DICOM: add null imageIO handler to allow parsing of DICOM data even with unsupported transfer syntax

core/file/dicom/mapper.cpp

@@ -18,6 +18,7 @@
 
 #include "header.h"
 #include "phase_encoding.h"
+#include "image_io/null.h"
 #include "image_io/default.h"
 #include "image_io/mosaic.h"
 #include "image_io/variable_scaling.h"
@@ -68,6 +69,8 @@ namespace MR {
         // build up sorted list of frames:
         vector<Frame*> frames;
 
+        bool transfer_syntax_supported = true;
+
         // loop over series list:
         for (const auto& series_it : series) {
           try {
@@ -82,13 +85,9 @@ namespace MR {
 
           // loop over images in each series:
           for (auto image_it : *series_it) {
-            if (!image_it->transfer_syntax_supported) {
-              Exception E ("unsupported transfer syntax found in DICOM data");
-              E.push_back ("consider using third-party tools to convert your data to standard uncompressed encoding");
-              E.push_back ("See the MRtrix3 documentation on DICOM handling for details:");
-              E.push_back ("   http://mrtrix.readthedocs.io/en/latest/tips_and_tricks/dicom_handling.html#error-unsupported-transfer-syntax");
-              throw E;
-            }
+            if (!image_it->transfer_syntax_supported)
+              transfer_syntax_supported = false;
+
             // if multi-frame, loop over frames in image:
             if (image_it->frames.size()) {
               std::sort (image_it->frames.begin(), image_it->frames.end(), compare_ptr_contents());
@@ -209,7 +208,7 @@ namespace MR {
         }
 
         size_t nchannels = image.samples_per_pixel;
-        if (nchannels == 1 && !image.frames.size()) {
+        if (nchannels == 1 && !image.frames.size() && transfer_syntax_supported) {
           // only guess number of samples per pixel if not explicitly set in
           // DICOM and not using multi-frame:
           nchannels = image.data_size / (frame.dim[0] * frame.dim[1] * (frame.bits_alloc/8));
@@ -363,6 +362,16 @@ namespace MR {
         }
 
 
+        if (!transfer_syntax_supported) {
+          WARN ("unsupported transfer syntax found in DICOM data");
+          WARN ("consider using third-party tools to convert your data to standard uncompressed encoding");
+          WARN ("See the MRtrix3 documentation on DICOM handling for details:");
+          WARN ("   http://mrtrix.readthedocs.io/en/latest/tips_and_tricks/dicom_handling.html#error-unsupported-transfer-syntax");
+
+          io_handler.reset (new MR::ImageIO::Null (H));
+          return io_handler;
+        }
+
         if (image.images_in_mosaic) {
 
           INFO ("DICOM image \"" + H.name() + "\" is in mosaic format");

core/image_io/null.cpp

@@ -0,0 +1,34 @@
+/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * Covered Software is provided under this License on an "as is"
+ * basis, without warranty of any kind, either expressed, implied, or
+ * statutory, including, without limitation, warranties that the
+ * Covered Software is free of defects, merchantable, fit for a
+ * particular purpose or non-infringing.
+ * See the Mozilla Public License v. 2.0 for more details.
+ *
+ * For more details, see http://www.mrtrix.org/.
+ */
+
+#include "image_io/null.h"
+#include "header.h"
+
+namespace MR {
+  namespace ImageIO {
+
+    void Null::load(const Header &header, size_t) {
+      throw Exception("No suitable handler to access data in \"" + header.name() +
+          "\"");
+    }
+
+    void Null::unload(const Header &header) {
+      throw Exception("No suitable handler to access data in \"" + header.name() +
+          "\"");
+    }
+
+  } // namespace ImageIO
+} // namespace MR

core/image_io/null.h

@@ -0,0 +1,38 @@
+/* Copyright (c) 2008-2023 the MRtrix3 contributors.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * Covered Software is provided under this License on an "as is"
+ * basis, without warranty of any kind, either expressed, implied, or
+ * statutory, including, without limitation, warranties that the
+ * Covered Software is free of defects, merchantable, fit for a
+ * particular purpose or non-infringing.
+ * See the Mozilla Public License v. 2.0 for more details.
+ *
+ * For more details, see http://www.mrtrix.org/.
+ */
+
+#ifndef __image_io_null_h__
+#define __image_io_null_h__
+
+#include "image_io/base.h"
+
+namespace MR {
+  namespace ImageIO {
+
+    class Null : public Base {
+      NOMEMALIGN
+      public:
+        Null(const Header &header) : Base(header) {}
+
+      protected:
+        virtual void load(const Header &, size_t);
+        virtual void unload(const Header &);
+    };
+
+  } // namespace ImageIO
+} // namespace MR
+
+#endif