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Subsequent feature: Modularized asm IO as proposed in scalismo #2

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Subsequent feature: Modularized asm IO as proposed in scalismo #2

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89 changes: 52 additions & 37 deletions src/main/scala/scalismo/asm/io/ActiveShapeModelIO.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -13,25 +13,19 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package scalismo.asm.io
package scalismo.io
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So far everything in scalismo-asm is in the scalismo.asm. package. Same for vtk. We can also change it everywhere to be part of scalismo itself as that would make less changes for people updating from scalismo 0.x.
Just need to be consistent.


import java.io.{File, IOException}
import breeze.linalg.{DenseMatrix, DenseVector}
import io.jhdf.api.Group
import scalismo.asm.statisticalmodel.{
ActiveShapeModel,
FeatureExtractorIOHandlers,
ImagePreprocessorIOHandlers,
Profile,
Profiles
}
import scalismo.common.PointId
import scalismo.geometry._3D
import scalismo.hdf5json.{FloatArray1D, HDFPath, IntArray1D}
import scalismo.io.statisticalmodel.*
import scalismo.io.statisticalmodel.{HDF5Writer, NDArray, StatismoIO, StatisticalModelIOUtils, StatisticalModelReader}
import scalismo.mesh.TriangleMesh
import scalismo.statisticalmodel.{MultivariateNormalDistribution, PointDistributionModel, StatisticalMeshModel}
import scalismo.statisticalmodel.asm.*

import java.io.{File, IOException}
import scala.collection.immutable
import scala.util.{Failure, Success, Try}

Expand All @@ -40,7 +34,7 @@ object ActiveShapeModelIO {
object Names {

object Group {
val ActiveShapeModel = "/activeShapeModel"
val ActiveShapeModel = "activeShapeModel"
val FeatureExtractor = "featureExtractor"
val ImagePreprocessor = "imagePreprocessor"
val Profiles = "profiles"
Expand All @@ -61,24 +55,38 @@ object ActiveShapeModelIO {
}

}

def writeActiveShapeModel(asm: ActiveShapeModel, file: File): Try[Unit] = {
for {
h5file <- StatisticalModelIOUtils.createFile(file)
_ <- writeAcitveShapeModel(asm, h5file, HDFPath("/"))
_ <- Try(h5file.close())
} yield ()
}

private[io] def writeAcitveShapeModel(asm: ActiveShapeModel, h5file: HDF5Writer, path: HDFPath): Try[Unit] = {
val pointModel = PointDistributionModel[_3D, TriangleMesh](asm.statisticalModel.gp)

for {
_ <- StatismoIO.writeStatismoPDM(pointModel, h5file, path)
_ <- writeAppearanceModel(asm, h5file, path)
_ <- h5file.write()
} yield ()
}

private def writeAppearanceModel(asm: ActiveShapeModel, h5file: HDF5Writer, path: HDFPath): Try[Unit] = {
val asmPath = HDFPath(path, Names.Group.ActiveShapeModel)
val fePath = HDFPath(asmPath, Names.Group.FeatureExtractor)
val ppPath = HDFPath(asmPath, Names.Group.ImagePreprocessor)
val profilesPath = HDFPath(asmPath, Names.Group.Profiles)

for {
_ <- StatismoIO.writeStatismoPDM(pointModel, file)
h5 <- StatisticalModelIOUtils.openFileForWriting(file)
asmPath = HDFPath(Names.Group.ActiveShapeModel)
fePath = HDFPath(asmPath, Names.Group.FeatureExtractor)
ppPath = HDFPath(asmPath, Names.Group.ImagePreprocessor)
profilesPath = HDFPath(asmPath, Names.Group.Profiles)
// for now, the version information is fixed to 1.0
_ <- h5.writeIntAttribute(asmPath, Names.Attribute.MajorVersion, 1)
_ <- h5.writeIntAttribute(asmPath, Names.Attribute.MinorVersion, 0)
_ <- ImagePreprocessorIOHandlers.save(asm.preprocessor, h5, ppPath)
_ <- FeatureExtractorIOHandlers.save(asm.featureExtractor, h5, fePath)
_ <- writeProfiles(h5, profilesPath, asm.profiles)
_ <- h5.write()
_ <- h5file.writeIntAttribute(asmPath, Names.Attribute.MajorVersion, 1)
_ <- h5file.writeIntAttribute(asmPath, Names.Attribute.MinorVersion, 0)
_ <- ImagePreprocessorIOHandlers.save(asm.preprocessor, h5file, ppPath)
_ <- FeatureExtractorIOHandlers.save(asm.featureExtractor, h5file, fePath)
_ <- writeProfiles(h5file, profilesPath, asm.profiles)
_ <- h5file.write()
} yield ()
}

