Utilize SamplesBatch class

Author: Alex Lapin

selene_sdk/evaluate_model.py

@@ -209,24 +209,17 @@ def evaluate(self):
         """
         batch_losses = []
         all_predictions = []
-        for (inputs, targets) in self._test_data:
-            inputs = torch.Tensor(inputs)
-            targets = torch.Tensor(targets[:, self._use_ixs])
+        for samples_batch in self._test_data:
+            inputs, targets = samples_batch.torch_inputs_and_targets(self.use_cuda)
+            targets = targets[:, self._use_ixs]
 
-            if self.use_cuda:
-                inputs = inputs.cuda()
-                targets = targets.cuda()
             with torch.no_grad():
-                inputs = Variable(inputs)
-                targets = Variable(targets)
-
                 predictions = None
                 if _is_lua_trained_model(self.model):
                     predictions = self.model.forward(
-                        inputs.transpose(1, 2).contiguous().unsqueeze_(2))
+                        inputs.contiguous().unsqueeze_(2))
                 else:
-                    predictions = self.model.forward(
-                        inputs.transpose(1, 2))
+                    predictions = self.model.forward(inputs)
                 predictions = predictions[:, self._use_ixs]
                 loss = self.criterion(predictions, targets)
 

selene_sdk/samplers/file_samplers/bed_file_sampler.py

@@ -1,6 +1,7 @@
 """
 This module provides the BedFileSampler class.
 """
+from selene_sdk.samplers.samples_batch import SamplesBatch
 import numpy as np
 
 from .file_sampler import FileSampler
@@ -96,8 +97,8 @@ def sample(self, batch_size=1):
 
         Returns
         -------
-        sequences, targets : tuple(numpy.ndarray, numpy.ndarray)
-            A tuple containing the numeric representation of the
+        SamplesBatch
+            A batch containing the numeric representation of the
             sequence examples and their corresponding labels. The
             shape of `sequences` will be
             :math:`B \\times L \\times N`, where :math:`B` is
@@ -163,8 +164,8 @@ def sample(self, batch_size=1):
         sequences = np.array(sequences)
         if self.targets_avail:
             targets = np.array(targets)
-            return (sequences, targets)
-        return sequences,
+            return SamplesBatch(sequences, target_batch=targets)
+        return SamplesBatch(sequences)
 
     def get_data(self, batch_size, n_samples=None):
         """
@@ -188,18 +189,21 @@ def get_data(self, batch_size, n_samples=None):
             and :math:`N` is the size of the sequence type's alphabet.
 
         """
+        # TODO: Should this method return a collection of samples_batch.inputs()?
+
         if not n_samples:
             n_samples = self.n_samples
         sequences = []
 
         count = batch_size
         while count < n_samples:
-            seqs, = self.sample(batch_size=batch_size)
-            sequences.append(seqs)
+            samples_batch = self.sample(batch_size=batch_size)
+            sequences.append(samples_batch.sequence_batch())
             count += batch_size
         remainder = batch_size - (count - n_samples)
-        seqs, = self.sample(batch_size=remainder)
-        sequences.append(seqs)
+        samples_batch = self.sample(batch_size=remainder)
+        sequences.append(samples_batch.sequence_batch())
+
         return sequences
 
     def get_data_and_targets(self, batch_size, n_samples=None):
@@ -216,11 +220,11 @@ def get_data_and_targets(self, batch_size, n_samples=None):
 
         Returns
         -------
-        sequences_and_targets, targets_matrix : \
-        tuple(list(tuple(numpy.ndarray, numpy.ndarray)), numpy.ndarray)
-            Tuple containing the list of sequence-target pairs, as well
+        batches, targets_matrix : \
+        tuple(list(SamplesBatch), numpy.ndarray)
+            Tuple containing the list of batches, as well
             as a single matrix with all targets in the same order.
-            Note that `sequences_and_targets`'s sequence elements are of
+            Note that `batches`'s sequence elements are of
             the shape :math:`B \\times L \\times N` and its target
             elements are of the shape :math:`B \\times F`, where
             :math:`B` is `batch_size`, :math:`L` is the sequence length,
@@ -236,18 +240,18 @@ def get_data_and_targets(self, batch_size, n_samples=None):
                 "Please use `get_data` instead.")
         if not n_samples:
             n_samples = self.n_samples
-        sequences_and_targets = []
+        batches = []
         targets_mat = []
 
