merge master

Dockerfile

@@ -36,24 +36,24 @@ RUN git clone -b $MRTRIX3_GIT_COMMITISH --depth 1 https://github.com/MRtrix3/mrt
     && rm -rf tmp
 
 # Download minified ART ACPCdetect (V2.0).
-FROM base-builder as acpcdetect-installer
+FROM base-builder AS acpcdetect-installer
 WORKDIR /opt/art
 RUN curl -fsSL https://osf.io/73h5s/download \
     | tar xz --strip-components 1
 
 # Download minified ANTs (2.3.4-2).
-FROM base-builder as ants-installer
+FROM base-builder AS ants-installer
 WORKDIR /opt/ants
 RUN curl -fsSL https://osf.io/yswa4/download \
     | tar xz --strip-components 1
 
 # Download FreeSurfer files.
-FROM base-builder as freesurfer-installer
+FROM base-builder AS freesurfer-installer
 WORKDIR /opt/freesurfer
 RUN curl -fsSLO https://raw.githubusercontent.com/freesurfer/freesurfer/v7.1.1/distribution/FreeSurferColorLUT.txt
 
 # Download minified FSL (6.0.7.7)
-FROM base-builder as fsl-installer
+FROM base-builder AS fsl-installer
 WORKDIR /opt/fsl
 RUN curl -fsSL https://osf.io/ph9ex/download \
     | tar xz --strip-components 1
@@ -108,4 +108,4 @@ RUN strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so
 
 RUN ln -s /usr/bin/python3 /usr/bin/python
 
-CMD ["/bin/bash"]
+CMD ["/bin/bash"]

Singularity

@@ -26,8 +26,8 @@ Include: apt
     export FSLDIR FSLOUTPUTTYPE FSLMULTIFILEQUIT FSLTCLSH FSLWISH
 
 # All
-    LD_LIBRARY_PATH="/.singularity.d/libs:/usr/lib:/opt/fsl/lib:$LD_LIBRARY_PATH"
-    PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/bin:$PATH"
+    LD_LIBRARY_PATH="/.singularity.d/libs:/usr/lib:$LD_LIBRARY_PATH"
+    PATH="/opt/mrtrix3/bin:/opt/ants/bin:/opt/art/bin:/opt/fsl/share/fsl/bin:$PATH"
     export LD_LIBRARY_PATH PATH
 
 %post
@@ -51,8 +51,8 @@ Include: apt
     mkdir -p /opt/ants && curl -fsSL https://osf.io/yswa4/download | tar xz -C /opt/ants --strip-components 1
     # Download FreeSurfer lookup table file (v7.1.1).
     mkdir -p /opt/freesurfer && curl -fsSL -o /opt/freesurfer/FreeSurferColorLUT.txt https://raw.githubusercontent.com/freesurfer/freesurfer/v7.1.1/distribution/FreeSurferColorLUT.txt
-    # Download minified FSL (6.0.4-2).
-    mkdir -p /opt/fsl && curl -fsSL https://osf.io/dtep4/download | tar xz -C /opt/fsl --strip-components 1
+    # Download minified FSL (6.0.7.7).
+    mkdir -p /opt/fsl && curl -fsSL https://osf.io/ph9ex/download | tar xz -C /opt/fsl --strip-components 1
 
 # Use Python3 for anything requesting Python, since Python2 is not installed
     ln -s /usr/bin/python3 /usr/bin/python

cmd/5ttcheck.cpp

@@ -145,7 +145,7 @@ void run ()
     }
   }
 
-  const std::string vox_option_suggestion = get_options ("masks").size() ? (" (suggest checking " + std::string(argument.size() > 1 ? "outputs from" : "output of") + " -masks option)") : " (suggest re-running using the -masks option to see voxels where tissue fractions do not sum to 1.0)";
+  const std::string vox_option_suggestion = get_options ("voxels").size() ? (" (suggest checking " + std::string(argument.size() > 1 ? "outputs from" : "output of") + " -voxels option)") : " (suggest re-running using the -voxels option to see voxels where tissue fractions do not sum to 1.0)";
 
   if (major_error_count) {
     if (argument.size() > 1)

configure

@@ -73,6 +73,9 @@ OPTIONS
     -conda       prevent stripping anaconda/miniconda from the PATH (only use if
                  you intend building with the conda toolchain - not recommended)
 