Expand All @@ -87,11 +95,11 @@ object ActiveShapeModelIO {
val numberOfPoints = profiles.data.length
val profileLength = if (numberOfPoints > 0) profiles.data.head.distribution.mean.size else 0
val means: NDArray[Float] = new NDArray(IndexedSeq[Long](numberOfPoints, profileLength),
profiles.data.flatMap(_.distribution.mean.toArray).toArray.map(_.toFloat)
profiles.data.flatMap(_.distribution.mean.toArray).toArray.map(_.toFloat)
)
val covariances: NDArray[Float] =
new NDArray(IndexedSeq[Long](numberOfPoints * profileLength, profileLength),
profiles.data.flatMap(_.distribution.cov.toArray).toArray.map(_.toFloat)
profiles.data.flatMap(_.distribution.cov.toArray).toArray.map(_.toFloat)
)

val result = for {
Expand All @@ -110,10 +118,24 @@ object ActiveShapeModelIO {
}.flatten

def readActiveShapeModel(fn: File): Try[ActiveShapeModel] = {
val modelPath = HDFPath("/")
for {
pdm <- StatismoIO.readStatismoPDM[_3D, TriangleMesh](fn)
modelReader <- StatisticalModelIOUtils.openFileForReading(fn)
asmPath = HDFPath(Names.Group.ActiveShapeModel)
pointModel <- StatismoIO.readStatismoPDM[_3D, TriangleMesh](modelReader, modelPath)
model <- readActiveShapeModel(modelReader, modelPath, pointModel)
} yield model
}

private[io] def readActiveShapeModel(modelReader: StatisticalModelReader,
modelPath: HDFPath,
pdm: PointDistributionModel[_3D, TriangleMesh]
): Try[ActiveShapeModel] = {
val asmPath = HDFPath(Names.Group.ActiveShapeModel)
val fePath = HDFPath(asmPath, Names.Group.FeatureExtractor)
val ppPath = HDFPath(asmPath, Names.Group.ImagePreprocessor)
val profilesGroup = HDFPath(asmPath, Names.Group.Profiles)

for {
asmVersionMajor <- modelReader.readIntAttribute(asmPath, Names.Attribute.MajorVersion)
asmVersionMinor <- modelReader.readIntAttribute(asmPath, Names.Attribute.MinorVersion)
_ <- {
Expand All @@ -122,23 +144,16 @@ object ActiveShapeModelIO {
case _ => Failure(new IOException(s"Unsupported ActiveShapeModel version: $asmVersionMajor.$asmVersionMinor"))
}
}
fePath = HDFPath(asmPath, Names.Group.FeatureExtractor)
ppPath = HDFPath(asmPath, Names.Group.ImagePreprocessor)
preprocessor <- ImagePreprocessorIOHandlers.load(modelReader, ppPath)
profilesGroup = HDFPath(asmPath, Names.Group.Profiles)
featureExtractor <- FeatureExtractorIOHandlers.load(modelReader, fePath)
profiles <- readProfiles(modelReader, profilesGroup, pdm.reference)
} yield {
val shapeModel = PointDistributionModel(pdm.gp)
ActiveShapeModel(shapeModel, profiles, preprocessor, featureExtractor)
}

} yield ActiveShapeModel(pdm, profiles, preprocessor, featureExtractor)
}

private[this] def readProfiles(modelReader: StatisticalModelReader,
path: HDFPath,
referenceMesh: TriangleMesh[_3D]
): Try[Profiles] = {
): Try[Profiles] = {

for {
profileLength <- modelReader.readIntAttribute(path, Names.Attribute.ProfileLength)
Expand Down