public HeaderMRC(BinaryReader reader)
{
Dimensions = new int3(reader.ReadBytes(3 * sizeof(int)));
Mode = (MRCDataType)reader.ReadInt32();
StartSubImage = new int3(reader.ReadBytes(3 * sizeof(int)));
Griddimensions = new int3(reader.ReadBytes(3 * sizeof(int)));
Pixelsize = new float3(reader.ReadBytes(3 * sizeof(float)));
Angles = new float3(reader.ReadBytes(3 * sizeof(float)));
MapOrder = new int3(reader.ReadBytes(3 * sizeof(int)));
MinValue = reader.ReadSingle();
MaxValue = reader.ReadSingle();
MeanValue = reader.ReadSingle();
SpaceGroup = reader.ReadInt32();
ExtendedBytes = reader.ReadInt32();
CreatorID = reader.ReadInt16();
ExtraData1 = reader.ReadBytes(30);
NInt = reader.ReadInt16();
NReal = reader.ReadInt16();
ExtraData2 = reader.ReadBytes(28);
IDType = reader.ReadInt16();
Lens = reader.ReadInt16();
ND1 = reader.ReadInt16();
ND2 = reader.ReadInt16();
VD1 = reader.ReadInt16();
VD2 = reader.ReadInt16();
TiltOriginal = new float3(reader.ReadBytes(3 * sizeof(float)));
TiltCurrent = new float3(reader.ReadBytes(3 * sizeof(float)));
Origin = new float3(reader.ReadBytes(3 * sizeof(float)));
CMap = reader.ReadBytes(4);
Stamp = reader.ReadBytes(4);
StdDevValue = reader.ReadSingle();
NumLabels = reader.ReadInt32();
for (int i = 0; i < 10; i++)
{
Labels[i] = reader.ReadBytes(80);
}
Extended = reader.ReadBytes(ExtendedBytes);
}
public override void SetValueType(Type t)
{
if (t == typeof(byte))
{
Mode = MRCDataType.Byte;
}
else if (t == typeof(float))
{
Mode = MRCDataType.Float;
}
else if (t == typeof(short))
{
Mode = MRCDataType.Short;
}
else if (t == typeof(ushort))
{
Mode = MRCDataType.UnsignedShort;
}
else
{
throw new Exception("Unknown data type.");
}
}
public HeaderMRC(BinaryReader reader)
{
Dimensions = new int3(reader.ReadBytes(3 * sizeof(int)));
Mode = (MRCDataType)reader.ReadInt32();
StartSubImage = new int3(reader.ReadBytes(3 * sizeof(int)));
Griddimensions = new int3(reader.ReadBytes(3 * sizeof(int)));
Pixelsize = new float3(reader.ReadBytes(3 * sizeof(float))) / new float3(Dimensions.X, Dimensions.Y, Dimensions.Z);
Angles = new float3(reader.ReadBytes(3 * sizeof(float)));
MapOrder = new int3(reader.ReadBytes(3 * sizeof(int)));
MinValue = reader.ReadSingle();
MaxValue = reader.ReadSingle();
MeanValue = reader.ReadSingle();
SpaceGroup = reader.ReadInt32();
ExtendedBytes = reader.ReadInt32();
CreatorID = reader.ReadInt16();
ExtraData1 = reader.ReadBytes(30);
NInt = reader.ReadInt16();
NReal = reader.ReadInt16();
ExtraData2 = reader.ReadBytes(28);
IDType = reader.ReadInt16();
Lens = reader.ReadInt16();
ND1 = reader.ReadInt16();
ND2 = reader.ReadInt16();
VD1 = reader.ReadInt16();
VD2 = reader.ReadInt16();
TiltOriginal = new float3(reader.ReadBytes(3 * sizeof(float)));
TiltCurrent = new float3(reader.ReadBytes(3 * sizeof(float)));
Origin = new float3(reader.ReadBytes(3 * sizeof(float)));
CMap = reader.ReadBytes(4);
Stamp = reader.ReadBytes(4);
StdDevValue = reader.ReadSingle();
NumLabels = reader.ReadInt32();
for (int i = 0; i < 10; i++)
Labels[i] = reader.ReadBytes(80);
// In case this is from SerialEM, check how big ExtendedBytes should be at least to read per-frame data
ImodHasTilt = (NReal & (1 << 0)) > 0;
ImodHasMontage = (NReal & (1 << 1)) > 0;
ImodHasStagePos = (NReal & (1 << 2)) > 0;
ImodHasMagnification = (NReal & (1 << 3)) > 0;
ImodHasIntensity = (NReal & (1 << 4)) > 0;
ImodHasExposure = (NReal & (1 << 5)) > 0;
int BytesPerSection = (ImodHasTilt ? 2 : 0) +
(ImodHasMontage ? 6 : 0) +
(ImodHasStagePos ? 4 : 0) +
(ImodHasMagnification ? 2 : 0) +
(ImodHasIntensity ? 2 : 0) +
(ImodHasExposure ? 4 : 0);
if (BytesPerSection * Dimensions.Z > ExtendedBytes) // Not from SerialEM, ignore extended header
{
Extended = reader.ReadBytes(ExtendedBytes);
}
else // SerialEM extended header, read one section per frame
{
if (ImodHasTilt)
ImodTilt = new float[Dimensions.Z];
if (ImodHasMagnification)
ImodMagnification = new float[Dimensions.Z];
if (ImodHasIntensity)
ImodIntensity = new float[Dimensions.Z];
if (ImodHasExposure)
ImodExposure = new float[Dimensions.Z];
for (int i = 0; i < Dimensions.Z; i++)
{
if (ImodHasTilt)
ImodTilt[i] = reader.ReadInt16() / 100f;
