Fix tiff writing bugs (out of order tiff tags)

Signed-off-by: Michael Jackson <[email protected]>

Source/Apps/generate_ipf_legends.cpp

@@ -339,6 +339,39 @@ int main(int argc, char* argv[])
 
   std::stringstream ss;
   int imageDim = 512;
+  {
+    TrigonalOps ops;
+    auto legend = ops.generateIPFTriangleLegend(imageDim, true);
+    ss.str("");
+    ss << k_Output_Dir << "/" << EbsdStringUtils::replace(ops.getSymmetryName(), "/", "_") << "/" << EbsdStringUtils::replace(ops.getSymmetryName(), "/", "_") << "_FULL.tiff";
+    auto result = TiffWriter::WriteColorImage(ss.str(), imageDim, imageDim, 3, legend->getPointer(0));
+    std::cout << ops.getSymmetryName() << " Result: " << result.first << ": " << result.second << std::endl;
+
+    legend = ops.generateIPFTriangleLegend(imageDim, false);
+    int xStart = imageDim * 0.05F;
+    int yStart = 0;
+    int numCols = imageDim * 0.75F;
+    int numRows = imageDim * 0.65F;
+    legend = EbsdLib::CropRGBImage<uint8_t>(legend, imageDim, imageDim, xStart, yStart, numCols, numRows);
+    ss.str("");
+    ss << k_Output_Dir << "/" << EbsdStringUtils::replace(ops.getSymmetryName(), "/", "_") << "/" << EbsdStringUtils::replace(ops.getSymmetryName(), "/", "_") << ".tiff";
+    result = TiffWriter::WriteColorImage(ss.str(), numCols, numRows, 3, legend->getPointer(0));
+    std::cout << ops.getSymmetryName() << " Result: " << result.first << ": " << result.second << std::endl;
+
+    std::vector<FloatVec3Type> referenceDirections = {
+        {0.0F, 0.0F, 1.0F},                    // Red  DONE
+        {0.0F, 1.0F, 0.0F},                    // Green
+        {-0.5F, std::sqrt(3.0F) / 2.0F, 0.0F}, // Aqua
+        {2.0F, 1.0F, 0.0F},                    // Blue
+        {0.0F, 1.0F, -1.0F},                   // Yellow  DONE
+        {1.0F, -1.0F, 1.0F},                   // Pink  DONE
+        {1.0F, 0.0F, 1.0F},                    // Flesh
+    };
+    std::vector<std::string> colorNames{"Red", "Green", "Aqua", "Blue", "Yellow", "Pink", "Flesh"};
+    GenerateTestIPFImages(referenceDirections, colorNames, 10);
+    // Generate Pole Figures for the Input Test Orientations
+    GeneratePoleFigures(ops, 2);
+  }
 
   {
     TriclinicOps ops;
@@ -630,40 +663,6 @@ int main(int argc, char* argv[])
     GeneratePoleFigures(ops, 2);
   }
 
