Exemplo n.º 1
0
// NdDataSchema returns the metadata in JSON for this Data
func (p *Properties) NdDataMetadata() (string, error) {
	var err error
	var size, offset dvid.Point

	dims := int(p.BlockSize.NumDims())
	if p.MinPoint == nil || p.MaxPoint == nil {
		zeroPt := make([]int32, dims)
		size, err = dvid.NewPoint(zeroPt)
		if err != nil {
			return "", err
		}
		offset = size
	} else {
		size = p.MaxPoint.Sub(p.MinPoint).AddScalar(1)
		offset = p.MinPoint
	}

	var axesName = []string{"X", "Y", "Z", "t", "c"}
	var metadata metadataT
	metadata.Axes = []axisT{}
	for dim := 0; dim < dims; dim++ {
		metadata.Axes = append(metadata.Axes, axisT{
			Label:      axesName[dim],
			Resolution: p.Resolution.VoxelSize[dim],
			Units:      p.Resolution.VoxelUnits[dim],
			Size:       size.Value(uint8(dim)),
			Offset:     offset.Value(uint8(dim)),
		})
	}
	metadata.Properties = *p

	m, err := json.Marshal(metadata)
	if err != nil {
		return "", err
	}
	return string(m), nil
}
Exemplo n.º 2
0
// GetGoogleSubvolGeom returns a google-specific voxel spec, which includes how the data is positioned relative to
// scaled volume boundaries.  Not that the size parameter is the desired size and not what is required to fit
// within a scaled volume.
func (d *Data) GetGoogleSubvolGeom(scaling Scaling, shape dvid.DataShape, offset dvid.Point3d, size dvid.Point) (*GoogleSubvolGeom, error) {
	gsg := new(GoogleSubvolGeom)
	if err := gsg.shape.FromShape(shape); err != nil {
		return nil, err
	}
	gsg.offset = offset

	// If 2d plane, convert combination of plane and size into 3d size.
	if size.NumDims() == 2 {
		size2d := size.(dvid.Point2d)
		sizeWant, err := dvid.GetPoint3dFrom2d(shape, size2d, 1)
		if err != nil {
			return nil, err
		}
		gsg.sizeWant = sizeWant
	} else {
		var ok bool
		gsg.sizeWant, ok = size.(dvid.Point3d)
		if !ok {
			return nil, fmt.Errorf("Can't convert %v to dvid.Point3d", size)
		}
	}

	// Determine which geometry is appropriate given the scaling and the shape/orientation
	tileSpec, err := GetGSpec(scaling, shape)
	if err != nil {
		return nil, err
	}
	geomIndex, found := d.GeomMap[*tileSpec]
	if !found {
		return nil, fmt.Errorf("Could not find scaled volume in %q for %s with scaling %d", d.DataName(), shape, scaling)
	}
	geom := d.Scales[geomIndex]
	gsg.gi = geomIndex
	gsg.channelCount = geom.ChannelCount
	gsg.channelType = geom.ChannelType

	// Get the # bytes for each pixel
	switch geom.ChannelType {
	case "UINT8":
		gsg.bytesPerVoxel = 1
	case "FLOAT":
		gsg.bytesPerVoxel = 4
	case "UINT64":
		gsg.bytesPerVoxel = 8
	default:
		return nil, fmt.Errorf("Unknown volume channel type in %s: %s", d.DataName(), geom.ChannelType)
	}

	// Check if the requested area is completely outside the volume.
	volumeSize := geom.VolumeSize
	if offset[0] >= volumeSize[0] || offset[1] >= volumeSize[1] || offset[2] >= volumeSize[2] {
		gsg.outside = true
		return gsg, nil
	}

	// Check if the requested shape is on the edge and adjust size.
	adjSize := gsg.sizeWant
	maxpt := offset.Add(adjSize)
	for i := uint8(0); i < 3; i++ {
		if maxpt.Value(i) > volumeSize[i] {
			gsg.edge = true
			adjSize[i] = volumeSize[i] - offset[i]
		}
	}
	gsg.size = adjSize

	return gsg, nil
}
Exemplo n.º 3
0
func (v *Voxels) readScaledBlock(block *storage.TKeyValue, blockSize dvid.Point, attenuation uint8) error {
	if blockSize.NumDims() > 3 {
		return fmt.Errorf("DVID voxel blocks currently only supports up to 3d, not 4+ dimensions")
	}
	blockBeg, dataBeg, dataEnd, err := v.ComputeTransform(block, blockSize)
	if err != nil {
		return err
	}
	data := v.Data()
	bytesPerVoxel := int64(v.Values().BytesPerElement())
	if bytesPerVoxel != 1 {
		return fmt.Errorf("Can only scale non-ROI blocks with 1 byte voxels")
	}

