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From: ImageAnalyst &lt;imageanalyst@mailinator.com&gt;
Newsgroups: comp.soft-sys.matlab
Subject: Re: Creating an image from a binary mask file using RESHAPE
Date: Tue, 3 Nov 2009 11:44:27 -0800 (PST)
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Arvind:
I don't know.  All I can say is to not use reshape.  Just read it out
slice by slice, like I do.  Here is a snippet of my code where I'm
reading slices into a 3D array using fread():
[snip]
	if(stHeader.BytesPerVoxel == 1)
		dataLengthString = '*uint8';	% You need the *, otherwise fread
returns doubles.
		% Initialize a 3D data array.
		data3D = uint8(zeros([subsampledXSize, subsampledYSize,
subsampledZSize]));

	elseif(stHeader.BytesPerVoxel == 2)
		dataLengthString = '*uint16';	% You need the *, otherwise fread
returns doubles.
		% Initialize a 3D data array.
		data3D = uint16(zeros([subsampledXSize, subsampledYSize,
subsampledZSize]));

	else
		error('Unsupported BytesPerVoxel %d', stHeader.BytesPerVoxel);
	end
	bytesPerVoxel = stHeader.BytesPerVoxel;

[snip]
	% Read in data slice by slice to avoid out of memory error.
	% We'll build up the 3D array slice by slice along the Z direction.
	sliceNumber = 1;
	for z = stValidParameters.ZStart : stValidParameters.Subsample :
stValidParameters.ZEnd
		% Read in slice z from input image and put into slice sliceNumber of
output image.
		% Reads from the current file pointer position.
		% Note: fread requires that x_size and y_size be doubles.
		oneFullSlice = fread(fileHandle, [x_size, y_size],
dataLengthString);
		if needToCropOrSubsample == 1
			% Crop it and subsample it.
			croppedSlice = oneFullSlice
(stValidParameters.XStart:stValidParameters.Subsample:stValidParameters.XEnd,
stValidParameters.YStart:stValidParameters.Subsample:stValidParameters.YEnd);
			% Assign it, but don't transpose it like in some other formats.
			data3D(:, :, sliceNumber) = croppedSlice;
		else
			% Take the full slice, (not transposed like in some other formats).
			data3D(:, :, sliceNumber) = oneFullSlice;
		end
		%disp(['Read in slice ' num2str(z) ' of input, slice ' num2str
(sliceNumber) ' of output']);
		% Skip the next slices if we are subsampling.
		% For example, if we just read slice 1 and the subsampling is 3, the
next slice we should
		% read is 4, so we need to skip slices 2 and 3 (skip subsampling-1
slices).
		if stValidParameters.Subsample &gt; 1
			% Calculate how many bytes to skip.
			bytesToSkip = int32(x_size * y_size * bytesPerVoxel *
(stValidParameters.Subsample - 1));
			% Skip that many past the current position, which is at the end of
the slice we just read.
			fseek(fileHandle, bytesToSkip, 'cof');
		end
		% Increment the slice we are on in the output array.
		sliceNumber = sliceNumber + 1;
	end

	% Close the file.
	fclose(fileHandle);

Pay particular attention to the line:
       oneFullSlice = fread(fileHandle, [x_size, y_size],
dataLengthString);
This is what allows you to read it in as a 2D array and stuff it
directly into your 3D array -- no reshape needed.  It's pretty fast
too.
Good luck,
ImageAnalyst

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