Added VOL and NRRD lazy loaders

@MappedTensor/arrayfun.m

@@ -290,9 +290,13 @@
       end
 
       % handle early return with single chunk
-      if bEarlyReturn && ~isempty(tData) && any(tData)
-        mtNewVar = tData;
-        return;
+      if bEarlyReturn
+        if ~isempty(tData) && any(tData(:))
+          mtNewVar = tData;
+          return;
+        else
+          continue;
+        end
       end
 
       % - Write results

@MappedTensor/arrayfun2.m

@@ -256,9 +256,13 @@
     end
 
     % handle early return with single chunk
-    if bEarlyReturn && ~isempty(tData1) && any(tData1)
-      mtNewVar = tData1;
-      return;
+    if bEarlyReturn
+      if ~isempty(tData1) && any(tData1)
+        mtNewVar = tData1;
+        return;
+      else
+        continue;
+      end
     end
 
     % - Write results

@MappedTensor/load.m

@@ -4,11 +4,14 @@
 %   | Extension         | Description               |
 %   |-------------------|---------------------------|
 %   | EDF               | ESRF Data Format          |
-%   | POS               | Atom Probe Tomography     |
-%   | NPY               | Python NumPy array        |
+%   | IMG SMV           | ADSC X-ray detector image |
+%   | MAR MCCD          | MAR CCD image             |
 %   | MRC MAP CCP4 RES  | MRC MRC/CCP4/MAP electronic density map |
-%   | MAR               | MAR CCD image             |
-%   | IMG MCCD          | ADSC X-ray detector image |
+%   | NRRD              | Nearly Raw Raster Data    |
+%   | NPY               | Python NumPy array        |
+%   | POS               | Atom Probe Tomography     |
+%   | VOL (PAR)         | PyHST2 volume (tomography)|
+%   
 %
 % Not implemented
 %     VOL + PAR PyHST2 volume reconstruction
@@ -77,20 +80,26 @@
 args = {}; header = [];
 switch upper(e)
 case '.EDF'
-  [Descr,args] = private_load_edf(filename);
-case '.POS'
-  [Descr,args] = private_load_pos(filename);
-case '.NPY'
-  [Descr,args,header] = private_load_npy(filename);
-case {'.MRC','.MAP','.CCP4','.RES'}
-  [Descr,args,header] = private_load_mrc(filename);
+  [Descr,args,header] = private_load_edf(filename);
+case '.IMG'
+  % ADSC (IMG/SMV)
+  [Descr,args,header] = private_load_smv(filename);
+  % could be a Mayo Clinic Analyze when supported...
 case {'.MAR','.MCCD'}
   [Descr,args,header] = private_load_mar(filename);
+case {'.MRC','.MAP','.CCP4','.RES'}
+  [Descr,args,header] = private_load_mrc(filename);
+case '.NPY'
+  [Descr,args,header] = private_load_npy(filename);
+case '.NRRD'
+  [Descr,args,header] = private_load_nrrd(filename);
+case '.POS'
+  [Descr,args,header] = private_load_pos(filename);
 case '.SMV' % ADSC (IMG/SMV)
   [Descr,args,header] = private_load_smv(filename);
-case '.IMG'
-  % ADSC (IMG/SMV)
-  [Descr,args,header] = private_load_smv(filename);
+case '.VOL'
+  [Descr,args,header] = private_load_vol(filename);
+
 otherwise
   error([ mfilename ': unsupported file type ' upper(e) ' for ' filename ]);
 end

@MappedTensor/plot.m

@@ -3,6 +3,10 @@
 %   H = PLOT(M) plots the array M as a vector, matrix/surface, or volume.
 %   Higher dimension tensors plot a projection.
 %
+%   PLOT(...,'log') transforms the signal in log-scale before plotting.
+%
+%   PLOT(..., 'PROP1',VALUE1,...) uses specified plot properties.
+%
 % Example: h=plot(MappedTensor(rand(100))); close(gcf); 1
 
 h = [];
@@ -22,6 +26,16 @@
 end
 signal = squeeze(double(signal));
 
