Fixed errors in computing layer output shapes and loading images (d5dad129) · Commits · 钟慕尧 / deepchem

deepchem/data/data_loader.py

+3 −0

Original line number	Diff line number	Diff line
		@@ -369,6 +369,7 @@ class ImageLoader(DataLoader):
		remainder = []
		for input_file in input_files:
		filename, extension = os.path.splitext(input_file)
		extension = extension.lower()
		# TODO(rbharath): Add support for more extensions
		if os.path.isdir(input_file):
		dirfiles = [
		@@ -386,6 +387,7 @@ class ImageLoader(DataLoader):
		]
		for zip_file in zip_files:
		_, extension = os.path.splitext(zip_file)
		extension = extension.lower()
		if extension in [".png", ".tif"]:
		image_files.append(zip_file)
		elif extension in [".png", ".tif"]:
		@@ -405,6 +407,7 @@ class ImageLoader(DataLoader):
		images = []
		for image_file in image_files:
		_, extension = os.path.splitext(image_file)
		extension = extension.lower()
		if extension == ".png":
		image = misc.imread(image_file)
		images.append(image)

deepchem/models/tensorgraph/layers.py

+27 −6

Original line number	Diff line number	Diff line
		@@ -485,7 +485,6 @@ class Conv1D(Layer):
		`(10, 128)` for sequences of 10 vectors of 128-dimensional vectors,
		or `(None, 128)` for variable-length sequences of 128-dimensional vectors.

		TODO(LESWING): Calculate output shape at construction time
		Arguments:
		filters: Integer, the dimensionality of the output space
		(i.e. the number output of filters in the convolution).
		@@ -541,6 +540,17 @@ class Conv1D(Layer):
		self.kernel_constraint = kernel_constraint
		self.bias_constraint = bias_constraint
		super(Conv1D, self).__init__(in_layers, **kwargs)
		try:
		parent_shape = self.in_layers[0].shape
		if isinstance(strides, int):
		strides = (strides,)
		if padding.lower() == 'same':
		self._shape = (parent_shape[0],
		int(np.ceil(parent_shape[1] / strides[0])), filters)
		else:
		self._shape = (parent_shape[0], parent_shape[1] // strides[0], filters)
		except:
		pass

		def _build_layer(self):
		return tf.keras.layers.Conv1D(
		@@ -1983,6 +1993,11 @@ class Conv2D(SharedVariableScope):
		strides = stride
		if isinstance(stride, int):
		strides = (stride, stride)
		if padding.lower() == 'same':
		self._shape = (parent_shape[0],
		int(np.ceil(parent_shape[1] / strides[0])),
		int(np.ceil(parent_shape[2] / strides[1])), num_outputs)
		else:
		self._shape = (parent_shape[0], parent_shape[1] // strides[0],
		parent_shape[2] // strides[1], num_outputs)
		except:
		@@ -2100,6 +2115,12 @@ class Conv3D(SharedVariableScope):
		strides = stride
		if isinstance(stride, int):
		strides = (stride, stride, stride)
		if padding.lower() == 'same':
		self._shape = (parent_shape[0],
		int(np.ceil(parent_shape[1] / strides[0])),
		int(np.ceil(parent_shape[2] / strides[1])),
		int(np.ceil(parent_shape[3] / strides[2])), num_outputs)
		else:
		self._shape = (parent_shape[0], parent_shape[1] // strides[0],
		parent_shape[2] // strides[1],
		parent_shape[3] // strides[2], num_outputs)

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