Package biopb.image
Class Pixels
java.lang.Object
com.google.protobuf.AbstractMessageLite
com.google.protobuf.AbstractMessage
com.google.protobuf.GeneratedMessageV3
biopb.image.Pixels
- All Implemented Interfaces:
PixelsOrBuilder,com.google.protobuf.Message,com.google.protobuf.MessageLite,com.google.protobuf.MessageLiteOrBuilder,com.google.protobuf.MessageOrBuilder,Serializable
The Pixels element represent generic 5D pixel data. The time axis is currently not being utilized, but is defined here for futire extensibility. This is modeled after OME-XML's Pixel structure.Protobuf type
biopb.image.Pixels- See Also:
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic final classThe Pixels element represent generic 5D pixel data.Nested classes/interfaces inherited from class com.google.protobuf.GeneratedMessageV3
com.google.protobuf.GeneratedMessageV3.BuilderParent, com.google.protobuf.GeneratedMessageV3.ExtendableBuilder<MessageT extends com.google.protobuf.GeneratedMessageV3.ExtendableMessage<MessageT>,BuilderT extends com.google.protobuf.GeneratedMessageV3.ExtendableBuilder<MessageT, BuilderT>>, com.google.protobuf.GeneratedMessageV3.ExtendableMessage<MessageT extends com.google.protobuf.GeneratedMessageV3.ExtendableMessage<MessageT>>, com.google.protobuf.GeneratedMessageV3.ExtendableMessageOrBuilder<MessageT extends com.google.protobuf.GeneratedMessageV3.ExtendableMessage<MessageT>>, com.google.protobuf.GeneratedMessageV3.FieldAccessorTable, com.google.protobuf.GeneratedMessageV3.UnusedPrivateParameter Nested classes/interfaces inherited from class com.google.protobuf.AbstractMessageLite
com.google.protobuf.AbstractMessageLite.InternalOneOfEnum -
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intstatic final intFields inherited from class com.google.protobuf.GeneratedMessageV3
alwaysUseFieldBuilders, unknownFieldsFields inherited from class com.google.protobuf.AbstractMessage
memoizedSizeFields inherited from class com.google.protobuf.AbstractMessageLite
memoizedHashCode -
Method Summary
Modifier and TypeMethodDescriptionbooleanPixel valuesPixel valuesstatic Pixelsstatic final com.google.protobuf.Descriptors.DescriptorA string describing the dimension order of the pixel data, e.g.com.google.protobuf.ByteStringA string describing the dimension order of the pixel data, e.g.getDtype()A string describing the data type using numpy's convention.com.google.protobuf.ByteStringA string describing the data type using numpy's convention.intoptional uint32 offset_c = 26;intoptional uint32 offset_t = 25;intfor large image dataset, it is necessary to send a stream of image patches instead of one monolithic data structure of the whole dataset.intoptional uint32 offset_y = 23;intoptional uint32 offset_z = 24;com.google.protobuf.Parser<Pixels>physical size unit, default "µm"com.google.protobuf.ByteStringphysical size unit, default "µm"floatPhysical size of a pixel.floatoptional float physical_size_y = 15;floatoptional float physical_size_z = 16;intintgetSizeC()uint32 size_c = 12;intgetSizeT()uint32 size_t = 13;intgetSizeX()Dimensional size of pixel data array [units:none]intgetSizeY()uint32 size_y = 10;intgetSizeZ()uint32 size_z = 11;floattime_increment is used for time series that have a global timing specification instead of per-timepoint timing info.time unit, default "s"com.google.protobuf.ByteStringtime unit, default "s"booleanPixel valuesinthashCode()booleanoptional uint32 offset_c = 26;booleanoptional uint32 offset_t = 25;booleanfor large image dataset, it is necessary to send a stream of image patches instead of one monolithic data structure of the whole dataset.booleanoptional uint32 offset_y = 23;booleanoptional uint32 offset_z = 24;booleanPhysical size of a pixel.booleanoptional float physical_size_y = 15;booleanoptional float physical_size_z = 16;booleantime_increment is used for time series that have a global timing specification instead of per-timepoint timing