2DRF Pulse Toolkit Expansion

rfPulseTools/2drfPulseTools/readNPY.m

@@ -0,0 +1,37 @@
+
+
+function data = readNPY(filename)
+% Function to read NPY files into matlab.
+% *** Only reads a subset of all possible NPY files, specifically N-D arrays of certain data types.
+% See https://github.com/kwikteam/npy-matlab/blob/master/tests/npy.ipynb for
+% more.
+%
+
+[shape, dataType, fortranOrder, littleEndian, totalHeaderLength, ~] = readNPYheader(filename);
+
+if littleEndian
+    fid = fopen(filename, 'r', 'l');
+else
+    fid = fopen(filename, 'r', 'b');
+end
+
+try
+
+    [~] = fread(fid, totalHeaderLength, 'uint8');
+
+    % read the data
+    data = fread(fid, prod(shape), [dataType '=>' dataType]);
+
+    if length(shape)>1 && ~fortranOrder
+        data = reshape(data, shape(end:-1:1));
+        data = permute(data, [length(shape):-1:1]);
+    elseif length(shape)>1
+        data = reshape(data, shape);
+    end
+
+    fclose(fid);
+
+catch me
+    fclose(fid);
+    rethrow(me);
+end

rfPulseTools/2drfPulseTools/readNPYheader.m

@@ -0,0 +1,72 @@
+
+
+function [arrayShape, dataType, fortranOrder, littleEndian, totalHeaderLength, npyVersion] = readNPYheader(filename)
+% function [arrayShape, dataType, fortranOrder, littleEndian, ...
+%       totalHeaderLength, npyVersion] = readNPYheader(filename)
+%
+% parse the header of a .npy file and return all the info contained
+% therein.
+%
+% Based on spec at http://docs.scipy.org/doc/numpy-dev/neps/npy-format.html
+
+fid = fopen(filename);
+
+% verify that the file exists
+if (fid == -1)
+    if ~isempty(dir(filename))
+        error('Permission denied: %s', filename);
+    else
+        error('File not found: %s', filename);
+    end
+end
+
+try
+
+    dtypesMatlab = {'uint8','uint16','uint32','uint64','int8','int16','int32','int64','single','double', 'logical'};
+    dtypesNPY = {'u1', 'u2', 'u4', 'u8', 'i1', 'i2', 'i4', 'i8', 'f4', 'f8', 'b1'};
+
+
+    magicString = fread(fid, [1 6], 'uint8=>uint8');
+
+    if ~all(magicString == [147,78,85,77,80,89])
+        error('readNPY:NotNUMPYFile', 'Error: This file does not appear to be NUMPY format based on the header.');
+    end
+
+    majorVersion = fread(fid, [1 1], 'uint8=>uint8');
+    minorVersion = fread(fid, [1 1], 'uint8=>uint8');
+
+    npyVersion = [majorVersion minorVersion];
+
+    headerLength = fread(fid, [1 1], 'uint16=>uint16');
+
+    totalHeaderLength = 10+headerLength;
+
+    arrayFormat = fread(fid, [1 headerLength], 'char=>char');
+
+    % to interpret the array format info, we make some fairly strict
+    % assumptions about its format...
+
+    r = regexp(arrayFormat, '''descr''\s*:\s*''(.*?)''', 'tokens');
+    if isempty(r)
+        error('Couldn''t parse array format: "%s"', arrayFormat);
+    end
+    dtNPY = r{1}{1};    
+
+    littleEndian = ~strcmp(dtNPY(1), '>');
+
+    dataType = dtypesMatlab{strcmp(dtNPY(2:3), dtypesNPY)};
+
+    r = regexp(arrayFormat, '''fortran_order''\s*:\s*(\w+)', 'tokens');
+    fortranOrder = strcmp(r{1}{1}, 'True');
+
+    r = regexp(arrayFormat, '''shape''\s*:\s*\((.*?)\)', 'tokens');
+    shapeStr = r{1}{1}; 
+    arrayShape = str2num(shapeStr(shapeStr~='L'));
+
+
+    fclose(fid);
+
+catch me
+    fclose(fid);
+    rethrow(me);
+end