	// Compute the strides (in bytes)
	bX := int64(blockSize.Value(0)) * bytesPerVoxel
	bY := int64(blockSize.Value(1)) * bX
	dX := int64(v.Stride())

	// Get the block beginning coordinates.
	blockBegX := int64(blockBeg.Value(0))
	blockBegY := int64(blockBeg.Value(1))
	blockBegZ := int64(blockBeg.Value(2))

	// Do the transfers depending on shape of the external voxels.
	switch {
	case v.DataShape().Equals(dvid.XY):
		blockI := blockBegZ*bY + blockBegY*bX + blockBegX*bytesPerVoxel
		dataI := int64(dataBeg.Value(1))*dX + int64(dataBeg.Value(0))*bytesPerVoxel
		for y := dataBeg.Value(1); y <= dataEnd.Value(1); y++ {
			for x := int64(dataBeg.Value(0)); x <= int64(dataEnd.Value(0)); x++ {
				data[dataI+x] = (block.V[blockI+x] >> attenuation)
			}
			blockI += bX
			dataI += dX
		}

	case v.DataShape().Equals(dvid.XZ):
		blockI := blockBegZ*bY + blockBegY*bX + blockBegX*bytesPerVoxel
		dataI := int64(dataBeg.Value(2))*dX + int64(dataBeg.Value(0))*bytesPerVoxel
		for y := dataBeg.Value(2); y <= dataEnd.Value(2); y++ {
			for x := int64(dataBeg.Value(0)); x <= int64(dataEnd.Value(0)); x++ {
				data[dataI+x] = (block.V[blockI+x] >> attenuation)
			}
			blockI += bY
			dataI += dX
		}

	case v.DataShape().Equals(dvid.YZ):
		bz := blockBegZ
		for y := int64(dataBeg.Value(2)); y <= int64(dataEnd.Value(2)); y++ {
			blockI := blockBegZ*bY + blockBegY*bX + blockBegX*bytesPerVoxel
			dataI := y*dX + int64(dataBeg.Value(1))*bytesPerVoxel
			for x := dataBeg.Value(1); x <= dataEnd.Value(1); x++ {
				data[dataI] = (block.V[blockI] >> attenuation)
				blockI += bX
				dataI += bytesPerVoxel
			}
			bz++
		}

	case v.DataShape().ShapeDimensions() == 2:
		// TODO: General code for handling 2d ExtData in n-d space.
		return fmt.Errorf("DVID currently does not support 2d in n-d space.")

	case v.DataShape().Equals(dvid.Vol3d):
		blockOffset := blockBegX * bytesPerVoxel
		dX := int64(v.Size().Value(0)) * bytesPerVoxel
		dY := int64(v.Size().Value(1)) * dX
		dataOffset := int64(dataBeg.Value(0)) * bytesPerVoxel
		blockZ := blockBegZ

		for dataZ := dataBeg.Value(2); dataZ <= dataEnd.Value(2); dataZ++ {
			blockY := blockBegY
			for dataY := dataBeg.Value(1); dataY <= dataEnd.Value(1); dataY++ {
				blockI := blockZ*bY + blockY*bX + blockOffset
				dataI := int64(dataZ)*dY + int64(dataY)*dX + dataOffset
				for x := int64(dataBeg.Value(0)); x <= int64(dataEnd.Value(0)); x++ {
					data[dataI+x] = (block.V[blockI+x] >> attenuation)
				}
				blockY++
			}
			blockZ++
		}

	default:
		return fmt.Errorf("Cannot readScaledBlock() unsupported voxels data shape %s", v.DataShape())
	}
	return nil
}
Exemplo n.º 4
0
func (v *Voxels) writeBlock(block *storage.TKeyValue, blockSize dvid.Point) error {
	if blockSize.NumDims() > 3 {
		return fmt.Errorf("DVID voxel blocks currently only supports up to 3d, not 4+ dimensions")
	}
	blockBeg, dataBeg, dataEnd, err := v.ComputeTransform(block, blockSize)
	if err != nil {
		return err
	}
	data := v.Data()
	bytesPerVoxel := int64(v.Values().BytesPerElement())