info.protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTablefinal booleanstatic Pixels.Builderstatic Pixels.BuildernewBuilder(Pixels prototype) protected Pixels.BuildernewBuilderForType(com.google.protobuf.GeneratedMessageV3.BuilderParent parent) protected ObjectnewInstance(com.google.protobuf.GeneratedMessageV3.UnusedPrivateParameter unused) static PixelsparseDelimitedFrom(InputStream input) static PixelsparseDelimitedFrom(InputStream input, com.google.protobuf.ExtensionRegistryLite extensionRegistry) static PixelsparseFrom(byte[] data) static PixelsparseFrom(byte[] data, com.google.protobuf.ExtensionRegistryLite extensionRegistry) static PixelsparseFrom(com.google.protobuf.ByteString data) static PixelsparseFrom(com.google.protobuf.ByteString data, com.google.protobuf.ExtensionRegistryLite extensionRegistry) static PixelsparseFrom(com.google.protobuf.CodedInputStream input) static PixelsparseFrom(com.google.protobuf.CodedInputStream input, com.google.protobuf.ExtensionRegistryLite extensionRegistry) static PixelsparseFrom(InputStream input) static PixelsparseFrom(InputStream input, com.google.protobuf.ExtensionRegistryLite extensionRegistry) static PixelsparseFrom(ByteBuffer data) static PixelsparseFrom(ByteBuffer data, com.google.protobuf.ExtensionRegistryLite extensionRegistry) static com.google.protobuf.Parser<Pixels>parser()voidwriteTo(com.google.protobuf.CodedOutputStream output) Methods inherited from class com.google.protobuf.GeneratedMessageV3
canUseUnsafe, computeStringSize, computeStringSizeNoTag, emptyBooleanList, emptyDoubleList, emptyFloatList, emptyIntList, emptyList, emptyLongList, getAllFields, getDescriptorForType, getField, getOneofFieldDescriptor, getRepeatedField, getRepeatedFieldCount, getUnknownFields, hasField, hasOneof, internalGetMapField, internalGetMapFieldReflection, isStringEmpty, makeExtensionsImmutable, makeMutableCopy, makeMutableCopy, mergeFromAndMakeImmutableInternal, mutableCopy, mutableCopy, mutableCopy, mutableCopy, mutableCopy, newBooleanList, newBuilderForType, newDoubleList, newFloatList, newIntList, newLongList, parseDelimitedWithIOException, parseDelimitedWithIOException, parseUnknownField, parseUnknownFieldProto3, parseWithIOException, parseWithIOException, parseWithIOException, parseWithIOException, serializeBooleanMapTo, serializeIntegerMapTo, serializeLongMapTo, serializeStringMapTo, writeReplace, writeString, writeStringNoTagMethods inherited from class com.google.protobuf.AbstractMessage
findInitializationErrors, getInitializationErrorString, hashBoolean, hashEnum, hashEnumList, hashFields, hashLong, toStringMethods inherited from class com.google.protobuf.AbstractMessageLite
addAll, addAll, checkByteStringIsUtf8, toByteArray, toByteString, writeDelimitedTo, writeToMethods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, waitMethods inherited from interface com.google.protobuf.MessageLite
toByteArray, toByteString, writeDelimitedTo, writeToMethods inherited from interface com.google.protobuf.MessageOrBuilder
findInitializationErrors, getAllFields, getDescriptorForType, getField, getInitializationErrorString, getOneofFieldDescriptor, getRepeatedField, getRepeatedFieldCount, getUnknownFields, hasField, hasOneof
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Field Details
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BINDATA_FIELD_NUMBER
public static final int BINDATA_FIELD_NUMBER- See Also:
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DIMENSION_ORDER_FIELD_NUMBER
public static final int DIMENSION_ORDER_FIELD_NUMBER- See Also:
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DTYPE_FIELD_NUMBER
public static final int DTYPE_FIELD_NUMBER- See Also:
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SIZE_X_FIELD_NUMBER
public static final int SIZE_X_FIELD_NUMBER- See Also:
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SIZE_Y_FIELD_NUMBER
public static final int SIZE_Y_FIELD_NUMBER- See Also:
