Add check for stored sizes in parsing (#103)

* added enum constant and check for stored sizes for dims other than x,y,m. * added to lax parsing. * clean-up. * clean-up and review comments. * ouput corrected. * added unit test, output correction * updated version. * added entry for verison history. * changed test data to restore test coverage.
ZEISS · Jun 20, 2024 · dedfa6e · dedfa6e
1 parent 067f3b0
commit dedfa6e
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Showing 5 changed files with 251 additions and 6 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,7 +3,7 @@ cmake_minimum_required(VERSION 3.15)
 cmake_policy(SET CMP0091 NEW) # enable new "MSVC runtime library selection" (https://cmake.org/cmake/help/latest/variable/CMAKE_MSVC_RUNTIME_LIBRARY.html)
 
 project(libCZI 
-      VERSION 0.58.4
+      VERSION 0.59.0
       HOMEPAGE_URL "https://github.com/ZEISS/libczi"
       DESCRIPTION "libCZI is an Open Source Cross-Platform C++ library to read and write CZI")
 

diff --git a/Src/libCZI/CziParse.cpp b/Src/libCZI/CziParse.cpp
@@ -573,6 +573,21 @@ using namespace libCZI;
         {
             libCZI::DimensionIndex dim = CCZIParse::DimensionCharToDimensionIndex(subBlkDirDV->DimensionEntries[i].Dimension, 4);
             entry.coordinate.Set(dim, subBlkDirDV->DimensionEntries[i].Start);
+
+            if(options.GetPhysicalDimensionOtherThanMMustHaveSizeOne())
+            { 
+                auto physicalSize = subBlkDirDV->DimensionEntries[i].StoredSize;
+                if(physicalSize != 1)
+                {
+                    stringstream string_stream;
+                    string_stream 
+                            << "Physical size for dimension '" << Utils::DimensionToChar(dim)
+                            << "' is expected to be 1, but found " << physicalSize
+                            << " (file-offset:" << subBlkDirDV->FilePosition << ").";
+                    throw LibCZICZIParseException(string_stream.str().c_str(), LibCZICZIParseException::ErrorCode::NonConformingSubBlockDimensionEntry);
+                }
+            }
+
             if (options.GetDimensionOtherThanMMustHaveSizeOne() && subBlkDirDV->DimensionEntries[i].Size != 1)
             {
                 stringstream string_stream;

diff --git a/Src/libCZI/CziParse.h b/Src/libCZI/CziParse.h
@@ -33,6 +33,7 @@ class CCZIParse
         {
             kDimensionXyMustBePresent = 0,
             kDimensionOtherThanMMustHaveSizeOne,
+            kPhysicalDimensionOtherThanMMustHaveSizeOne,
             kDimensionMMustHaveSizeOneExceptForPyramidSubblocks,
             kDimensionMMustHaveSizeOne,
 
@@ -45,11 +46,16 @@ class CCZIParse
         /// \param  enable  True to enable, false to disable.
         void SetDimensionXyMustBePresent(bool enable) { return this->SetFlag(ParseFlags::kDimensionXyMustBePresent, enable); }
 
+        /// Require that for each subblock the physical size (for all dimensions other than X, Y and M) is "1".
+        ///
+        /// \param  enable  True to enable, false to disable.
+        void SetPhysicalDimensionOtherThanMMustHaveSizeOne(bool enable) { return this->SetFlag(ParseFlags::kPhysicalDimensionOtherThanMMustHaveSizeOne, enable); }
+
         /// Require that for each subblock the size (for all dimensions other than X, Y and M) is "1".
         ///
         /// \param  enable  True to enable, false to disable.
-        void SetDimensionOtherThanMMustHaveSizeOne(bool enable) { return this->SetFlag(ParseFlags::kDimensionOtherThanMMustHaveSizeOne, enable); }
 
+        void SetDimensionOtherThanMMustHaveSizeOne(bool enable) { return this->SetFlag(ParseFlags::kDimensionOtherThanMMustHaveSizeOne, enable); }
         /// Require that for all subblocks that the size of dimension M is "1" except for pyramid subblocks.
         ///
         /// \param  enable  True to enable, false to disable.
@@ -70,6 +76,11 @@ class CCZIParse
         /// \returns    True if it is to be checked that the size of all dimensions other than X, Y and M is "1" for each subblock; false otherwise.
         bool GetDimensionOtherThanMMustHaveSizeOne() const { return this->GetFlag(ParseFlags::kDimensionOtherThanMMustHaveSizeOne); }
 
+        /// Gets a boolean indicating whether to check that the physical size of all dimensions other than X, Y and M is "1" for each subblock.
+        ///
+        /// \returns    True if it is to be checked that the physical size of all dimensions other than X, Y and M is "1" for each subblock; false otherwise.
+        bool GetPhysicalDimensionOtherThanMMustHaveSizeOne() const { return this->GetFlag(ParseFlags::kPhysicalDimensionOtherThanMMustHaveSizeOne); }
+
         /// Gets a boolean indicating whether to check that the size is "1" for dimension M for all non-pyramid-subblocks.
         /// This flag is more specific than the flag "DimensionMMustHaveSizeOne".
         ///
@@ -86,13 +97,15 @@ class CCZIParse
         {
             this->SetDimensionXyMustBePresent(false);
             this->SetDimensionOtherThanMMustHaveSizeOne(false);
+            this->SetPhysicalDimensionOtherThanMMustHaveSizeOne(false);
             this->SetDimensionMMustHaveSizeOne(false);
         }
 
         /// Sets strict parsing - all options are enabled.
         void SetStrictParsing()
         {
             this->SetDimensionXyMustBePresent(true);
+            this->SetPhysicalDimensionOtherThanMMustHaveSizeOne(true);
             this->SetDimensionOtherThanMMustHaveSizeOne(true);
             this->SetDimensionMMustHaveSizeOne(true);
         }

diff --git a/Src/libCZI/Doc/version-history.markdown b/Src/libCZI/Doc/version-history.markdown
@@ -20,4 +20,5 @@ version history                 {#version_history}
  0.58.1             | [95](https://github.com/ZEISS/libczi/pull/95)        | some fixes for CziReaderWriter
  0.58.2             | [96](https://github.com/ZEISS/libczi/pull/96)        | small fixes for deficiencies reported by CodeQL
  0.58.3             | [97](https://github.com/ZEISS/libczi/pull/97)        | update zstd to [version 1.5.6](https://github.com/facebook/zstd/releases/tag/v1.5.6)
- 0.58.4             | [99](https://github.com/ZEISS/libczi/pull/99)        | fix a rare issue with curl_http_inputstream which would fail to read CZIs with an attachment-directory containing zero entries
+ 0.58.4             | [99](https://github.com/ZEISS/libczi/pull/99)        | fix a rare issue with curl_http_inputstream which would fail to read CZIs with an attachment-directory containing zero entries
+ 0.59.0             | [99](https://github.com/ZEISS/libczi/pull/103)        | add a check for physical size for dimensions other than X,Y,M, they must not be >1, active for strict parsing.