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/*
* Copyright 2015 University of Basel, Graphics and Vision Research Group
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package scalismo.io
import java.io._
import scalismo.common.{Scalar, UnstructuredPointsDomain, Vectorizer}
import scalismo.geometry.{_1D, _2D, _3D, EuclideanVector}
import scalismo.image.DiscreteImageDomain
import scalismo.mesh.{LineMesh, TetrahedralMesh, TriangleMesh}
import scalismo.statisticalmodel.{DiscreteLowRankGaussianProcess, PointDistributionModel, StatisticalMeshModel}
import scala.util.Try
object StatisticalModelIO {
/**
* Reads and write of point distribution models with different domain types.
* The model file type is determined based on the extension.
* Currently only the Scalismo format (.h5) is supported.
*/
/**
* Reads a PDM with TriangleMesh[_2D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def readStatisticalTriangleMeshModel2D(file: File,
modelPath: String = "/"): Try[PointDistributionModel[_2D, TriangleMesh]] = {
StatismoIO.readStatismoPDM[_2D, TriangleMesh](file, modelPath)
}
/**
* Writes a PDM with TriangleMesh[_2D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def writeStatisticalTriangleMeshModel2D(model: PointDistributionModel[_2D, TriangleMesh],
file: File,
modelPath: String = "/"): Try[Unit] = {
StatismoIO.writeStatismoPDM[_2D, TriangleMesh](model, file, modelPath)
}
/**
* Reads a PDM with TriangleMesh[_3D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def readStatisticalTriangleMeshModel3D(file: File,
modelPath: String = "/"): Try[PointDistributionModel[_3D, TriangleMesh]] = {
StatismoIO.readStatismoPDM[_3D, TriangleMesh](file, modelPath)
}
/**
* Writes a PDM with TriangleMesh[_3D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def writeStatisticalTriangleMeshModel3D(model: PointDistributionModel[_3D, TriangleMesh],
file: File,
modelPath: String = "/"): Try[Unit] = {
StatismoIO.writeStatismoPDM[_3D, TriangleMesh](model, file, modelPath)
}
/**
* Reads a PDM with LineMesh[_2D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def readStatisticalLineMeshModel2D(file: File,
modelPath: String = "/"): Try[PointDistributionModel[_2D, LineMesh]] = {
StatismoIO.readStatismoPDM[_2D, LineMesh](file, modelPath)
}
/**
* Writes a PDM with LineMesh[_2D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def writeStatisticalLineMeshModel2D(model: PointDistributionModel[_2D, LineMesh],
file: File,
modelPath: String = "/"): Try[Unit] = {
StatismoIO.writeStatismoPDM[_2D, LineMesh](model, file, modelPath)
}
/**
* Reads a PDM with TriangleMesh[_3D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def readStatisticalLineMeshModel3D(file: File,
modelPath: String = "/"): Try[PointDistributionModel[_3D, LineMesh]] = {
StatismoIO.readStatismoPDM[_3D, LineMesh](file, modelPath)
}
/**
* Writes a PDM with TriangleMesh[_3D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def writeStatisticalLineMeshModel3D(model: PointDistributionModel[_3D, LineMesh],
file: File,
modelPath: String = "/"): Try[Unit] = {
StatismoIO.writeStatismoPDM[_3D, LineMesh](model, file, modelPath)
}
/**
* Reads a PDM with TetrahedralMesh[_3D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def readStatisticalTetrahedralMeshModel3D(
file: File,
modelPath: String = "/"
): Try[PointDistributionModel[_3D, TetrahedralMesh]] = {
StatismoIO.readStatismoPDM[_3D, TetrahedralMesh](file, modelPath)
}
/**
* Writes a PDM with TetrahedralMesh[_3D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def writeStatisticalTetrahedralMeshModel3D(model: PointDistributionModel[_3D, TetrahedralMesh],
file: File,
