Multiple changes to PNG handling

- Do not attempt to support writing bitwise images, even if the number of pixels in the width direction is a factor of 8.
- Fix intensity scaling of bitwise images such that values of 0 and 255 are used in the output uint8 image.
 Add test data and tests for verifying operation of PNG export.

core/file/png.cpp

@@ -183,6 +183,7 @@ namespace MR
           bit_depth (0),
           filename (filename),
           data_type (H.datatype()),
+          multiplier (1.0),
           outfile (NULL)
       {
         if (Path::exists (filename) && !App::overwrite_files)
@@ -231,17 +232,23 @@ namespace MR
             png_destroy_write_struct (&png_ptr, &info_ptr);
             throw Exception ("Undefined data type in image \"" + H.name() + "\" for PNG writer");
           case DataType::Bit:
-            bit_depth = 1;
+            assert (false);
             break;
           case DataType::UInt8:
+            bit_depth = 8;
+            break;
           case DataType::Float32:
             bit_depth = 8;
+            multiplier = std::numeric_limits<uint8_t>::max(); break;
             break;
           case DataType::UInt16:
           case DataType::UInt32:
           case DataType::UInt64:
+            bit_depth = 16;
+            break;
           case DataType::Float64:
             bit_depth = 16;
+            multiplier = std::numeric_limits<uint16_t>::max(); break;
             break;
         }
         // Detect cases where one axis has a size of 1, and hence represents the image plane
@@ -327,7 +334,7 @@ namespace MR
         };
 
 
-        if (bit_depth == 1 || data_type == DataType::UInt8 || data_type == DataType::UInt16BE) {
+        if (data_type == DataType::UInt8 || data_type == DataType::UInt16BE) {
           finish (data);
         } else {
           uint8_t scratch[row_bytes * height];

core/file/png.h

@@ -83,6 +83,7 @@ namespace MR
           int color_type, bit_depth;
           std::string filename;
           DataType data_type;
+          default_type multiplier;
           FILE* outfile;
 
           static void error_handler (png_struct_def*, const char*);
@@ -100,16 +101,8 @@ namespace MR
         std::function<default_type(const void*,size_t,default_type,default_type)> fetch_func;
         std::function<void(default_type,void*,size_t,default_type,default_type)> store_func;
         __set_fetch_store_functions<default_type> (fetch_func, store_func, data_type);
-        default_type multiplier = 1.0;
-        switch (data_type() & DataType::Type) {
-          case DataType::Float32: multiplier = std::numeric_limits<uint8_t>::max(); break;
-          case DataType::Float64: multiplier = std::numeric_limits<uint16_t>::max(); break;
-        }
-        for (size_t i = 0; i != num_elements; ++i) {
-          Raw::store_BE<T> (std::min (default_type(std::numeric_limits<T>::max()), std::max (0.0, std::round(multiplier * fetch_func (in_ptr, 0, 0.0, 1.0)))), out_ptr);
-          in_ptr += data_type.bytes();
-          out_ptr += sizeof(T);
-        }
+        for (size_t i = 0; i != num_elements; ++i)
+          Raw::store_BE<T> (std::min (default_type(std::numeric_limits<T>::max()), std::max (0.0, std::round(multiplier * fetch_func (in_ptr, i, 0.0, 1.0)))), out_ptr, i);
       };
 
 

core/formats/png.cpp

@@ -149,7 +149,8 @@ namespace MR
       // - 4 volumes (save as RGBA)
       // This needs to be compatible with NameParser used in Header::create():
       //   "num_axes" subtracts from H.ndim() however many instances of [] there are
-      size_t width_axis = 0, axis_to_zero = 3;
+      // size_t width_axis = 0;
+      size_t axis_to_zero = 3;
       if (H.ndim() - num_axes > 1)
         throw Exception ("Cannot nominate more than one axis using square-bracket notation for PNG format");
       switch (num_axes) {
@@ -170,7 +171,7 @@ namespace MR
             axis_to_zero = 1;
           } else if (H.size(0) == 1) {
             axis_to_zero = 0;
-            width_axis = 1;
+            //width_axis = 1;
           } else {
             // If image is 3D, and all three axes have size greater than one, and we
             //   haven't used the square-bracket notation, we can't export genuine 3D data
@@ -192,8 +193,8 @@ namespace MR
           }
           if (axis < 0)
             throw Exception ("Cannot export 4D image to PNG format if all three spatial axes have size greater than 1 and square-bracket notation is not used");
-          if (!axis_to_zero)
-            width_axis = 1;
+          // if (!axis_to_zero)
+          //   width_axis = 1;
           break;
         default:
           throw Exception ("Cannot generate PNG file(s) from image with more than 4 axes");
@@ -223,9 +224,10 @@ namespace MR
 
       H.transform().setIdentity();
 
-      if (H.datatype() == DataType::Bit && H.size (width_axis) % 8) {
-        WARN ("Cannot write bitwise PNG image with width not a factor of 8; will instead write with 8-bit depth");
+      if (H.datatype() == DataType::Bit) {
+        WARN ("Cannot write bitwise PNG images; will instead write with 8-bit depth");
         H.datatype() = DataType::UInt8;
+        H.intensity_scale() = 1.0 / 255.0;
       }
 
       return true;

testing/binaries/tests/mrconvert

@@ -16,4 +16,9 @@ mrconvert mrcat/voxel[].mih - | testing_diff_header -keyval - mrcat/all_axis0.mi
 mrconvert mrcat/all_axis3.mif tmp-[].mif -force && testing_diff_header -keyval tmp-0.mif mrcat/voxel1.mih && testing_diff_header -keyval tmp-1.mif mrcat/voxel2.mih && testing_diff_header -keyval tmp-2.mif mrcat/voxel3.mih && testing_diff_header -keyval tmp-3.mif mrcat/voxel4.mih && testing_diff_header -keyval tmp-4.mif mrcat/voxel5.mih && testing_diff_header -keyval tmp-5.mif mrcat/voxel6.mih
 mrconvert dwi.mif tmp-[]-[].mif -force && testing_diff_image dwi.mif tmp-[]-[].mif
 mrconvert dwi.mif -coord 3 1:2:end -axes 0:2,-1,3 - | testing_diff_image - mrconvert/dwi_select_axes.mif
-
+mrinfo template.mif.gz -transform > tmp.txt && mrconvert template.mif.gz tmp[].png -force && mrconvert tmp[].png -vox 2.5 - | mrtransform - -replace tmp.txt - | mrcalc - 255 -div - | testing_diff_image - $(mrcalc template.mif.gz 1.0 -min -) -abs 0.002
+rm -f tmpaxial*.png && mrconvert template.mif.gz -coord 2 9,19,29,39,49 tmpaxial[].png && testing_diff_image tmpaxial[].png mrconvert/axial[].png
+rm -f tmpcoronal*.png && mrconvert template.mif.gz -coord 1 17,32,47,62,77 -axes 0,2,1 tmpcoronal[].png && testing_diff_image tmpcoronal[].png mrconvert/coronal[].png
+rm -f tmpsagittal*.png && mrconvert template.mif.gz -coord 0 27,47,67 -axes 1,2,0 tmpsagittal[].png && testing_diff_image tmpsagittal[].png mrconvert/sagittal[].png
+rm -f tmpmask*.png && mrconvert mask.mif tmpmask[].png && testing_diff_image tmpmask[].png mrconvert/mask[].png
+rm -f tmptissues*.png && mrconvert dwi2fod/msmt/tissues.mif tmptissues[].png && testing_diff_image tmptissues[].png mrconvert/tissues[].png