+% handle special 'log' option
+for index=1:numel(varargin)
+  if ischar(varargin{index}) && strcmp(varargin{index}, 'log')
+    varargin(index) = [];
+    signal = signal - min(signal(:));
+    signal(signal <=0) = nan;
+    signal = log10(signal);
+  end
+end
+
 if ~isempty(inputname(1))
   iname = inputname(1);
 else
@@ -39,9 +53,9 @@
 
 % call the single plot method
 try
-  h = iFunc_plot(name, signal);
+  h = single_plot(name, signal, varargin{:});
   if ~isempty(h)
-    h = iFunc_plot_menu(h, a, name);
+    h = single_plot_menu(h, a, name);
   end
 catch ME
   warning(getReport(ME))
@@ -51,7 +65,7 @@
 
 % ------------------------------------------------------------------------------
 % simple plot of the array
-function h=iFunc_plot(name, signal, varargin)
+function h=single_plot(name, signal, varargin)
 % this internal function plots a single model, 1D, 2D or 3D.
 h=[];
 if isempty(signal) || isscalar(signal)
@@ -74,7 +88,7 @@
 set(h, 'DisplayName', name);
 
 %-------------------------------------------------------------------------------
-function h=iFunc_plot_menu(h, a, name)
+function h=single_plot_menu(h, a, name)
 % contextual menu for the single object being displayed
 % internal functions must be avoided as it uses LOTS of memory
 