modelPath: String = "/"): Try[Unit] = {
StatismoIO.writeStatismoPDM[_3D, TetrahedralMesh](model, file, modelPath)
}
/**
* Reads a PDM with UnstructuredPointsDomain[_3D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def readStatisticalPointModel3D(
file: File,
modelPath: String = "/"
): Try[PointDistributionModel[_3D, UnstructuredPointsDomain]] = {
StatismoIO.readStatismoPDM[_3D, UnstructuredPointsDomain](file, modelPath)
}
/**
* Writes a PDM with UnstructuredPointsDomain[_3D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def writeStatisticalPointModel3D(model: PointDistributionModel[_3D, UnstructuredPointsDomain],
file: File,
modelPath: String = "/"): Try[Unit] = {
StatismoIO.writeStatismoPDM[_3D, UnstructuredPointsDomain](model, file, modelPath)
}
/**
* Reads a PDM with UnstructuredPointsDomain[_2D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def readStatisticalPointModel2D(
file: File,
modelPath: String = "/"
): Try[PointDistributionModel[_2D, UnstructuredPointsDomain]] = {
StatismoIO.readStatismoPDM[_2D, UnstructuredPointsDomain](file, modelPath)
}
/**
* Writes a PDM with UnstructuredPointsDomain[_2D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def writeStatisticalPointModel2D(model: PointDistributionModel[_2D, UnstructuredPointsDomain],
file: File,
modelPath: String = "/"): Try[Unit] = {
StatismoIO.writeStatismoPDM[_2D, UnstructuredPointsDomain](model, file, modelPath)
}
/**
* Reads a PDM with UnstructuredPointsDomain[_1D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def readStatisticalPointModel1D(
file: File,
modelPath: String = "/"
): Try[PointDistributionModel[_1D, UnstructuredPointsDomain]] = {
StatismoIO.readStatismoPDM[_1D, UnstructuredPointsDomain](file, modelPath)
}
/**
* Writes a PDM with UnstructuredPointsDomain[_1D] as the domain
* @param file The statismo file
* @param modelPath in the hdf5 directory
* @return A PointDistributionModel or the Failure
*/
def writeStatisticalPointModel1D(model: PointDistributionModel[_1D, UnstructuredPointsDomain],
file: File,
modelPath: String = "/"): Try[Unit] = {
StatismoIO.writeStatismoPDM[_1D, UnstructuredPointsDomain](model, file, modelPath)
}
/**
* Conversion between old format only supporting TriangleMesh PDMs and the new general PDM format
* @param model statisticalMeshModel
* @return PointDistributionModel with a TriangleMesh[_3D] as the domain
*/
private def modelConverterToPointDistribution(
model: StatisticalMeshModel
): PointDistributionModel[_3D, TriangleMesh] = {
PointDistributionModel(model.gp)
}
/**
* Conversion between new general PDM format and the old format only supporting TriangleMesh PDMs
* @param model PointDistributionModel with a TriangleMesh[_3D] as the domain
* @return statisticalMeshModel
*/
private def modelConverterToMeshModel(model: PointDistributionModel[_3D, TriangleMesh]): StatisticalMeshModel = {
StatisticalMeshModel(model.reference, model.gp)
}
/**
* Reads a statistical mesh model. The file type is determined
* based on the extension. Currently on the Scalismo format (.h5)
* is supported.
*
* @param file The statismo file
* @return A StatisticalMeshModel or the Failure
*/
def readStatisticalMeshModel(file: File, modelPath: String = "/"): Try[StatisticalMeshModel] = {
val pModel = readStatisticalTriangleMeshModel3D(file, modelPath)
for {
model <- pModel
} yield modelConverterToMeshModel(model)
}
/**
* Writes a statistical mesh model. The file type is determined
* based on the extension. Currently on the Scalismo format (.h5)
* is supported.
*
* @param model The statistical model
* @param file The file to which the model is written
* @return In case of Failure, the Failure is returned.
