DICOM: better handling of unsupported transfer syntax

core/file/dicom/element.cpp

@@ -20,14 +20,13 @@ namespace MR {
   namespace File {
     namespace Dicom {
 
-      const char* Element::error_message = nullptr;
-
       void Element::set (const std::string& filename, bool force_read, bool read_write)
       {
         group = element = VR = 0;
         size = 0;
         start = data = next = NULL;
         is_BE = is_transfer_syntax_BE = false;
+        transfer_syntax_supported = true;
         parents.clear();
 
         fmap.reset (new File::MMap (filename, read_write));
@@ -158,35 +157,39 @@ namespace MR {
           size = Raw::fetch_<uint32_t> (start+4, is_BE);
         }
 
-
         next = data;
+
         if (size == LENGTH_UNDEFINED) {
-          if (VR != VR_SQ && !(group == GROUP_SEQUENCE && element == ELEMENT_SEQUENCE_ITEM)) {
+          if (VR != VR_SQ && !(group == GROUP_SEQUENCE && element == ELEMENT_SEQUENCE_ITEM)) 
             INFO ("undefined length used for DICOM tag " + ( tag_name().size() ? tag_name().substr (2) : "" )
                 + MR::printf ("(%04X, %04X) in file \"", group, element) + fmap->name() + "\"");
-            size = 0;
-          }
         }
         else if (next+size > fmap->address() + fmap->size())
           throw Exception ("file \"" + fmap->name() + "\" is too small to contain DICOM elements specified");
         else {
           if (size%2)
             DEBUG ("WARNING: odd length (" + str (size) + ") used for DICOM tag " + ( tag_name().size() ? tag_name().substr (2) : "" )
                 + " (" + str (group) + ", " + str (element) + ") in file \"" + fmap->name() + "");
-          if (VR != VR_SQ && ( group != GROUP_SEQUENCE || element != ELEMENT_SEQUENCE_ITEM ) )
-            next += size;
+          if (VR != VR_SQ) {
+            if (group == GROUP_SEQUENCE && element == ELEMENT_SEQUENCE_ITEM) {
+              if (parents.size() && parents.back().group == GROUP_DATA && parents.back().element == ELEMENT_DATA)
+                next += size;
+            }
+            else
+              next += size;
+          }
         }
 
 
 
-        if (parents.size())
+        if (parents.size()) 
           if ((parents.back().end && data > parents.back().end) ||
-              (group == GROUP_SEQUENCE && element == ELEMENT_SEQUENCE_DELIMITATION_ITEM))
+              (group == GROUP_SEQUENCE && element == ELEMENT_SEQUENCE_DELIMITATION_ITEM)) 
             parents.pop_back();
 
-        if (VR == VR_SQ) {
+        if (is_new_sequence()) {
           if (size == LENGTH_UNDEFINED)
-            parents.push_back (Sequence (group, element, NULL));
+            parents.push_back (Sequence (group, element, nullptr));
           else
             parents.push_back (Sequence (group, element, data + size));
         }
@@ -214,10 +217,7 @@ namespace MR {
                   throw Exception ("DICOM deflated explicit VR little endian transfer syntax not supported");
                 }
                 else {
-                  error_message =
-                    "unsupported transfer syntax found in DICOM data\n"
-                    "consider using third-party tools to convert your data to standard uncompressed encoding\n"
-                    "e.g. dcmtk: http://dicom.offis.de/dcmtk.php.en";
+                  transfer_syntax_supported = false;
                   INFO ("unsupported DICOM transfer syntax: \"" + std::string (reinterpret_cast<const char*> (data), size)
                     + "\" in file \"" + fmap->name() + "\"");
                 }
@@ -376,7 +376,7 @@ namespace MR {
         size_t indent = item.level() - ( item.VR == VR_SQ ? 1 : 0 );
         for (size_t i = 0; i < indent; i++)
           tmp += "  ";
-        if (item.VR == VR_SQ)
+        if (item.is_new_sequence())
           tmp += "> ";
         else if (item.group == GROUP_SEQUENCE && item.element == ELEMENT_SEQUENCE_ITEM)
           tmp += "- ";

