
metadata['augmentation'] = 'fmask'
success = True
except Exception as e:
sample_fname = Path(sample_path).stem
self.log.err(
f"Failed to time shift on {sample_fname} ({repr(e)})")
elif method == ImgAugMethod.TMASK:
try:
# Vertical bands:
new_spectro, out_fname = SoundProcessor.time_mask(
spectro,
max_width=15 # num time ticks
)
metadata['augmentation'] = 'tmask'
success = True
except Exception as e:
sample_fname = Path(sample_path).stem
self.log.err(
f"Failed to time shift on {sample_fname} ({repr(e)})")
if success:
sample_p = Path(sample_path)
appended_fname = sample_p.stem + out_fname + sample_p.suffix
out_path = os.path.join(out_dir, appended_fname)
SoundProcessor.save_image(new_spectro, out_path, metadata)
return out_path if success else None