	// Compute the strides (in bytes)
	bX := int64(blockSize.Value(0)) * bytesPerVoxel
	bY := int64(blockSize.Value(1)) * bX
	dX := int64(v.Stride())

	blockBegX := int64(blockBeg.Value(0))
	blockBegY := int64(blockBeg.Value(1))
	blockBegZ := int64(blockBeg.Value(2))

	// Do the transfers depending on shape of the external voxels.
	switch {
	case v.DataShape().Equals(dvid.XY):
		dataI := int64(dataBeg.Value(1))*dX + int64(dataBeg.Value(0))*bytesPerVoxel
		blockI := blockBegZ*bY + blockBegY*bX + blockBegX*bytesPerVoxel
		bytes := int64(dataEnd.Value(0)-dataBeg.Value(0)+1) * bytesPerVoxel
		for y := dataBeg.Value(1); y <= dataEnd.Value(1); y++ {
			copy(block.V[blockI:blockI+bytes], data[dataI:dataI+bytes])
			blockI += bX
			dataI += dX
		}

	case v.DataShape().Equals(dvid.XZ):
		dataI := int64(dataBeg.Value(2))*dX + int64(dataBeg.Value(0))*bytesPerVoxel
		blockI := blockBegZ*bY + blockBegY*bX + blockBegX*bytesPerVoxel
		bytes := int64(dataEnd.Value(0)-dataBeg.Value(0)+1) * bytesPerVoxel
		for y := dataBeg.Value(2); y <= dataEnd.Value(2); y++ {
			copy(block.V[blockI:blockI+bytes], data[dataI:dataI+bytes])
			blockI += bY
			dataI += dX
		}

	case v.DataShape().Equals(dvid.YZ):
		bz := blockBegZ
		for y := int64(dataBeg.Value(2)); y <= int64(dataEnd.Value(2)); y++ {
			dataI := y*dX + int64(dataBeg.Value(1))*bytesPerVoxel
			blockI := bz*bY + blockBegY*bX + blockBegX*bytesPerVoxel
			for x := dataBeg.Value(1); x <= dataEnd.Value(1); x++ {
				copy(block.V[blockI:blockI+bytesPerVoxel], data[dataI:dataI+bytesPerVoxel])
				blockI += bX
				dataI += bytesPerVoxel
			}
			bz++
		}

	case v.DataShape().ShapeDimensions() == 2:
		// TODO: General code for handling 2d ExtData in n-d space.
		return fmt.Errorf("DVID currently does not support 2d in n-d space.")

	case v.DataShape().Equals(dvid.Vol3d):
		blockOffset := blockBegX * bytesPerVoxel
		dX := int64(v.Size().Value(0)) * bytesPerVoxel
		dY := int64(v.Size().Value(1)) * dX
		dataOffset := int64(dataBeg.Value(0)) * bytesPerVoxel
		bytes := int64(dataEnd.Value(0)-dataBeg.Value(0)+1) * bytesPerVoxel
		blockZ := blockBegZ

		for dataZ := int64(dataBeg.Value(2)); dataZ <= int64(dataEnd.Value(2)); dataZ++ {
			blockY := blockBegY
			for dataY := int64(dataBeg.Value(1)); dataY <= int64(dataEnd.Value(1)); dataY++ {
				dataI := dataZ*dY + dataY*dX + dataOffset
				blockI := blockZ*bY + blockY*bX + blockOffset
				copy(block.V[blockI:blockI+bytes], data[dataI:dataI+bytes])
				blockY++
			}
			blockZ++
		}

	default:
		return fmt.Errorf("Cannot writeBlock() unsupported voxels data shape %s", v.DataShape())
	}
	return nil
}
Exemplo n.º 5
0
func (v *Labels) readMappedBlock(block *storage.TKeyValue, blockSize dvid.Point, m *labels.Mapping) error {
	if blockSize.NumDims() > 3 {
		return fmt.Errorf("DVID voxel blocks currently only supports up to 3d, not 4+ dimensions")
	}
	blockBeg, dataBeg, dataEnd, err := v.ComputeTransform(block, blockSize)
	if err != nil {
		return err
	}
	data := v.Data()