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SIZE_Z_FIELD_NUMBER
public static final int SIZE_Z_FIELD_NUMBER- See Also:
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SIZE_C_FIELD_NUMBER
public static final int SIZE_C_FIELD_NUMBER- See Also:
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SIZE_T_FIELD_NUMBER
public static final int SIZE_T_FIELD_NUMBER- See Also:
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PHYSICAL_SIZE_X_FIELD_NUMBER
public static final int PHYSICAL_SIZE_X_FIELD_NUMBER- See Also:
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PHYSICAL_SIZE_Y_FIELD_NUMBER
public static final int PHYSICAL_SIZE_Y_FIELD_NUMBER- See Also:
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PHYSICAL_SIZE_Z_FIELD_NUMBER
public static final int PHYSICAL_SIZE_Z_FIELD_NUMBER- See Also:
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PHYSICAL_SIZE_UNIT_FIELD_NUMBER
public static final int PHYSICAL_SIZE_UNIT_FIELD_NUMBER- See Also:
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TIME_INCREMENT_FIELD_NUMBER
public static final int TIME_INCREMENT_FIELD_NUMBER- See Also:
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TIME_INCREMENT_UNIT_FIELD_NUMBER
public static final int TIME_INCREMENT_UNIT_FIELD_NUMBER- See Also:
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OFFSET_X_FIELD_NUMBER
public static final int OFFSET_X_FIELD_NUMBER- See Also:
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OFFSET_Y_FIELD_NUMBER
public static final int OFFSET_Y_FIELD_NUMBER- See Also:
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OFFSET_Z_FIELD_NUMBER
public static final int OFFSET_Z_FIELD_NUMBER- See Also:
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OFFSET_T_FIELD_NUMBER
public static final int OFFSET_T_FIELD_NUMBER- See Also:
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OFFSET_C_FIELD_NUMBER
public static final int OFFSET_C_FIELD_NUMBER- See Also:
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Method Details
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newInstance
- Overrides:
newInstancein classcom.google.protobuf.GeneratedMessageV3
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getDescriptor
public static final com.google.protobuf.Descriptors.Descriptor getDescriptor() -
internalGetFieldAccessorTable
protected com.google.protobuf.GeneratedMessageV3.FieldAccessorTable internalGetFieldAccessorTable()- Specified by:
internalGetFieldAccessorTablein classcom.google.protobuf.GeneratedMessageV3
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hasBindata
public boolean hasBindata()Pixel values
.biopb.image.BinData bindata = 3;- Specified by:
hasBindatain interfacePixelsOrBuilder- Returns:
- Whether the bindata field is set.
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getBindata
Pixel values
.biopb.image.BinData bindata = 3;- Specified by:
getBindatain interfacePixelsOrBuilder- Returns:
- The bindata.
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getBindataOrBuilder
Pixel values
.biopb.image.BinData bindata = 3;- Specified by:
getBindataOrBuilderin interfacePixelsOrBuilder
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getDimensionOrder
A string describing the dimension order of the pixel data, e.g. "XYZCT" The string must be a permutaion of these 5 letters even if some of the dimension doesn't exist in the data.
string dimension_order = 4;- Specified by:
getDimensionOrderin interfacePixelsOrBuilder- Returns:
- The dimensionOrder.
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getDimensionOrderBytes
public com.google.protobuf.ByteString getDimensionOrderBytes()A string describing the dimension order of the pixel data, e.g. "XYZCT" The string must be a permutaion of these 5 letters even if some of the dimension doesn't exist in the data.
string dimension_order = 4;- Specified by:
getDimensionOrderBytesin interfacePixelsOrBuilder- Returns:
- The bytes for dimensionOrder.
