ZEISS · ptahmose · Feb 20, 2025 · Feb 20, 2025 · Feb 20, 2025 · Feb 20, 2025
diff --git a/.github/workflows/mega-linter.yml b/.github/workflows/mega-linter.yml
@@ -22,14 +22,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # MegaLinter
       - name: MegaLinter
         id: ml
         # You can override MegaLinter flavor used to have faster performances
         # More info at https://megalinter.io/flavors/
-        uses: oxsecurity/megalinter/flavors/dotnet@v6
+        uses: oxsecurity/megalinter/flavors/dotnet@v7
         env:
           # All available variables are described in documentation
           # https://megalinter.io/configuration/
@@ -38,7 +38,7 @@ jobs:
       # Upload MegaLinter artifacts
       - name: Archive production artifacts
         if: ${{ success() || failure() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: MegaLinter reports
           path: |

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -5,7 +5,7 @@
 cmake_minimum_required(VERSION 3.15)
 
 project(CZICheck 
-      VERSION 0.6.0
+      VERSION 0.6.1
       HOMEPAGE_URL "https://github.com/ZEISS/czicheck"
       DESCRIPTION "CZICheck is a validator for CZI-documents")
 

diff --git a/CZICheck/checkers/schema/ZEN/flatten/ImageMetadata.xsd b/CZICheck/checkers/schema/ZEN/flatten/ImageMetadata.xsd
diff --git a/CZICheck/resultgathererfactory.cpp b/CZICheck/resultgathererfactory.cpp
@@ -23,4 +23,3 @@ std::unique_ptr<IResultGatherer> CreateResultGatherer(const CCmdLineOptions& opt
             throw std::invalid_argument("Unknown output encoding format");
     }
 }
-
diff --git a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.json
@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml b/Test/CZICheckSamples/differentpixeltypeinchannel.txt.xml
@@ -99,6 +99,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/duplicate_coordinates.txt.json b/Test/CZICheckSamples/duplicate_coordinates.txt.json
@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/duplicate_coordinates.txt.xml b/Test/CZICheckSamples/duplicate_coordinates.txt.xml
@@ -99,6 +99,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/edf-missing-texture.txt b/Test/CZICheckSamples/edf-missing-texture.txt
@@ -11,8 +11,8 @@ Test "Basic semantic checks of the XML-metadata" : OK
 Test "validate the XML-metadata against XSD-schema" :
   (101,22): no declaration found for element 'RotationCenter'
   (105,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'
-  (112,21): no declaration found for element 'LookupTables'
-  <3 more findings omitted> 
+  (188,29): attribute 'Id' is not declared for element 'Scaling'
+  <1 more finding omitted> 
  FAIL
 Test "check if subblocks at pyramid-layer 0 of different scenes are overlapping" : OK
 Test "SubBlock-Segments in SubBlockDirectory are valid and valid content" : OK

diff --git a/Test/CZICheckSamples/edf-missing-texture.txt.json b/Test/CZICheckSamples/edf-missing-texture.txt.json
@@ -76,16 +76,6 @@
                     "description": "(105,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'",
                     "details": ""
                 },
-                {
-                    "severity": "FATAL",
-                    "description": "(112,21): no declaration found for element 'LookupTables'",
-                    "details": ""
-                },
-                {
-                    "severity": "FATAL",
-                    "description": "(113,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)'",
-                    "details": ""
-                },
                 {
                     "severity": "FATAL",
                     "description": "(188,29): attribute 'Id' is not declared for element 'Scaling'",
@@ -125,6 +115,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/edf-missing-texture.txt.xml b/Test/CZICheckSamples/edf-missing-texture.txt.xml
@@ -65,16 +65,6 @@
           <Description>(105,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'</Description>
           <Details></Details>
         </Finding>
-        <Finding>
-          <Severity>FATAL</Severity>
-          <Description>(112,21): no declaration found for element 'LookupTables'</Description>
-          <Details></Details>
-        </Finding>
-        <Finding>
-          <Severity>FATAL</Severity>
-          <Description>(113,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)'</Description>
-          <Details></Details>
-        </Finding>
         <Finding>
           <Severity>FATAL</Severity>
           <Description>(188,29): attribute 'Id' is not declared for element 'Scaling'</Description>
@@ -112,6 +102,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.json
@@ -136,6 +136,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml b/Test/CZICheckSamples/edf-superfluous-missing-channel-subblock.txt.xml
@@ -123,6 +123,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/edf-superfluous.txt b/Test/CZICheckSamples/edf-superfluous.txt
@@ -11,8 +11,8 @@ Test "Basic semantic checks of the XML-metadata" : OK
 Test "validate the XML-metadata against XSD-schema" :
   (121,22): no declaration found for element 'RotationCenter'
   (125,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'
-  (139,21): no declaration found for element 'LookupTables'
-  <3 more findings omitted> 
+  (222,29): attribute 'Id' is not declared for element 'Scaling'
+  <1 more finding omitted> 
  FAIL
 Test "check if subblocks at pyramid-layer 0 of different scenes are overlapping" : OK
 Test "SubBlock-Segments in SubBlockDirectory are valid and valid content" : OK