@MappedTensor/private/private_load_nrrd.m

@@ -0,0 +1,214 @@
+function [Descr, args, header] = private_load_nrrd(filename)
+% PRIVATE_LOAD_NRRD Read NRRD Nearly Raw Raster Data.
+%
+% A NRRD file is a simple binary block, preceeded by a text header until an
+% empty line.
+%
+% See http://teem.sourceforge.net/nrrd/format.html
+
+Descr=''; args = [];
+
+header = nrrdread(filename);
+
+Descr= 'Nearly Raw Raster Data';
+args = {
+  'Offset',         header.Offset, ...
+  'Format',         header.Format, ...
+  'MachineFormat',  header.MachineFormat, ...
+  'Dimension' ,     header.Dimension' };
+
+% ------------------------------------------------------------------------------
+% https://www.mathworks.com/matlabcentral/fileexchange/34653-nrrd-format-file-reader
+% ------------------------------------------------------------------------------
+
+%  Copyright (c) 2016, The MathWorks, Inc.
+%  All rights reserved.
+
+%  Redistribution and use in source and binary forms, with or without
+%  modification, are permitted provided that the following conditions are met:
+
+%  * Redistributions of source code must retain the above copyright notice, this
+%    list of conditions and the following disclaimer.
+
+%  * Redistributions in binary form must reproduce the above copyright notice,
+%    this list of conditions and the following disclaimer in the documentation
+%    and/or other materials provided with the distribution.
+%  * In all cases, the software is, and all modifications and derivatives of the
+%    software shall be, licensed to you solely for use in conjunction with
+%    MathWorks products and service offerings.
+
+%  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+%  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+%  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+%  DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
+%  FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+%  DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+%  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+%  CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+%  OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+%  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+function [meta] = nrrdread(filename)
+%NRRDREAD  Import NRRD imagery and metadata.
+%   [X, META] = NRRDREAD(FILENAME) reads the image volume and associated
+%   metadata from the NRRD-format file specified by FILENAME.
+%
+%   Current limitations/caveats:
+%   * "Block" datatype is not supported.
+%   * Only tested with "gzip" and "raw" file encodings.
+%   * Very limited testing on actual files.
+%   * I only spent a couple minutes reading the NRRD spec.
+%
+%   See the format specification online:
+%   http://teem.sourceforge.net/nrrd/format.html
+% Copyright 2012 The MathWorks, Inc.
+% Open file.
+fid = fopen(filename, 'rb');
+assert(fid > 0, 'Could not open file.');
+cleaner = onCleanup(@() fclose(fid));
+% Magic line.
+theLine = fgetl(fid);
+assert(numel(theLine) >= 4, 'Bad signature in file.')
+assert(isequal(theLine(1:4), 'NRRD'), 'Bad signature in file.')
+% The general format of a NRRD file (with attached header) is:
+% 
+%     NRRD000X
+%     <field>: <desc>
+%     <field>: <desc>
+%     # <comment>
+%     ...
+%     <field>: <desc>
+%     <key>:=<value>
+%     <key>:=<value>
+%     <key>:=<value>
+%     # <comment>
+% 
+%     <data><data><data><data><data><data>...
+meta = struct([]);
+% Parse the file a line at a time.
+while (true)
+  theLine = fgetl(fid);
+
+  if (isempty(theLine) || feof(fid))
+    % End of the header.
+    break;
+  end
+
+  if (isequal(theLine(1), '#'))
+      % Comment line.
+      continue;
+  end
+
+  % "fieldname:= value" or "fieldname: value" or "fieldname:value"
+  parsedLine = regexp(theLine, ':=?\s*', 'split','once');
+
+  assert(numel(parsedLine) == 2, 'Parsing error')
+
+  field = lower(parsedLine{1});
+  value = parsedLine{2};
+
+  field(isspace(field)) = '';
+  meta(1).(field) = value;
+
+end
+datatype = getDatatype(meta.type);
+% Get the size of the data.
+assert(isfield(meta, 'sizes') && ...
+       isfield(meta, 'encoding') , ...
+       'Missing required metadata fields.')
+dims = sscanf(meta.sizes, '%d');
+if isfield(meta,'dimension')
+  ndims = sscanf(meta.dimension, '%d');
+  assert(numel(dims) == ndims);
+end
+meta.Offset = ftell(fid);
+%data = readData(fid, meta, datatype);
+%data = adjustEndian(data, meta);
+% Reshape and get into MATLAB's order.
+meta.Dimension = dims;
+%X = reshape(data, dims');
+%X = permute(X, [2 1 3]);
+
+% prepare for MappedTensor
+meta.Format = datatype;
+meta.MachineFormat = '';
+if isfield(meta, 'endian')
+  switch meta.endian
+  case {'little','L','le'}
+    meta.MachineFormat = 'ieee-le';
+  case {'big','B','be'}
+    meta.MachineFormat = 'ieee-be';
+  end
+end  
+
+% ------------------------------------------------------------------------------
+
+function datatype = getDatatype(metaType)
+% Determine the datatype
+switch (metaType)
+ case {'signed char', 'int8', 'int8_t'}
+  datatype = 'int8';
+
+ case {'uchar', 'unsigned char', 'uint8', 'uint8_t'}
+  datatype = 'uint8';
+ case {'short', 'short int', 'signed short', 'signed short int', ...
+       'int16', 'int16_t'}
+  datatype = 'int16';
+
+ case {'ushort', 'unsigned short', 'unsigned short int', 'uint16', ...
+       'uint16_t'}
+  datatype = 'uint16';
+
+ case {'int', 'signed int', 'int32', 'int32_t'}
+  datatype = 'int32';
+
+ case {'uint', 'unsigned int', 'uint32', 'uint32_t'}
+  datatype = 'uint32';
+
+ case {'longlong', 'long long', 'long long int', 'signed long long', ...
+       'signed long long int', 'int64', 'int64_t'}
+  datatype = 'int64';
+
+ case {'ulonglong', 'unsigned long long', 'unsigned long long int', ...
+       'uint64', 'uint64_t'}
+  datatype = 'uint64';
+
+ case {'float'}
+  datatype = 'single';
+
+ case {'double'}
+  datatype = 'double';
+
+ otherwise
+  assert(false, 'Unknown datatype')
+end
+
+
+function data = readData(fidIn, meta, datatype)
+switch (meta.encoding)
+ case {'raw'}
+
+  data = fread(fidIn, inf, [datatype '=>' datatype]);
+
+ case {'gzip', 'gz'}
+  error('Compressed NRRD is not supported')
+
+ case {'txt', 'text', 'ascii'}
+
+  data = fscanf(fidIn, '%f');
+  data = cast(data, datatype);
+
+ otherwise
+  assert(false, 'Unsupported encoding')
+end
+
+
+function data = adjustEndian(data, meta)
+if ~isfield(meta, 'endian'), return; end
+[~,~,endian] = computer();
+needToSwap = (isequal(endian, 'B') && isequal(lower(meta.endian), 'little')) || ...
+             (isequal(endian, 'L') && isequal(lower(meta.endian), 'big'));
+
+if (needToSwap)
+    data = swapbytes(data);
+end