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getDtype
A string describing the data type using numpy's convention. E.g., 'i8' represent int64. Endianness indicator, e.g. '=i8', is allowed but will be ignored. Instead the endianness will be determined by the field within the Bindata structure.
string dtype = 5;- Specified by:
getDtypein interfacePixelsOrBuilder- Returns:
- The dtype.
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getDtypeBytes
public com.google.protobuf.ByteString getDtypeBytes()A string describing the data type using numpy's convention. E.g., 'i8' represent int64. Endianness indicator, e.g. '=i8', is allowed but will be ignored. Instead the endianness will be determined by the field within the Bindata structure.
string dtype = 5;- Specified by:
getDtypeBytesin interfacePixelsOrBuilder- Returns:
- The bytes for dtype.
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getSizeX
public int getSizeX()Dimensional size of pixel data array [units:none]
uint32 size_x = 9;- Specified by:
getSizeXin interfacePixelsOrBuilder- Returns:
- The sizeX.
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getSizeY
public int getSizeY()uint32 size_y = 10;- Specified by:
getSizeYin interfacePixelsOrBuilder- Returns:
- The sizeY.
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getSizeZ
public int getSizeZ()uint32 size_z = 11;- Specified by:
getSizeZin interfacePixelsOrBuilder- Returns:
- The sizeZ.
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getSizeC
public int getSizeC()uint32 size_c = 12;- Specified by:
getSizeCin interfacePixelsOrBuilder- Returns:
- The sizeC.
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getSizeT
public int getSizeT()uint32 size_t = 13;- Specified by:
getSizeTin interfacePixelsOrBuilder- Returns:
- The sizeT.
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hasPhysicalSizeX
public boolean hasPhysicalSizeX()Physical size of a pixel.
optional float physical_size_x = 14;- Specified by:
hasPhysicalSizeXin interfacePixelsOrBuilder- Returns:
- Whether the physicalSizeX field is set.
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getPhysicalSizeX
public float getPhysicalSizeX()Physical size of a pixel.
optional float physical_size_x = 14;- Specified by:
getPhysicalSizeXin interfacePixelsOrBuilder- Returns:
- The physicalSizeX.
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hasPhysicalSizeY
public boolean hasPhysicalSizeY()optional float physical_size_y = 15;- Specified by:
hasPhysicalSizeYin interfacePixelsOrBuilder- Returns:
- Whether the physicalSizeY field is set.
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getPhysicalSizeY
public float getPhysicalSizeY()optional float physical_size_y = 15;- Specified by:
getPhysicalSizeYin interfacePixelsOrBuilder- Returns:
- The physicalSizeY.
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hasPhysicalSizeZ
public boolean hasPhysicalSizeZ()optional float physical_size_z = 16;- Specified by:
hasPhysicalSizeZin interfacePixelsOrBuilder- Returns:
- Whether the physicalSizeZ field is set.
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getPhysicalSizeZ
public float getPhysicalSizeZ()optional float physical_size_z = 16;- Specified by:
getPhysicalSizeZin interfacePixelsOrBuilder- Returns:
- The physicalSizeZ.
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getPhysicalSizeUnit
physical size unit, default "µm"
string physical_size_unit = 17;- Specified by:
getPhysicalSizeUnitin interfacePixelsOrBuilder- Returns:
- The physicalSizeUnit.
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getPhysicalSizeUnitBytes
public com.google.protobuf.ByteString getPhysicalSizeUnitBytes()physical size unit, default "µm"
string physical_size_unit = 17;- Specified by:
getPhysicalSizeUnitBytesin interfacePixelsOrBuilder- Returns:
- The bytes for physicalSizeUnit.
