Merge branch 'master' into 'master'

add doc for parakeet.data, python2 compatability for DataIterator and  lazy CacheDataset

See merge request !32

doc/data.md

+# parakeet.data
+
+This short guide shows the design of `parakeet.data` and how we use it in an experiment.
+
+The most concepts of parakeet are Dataset, DataCargo, Sampler, batch function and DataIterator.
+
+## Dataset
+
+`Dataset`, as we assume here, is a list of examples. You gen get its length by `len(dataset)`(which means it length is known, and we have to implement `__len__` method for it). And you can access its items randomly by `dataset[i]`(which means we have to implement `__getitem__` method for it). Furthermore,  you can iterable over it by `iter(dataset)` or `for example in dataset`, which means we have to implement `__iter__` method for it.
+
+We provide an `DatasetMixin` object which provides the above methods. You can inherit `DatasetMixin` and implement `get_example` method for it to define your own dataset class. The `get_example` method is called by `__getitem__` method automatically.
+
+We also provide several other datasets that is built based on other datasets.
+
+### TupleDataset
+
+Dataset that is combined by sevral datasets of the same length. An `example` of a tupledataset is a tuple of examples of its constituent datasets.
+
+### DictDataset
+
+Dataset that is combined by sevral datasets of the same length. An `example` of the tupledataset is a dict of examples of its constituent datasets.
+
+### SliceDataset
+
+SliceDataset is a slice of the base dataset.
+
+### SubsetDataset
+
+SubsetDataset is a subset of the base dataset.
+
+### ChainDataset
+
+ChainDataset is the concatenation of several datastes with the same fields.
+
+### TransformDataset
+
+A `TransformeDataset` is created by applying a `transform` to the base dataset. The `transform` is a callable object which takes an `example` of the base dataset and returns an `example` of the `TransformDataset`. The transform is lazy, which means it is applied to an example only when requested.
+
+### FilterDataset
+
+A `FilterDataset` is created by applying a `filter` to the base dataset. A `filter` is a predicate that takes an `example` of the base dataset and returns a boolean. Only those examples that pass the filter are included in the FilterDataset.
+
+Note that filter is applied to all the examples in the base dataset when initializing a FilterDataset.
+
+### CacheDataset
+
+By default, we preprocess dataset lazily in `DatasetMixin.get_example`. An example is preprocessed only only requested. But `CacheDataset` caches a base dataset (preprocesses all examples and cache s them eagerly beforehand). When preprocessing the dataset is slow, you can use Cachedataset to speed it up, but caching may consume a lot of RAM if the dataset is large.
+
+Finally, if preprocessing the dataset is slow and the processed dataset is too large to cache, you can write your own code to save them into files or databases and defines a Dataset to load them. Dataset is flexible, so you can create your own dataset painlessly.
+
+## DataCargo
+
+`DataCargo`, like `Dataset`, is an iterable of batches. We need datacargo because in deep learning, batching examples into batches exploits the computational resources of modern hardwares. You can iterate over it by `iter(datacargo)` or `for batch in datacargo`. It is an iterable but not an iterator, in that in can be iterated more than once.
+
+### batch function
+
+The concept of `batch` is something transformed from a list of examples. Assume that an example is a structure(tuple in python, or struct in C and C++) consists of several fields, then a list of examples is an array of structure(AOS, a dataset is an AOS). Then a batch here is a structure of arrays (SOA). Here is an example:
+
+The table below represents 2 examples, each of which contains 5 fields.
+
+| weight | height | width | depth | density |
+| ------ | ------ | ----- | ----- | ------- |
+| 1.2    | 1.1    | 1.3   | 1.4   | 0.8     |
+| 1.6    | 1.4    | 1.2   | 0.6   | 1.4     |
+
+The AOS representation and SOA representation of the table is show below.
+
+AOS:
+```text
+[(1.2, 1,1, 1,3, 1,4, 0.8),
+
+ (1.6, 1.4, 1.2, 0.6, 1.4)]
+```
+
+SOA:
+```text
+([1,2, 1.6],
+ [1.1, 1.4],
+ [1.3, 1.2],
+ [1.4, 0.6],
+ [0.8, 1.4])
+```
+
+For the example above, converting an AOS to an SOA is trivial, just stack every field for all the examples. But it is not always the case. When a field contains a sequence, you may have to pad all the sequences to the largest length then stack them together. In some other cases, we may want to add a field for the batch, for example, `valid_length` for each example. So in general, a function to transform an AOS to SOA is needed to build a datacargo from a dataset. We call this the batch function (`batch_fn`), but you can use any callable if you need to.
+
+Usually we need to define an callable object which stores all the options and configurations as its members as our `batch_fn`. Its `__call__` method transforms a list of examples into a batch.
+
+### sampler
+
+Equipped with a batch function(we have known __how to batch__), here comes the next question. __What to batch?__ We need to decide which examples to pick when creating a batch. Since a dataset is a list of examples, we only need to pick indices for the corresponding examples. A sampler object is what we use to do this.