+    -fsl         prevent stripping FSL from the PATH (only use if you intend
+                 building with the FSL toolchain - not recommended)
+
 
 ENVIRONMENT VARIABLES
 
@@ -194,6 +197,7 @@ R_module = False
 openmp = False
 dev = False
 conda = False
+fsl = False
 
 optimlevel = 3
 
@@ -227,6 +231,8 @@ for arg in sys.argv[1:]:
     openmp = True
   elif '-conda'.startswith (arg):
     conda = True
+  elif '-fsl'.startswith (arg):
+    fsl = True
   else:
     sys.stdout.write (usage_string)
     sys.exit (1)
@@ -292,15 +298,30 @@ if conda:
 else:
   path = []
   for entry in os.environ['PATH'].split(os.pathsep):
-    if 'conda' in entry:
+    if 'conda' in entry.lower():
       report ('WARNING: anaconda/miniconda detected in PATH ("' + entry + '") - removed to avoid conflicts\n')
       issue_conda_warning = True
     else:
       path += [ entry ]
   path = os.pathsep.join(path)
   os.environ['PATH'] = path
 
-log ('PATH set to: ' + path)
+# if not using FSL, remove any mention of FSL from PATH:
+issue_fsl_warning = False
+if fsl:
+  path = os.environ['PATH']
+else:
+  path = []
+  for entry in os.environ['PATH'].split(os.pathsep):
+    if 'fsl' in entry.lower():
+      report ('WARNING: FSL detected in PATH ("' + entry + '") - removed to avoid conflicts\n')
+      issue_fsl_warning = True
+    else:
+      path += [ entry ]
+  path = os.pathsep.join(path)
+  os.environ['PATH'] = path
+
+log ('\nPATH set to: ' + path)
 
 
 
@@ -741,7 +762,10 @@ if 'LINKLIB_ARGS' in os.environ.keys():
 
 
 if issue_conda_warning:
-  report ('\nNOTE: if you intend to build with anaconda/miniconda (not recommended), pass the -conda flag to ./configure\n\n')
+  report ('NOTE: if you intend to build with anaconda/miniconda (not recommended), pass the -conda flag to ./configure\n')
+if issue_fsl_warning:
+  report ('NOTE: if you intend to build with the FSL toolchain (not recommended), pass the -fsl flag to ./configure\n')
+report ('\n')
 
 
 

core/file/png.cpp

@@ -38,6 +38,7 @@ namespace MR
 
 
       Reader::Reader (const std::string& filename) :
+          infile (fopen (filename.c_str(), "rb")),
           png_ptr (NULL),
           info_ptr (NULL),
           width (0),
@@ -46,7 +47,6 @@ namespace MR
           color_type (0),
           channels (0)
       {
-        FILE* infile = fopen (filename.c_str(), "rb");
         unsigned char sig[8];
         if (fread (sig, 1, 8, infile) < 8)
           throw Exception ("error reading from PNG file \"" + filename + "\"");
@@ -130,6 +130,10 @@ namespace MR
           png_ptr = NULL;
           info_ptr = NULL;
         }
+        if (infile) {
+          fclose(infile);
+          infile = NULL;
+        }
       }
 
 
@@ -183,6 +187,7 @@ namespace MR
           bit_depth (0),
           filename (filename),
           data_type (H.datatype()),
+          multiplier (1.0),
           outfile (NULL)
       {
         if (Path::exists (filename) && !App::overwrite_files)
@@ -196,6 +201,8 @@ namespace MR
           throw Exception ("Unable to set jump buffer for PNG structure for image \"" + filename + "\"");
         }
         outfile = fopen (filename.c_str(), "wb");
+        if (!outfile)
+          throw Exception ("Unable to open PNG file for writing for image \"" + filename + "\": " + strerror (errno));
         png_init_io (png_ptr, outfile);
         png_set_compression_level (png_ptr, Z_DEFAULT_COMPRESSION);
         switch (H.ndim()) {
@@ -231,17 +238,23 @@ 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
@@ -302,6 +315,10 @@ namespace MR
           png_ptr = NULL;
           info_ptr = NULL;
         }
+        if (outfile) {
+          fclose(outfile);
+          outfile = NULL;
+        }
       }
 