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hasTimeIncrement
public boolean hasTimeIncrement()time_increment is used for time series that have a global timing specification instead of per-timepoint timing info. For example in a video stream. Units are set by TimeIncrementUnit.
optional float time_increment = 18;- Specified by:
hasTimeIncrementin interfacePixelsOrBuilder- Returns:
- Whether the timeIncrement field is set.
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getTimeIncrement
public float getTimeIncrement()time_increment is used for time series that have a global timing specification instead of per-timepoint timing info. For example in a video stream. Units are set by TimeIncrementUnit.
optional float time_increment = 18;- Specified by:
getTimeIncrementin interfacePixelsOrBuilder- Returns:
- The timeIncrement.
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getTimeIncrementUnit
time unit, default "s"
string time_increment_unit = 21;- Specified by:
getTimeIncrementUnitin interfacePixelsOrBuilder- Returns:
- The timeIncrementUnit.
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getTimeIncrementUnitBytes
public com.google.protobuf.ByteString getTimeIncrementUnitBytes()time unit, default "s"
string time_increment_unit = 21;- Specified by:
getTimeIncrementUnitBytesin interfacePixelsOrBuilder- Returns:
- The bytes for timeIncrementUnit.
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hasOffsetX
public boolean hasOffsetX()for large image dataset, it is necessary to send a stream of image patches instead of one monolithic data structure of the whole dataset. The offset values allows one to specify the relative locations of each patch. These include spatial (x,y,z), channel (c), and time (t) offsets.
optional uint32 offset_x = 22;- Specified by:
hasOffsetXin interfacePixelsOrBuilder- Returns:
- Whether the offsetX field is set.
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getOffsetX
public int getOffsetX()for large image dataset, it is necessary to send a stream of image patches instead of one monolithic data structure of the whole dataset. The offset values allows one to specify the relative locations of each patch. These include spatial (x,y,z), channel (c), and time (t) offsets.
optional uint32 offset_x = 22;- Specified by:
getOffsetXin interfacePixelsOrBuilder- Returns:
- The offsetX.
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hasOffsetY
public boolean hasOffsetY()optional uint32 offset_y = 23;- Specified by:
hasOffsetYin interfacePixelsOrBuilder- Returns:
- Whether the offsetY field is set.
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getOffsetY
public int getOffsetY()optional uint32 offset_y = 23;- Specified by:
getOffsetYin interfacePixelsOrBuilder- Returns:
- The offsetY.
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hasOffsetZ
public boolean hasOffsetZ()optional uint32 offset_z = 24;- Specified by:
hasOffsetZin interfacePixelsOrBuilder- Returns:
- Whether the offsetZ field is set.
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getOffsetZ
public int getOffsetZ()optional uint32 offset_z = 24;- Specified by:
getOffsetZin interfacePixelsOrBuilder- Returns:
- The offsetZ.
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hasOffsetT
public boolean hasOffsetT()optional uint32 offset_t = 25;- Specified by:
hasOffsetTin interfacePixelsOrBuilder- Returns:
- Whether the offsetT field is set.
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getOffsetT
public int getOffsetT()optional uint32 offset_t = 25;- Specified by:
getOffsetTin interfacePixelsOrBuilder- Returns:
- The offsetT.
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hasOffsetC
public boolean hasOffsetC()optional uint32 offset_c = 26;- Specified by:
hasOffsetCin interfacePixelsOrBuilder- Returns:
- Whether the offsetC field is set.
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getOffsetC
public int getOffsetC()optional uint32 offset_c = 26;- Specified by:
getOffsetCin interfacePixelsOrBuilder- Returns:
- The offsetC.
