Expose setters for undistortion parameters in Andor device (#756)

* ENH: Add setters for Andor camera undistortion parameters

* ENH: Andor camera processed images converted to counts/seconds

* BUG: Andor correction images loaded in as uint8 but should be uint16

Author: adamaji

src/PlusDataCollection/Andor/vtkPlusAndorVideoSource.cxx

@@ -670,7 +670,7 @@ void vtkPlusAndorVideoSource::ApplyCosmicRayCorrection(int bin, cv::Mat& floatIm
 }
 
 // ----------------------------------------------------------------------------
-void vtkPlusAndorVideoSource::ApplyFrameCorrections(int binning)
+void vtkPlusAndorVideoSource::ApplyFrameCorrections(int binning, float exposureTime)
 {
   cv::Mat cvIMG(frameSize[0], frameSize[1], CV_16UC1, &rawFrame[0]); // uses rawFrame as buffer
   CorrectBadPixels(binning, cvIMG);
@@ -696,6 +696,9 @@ void vtkPlusAndorVideoSource::ApplyFrameCorrections(int binning)
   // Divide the image by the 32-bit floating point correction image
   cv::divide(result, cvFlatCorrection, result, 1, CV_32FC1);
   LOG_INFO("Applied multiplicative flat correction");
+
+  // Convert image from count to counts/seconds
+  cv::divide(result, exposureTime, result, 1, CV_32FC1);
   result.convertTo(cvIMG, CV_16UC1);
 }
 
@@ -709,7 +712,7 @@ PlusStatus vtkPlusAndorVideoSource::AcquireBLIFrame(int binning, int vsSpeed, in
 
   if(this->UseFrameCorrections)
   {
-    ApplyFrameCorrections(binning);
+    ApplyFrameCorrections(binning, exposureTime);
     AddFrameToDataSource(BLICorrected);
   }
 
@@ -726,7 +729,7 @@ PlusStatus vtkPlusAndorVideoSource::AcquireGrayscaleFrame(int binning, int vsSpe
 
   if(this->UseFrameCorrections)
   {
-    ApplyFrameCorrections(binning);
+    ApplyFrameCorrections(binning, exposureTime);
     AddFrameToDataSource(GrayCorrected);
   }
 
@@ -775,7 +778,7 @@ PlusStatus vtkPlusAndorVideoSource::SetBiasDarkCorrectionImage(const std::string
 {
   try
   {
-    cvBiasDarkCorrection = cv::imread(biasDarkFilePath, cv::IMREAD_GRAYSCALE);
+    cvBiasDarkCorrection = cv::imread(biasDarkFilePath, cv::IMREAD_UNCHANGED);
     if(cvBiasDarkCorrection.empty())
     {
       throw "Bias+dark correction image empty!";
@@ -794,7 +797,7 @@ PlusStatus vtkPlusAndorVideoSource::SetFlatCorrectionImage(std::string flatFileP
 {
   try
   {
-    cvFlatCorrection = cv::imread(flatFilePath, cv::IMREAD_GRAYSCALE);
+    cvFlatCorrection = cv::imread(flatFilePath, cv::IMREAD_UNCHANGED);
     if(cvFlatCorrection.empty())
     {
       throw "Flat correction image empty!";
@@ -993,6 +996,36 @@ bool vtkPlusAndorVideoSource::GetUseCosmicRayCorrection()
   return this->UseCosmicRayCorrection;
 }
 
+// ----------------------------------------------------------------------------
+PlusStatus vtkPlusAndorVideoSource::SetCameraIntrinsics(std::array<double, 9> intrinsics)
+{
+  std::copy(std::begin(intrinsics), std::end(intrinsics), this->cameraIntrinsics);
+  return PLUS_SUCCESS;
+}
+
+// ----------------------------------------------------------------------------
+std::array<double, 9> vtkPlusAndorVideoSource::GetCameraIntrinsics()
+{
+  std::array<double, 9> returnIntrinsics;
+  std::copy(this->cameraIntrinsics, this->cameraIntrinsics + 9, std::begin(returnIntrinsics));
+  return returnIntrinsics;
+}
+
+// ----------------------------------------------------------------------------
+PlusStatus vtkPlusAndorVideoSource::SetDistanceCoefficients(std::array<double, 4> coefficients)
+{
+  std::copy(std::begin(coefficients), std::end(coefficients), this->distanceCoefficients);
+  return PLUS_SUCCESS;
+}
+
+// ----------------------------------------------------------------------------
+std::array<double, 4> vtkPlusAndorVideoSource::GetDistanceCoefficients()
+{
+  std::array<double, 4> returnCoefficients;
+  std::copy(this->distanceCoefficients, this->distanceCoefficients + 4, std::begin(returnCoefficients));
+  return returnCoefficients;
+}
+
 // ----------------------------------------------------------------------------
 PlusStatus vtkPlusAndorVideoSource::SetRequireCoolTemp(bool requireCoolTemp)
 {

src/PlusDataCollection/Andor/vtkPlusAndorVideoSource.h

@@ -159,6 +159,12 @@ class vtkPlusDataCollectionExport vtkPlusAndorVideoSource: public vtkPlusDevice
     return flatCorrection;
   }
 
+  /*! Data for setting undistortion coefficients. */
+  PlusStatus SetCameraIntrinsics(std::array<double, 9> intrinsics);
+  std::array<double, 9> GetCameraIntrinsics();
+  PlusStatus SetDistanceCoefficients(std::array<double, 4> coefficients);
+  std::array<double, 4> GetDistanceCoefficients();
+
   /*! -1 uses currently active settings. */
   PlusStatus AcquireBLIFrame(int binning, int vsSpeed, int hsSpeed, float exposureTime);
 
@@ -247,7 +253,7 @@ class vtkPlusDataCollectionExport vtkPlusAndorVideoSource: public vtkPlusDevice
   void ApplyCosmicRayCorrection(int binning, cv::Mat& floatImage);
 
   /*! Applies bias correction for dark current, flat correction and lens distortion. */
-  void ApplyFrameCorrections(int binning);
+  void ApplyFrameCorrections(int binning, float exposureTime);
 
   /*! Flag whether to call ApplyFrameCorrections on the raw acquired frame on acquisition
       or to skip frame corrections.