	// Compute the strides (in bytes)
	bX := int64(blockSize.Value(0)) * 8
	bY := int64(blockSize.Value(1)) * bX
	dX := int64(v.Stride())

	blockBegX := int64(blockBeg.Value(0))
	blockBegY := int64(blockBeg.Value(1))
	blockBegZ := int64(blockBeg.Value(2))

	// Do the transfers depending on shape of the external voxels.
	switch {
	case v.DataShape().Equals(dvid.XY):
		dataI := int64(dataBeg.Value(1))*dX + int64(dataBeg.Value(0))*8
		blockI := blockBegZ*bY + blockBegY*bX + blockBegX*8
		for y := int64(dataBeg.Value(1)); y <= int64(dataEnd.Value(1)); y++ {
			bI := blockI
			dI := dataI
			for x := dataBeg.Value(0); x <= dataEnd.Value(0); x++ {
				orig := binary.LittleEndian.Uint64(block.V[bI : bI+8])
				mapped, found := m.FinalLabel(orig)
				if found {
					binary.LittleEndian.PutUint64(data[dI:dI+8], mapped)
				} else {
					copy(data[dI:dI+8], block.V[bI:bI+8])
				}
				bI += 8
				dI += 8
			}
			blockI += bX
			dataI += dX
		}

	case v.DataShape().Equals(dvid.XZ):
		dataI := int64(dataBeg.Value(2))*dX + int64(dataBeg.Value(0))*8
		blockI := blockBegZ*bY + blockBegY*bX + blockBegX*8
		for y := int64(dataBeg.Value(2)); y <= int64(dataEnd.Value(2)); y++ {
			bI := blockI
			dI := dataI
			for x := dataBeg.Value(0); x <= dataEnd.Value(0); x++ {
				orig := binary.LittleEndian.Uint64(block.V[bI : bI+8])
				mapped, found := m.FinalLabel(orig)
				if found {
					binary.LittleEndian.PutUint64(data[dI:dI+8], mapped)
				} else {
					copy(data[dI:dI+8], block.V[bI:bI+8])
				}
				bI += 8
				dI += 8
			}
			blockI += bY
			dataI += dX
		}

	case v.DataShape().Equals(dvid.YZ):
		bz := blockBegZ
		for y := int64(dataBeg.Value(2)); y <= int64(dataEnd.Value(2)); y++ {
			dataI := y*dX + int64(dataBeg.Value(1))*8
			blockI := bz*bY + blockBegY*bX + blockBegX*8
			for x := dataBeg.Value(1); x <= dataEnd.Value(1); x++ {
				orig := binary.LittleEndian.Uint64(block.V[blockI : blockI+8])
				mapped, found := m.FinalLabel(orig)
				if found {
					binary.LittleEndian.PutUint64(data[dataI:dataI+8], mapped)
				} else {
					copy(data[dataI:dataI+8], block.V[blockI:blockI+8])
				}
				blockI += bX
				dataI += 8
			}
			bz++
		}

	case v.DataShape().ShapeDimensions() == 2:
		// TODO: General code for handling 2d ExtData in n-d space.
		return fmt.Errorf("DVID currently does not support 2d in n-d space.")

	case v.DataShape().Equals(dvid.Vol3d):
		blockOffset := blockBegX * 8
		dX := int64(v.Size().Value(0)) * 8
		dY := int64(v.Size().Value(1)) * dX
		dataOffset := int64(dataBeg.Value(0)) * 8
		blockZ := blockBegZ

		for dataZ := int64(dataBeg.Value(2)); dataZ <= int64(dataEnd.Value(2)); dataZ++ {
			blockY := blockBegY
			for dataY := int64(dataBeg.Value(1)); dataY <= int64(dataEnd.Value(1)); dataY++ {
				bI := blockZ*bY + blockY*bX + blockOffset
				dI := dataZ*dY + dataY*dX + dataOffset
				for x := dataBeg.Value(0); x <= dataEnd.Value(0); x++ {
					orig := binary.LittleEndian.Uint64(block.V[bI : bI+8])
					mapped, found := m.FinalLabel(orig)
					if found {
						binary.LittleEndian.PutUint64(data[dI:dI+8], mapped)
					} else {
						copy(data[dI:dI+8], block.V[bI:bI+8])
					}
					bI += 8
					dI += 8
				}
				blockY++
			}
			blockZ++
		}

	default:
		return fmt.Errorf("Cannot readBlock() unsupported voxels data shape %s", v.DataShape())
	}
	return nil
}