diff --git a/Test/CZICheckSamples/edf-superfluous.txt.json b/Test/CZICheckSamples/edf-superfluous.txt.json
@@ -76,16 +76,6 @@
                     "description": "(125,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'",
                     "details": ""
                 },
-                {
-                    "severity": "FATAL",
-                    "description": "(139,21): no declaration found for element 'LookupTables'",
-                    "details": ""
-                },
-                {
-                    "severity": "FATAL",
-                    "description": "(140,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)'",
-                    "details": ""
-                },
                 {
                     "severity": "FATAL",
                     "description": "(222,29): attribute 'Id' is not declared for element 'Scaling'",
@@ -125,6 +115,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/edf-superfluous.txt.xml b/Test/CZICheckSamples/edf-superfluous.txt.xml
@@ -65,16 +65,6 @@
           <Description>(125,15): element 'RotationCenter' is not allowed for content model 'All(SessionMatrix?,HolderZeissName?,HolderZeissId?,HolderCwsId?,SessionCount?,SessionRotationAtStart?,CustomAttributes?)'</Description>
           <Details></Details>
         </Finding>
-        <Finding>
-          <Severity>FATAL</Severity>
-          <Description>(139,21): no declaration found for element 'LookupTables'</Description>
-          <Details></Details>
-        </Finding>
-        <Finding>
-          <Severity>FATAL</Severity>
-          <Description>(140,12): element 'LookupTables' is not allowed for content model 'All(SizeX?,SizeY?,SizeC?,SizeZ?,SizeT?,SizeH?,SizeR?,SizeV?,SizeS?,SizeI?,SizeM?,SizeB?,PixelType?,ComponentBitCount?,OriginalScanData?,AcquisitionDateAndTime?,AcquisitionDuration?,OriginalCompressionMethod?,OriginalEncodingQuality?,OriginalCompressionParameters?,CurrentCompressionParameters?,Dimensions?,MicroscopeRef?,MicroscopeSettings?,ObjectiveSettings?,TubeLenses?,Specimen?,Session?,SpatialRelations?,CustomAttributes?)'</Description>
-          <Details></Details>
-        </Finding>
         <Finding>
           <Severity>FATAL</Severity>
           <Description>(222,29): attribute 'Id' is not declared for element 'Scaling'</Description>
@@ -112,6 +102,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/inconsistent_coordinates.txt.json b/Test/CZICheckSamples/inconsistent_coordinates.txt.json
@@ -112,6 +112,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/inconsistent_coordinates.txt.xml b/Test/CZICheckSamples/inconsistent_coordinates.txt.xml
@@ -99,6 +99,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/invalid_componentbitcount.txt.json b/Test/CZICheckSamples/invalid_componentbitcount.txt.json
@@ -94,6 +94,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/invalid_componentbitcount.txt.xml b/Test/CZICheckSamples/invalid_componentbitcount.txt.xml
@@ -81,6 +81,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.json
@@ -100,6 +100,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_pixeltype.txt.xml
@@ -87,6 +87,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.json
@@ -100,6 +100,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml b/Test/CZICheckSamples/jpgxrcompressed_inconsistent_size.txt.xml
@@ -87,6 +87,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.json
@@ -100,6 +100,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml b/Test/CZICheckSamples/layer_0_subblocks_with_no_m_index.txt.xml
@@ -87,6 +87,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/negative_plane_start_index.txt.json b/Test/CZICheckSamples/negative_plane_start_index.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/negative_plane_start_index.txt.xml b/Test/CZICheckSamples/negative_plane_start_index.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/overlapping_scenes.txt.json b/Test/CZICheckSamples/overlapping_scenes.txt.json
@@ -136,6 +136,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/overlapping_scenes.txt.xml b/Test/CZICheckSamples/overlapping_scenes.txt.xml
@@ -123,6 +123,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.json
@@ -181,6 +181,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml b/Test/CZICheckSamples/pixeltype_mismatch_between_metadata_and_subblocks.txt.xml
@@ -168,6 +168,6 @@
   <AggregatedResult>FAIL</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/positive_plane_start_index.txt.json b/Test/CZICheckSamples/positive_plane_start_index.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/positive_plane_start_index.txt.xml b/Test/CZICheckSamples/positive_plane_start_index.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
diff --git a/Test/CZICheckSamples/sparse_planes.txt.json b/Test/CZICheckSamples/sparse_planes.txt.json
@@ -105,6 +105,6 @@
     ],
     "output_version": {
         "command": "CZICheck",
-        "version": "0.6.0"
+        "version": "0.6.1"
     }
 }
diff --git a/Test/CZICheckSamples/sparse_planes.txt.xml b/Test/CZICheckSamples/sparse_planes.txt.xml
@@ -92,6 +92,6 @@
   <AggregatedResult>WARN</AggregatedResult>
   <OutputVersion>
     <Command>CZICheck</Command>
-    <Version>0.6.0</Version>
+    <Version>0.6.1</Version>
   </OutputVersion>
 </TestResults>
Original file line number	Diff line number	Diff line change
Expand Up		@@ -23,4 +23,3 @@ std::unique_ptr<IResultGatherer> CreateResultGatherer(const CCmdLineOptions& opt
		throw std::invalid_argument("Unknown output encoding format");
		}
		}