Keep discriminating volumes until all files grouped

InsightSoftwareConsortium · Mar 19, 2024 · f892552 · f892552
1 parent 0775d5b
commit f892552
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Showing 4 changed files with 78 additions and 67 deletions.
diff --git a/packages/dicom/gdcm/discriminate-volume.cxx → packages/dicom/gdcm/gdcmDiscriminateVolume.h b/packages/dicom/gdcm/discriminate-volume.cxx → packages/dicom/gdcm/gdcmDiscriminateVolume.h
@@ -1,3 +1,38 @@
+/*=========================================================================
+
+  Program: GDCM (Grassroots DICOM). A DICOM library
+
+  Copyright (c) 2006-2011 Mathieu Malaterre
+  All rights reserved.
+  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+
+/*=========================================================================
+
+ *  Copyright NumFOCUS
+ *
+ *  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
+ *
+ *         https://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ *  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.
+ *
+ *=========================================================================*/
+
+#ifndef DISCRIMINATE_VOLUME_H
+#define DISCRIMINATE_VOLUME_H
+
 #include "gdcmScanner.h"
 #include "gdcmTesting.h"
 #include "gdcmIPPSorter.h"
@@ -220,45 +255,4 @@ namespace gdcm
 
 } // namespace gdcm
 
-// int main(int argc, char *argv[])
-// {
-//     std::string dir1;
-//     if (argc < 2)
-//     {
-//         const char *extradataroot = nullptr;
-// #ifdef GDCM_BUILD_TESTING
-//         extradataroot = gdcm::Testing::GetDataExtraRoot();
-// #endif
-//         if (!extradataroot)
-//         {
-//             return 1;
-//         }
-//         dir1 = extradataroot;
-//         dir1 += "/gdcmSampleData/ForSeriesTesting/VariousIncidences/ST1";
-//     }
-//     else
-//     {
-//         dir1 = argv[1];
-//     }
-
-//     gdcm::Directory d;
-//     d.Load(dir1, true); // recursive !
-
-//     gdcm::Scanner s;
-//     s.AddTag(gdcm::t1);
-//     s.AddTag(gdcm::t2);
-//     s.AddTag(gdcm::t3);
-//     s.AddTag(gdcm::t4);
-//     bool b = s.Scan(d.GetFilenames());
-//     if (!b)
-//     {
-//         std::cerr << "Scanner failed" << std::endl;
-//         return 1;
-//     }
-
-//     gdcm::DiscriminateVolume dv;
-//     dv.ProcessIntoVolume(s);
-//     dv.Print(std::cout);
-
-//     return 0;
-// }
+#endif // DISCRIMINATE_VOLUME_H
diff --git a/packages/dicom/gdcm/image-sets-normalization.cxx b/packages/dicom/gdcm/image-sets-normalization.cxx
@@ -23,7 +23,7 @@
 #include "rapidjson/stringbuffer.h"
 #include "rapidjson/writer.h"
 
-#include "discriminate-volume.cxx"
+#include "gdcmDiscriminateVolume.h"
 
 int main(int argc, char *argv[])
 {
@@ -37,6 +37,7 @@ int main(int argc, char *argv[])
 
   ITK_WASM_PARSE(pipeline);
 
+  std::vector<gdcm::Directory::FilenamesType> volumes;
   gdcm::Scanner s;
 
   const gdcm::Tag t1(0x0020, 0x000d); // Study Instance UID
@@ -59,18 +60,26 @@ int main(int argc, char *argv[])
   gdcm::DiscriminateVolume dv;
   dv.ProcessIntoVolume(s);
 
-  std::vector<gdcm::Directory::FilenamesType> sortedFiles = dv.GetSortedFiles();
+  std::vector<gdcm::Directory::FilenamesType> sorted = dv.GetSortedFiles();
+  for (gdcm::Directory::FilenamesType &volume : sorted)
+  {
+    volumes.push_back(volume);
+  }
+
+  std::vector<gdcm::Directory::FilenamesType> unsorted = dv.GetUnsortedFiles();
+  for (gdcm::Directory::FilenamesType fileGroups : unsorted)
+  {
+    volumes.push_back(fileGroups);
+  }
 
   rapidjson::Document imageSetsJson;
   rapidjson::Document::AllocatorType &allocator = imageSetsJson.GetAllocator();
   imageSetsJson.SetObject();
 
