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JobMetadataBuilderFactory.cs
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JobMetadataBuilderFactory.cs
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/*
* Apache License, Version 2.0
* Copyright 2021 NVIDIA Corporation
*
* 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.
*/
using Ardalis.GuardClauses;
using Dicom;
using Microsoft.Extensions.Logging;
using Nvidia.Clara.DicomAdapter.Common;
using System;
using System.Collections.Generic;
using System.Diagnostics;
using System.Linq;
namespace Nvidia.Clara.DicomAdapter.API
{
public interface IJobMetadataBuilderFactory
{
JobMetadataBuilder Build(bool uploadMetadata, IReadOnlyList<string> dicomTags, IReadOnlyList<string> files);
}
public class JobMetadataBuilderFactory : IJobMetadataBuilderFactory
{
private const int VALUE_LENGTH_LIMIT = 256;
private readonly ILogger<JobMetadataBuilderFactory> _logger;
private readonly IDicomToolkit _dicomToolkit;
public JobMetadataBuilderFactory(ILogger<JobMetadataBuilderFactory> logger, IDicomToolkit dicomToolkit)
{
_logger = logger ?? throw new ArgumentNullException(nameof(logger));
_dicomToolkit = dicomToolkit ?? throw new ArgumentNullException(nameof(dicomToolkit));
}
public JobMetadataBuilder Build(bool uploadMetadata, IReadOnlyList<string> dicomTags, IReadOnlyList<string> files)
{
Guard.Against.Null(files, nameof(files));
var metadata = new JobMetadataBuilder();
metadata.AddInstanceCount(files.Count);
if (!uploadMetadata || dicomTags.IsNullOrEmpty())
{
return metadata;
}
var stopwatch = new Stopwatch();
stopwatch.Start();
var dicomTagsToExtract = ConvertToDicomTags(dicomTags);
var uniqueBags = ExtractValues(dicomTagsToExtract, files);
foreach (var tag in uniqueBags.Keys)
{
AddToMetadataDictionary(metadata, tag, uniqueBags[tag].ToList());
}
stopwatch.Stop();
_logger.Log(LogLevel.Debug, $"Metadata built with {dicomTags.Count} DICOM tags and {files.Count} files in {stopwatch.ElapsedMilliseconds}ms.");
return metadata;
}
private void AddToMetadataDictionary(JobMetadataBuilder metadata, DicomTag dicomTag, IList<string> values)
{
Guard.Against.Null(metadata, nameof(metadata));
Guard.Against.Null(values, nameof(values));
if (values.Count() == 0)
{
return;
}
else if (values.Count() == 1)
{
metadata.Add($"{dicomTag.Group:X4}{dicomTag.Element:X4}", values.First());
}
else
{
for (var i = 0; i < values.Count(); i++)
{
metadata.Add($"{dicomTag.Group:X4}{dicomTag.Element:X4}-{i}", values.ElementAt(i));
}
}
}
private Dictionary<DicomTag, HashSet<string>> ExtractValues(List<DicomTag> dicomTagsToExtract, IReadOnlyList<string> files)
{
Guard.Against.Null(dicomTagsToExtract, nameof(dicomTagsToExtract));
Guard.Against.Null(files, nameof(files));
var bags = new Dictionary<DicomTag, HashSet<string>>();
foreach (var dicomTag in dicomTagsToExtract)
{
if (!bags.ContainsKey(dicomTag))
{
bags.Add(dicomTag, new HashSet<string>());
}
}
foreach (var file in files)
{
DicomFile dicomFile = null;
try
{
if (!_dicomToolkit.HasValidHeader(file))
{
continue;
}
dicomFile = _dicomToolkit.Open(file);
}
catch (Exception ex)
{
_logger.Log(LogLevel.Debug, ex, $"Error opening file {file}.");
continue;
}
foreach (var dicomTag in dicomTagsToExtract)
{
try
{
if (_dicomToolkit.TryGetString(dicomFile, dicomTag, out var value) &&
!string.IsNullOrWhiteSpace(value))
{
bags[dicomTag].Add(value.Substring(0, Math.Min(value.Length, VALUE_LENGTH_LIMIT)));
}
}
catch (Exception ex)
{
_logger.Log(LogLevel.Error, ex, $"Error extracting metadata from file {file}, DICOM tag {dicomTag}.");
}
}
}
return bags;
}
private List<DicomTag> ConvertToDicomTags(IReadOnlyList<string> metadata)
{
Guard.Against.Null(metadata, nameof(metadata));
var list = new List<DicomTag>();
foreach (var tag in metadata)
{
// Validation already done in ConfigurationValidator.
list.Add(DicomTag.Parse(tag));
_logger.Log(LogLevel.Debug, $"DICOM Tag added for metadata extraction: {tag}");
}
return list;
}
}
}