 
@@ -323,10 +340,11 @@ namespace MR
             row_pointers[row] = to_write + row * row_bytes;
           png_write_image (png_ptr, row_pointers);
           png_write_end (png_ptr, info_ptr);
+          delete [] row_pointers;
         };
 
 
-        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

@@ -54,6 +54,7 @@ namespace MR
           void load (uint8_t*);
 
         private:
+          FILE* infile;
           png_structp png_ptr;
           png_infop info_ptr;
           png_uint_32 width, height;
@@ -83,6 +84,7 @@ 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 +102,8 @@ 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

@@ -70,16 +70,16 @@ namespace MR
       }
 
       H.size(0) = png.get_width();
-      H.stride(0) = -3;
+      H.stride(0) = -2;
 
       H.size(1) = png.get_height();
-      H.stride(1) = -4;
+      H.stride(1) = -3;
 
       H.size(2) = 1;
-      H.stride(2) = 1;
+      H.stride(2) = 4;
 
       if (H.ndim() == 4)
-        H.stride(3) = 2;
+        H.stride(3) = 1;
 
       H.spacing (0) = H.spacing (1) = H.spacing (2) = 1.0;
       H.transform().setIdentity();
@@ -132,14 +132,14 @@ namespace MR
       if (H.ndim() == 4 && H.size(3) > 4)
         throw Exception ("A 4D image written to PNG must have between one and four volumes (requested: " + str(H.size(3)) + ")");
 
-      // TODO After looping over axes via square-bracket notation,
+      // After looping over axes via square-bracket notation,
       //   there needs to be at least two axes with size greater than one
-      size_t unity_axes = 0;
+      size_t nonunity_axes = 0;
       for (size_t axis = 0; axis != H.ndim(); ++axis) {
-        if (H.size (axis) == 1)
-          ++unity_axes;
+        if (H.size (axis) > 1)
+          ++nonunity_axes;
       }
-      if (unity_axes - (H.ndim() - num_axes) < 2)
+      if (nonunity_axes - (H.ndim() - num_axes) < 2)
         throw Exception ("Too few (non-unity) image axes to support PNG export");
 
       // For 4D images, can support:
@@ -149,7 +149,7 @@ 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 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 +170,6 @@ namespace MR
             axis_to_zero = 1;
           } else if (H.size(0) == 1) {
             axis_to_zero = 0;
-            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 +191,6 @@ 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;
           break;
         default:
           throw Exception ("Cannot generate PNG file(s) from image with more than 4 axes");
@@ -209,7 +206,7 @@ namespace MR
       H.stride(1) = -3;
       H.spacing(1) = 1.0;
       if (H.ndim() > 2) {
-        H.stride(2) = 4;
+        H.stride(2) = -4;
         H.spacing(2) = 1.0;
       }
       if (H.ndim() > 3) {
@@ -223,9 +220,10 @@ 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;

core/header.cpp

@@ -785,12 +785,13 @@ namespace MR
     Header result (headers[0]);
 
     if (axis_to_concat >= result.ndim()) {
+      Stride::symbolise (result);
       result.ndim() = axis_to_concat + 1;
       result.size(axis_to_concat) = 1;
+      result.stride(axis_to_concat) = axis_to_concat+1;
+      Stride::actualise (result);
     }
 
-    result.stride (axis_to_concat) = result.ndim()+1;
-
     for (size_t axis = 0; axis != result.ndim(); ++axis) {
       if (axis != axis_to_concat && result.size (axis) <= 1) {
         for (const auto& H : headers) {