if (ImodHasMontage)
reader.ReadBytes(6);
if (ImodHasStagePos)
reader.ReadBytes(4);
if (ImodHasMagnification)
ImodMagnification[i] = reader.ReadInt16() / 100f;
if (ImodHasIntensity)
ImodIntensity[i] = reader.ReadInt16() / 2500f;
if (ImodHasExposure)
{
float val = reader.ReadSingle();
/*int s1 = reader.ReadInt16();
int s2 = reader.ReadInt16();
float val = Math.Sign(s1) * (Math.Abs(s1) * 256 + (Math.Abs(s2) % 256)) * (float)Math.Pow(2, Math.Sign(s2) * (Math.Abs(s2) / 256f));*/
ImodExposure[i] = val;
}
}
}
}
public override void SetValueType(Type t)
{
if (t == typeof(byte))
Mode = MRCDataType.Byte;
else if (t == typeof(float))
Mode = MRCDataType.Float;
else if (t == typeof(short))
Mode = MRCDataType.Short;
else if (t == typeof(ushort))
Mode = MRCDataType.UnsignedShort;
else
throw new Exception("Unknown data type.");
}
public HeaderMRC(BinaryReader reader)
{
Dimensions = new int3(reader.ReadInt32(), reader.ReadInt32(), reader.ReadInt32());
Mode = (MRCDataType)reader.ReadInt32();
StartSubImage = new int3(reader.ReadInt32(), reader.ReadInt32(), reader.ReadInt32());
Griddimensions = new int3(reader.ReadInt32(), reader.ReadInt32(), reader.ReadInt32());
PixelSize = new float3(reader.ReadSingle(), reader.ReadSingle(), reader.ReadSingle()) / new float3(Dimensions);
Angles = new float3(reader.ReadSingle(), reader.ReadSingle(), reader.ReadSingle());
MapOrder = new int3(reader.ReadInt32(), reader.ReadInt32(), reader.ReadInt32());
MinValue = reader.ReadSingle();
MaxValue = reader.ReadSingle();
MeanValue = reader.ReadSingle();
SpaceGroup = reader.ReadInt32();
ExtendedBytes = reader.ReadInt32();
CreatorID = reader.ReadInt16();
ExtraData10 = reader.ReadBytes(6);
ExtID = reader.ReadBytes(4);
ExtraData11 = reader.ReadBytes(20);
NInt = reader.ReadInt16();
NReal = reader.ReadInt16();
ExtraData2 = reader.ReadBytes(28);
IDType = reader.ReadInt16();
Lens = reader.ReadInt16();
ND1 = reader.ReadInt16();
ND2 = reader.ReadInt16();
VD1 = reader.ReadInt16();
VD2 = reader.ReadInt16();
TiltOriginal = new float3(reader.ReadSingle(), reader.ReadSingle(), reader.ReadSingle());
TiltCurrent = new float3(reader.ReadSingle(), reader.ReadSingle(), reader.ReadSingle());
Origin = new float3(reader.ReadSingle(), reader.ReadSingle(), reader.ReadSingle());
CMap = reader.ReadBytes(4);
Stamp = reader.ReadBytes(4);
StdDevValue = reader.ReadSingle();
NumLabels = reader.ReadInt32();
for (int i = 0; i < 10; i++)
{
Labels[i] = reader.ReadBytes(80);
}
// In case this is from SerialEM, check how big ExtendedBytes should be at least to read per-frame data
ImodHasTilt = (NReal & (1 << 0)) > 0;
ImodHasMontage = (NReal & (1 << 1)) > 0;
ImodHasStagePos = (NReal & (1 << 2)) > 0;
ImodHasMagnification = (NReal & (1 << 3)) > 0;
ImodHasIntensity = (NReal & (1 << 4)) > 0;
ImodHasExposure = (NReal & (1 << 5)) > 0;
int BytesPerSection = (ImodHasTilt ? 2 : 0) +
(ImodHasMontage ? 6 : 0) +
(ImodHasStagePos ? 4 : 0) +
(ImodHasMagnification ? 2 : 0) +
(ImodHasIntensity ? 2 : 0) +
(ImodHasExposure ? 4 : 0);
if (BytesPerSection * Dimensions.Z > ExtendedBytes) // Not from SerialEM, ignore extended header
{
Extended = reader.ReadBytes(ExtendedBytes);
}
else // SerialEM extended header, read one section per frame
{
if (ImodHasTilt)
{
ImodTilt = new float[Dimensions.Z];
}
if (ImodHasMagnification)
{
ImodMagnification = new float[Dimensions.Z];
}
if (ImodHasIntensity)
{
ImodIntensity = new float[Dimensions.Z];
}
if (ImodHasExposure)
{
ImodExposure = new float[Dimensions.Z];
}
for (int i = 0; i < Dimensions.Z; i++)
{
if (ImodHasTilt)
{
ImodTilt[i] = reader.ReadInt16() / 100f;
}
if (ImodHasMontage)
{
reader.ReadBytes(6);
}
if (ImodHasStagePos)
{
reader.ReadBytes(4);
}
if (ImodHasMagnification)
{
ImodMagnification[i] = reader.ReadInt16() / 100f;
}
if (ImodHasIntensity)
{
ImodIntensity[i] = reader.ReadInt16() / 2500f;
}
if (ImodHasExposure)
{
float val = reader.ReadSingle();
/*int s1 = reader.ReadInt16();
* int s2 = reader.ReadInt16();
*
* float val = Math.Sign(s1) * (Math.Abs(s1) * 256 + (Math.Abs(s2) % 256)) * (float)Math.Pow(2, Math.Sign(s2) * (Math.Abs(s2) / 256f));*/
ImodExposure[i] = val;
}
}
}
}