-  {
-    TrigonalOps ops;
-    auto legend = ops.generateIPFTriangleLegend(imageDim, true);
-    ss.str("");
-    ss << k_Output_Dir << "/" << EbsdStringUtils::replace(ops.getSymmetryName(), "/", "_") << "/" << EbsdStringUtils::replace(ops.getSymmetryName(), "/", "_") << "_FULL.tiff";
-    auto result = TiffWriter::WriteColorImage(ss.str(), imageDim, imageDim, 3, legend->getPointer(0));
-    std::cout << ops.getSymmetryName() << " Result: " << result.first << ": " << result.second << std::endl;
-
-    legend = ops.generateIPFTriangleLegend(imageDim, false);
-    int xStart = imageDim * 0.05F;
-    int yStart = 0;
-    int numCols = imageDim * 0.75F;
-    int numRows = imageDim * 0.65F;
-    legend = EbsdLib::CropRGBImage<uint8_t>(legend, imageDim, imageDim, xStart, yStart, numCols, numRows);
-    ss.str("");
-    ss << k_Output_Dir << "/" << EbsdStringUtils::replace(ops.getSymmetryName(), "/", "_") << "/" << EbsdStringUtils::replace(ops.getSymmetryName(), "/", "_") << ".tiff";
-    result = TiffWriter::WriteColorImage(ss.str(), numCols, numRows, 3, legend->getPointer(0));
-    std::cout << ops.getSymmetryName() << " Result: " << result.first << ": " << result.second << std::endl;
-
-    std::vector<FloatVec3Type> referenceDirections = {
-        {0.0F, 0.0F, 1.0F},                    // Red  DONE
-        {0.0F, 1.0F, 0.0F},                    // Green
-        {-0.5F, std::sqrt(3.0F) / 2.0F, 0.0F}, // Aqua
-        {2.0F, 1.0F, 0.0F},                    // Blue
-        {0.0F, 1.0F, -1.0F},                   // Yellow  DONE
-        {1.0F, -1.0F, 1.0F},                   // Pink  DONE
-        {1.0F, 0.0F, 1.0F},                    // Flesh
-    };
-    std::vector<std::string> colorNames{"Red", "Green", "Aqua", "Blue", "Yellow", "Pink", "Flesh"};
-    GenerateTestIPFImages(referenceDirections, colorNames, 10);
-    // Generate Pole Figures for the Input Test Orientations
-    GeneratePoleFigures(ops, 2);
-  }
-
   {
     TrigonalLowOps ops;
     auto legend = ops.generateIPFTriangleLegend(imageDim, true);

Source/EbsdLib/Core/Quaternion.hpp

@@ -397,7 +397,7 @@ class Quaternion
 
   /**
    * @brief Conjugate Converts quaternion q into its conjugate
-   * @return new quaternioin that is the conjugate of the current quaternion
+   * @return new quaternion that is the conjugate of the current quaternion
    */
   Quaternion conjugate() const
   {

Source/EbsdLib/LaueOps/LaueOps.cpp

@@ -187,6 +187,7 @@ OrientationD LaueOps::calculateMisorientationInternal(const std::vector<QuatD>&
   QuatD qc;
   QuatD qr = q1 * (q2.conjugate());
   size_t numsym = quatsym.size();
+  // Loop through all the symmetry operators and find the Axis Angle with the smallest angular part.
   for(size_t i = 0; i < numsym; i++)
   {
     qc = quatsym[i] * qr;
@@ -211,15 +212,19 @@ OrientationD LaueOps::calculateMisorientationInternal(const std::vector<QuatD>&
     }
   }
   double denom = sqrt((axisAngleMin[0] * axisAngleMin[0] + axisAngleMin[1] * axisAngleMin[1] + axisAngleMin[2] * axisAngleMin[2]));
-  axisAngleMin[0] = axisAngleMin[0] / denom;
-  axisAngleMin[1] = axisAngleMin[1] / denom;
-  axisAngleMin[2] = axisAngleMin[2] / denom;
+
   if(denom == 0.0 || axisAngleMin[3] == 0.0)
   {
     axisAngleMin[0] = 0.0;
     axisAngleMin[1] = 0.0;
     axisAngleMin[2] = 1.0;
   }
+  else
+  {
+    axisAngleMin[0] = axisAngleMin[0] / denom;
+    axisAngleMin[1] = axisAngleMin[1] / denom;
+    axisAngleMin[2] = axisAngleMin[2] / denom;
+  }
 
   return axisAngleMin;
 }

Source/EbsdLib/LaueOps/LaueOps.h

@@ -204,7 +204,7 @@ class EbsdLib_EXPORT LaueOps
   virtual QuatF getNearestQuat(const QuatF& q1f, const QuatF& q2f) const = 0;
 
   /**
-   * @brief getFZQuat Returns a Quaternioni that lies in the Fundemental Zone (FZ)
+   * @brief getFZQuat Returns a Quaternion that lies in the Fundamental Zone (FZ)
    * @param qr Input Quaternion
    * @return
    */