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isInitialized
public final boolean isInitialized()- Specified by:
isInitializedin interfacecom.google.protobuf.MessageLiteOrBuilder- Overrides:
isInitializedin classcom.google.protobuf.GeneratedMessageV3
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writeTo
- Specified by:
writeToin interfacecom.google.protobuf.MessageLite- Overrides:
writeToin classcom.google.protobuf.GeneratedMessageV3- Throws:
IOException
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getSerializedSize
public int getSerializedSize()- Specified by:
getSerializedSizein interfacecom.google.protobuf.MessageLite- Overrides:
getSerializedSizein classcom.google.protobuf.GeneratedMessageV3
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equals
- Specified by:
equalsin interfacecom.google.protobuf.Message- Overrides:
equalsin classcom.google.protobuf.AbstractMessage
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hashCode
public int hashCode()- Specified by:
hashCodein interfacecom.google.protobuf.Message- Overrides:
hashCodein classcom.google.protobuf.AbstractMessage
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parseFrom
public static Pixels parseFrom(ByteBuffer data) throws com.google.protobuf.InvalidProtocolBufferException - Throws:
com.google.protobuf.InvalidProtocolBufferException
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parseFrom
public static Pixels parseFrom(ByteBuffer data, com.google.protobuf.ExtensionRegistryLite extensionRegistry) throws com.google.protobuf.InvalidProtocolBufferException - Throws:
com.google.protobuf.InvalidProtocolBufferException
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parseFrom
public static Pixels parseFrom(com.google.protobuf.ByteString data) throws com.google.protobuf.InvalidProtocolBufferException - Throws:
com.google.protobuf.InvalidProtocolBufferException
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parseFrom
public static Pixels parseFrom(com.google.protobuf.ByteString data, com.google.protobuf.ExtensionRegistryLite extensionRegistry) throws com.google.protobuf.InvalidProtocolBufferException - Throws:
com.google.protobuf.InvalidProtocolBufferException
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parseFrom
public static Pixels parseFrom(byte[] data) throws com.google.protobuf.InvalidProtocolBufferException - Throws:
com.google.protobuf.InvalidProtocolBufferException
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parseFrom
public static Pixels parseFrom(byte[] data, com.google.protobuf.ExtensionRegistryLite extensionRegistry) throws com.google.protobuf.InvalidProtocolBufferException - Throws:
com.google.protobuf.InvalidProtocolBufferException
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parseFrom
- Throws:
IOException
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parseFrom
public static Pixels parseFrom(InputStream input, com.google.protobuf.ExtensionRegistryLite extensionRegistry) throws IOException - Throws:
IOException
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parseDelimitedFrom
- Throws:
IOException
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parseDelimitedFrom
public static Pixels parseDelimitedFrom(InputStream input, com.google.protobuf.ExtensionRegistryLite extensionRegistry) throws IOException - Throws:
IOException
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parseFrom
- Throws:
IOException
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parseFrom
public static Pixels parseFrom(com.google.protobuf.CodedInputStream input, com.google.protobuf.ExtensionRegistryLite extensionRegistry) throws IOException - Throws:
IOException
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newBuilderForType
- Specified by:
newBuilderForTypein interfacecom.google.protobuf.Message- Specified by:
newBuilderForTypein interfacecom.google.protobuf.MessageLite
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newBuilder
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newBuilder
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toBuilder
- Specified by:
toBuilderin interfacecom.google.protobuf.Message- Specified by:
toBuilderin interfacecom.google.protobuf.MessageLite
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newBuilderForType
protected Pixels.Builder newBuilderForType(com.google.protobuf.GeneratedMessageV3.BuilderParent parent) - Specified by:
newBuilderForTypein classcom.google.protobuf.GeneratedMessageV3
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getDefaultInstance
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parser
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getParserForType
- Specified by:
getParserForTypein interfacecom.google.protobuf.Message- Specified by:
getParserForTypein interfacecom.google.protobuf.MessageLite- Overrides:
getParserForTypein classcom.google.protobuf.GeneratedMessageV3
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getDefaultInstanceForType
- Specified by:
getDefaultInstanceForTypein interfacecom.google.protobuf.MessageLiteOrBuilder- Specified by:
getDefaultInstanceForTypein interfacecom.google.protobuf.MessageOrBuilder
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