*/
def writeStatisticalMeshModel(model: StatisticalMeshModel, file: File, modelPath: String = "/"): Try[Unit] = {
val pModel = modelConverterToPointDistribution(model)
writeStatisticalTriangleMeshModel3D(pModel, file, modelPath)
}
/**
* Reads a model of 2D deformation fields defined on a 2D image domain
* @param file the file from which the model is read
* @return a 2D deformation model
*/
def readDeformationModel2D(
file: java.io.File
): Try[DiscreteLowRankGaussianProcess[_2D, DiscreteImageDomain, EuclideanVector[_2D]]] = {
StatismoIO.readStatismoImageModel[_2D, EuclideanVector[_2D]](file, "/")
}
/**
* Reads a model of 3D deformation fields defined on a 3D image domain
* @param file the file from which the model is read
* @return a 3D deformation model
*/
def readDeformationModel3D(
file: java.io.File
): Try[DiscreteLowRankGaussianProcess[_3D, DiscreteImageDomain, EuclideanVector[_3D]]] = {
StatismoIO.readStatismoImageModel[_3D, EuclideanVector[_3D]](file, "/")
}
/**
* Writes a model of 2D deformation fields defined on a 2D image domain
*
* @param gp the deformation model
* @param file the file to which the model is written
* @return Success if model could be read, Failure otherwise
*/
def writeDeformationModel2D(gp: DiscreteLowRankGaussianProcess[_2D, DiscreteImageDomain, EuclideanVector[_2D]],
file: File): Try[Unit] = {
StatismoIO.writeStatismoImageModel[_2D, EuclideanVector[_2D]](gp, file, "/")
}
/**
* Writes a model of 3D deformation fields defined on a 3D image domain
*
* @param gp the deformation model
* @param file the file to which the model is written
* @return Success if model could be read, Failure otherwise
*/
def writeDeformationModel3D(gp: DiscreteLowRankGaussianProcess[_3D, DiscreteImageDomain, EuclideanVector[_3D]],
file: File): Try[Unit] = {
StatismoIO.writeStatismoImageModel[_3D, EuclideanVector[_3D]](gp, file, "/")
}
/**
* Reads an intensity model defined on a tetrahedral mesh
*
* @param file the file to which the model is written
* @return A try, where the success case holds the model, and the failure case the corresponding exception
*/
def readVolumeMeshIntensityModel3D(
file: File
): Try[DiscreteLowRankGaussianProcess[_3D, TetrahedralMesh, Float]] = {
StatismoIO.readIntensityModel[_3D, TetrahedralMesh, Float](file, "/")
}
/**
* Writes a model of 3D deformation fields defined on a 3D tetrahedral mesh
*
* @param gp the deformation model
* @param file the file to which the model is written
* @return Success if model could be read, Failure otherwise
*/
def writeVolumeMeshIntensityModel3D(gp: DiscreteLowRankGaussianProcess[_3D, TetrahedralMesh, Float],
file: File): Try[Unit] = {
StatismoIO.writeIntensityModel[_3D, TetrahedralMesh, Float](gp, file, "/")
}
/**
* Reads an intensity model defined on an image domain
*
* @param file the file to which the model is written
* @return A try, where the success case holds the model, and the failure case the corresponding exception
*/
def readImageIntensityModel3D(
file: File
): Try[DiscreteLowRankGaussianProcess[_3D, DiscreteImageDomain, Float]] = {
StatismoIO.readStatismoImageModel[_3D, Float](file, "/")
}
/** Writes a model of 3D deformation fields defined on a 3D image domain
*
* @param gp the deformation model
* @param file the file to which the model is written
* @return Success if model could be read, Failure otherwise
*/
def writeImageIntensityModel3D[Domain[D] <: DiscreteImageDomain[D]](
gp: DiscreteLowRankGaussianProcess[_3D, DiscreteImageDomain, Float],
file: File
): Try[Unit] = {
StatismoIO.writeStatismoImageModel[_3D, Float](gp, file, "/")
}
}
