public Option <Scan> Read(ScanFile scanFile)
{
{
using var scan = Hdf.Open(scanFile.Filepath);
if (scan.FileIdentifier < 0L)
{
return(Optional.None <Scan>($"The scan file at '{scanFile.Filepath}' does not exist or is not a valid HDF document"));
}
var outcome = Optional.Some();
var regions = new List <Region>();
scan.IterateGroup("/entry1/instrument", (n, t, _) =>
{
foreach (var __ in outcome)
{
if (t == ObjectType.Group)
{
var energies = scan.GetData <double>($"/entry1/instrument/{n}/energies");
if (energies != null)
{
// Starting energy value (energies), counts / creation time Unix (image_data)
energies.Value.FirstOrNone("The 'energies' array must contain at least one value")
.FlatMap(sev => scan.GetData <double>($"/entry1/instrument/{n}/image_data").SomeNotNull("Region must contain dataset 'image_data'")
.Filter(id => id.ChangeTime.HasValue, "Dataset 'image_data' does not specify a change time")
.Map(id => new
{
StartingEnergyValue = sev,
CreationTimeUnix = id.ChangeTime.Value,
ImageData = id.Value
}))
// Excitation energy (excitation_energy)
.FlatMap(d => scan.GetData <double>($"/entry1/instrument/{n}/excitation_energy").Value.SingleOrNone("The 'excitation_energy' array must contain exactly one value")
.FlatMap(ee =>
{
try
{
return(Optional.Some(Convert.ToUInt16(ee)));
}
catch
{
return(Optional.None <ushort>($"Excitation energy value must be convertible to a 16-bit unsigned integer (was {ee})"));
}
})
.Map(ee => new
{
d.StartingEnergyValue,
d.CreationTimeUnix,
d.ImageData,
ExcitationEnergy = ee
})
)
// Step time (step_time)
.FlatMap(d => scan.GetData <double>($"/entry1/instrument/{n}/step_time").SomeNotNull("Region must contain dataset 'step_time'")
.FlatMap(st => st.Value.SingleOrNone("The 'step_time' array must contain exactly one value"))
.Map(st => new
{
d.StartingEnergyValue,
d.CreationTimeUnix,
d.ImageData,
d.ExcitationEnergy,
StepTime = st
}))
// Energy step (energy_step)
.FlatMap(d => scan.GetData <double>($"/entry1/instrument/{n}/energy_step").SomeNotNull("Region must contain dataset 'energy_step'")
.FlatMap(es => es.Value.SingleOrNone("The 'energy_step' array must contain exactly one value"))
.Map(es => new
{
d.StartingEnergyValue,
d.CreationTimeUnix,
d.ImageData,
d.ExcitationEnergy,
d.StepTime,
EnergyStep = es
}))
// Energy mode (energy_mode)
.FlatMap(d => scan.GetString($"/entry1/instrument/{n}/energy_mode").SomeNotNull("Region must contain dataset 'energy_mode'")
.Map(em => new
{
d.StartingEnergyValue,
d.CreationTimeUnix,
d.ImageData,
d.ExcitationEnergy,
d.StepTime,
d.EnergyStep,
EnergyMode = em
}))
.FlatMap(d => Region.Create(n, d.CreationTimeUnix, d.StartingEnergyValue, d.ImageData, d.ExcitationEnergy, d.StepTime, d.EnergyStep, d.EnergyMode))
.Match(
some: r => regions.Add(r),
none: e => outcome = Optional.None(Error.Create($"Failed to read region '{n}' in file '{scanFile.Filename}'").CausedBy(e))
);
}
}
}
});
return(outcome.FlatMap(() => Scan.Create(scanFile, regions)));
}
}
public Option <Scan> Read(string filepath)
{
return(ScanFile.Create(filepath).FlatMap(Read));
}