+
+A sampler is represented as an iterable of integers. Assume the dataset has `N` examples, then an iterable of intergers in the range`[0, N)` is an appropriate sampler for this dataset to build a `DataCargo`.
+
+We provide several samplers that is ready to use. The `SequentialSampler`, `RandomSampler` and so on.
+
+## DataIterator
+
+`DataIterator` is what returned by `iter(data_cargo)`. It can only be iterated over once.
+
+Here's the analogy.
+
+```text
+Dataset   -->  Iterable[Example]  | iter(Dataset)    ->  Iterator[Example]
+DataCargo -->  Iterable[Batch]    | iter(DataCargo)  ->  Iterator[Batch]
+```
+
+ In order to construct an iterator of batches from an iterator of examples, we construct a DataCargo from a Dataset.
+
+
+
+## Code Example
+
+Here's an example of how we use `parakeet.data` to process the `LJSpeech` dataset with a wavenet model.
+
+First, we would like to define a class which represents the LJSpeech dataset and loads it as-is. We try not to apply any preprocessings here.
+
+```python
+import csv
+import numpy as np
+import librosa
+from pathlib import Path
+import pandas as pd
+
+from parakeet.data import DatasetMixin
+from parakeet.data import batch_spec, batch_wav
+
+class LJSpeechMetaData(DatasetMixin):
+    def __init__(self, root):
+        self.root = Path(root)
+        self._wav_dir = self.root.joinpath("wavs")
+        csv_path = self.root.joinpath("metadata.csv")
+        self._table = pd.read_csv(
+            csv_path,
+            sep="|",
+            header=None,
+            quoting=csv.QUOTE_NONE,
+            names=["fname", "raw_text", "normalized_text"])
+
+    def get_example(self, i):
+        fname, raw_text, normalized_text = self._table.iloc[i]
+        fname = str(self._wav_dir.joinpath(fname + ".wav"))
+        return fname, raw_text, normalized_text
+
+    def __len__(self):
+        return len(self._table)
+```
+
+We make this dataset simple in purpose. It requires only the path of the dataset, nothing more. It only loads the `metadata.csv` in the dataset when it is initialized, which includes file names of the audio files, and the transcriptions. We do not even load the audio files at `get_example`.
+
+Then we define a `Transform` object to transform an example of `LJSpeechMetaData` into an example we want for the model.
+
+```python
+class Transform(object):
+    def __init__(self, sample_rate, n_fft, win_length, hop_length, n_mels):
+        self.sample_rate = sample_rate
+        self.n_fft = n_fft
+        self.win_length = win_length
+        self.hop_length = hop_length
+        self.n_mels = n_mels
+
+    def __call__(self, example):
+        wav_path, _, _ = example
+
+        sr = self.sample_rate
+        n_fft = self.n_fft
+        win_length = self.win_length
+        hop_length = self.hop_length
+        n_mels = self.n_mels
+
+        wav, loaded_sr = librosa.load(wav_path, sr=None)
+        assert loaded_sr == sr, "sample rate does not match, resampling applied"
+
+        # Pad audio to the right size.
+        frames = int(np.ceil(float(wav.size) / hop_length))
+        fft_padding = (n_fft - hop_length) // 2  # sound
+        desired_length = frames * hop_length + fft_padding * 2
+        pad_amount = (desired_length - wav.size) // 2
+
+        if wav.size % 2 == 0:
+            wav = np.pad(wav, (pad_amount, pad_amount), mode='reflect')
+        else:
+            wav = np.pad(wav, (pad_amount, pad_amount + 1), mode='reflect')
+
+        # Normalize audio.
+        wav = wav / np.abs(wav).max() * 0.999
+
+        # Compute mel-spectrogram.
+        # Turn center to False to prevent internal padding.
+        spectrogram = librosa.core.stft(
+            wav,
+            hop_length=hop_length,
+            win_length=win_length,
+            n_fft=n_fft,
+            center=False)
+        spectrogram_magnitude = np.abs(spectrogram)
+
+        # Compute mel-spectrograms.
+        mel_filter_bank = librosa.filters.mel(sr=sr,
+                                              n_fft=n_fft,
+                                              n_mels=n_mels)
+        mel_spectrogram = np.dot(mel_filter_bank, spectrogram_magnitude)
+        mel_spectrogram = mel_spectrogram
+
+        # Rescale mel_spectrogram.
+        min_level, ref_level = 1e-5, 20  # hard code it
+        mel_spectrogram = 20 * np.log10(np.maximum(min_level, mel_spectrogram))
+        mel_spectrogram = mel_spectrogram - ref_level
+        mel_spectrogram = np.clip((mel_spectrogram + 100) / 100, 0, 1)
+
+        # Extract the center of audio that corresponds to mel spectrograms.
+        audio = wav[fft_padding:-fft_padding]
+        assert mel_spectrogram.shape[1] * hop_length == audio.size
+
+        # there is no clipping here
+        return audio, mel_spectrogram
+```
+
+`Transform` loads the audio file, and extracts `mel_spectrogram` from the audio. This transform actually needs a lot of options to specify, namely, the sample rate of the audio files, the `n_fft`, `win_length`, `hop_length` of `stft` transformation, and `n_mels` for transforming spectrogram into mel_spectrogram. So we define it as a callable class. You can also use a closure, or a `partial` if you want to.