         count = batch_size
         while count < n_samples:
-            seqs, tgts = self.sample(batch_size=batch_size)
-            sequences_and_targets.append((seqs, tgts))
-            targets_mat.append(tgts)
+            samples_batch = self.sample(batch_size=batch_size)
+            batches.append(samples_batch)
+            targets_mat.append(samples_batch.targets())
             count += batch_size
         remainder = batch_size - (count - n_samples)
-        seqs, tgts = self.sample(batch_size=remainder)
-        sequences_and_targets.append((seqs, tgts))
-        targets_mat.append(tgts)
+        samples_batch = self.sample(batch_size=remainder)
+        batches.append(samples_batch)
+        targets_mat.append(samples_batch.targets())
         targets_mat = np.vstack(targets_mat).astype(int)
-        return sequences_and_targets, targets_mat
+        return batches, targets_mat

selene_sdk/samplers/file_samplers/file_sampler.py

@@ -8,6 +8,8 @@
 from abc import ABCMeta
 from abc import abstractmethod
 
+from selene_sdk.samplers.samples_batch import SamplesBatch
+
 
 class FileSampler(metaclass=ABCMeta):
     """
@@ -26,7 +28,7 @@ def __init__(self):
         """
 
     @abstractmethod
-    def sample(self, batch_size=1):
+    def sample(self, batch_size=1) -> SamplesBatch:
         """
         Fetches a mini-batch of the data from the sampler.
 

selene_sdk/samplers/file_samplers/mat_file_sampler.py

@@ -5,6 +5,7 @@
 import h5py
 import numpy as np
 import scipy.io
+from selene_sdk.samplers.samples_batch import SamplesBatch
 
 from .file_sampler import FileSampler
 
@@ -126,8 +127,8 @@ def sample(self, batch_size=1):
 
         Returns
         -------
-        sequences, targets : tuple(numpy.ndarray, numpy.ndarray)
-            A tuple containing the numeric representation of the
+        SamplesBatch
+            A batch containing the numeric representation of the
             sequence examples and their corresponding labels. The
             shape of `sequences` will be
             :math:`B \\times L \\times N`, where :math:`B` is
@@ -166,8 +167,8 @@ def sample(self, batch_size=1):
                 targets = self._sample_tgts[:, use_indices].astype(float)
                 targets = np.transpose(
                     targets, (1, 0))
-            return (sequences, targets)
-        return sequences,
+            return SamplesBatch(sequences, target_batch=targets)
+        return SamplesBatch(sequences)
 
     def get_data(self, batch_size, n_samples=None):
         """
@@ -190,18 +191,20 @@ def get_data(self, batch_size, n_samples=None):
             is `batch_size`, :math:`L` is the sequence length,
             and :math:`N` is the size of the sequence type's alphabet.
         """
+        # TODO: Should this method return a collection of samples_batch.inputs()?
+
         if not n_samples:
             n_samples = self.n_samples
         sequences = []
 
         count = batch_size
         while count < n_samples:
-            seqs, = self.sample(batch_size=batch_size)
-            sequences.append(seqs)
+            samples_batch = self.sample(batch_size=batch_size)
+            sequences.append(samples_batch.sequence_batch())
             count += batch_size
         remainder = batch_size - (count - n_samples)
-        seqs, = self.sample(batch_size=remainder)
-        sequences.append(seqs)
+        samples_batch = self.sample(batch_size=remainder)
+        sequences.append(samples_batch.sequence_batch())
         return sequences
 
     def get_data_and_targets(self, batch_size, n_samples=None):
@@ -218,11 +221,11 @@ def get_data_and_targets(self, batch_size, n_samples=None):
 