-  int groupId = 0;
   for (
-      std::vector<gdcm::Directory::FilenamesType>::const_iterator fileNames = sortedFiles.begin();
-      fileNames != sortedFiles.end(); ++fileNames)
+      std::vector<gdcm::Directory::FilenamesType>::const_iterator fileNames = volumes.begin();
+      fileNames != volumes.end(); ++fileNames)
   {
-    groupId++;
     rapidjson::Value sortedFileNameArray(rapidjson::kArrayType);
 
     for (
@@ -83,7 +92,7 @@ int main(int argc, char *argv[])
     }
 
     std::string fileName = fileNames->front();
-    const char* studyInstanceUID = s.GetValue(fileName.c_str(), t1);
+    const char *studyInstanceUID = s.GetValue(fileName.c_str(), t1);
 
     rapidjson::Value groupIdKey(studyInstanceUID, allocator);
     imageSetsJson.AddMember(groupIdKey, sortedFileNameArray, allocator);

diff --git a/...hon/itkwasm-dicom-wasi/itkwasm_dicom_wasi/wasm_modules/image-sets-normalization.wasi.wasm b/...hon/itkwasm-dicom-wasi/itkwasm_dicom_wasi/wasm_modules/image-sets-normalization.wasi.wasm
diff --git a/packages/dicom/python/itkwasm-dicom-wasi/tests/test_image_sets_normalization.py b/packages/dicom/python/itkwasm-dicom-wasi/tests/test_image_sets_normalization.py
@@ -9,29 +9,37 @@ def test_one_series():
         test_input_path / "DicomImageOrientationTest" / "ImageOrientation.1.dcm",
         test_input_path / "DicomImageOrientationTest" / "ImageOrientation.2.dcm",
     ]
-
     assert files[0].exists()
-
     image_sets = image_sets_normalization(files)
-    print(image_sets)
-    # assert image_sets
-
-    assert image_sets == [
+    assert image_sets
+    sorted_files = list(image_sets.values())[0]
+    assert sorted_files == [
         str(files[1]),
         str(files[2]),
         str(files[0]),
     ]
 
-# def test_two_series():
-#     files = [
-#         test_input_path / "DicomImageOrientationTest" / "ImageOrientation.3.dcm",
-#         test_input_path / "DicomImageOrientationTest" / "ImageOrientation.1.dcm",
-#         test_input_path / "DicomImageOrientationTest" / "ImageOrientation.2.dcm",
-#         test_input_path / "dicom-images" / "CT" / "1-1.dcm",
-#         test_input_path / "dicom-images" / "CT" / "1-2.dcm",
-#     ]
-
-#     assert files[0].exists()
+def test_two_series():
+    files = [
+        test_input_path / "DicomImageOrientationTest" / "ImageOrientation.3.dcm",
+        test_input_path / "DicomImageOrientationTest" / "ImageOrientation.1.dcm",
+        test_input_path / "DicomImageOrientationTest" / "ImageOrientation.2.dcm",
+        test_input_path / "dicom-images" / "MR" / "1-001.dcm",
+        test_input_path / "dicom-images" / "MR" / "1-002.dcm",
+        test_input_path / "dicom-images" / "MR" / "1-003.dcm",
+        test_input_path / "dicom-images" / "MR" / "1-004.dcm",
+        test_input_path / "dicom-images" / "MR" / "1-005.dcm",
+    ]
+    assert files[0].exists()
+    image_sets = image_sets_normalization(files)
+    assert image_sets
+    assert len(image_sets.keys()) == 2
 
-#     image_sets = image_sets_normalization(files)
-#     assert image_sets
+def test_strange_ct():
+    files = [
+        test_input_path / "dicom-images" / "CT" / "1-1.dcm",
+        test_input_path / "dicom-images" / "CT" / "1-2.dcm",
+    ]
+    image_sets = image_sets_normalization(files)
+    assert image_sets
+    print(image_sets)