Source/EbsdLib/Utilities/TiffWriter.cpp

@@ -70,27 +70,29 @@ std::pair<int32_t, std::string> TiffWriter::WriteColorImage(const std::string& f
   // Generate the offset into the Image File Directory (ifd) which we are going to write first
   constexpr uint32_t ifd_Offset = 8;
   outputFile.write(reinterpret_cast<const char*>(&ifd_Offset), sizeof(ifd_Offset));
-
+  const int k_NumTags = 12;
   std::vector<TIFTAG> tags;
-  tags.push_back(TIFTAG{0x00FE, 0x0004, 1, 0x00000000});                       // NewSubfileType
-  tags.push_back(TIFTAG{0x0100, 0x0004, 1, width});                            // ImageWidth
-  tags.push_back(TIFTAG{0x0101, 0x0004, 1, height});                           // ImageLength
-  tags.push_back(TIFTAG{0x0102, 0x0003, 1, 8 * sizeof(char)});                 // BitsPerSample
-  tags.push_back(TIFTAG{0x0103, 0x0003, 1, 0x0001});                           // Compression
-  tags.push_back(TIFTAG{0x0106, 0x0003, 1, PHOTOMETRIC_RGB});                  // PhotometricInterpretation  // For SamplesPerPixel = 3 or 4 (RGB or RGBA)
+  tags.push_back(TIFTAG{0x00FE, 0x0004, 1, 0x00000000});       // NewSubfileType
+  tags.push_back(TIFTAG{0x0100, 0x0004, 1, width});            // ImageWidth
+  tags.push_back(TIFTAG{0x0101, 0x0004, 1, height});           // ImageLength
+  tags.push_back(TIFTAG{0x0102, 0x0003, 1, 8 * sizeof(char)}); // BitsPerSample
+  tags.push_back(TIFTAG{0x0103, 0x0003, 1, 0x0001});           // Compression
+  tags.push_back(TIFTAG{0x0106, 0x0003, 1, PHOTOMETRIC_RGB});  // PhotometricInterpretation  // For SamplesPerPixel = 3 or 4 (RGB or RGBA)
+  // Now compute the offset to the image data so that we can put that into the tag.
+  // The math on this ONLY Works if we have 11 total Tags.
+  // IF YOU ADD MORE TAGS, YOU NEED TO ADJUST THE NEXT LINE OF CODE
+  int32_t imageDataOffset = static_cast<int32_t>(8 + (k_NumTags * 12) + 6); // Header + tags + IDF Tag entry count and Next IFD Offset
+  tags.push_back(TIFTAG{0x0111, 0x0004, 1, imageDataOffset});               // StripOffsets
+
   tags.push_back(TIFTAG{0x0112, 0x0003, 1, 1});                                // Orientation
   tags.push_back(TIFTAG{0x0115, 0x0003, 1, samplesPerPixel});                  // SamplesPerPixel
   tags.push_back(TIFTAG{0x0116, 0x0004, 1, height});                           // RowsPerStrip
   tags.push_back(TIFTAG{0x0117, 0x0004, 1, width * height * samplesPerPixel}); // StripByteCounts
+
   // TIFTAG XResolution;
   // TIFTAG YResolution;
   // TIFTAG ResolutionUnit;
-  tags.push_back(TIFTAG{0x011c, 0x0003, 1, 0x0001}); // PlanarConfiguration
-
-  // Now compute the offset to the image data so that we can put that into the tag.
-  // THESE NEXT 2 LINES MUST BE THE LAST TAG TO BE PUSHED BACK INTO THE VECTOR OR THE MATH WILL BE WRONG
-  int32_t imageDataOffset = static_cast<int32_t>(8 + ((tags.size() + 1) * 12) + 6); // Header + tags + IDF Tag entry count and Next IFD Offset
-  tags.push_back(TIFTAG{0x0111, 0x0004, 1, imageDataOffset});                       // StripOffsets
+  tags.push_back(TIFTAG{0x011c, 0x0003, 1, 0x0001}); // PlanarConfiguration // 284
 
   // Write the number of tags to the IFD section
   uint16_t numEntries = static_cast<uint16_t>(tags.size());