core/file/dicom/element.h

@@ -55,6 +55,7 @@ namespace MR {
           uint32_t size;
           uint8_t* data;
           vector<Sequence> parents;
+          bool transfer_syntax_supported;
 
           void set (const std::string& filename, bool force_read = false, bool read_write = false);
           bool read ();
@@ -89,6 +90,9 @@ namespace MR {
           bool is_big_endian () const {
             return is_BE;
           }
+          bool is_new_sequence () const {
+            return VR == VR_SQ || ( group == GROUP_DATA && element == ELEMENT_DATA && size == LENGTH_UNDEFINED );
+          }
 
           Type type () const;
           vector<int32_t> get_int () const;
@@ -104,7 +108,6 @@ namespace MR {
                     "----- ---- ---- --  -------  -------   -------------------------------------  ---------------------------------------\n";
           }
 
-          static const char* get_error () { return error_message; }
 
         protected:
 
@@ -118,7 +121,6 @@ namespace MR {
 
           vector<uint8_t*>  end_seq;
 
-          static const char* error_message;
 
           uint16_t get_VR_from_tag_name (const std::string& name) {
             union {

core/file/dicom/image.h

@@ -42,6 +42,7 @@ namespace MR {
             bvalue = G[0] = G[1] = G[2] = NAN;
             data = bits_alloc = data_size = frame_offset = 0;
             DW_scheme_wrt_image = false;
+            transfer_syntax_supported = true;
             pe_axis = 3;
             pe_sign = 0;
             pixel_bandwidth = bandwidth_per_pixel_phase_encode = echo_time = NAN;
@@ -53,7 +54,7 @@ namespace MR {
           default_type distance, pixel_size[2], slice_thickness, slice_spacing, scale_slope, scale_intercept, bvalue;
           size_t data, bits_alloc, data_size, frame_offset;
           std::string filename;
-          bool DW_scheme_wrt_image;
+          bool DW_scheme_wrt_image, transfer_syntax_supported;
           size_t pe_axis;
           int pe_sign;
           default_type pixel_bandwidth, bandwidth_per_pixel_phase_encode, echo_time;

core/file/dicom/mapper.cpp

@@ -60,6 +60,12 @@ 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 ("e.g. dcmtk: http://dicom.offis.de/dcmtk.php.en");
+              throw E;
+            }
             // 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());

core/file/dicom/quick_scan.cpp

@@ -37,6 +37,7 @@ namespace MR {
         series_time.clear();
         sequence.clear();
         series_number = bits_alloc = dim[0] = dim[1] = data = 0;
+        transfer_syntax_supported = true;
 
         Element item;
         try {
@@ -82,6 +83,8 @@ namespace MR {
             }
           }
 
+          transfer_syntax_supported = item.transfer_syntax_supported;
+
         }
         catch (Exception& E) { 
           E.display (3);

core/file/dicom/quick_scan.h

@@ -31,6 +31,7 @@ namespace MR {
           std::string study, study_ID, study_date, study_time;
           std::string series, series_date, series_time, sequence;
           size_t series_number, bits_alloc, dim[2], data;
+          bool transfer_syntax_supported;
       };
 
       std::ostream& operator<< (std::ostream& stream, const QuickScan& file);

core/file/dicom/tree.cpp

@@ -102,6 +102,7 @@ namespace MR {
         image->filename = filename;
         image->series = series.get();
         image->sequence_name = reader.sequence;
+        image->transfer_syntax_supported = reader.transfer_syntax_supported;
         series->push_back (image);
       }
 
@@ -125,14 +126,6 @@ namespace MR {
         if (size() > 0)
           return;
 
-        auto error_msg = Element::get_error();
-        if (error_msg) {
-          auto lines = split_lines (error_msg);
-          Exception E ("unable to read DICOM images in \"" + filename + "\":");
-          for (const auto& line: lines)
-            E.push_back ("  " + line);
-          throw E;
-        }
         throw Exception ("no DICOM images found in \"" + filename + "\"");
       }