+
+Then we defines a functor to batch examples into a batch. Because the two fields ( `audio` and `mel_spectrogram`) are both sequences, batching them is not trivial. Also, because the wavenet model trains in audio clips of a fixed length(0.5 seconds, for example), we have to truncate the audio when creating batches. We want to crop it randomly when creating batches, instead of truncating it when preprocessing each example, because it allows for an audio to be truncated at different positions.
+
+```python
+class DataCollector(object):
+    def __init__(self,
+                 context_size,
+                 sample_rate,
+                 hop_length,
+                 train_clip_seconds,
+                 valid=False):
+        frames_per_second = sample_rate // hop_length
+        train_clip_frames = int(
+            np.ceil(train_clip_seconds * frames_per_second))
+        context_frames = context_size // hop_length
+        self.num_frames = train_clip_frames + context_frames
+
+        self.sample_rate = sample_rate
+        self.hop_length = hop_length
+        self.valid = valid
+
+    def random_crop(self, sample):
+        audio, mel_spectrogram = sample
+        audio_frames = int(audio.size) // self.hop_length
+        max_start_frame = audio_frames - self.num_frames
+        assert max_start_frame >= 0, "audio is too short to be cropped"
+
+        frame_start = np.random.randint(0, max_start_frame)
+        # frame_start = 0  # norandom
+        frame_end = frame_start + self.num_frames
+
+        audio_start = frame_start * self.hop_length
+        audio_end = frame_end * self.hop_length
+
+        audio = audio[audio_start:audio_end]
+        return audio, mel_spectrogram, audio_start
+
+    def __call__(self, samples):
+        # transform them first
+        if self.valid:
+            samples = [(audio, mel_spectrogram, 0)
+                       for audio, mel_spectrogram in samples]
+        else:
+            samples = [self.random_crop(sample) for sample in samples]
+        # batch them
+        audios = [sample[0] for sample in samples]
+        audio_starts = [sample[2] for sample in samples]
+        mels = [sample[1] for sample in samples]
+
+        mels = batch_spec(mels)
+
+        if self.valid:
+            audios = batch_wav(audios, dtype=np.float32)
+        else:
+            audios = np.array(audios, dtype=np.float32)
+        audio_starts = np.array(audio_starts, dtype=np.int64)
+        return audios, mels, audio_starts
+```
+
+When these 3 components are defined, we can start building our dataset with them.
+
+```python
+# building the ljspeech dataset
+ljspeech_meta = LJSpeechMetaData(root)
+transform = Transform(sample_rate, n_fft, win_length, hop_length, n_mels)
+ljspeech = TransformDataset(ljspeech_meta, transform)
+
+# split them into train and valid dataset
+ljspeech_valid = SliceDataset(ljspeech, 0, valid_size)
+ljspeech_train = SliceDataset(ljspeech, valid_size, len(ljspeech))
+
+# building batch functions (they can be differnt for training and validation if you need it)
+train_batch_fn = DataCollector(context_size, sample_rate, hop_length,
+                               train_clip_seconds)
+valid_batch_fn = DataCollector(
+  context_size, sample_rate, hop_length, train_clip_seconds, valid=True)
+
+# building the data cargo
+train_cargo = DataCargo(
+  ljspeech_train,
+  train_batch_fn,
+  batch_size,
+  sampler=RandomSampler(ljspeech_train))
+
+valid_cargo = DataCargo(
+  ljspeech_valid,
+  valid_batch_fn,
+  batch_size=1, # only batch=1 for validation is enabled
+  sampler=SequentialSampler(ljspeech_valid))
+```
+
+Here comes the next question, how to bring batches into Paddle's computation. Do we need some adaptor to transform numpy.ndarray into Paddle's native Variable type? Yes.
+
+First we can use `var = dg.to_variable(array)` to transform ndarray into Variable.
+
+```python
+for batch in train_cargo:
+    audios, mels, audio_starts = batch
+    audios = dg.to_variable(audios)
+    mels = dg.to_variable(mels)
+    audio_starts = dg.to_variable(audio_starts)
+
+    # your training code here
+```
+
+In the code above, processing of the data and training of the model runs in the same process. So the next batch starts to load after the training of the current batch has finished. There is actually better solution for this. Data processing and model training can be run asynchronously. To accomplish this, we would use `DataLoader` from Paddle. This serves as an adapter to transform an Iterable of batches into another iterable of batches, which runs asynchronously and transform each ndarray into `Variable`.
+
+```python
+# connects our data cargos with corresponding DataLoader
+# now the data cargo is connected with paddle
+with dg.guard(place):
+  train_loader = fluid.io.DataLoader.from_generator(
+   capacity=10,return_list=True).set_batch_generator(train_cargo, place)
+  valid_loader = fluid.io.DataLoader.from_generator(
+   capacity=10, return_list=True).set_batch_generator(valid_cargo, place)
+
+  # iterate over the dataloader
+  for batch in train_loader:
+    audios, mels, audio_starts = batch
+    # your trains cript here
+```