         Returns
         -------
-        sequences_and_targets, targets_matrix : \
-        tuple(list(tuple(numpy.ndarray, numpy.ndarray)), numpy.ndarray)
-            Tuple containing the list of sequence-target pairs, as well
+        batches, targets_matrix : \
+        tuple(list(SamplesBatch), numpy.ndarray)
+            Tuple containing the list of batches, as well
             as a single matrix with all targets in the same order.
-            Note that `sequences_and_targets`'s sequence elements are of
+            Note that `batches`'s sequence elements are of
             the shape :math:`B \\times L \\times N` and its target
             elements are of the shape :math:`B \\times F`, where
             :math:`B` is `batch_size`, :math:`L` is the sequence length,
@@ -237,19 +240,19 @@ def get_data_and_targets(self, batch_size, n_samples=None):
                 "initialization. Please use `get_data` instead.")
         if not n_samples:
             n_samples = self.n_samples
-        sequences_and_targets = []
+        batches = []
         targets_mat = []
 
         count = batch_size
         while count < n_samples:
-            seqs, tgts = self.sample(batch_size=batch_size)
-            sequences_and_targets.append((seqs, tgts))
-            targets_mat.append(tgts)
+            samples_batch = self.sample(batch_size=batch_size)
+            batches.append(samples_batch)
+            targets_mat.append(samples_batch.targets())
             count += batch_size
         remainder = batch_size - (count - n_samples)
-        seqs, tgts = self.sample(batch_size=remainder)
-        sequences_and_targets.append((seqs, tgts))
-        targets_mat.append(tgts)
+        samples_batch = self.sample(batch_size=remainder)
+        batches.append(samples_batch)
+        targets_mat.append(samples_batch.targets())
         # TODO: should not assume targets are always integers
         targets_mat = np.vstack(targets_mat).astype(float)
-        return sequences_and_targets, targets_mat
+        return batches, targets_mat

selene_sdk/samplers/intervals_sampler.py

@@ -2,14 +2,15 @@
 This module provides the `IntervalsSampler` class and supporting
 methods.
 """
-from collections import namedtuple
 import logging
 import random
+from collections import namedtuple
 
 import numpy as np
 
-from .online_sampler import OnlineSampler
+from selene_sdk.samplers.samples_batch import SamplesBatch
 from ..utils import get_indices_and_probabilities
+from .online_sampler import OnlineSampler
 
 logger = logging.getLogger(__name__)
 
@@ -388,8 +389,8 @@ def sample(self, batch_size=1):
 
         Returns
         -------
-        sequences, targets : tuple(numpy.ndarray, numpy.ndarray)
-            A tuple containing the numeric representation of the
+        SamplesBatch
+            A batch containing the numeric representation of the
             sequence examples and their corresponding labels. The
             shape of `sequences` will be
             :math:`B \\times L \\times N`, where :math:`B` is
@@ -426,4 +427,4 @@ def sample(self, batch_size=1):
             sequences[n_samples_drawn, :, :] = seq
             targets[n_samples_drawn, :] = seq_targets
             n_samples_drawn += 1
-        return (sequences, targets)
+        return SamplesBatch(sequences, target_batch=targets)

selene_sdk/samplers/multi_file_sampler.py

@@ -186,11 +186,11 @@ def get_test_set(self, batch_size, n_samples=None):
 
         Returns
         -------
-        sequences_and_targets, targets_matrix : \
-        tuple(list(tuple(numpy.ndarray, numpy.ndarray)), numpy.ndarray)
-            Tuple containing the list of sequence-target pairs, as well
+        batches, targets_matrix : \
+        tuple(list(SamplesBatch), numpy.ndarray)
+            Tuple containing the list of batches, as well
             as a single matrix with all targets in the same order.
-            Note that `sequences_and_targets`'s sequence elements are of
+            Note that `batches`'s sequence elements are of
             the shape :math:`B \\times L \\times N` and its target
             elements are of the shape :math:`B \\times F`, where
             :math:`B` is `batch_size`, :math:`L` is the sequence length,