parakeet/data/datacargo.py

@@ -98,6 +98,8 @@ class DataIterator(object):
         minibatch = self._batch_fn(minibatch)  # list[Example] -> Batch
         return minibatch
 
+    next = __next__  # Python 2 compatibility
+
     def _next_index(self):
         if six.PY3:
             return next(self._sampler_iter)

parakeet/data/dataset.py

@@ -59,6 +59,20 @@ class TransformDataset(DatasetMixin):
         return self._transform(in_data)
 
 
+class CacheDataset(DatasetMixin):
+    def __init__(self, dataset):
+        self._dataset = dataset
+        self._cache = dict()
+
+    def __len__(self):
+        return len(self._dataset)
+
+    def get_example(self, i):
+        if not i in self._cache:
+            self._cache[i] = self._dataset[i]
+        return self._cache[i]
+
+
 class TupleDataset(object):
     def __init__(self, *datasets):
         if not datasets:

parakeet/utils/layer_tools.py

@@ -36,14 +36,3 @@ def freeze(layer):
 def unfreeze(layer):
     for param in layer.parameters():
         param.trainable = True
-
-
-def torch_summary(layer):
-    num_params = num_elements = 0
-    print("layer summary:")
-    for name, param in layer.named_parameters():
-        print("{}|{}|{}".format(name, param.shape, np.prod(param.shape)))
-        num_elements += np.prod(param.shape)
-        num_params += 1
-    print("layer has {} parameters, {} elements.".format(num_params,
-                                                         num_elements))