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David Verrelli

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23 Feb 2013 export_fig Exports figures nicely to a number of vector & bitmap formats. Author: Oliver Woodford

Hi, Oliver,
I had played around with the relevant commands to copy figures as high-resolution bitmaps, using the undocumented "hardcopy" function suggested by TMW staff
e.g. hardcopy(hF_StatsAVI, '-Dopengl', '-r100')
In comparison, your function is more convenient to use, and much better documented.

I am using it to save out PNG files with either whigte or transparent figure background. However, I was baffled when running the same commands which had been succesful previously began outputting images with black backgrounds, despite my setting
set(gcf, 'color','white');
The problem seems to be that it is necessary to _manually_ select "Use figure color" in the "Copy Options" dialogue box, under "Edit" from the figure's menu bar.
I would normally want to produce a metafile with "Transparent background" when _copying_ the figure, except for some recalcitrant plots; hence, I don't usually have "Use figure color" selected.
I thought it might be possible to toggle this programatically, but the command
set(gcf, 'InvertHardCopy', 'off');
was not effective.

Anyway, these issues seem to point to flaws in MATLAB, rather than in your code.

~~~~~

By the way
set(gcf, 'color','none');
is generates this message:
"Warning: Setting the ColorSpec to 'none' for a figure will not be allowed in a future release."
It still works at the moment, and personally I would rather it continued to work. I hope it is replaced by an alternative, and not just removed.

—DIV

29 Jan 2013 imread for multiple life science image file formats imports images and metadata using the LOCI Bioformats package Author: Christoph Moehl

Sorry, I accidentally submitted twice.

I also want to ask/comment about two specific problems:

(1) Reading a uint8 file
I open a LIF file which should have intensities 0 to 255, I guess (unless the bit depth is higher???). However, the results returned from this M-file are in the range of int8, that is from -128 to +127. Looking at the frequency histogram, this is clearly wrong. I can fix it like this:
% Begin DIV edit 2013-01-22 %
if sgn == 0,
whos sgn arr
arr = uint8(arr >= 0) .* uint8(arr) + uint8(arr < 0) .* (uint8(arr + 128) + 128);
end;
% End DIV edit 2013-01-22 %

but I notice that the variable
sgn = loci.formats.FormatTools.isSigned(pixelType);
is already defined in the code, but never used for anything (see my previous post). Is there some bug there?

(2) Opening a LIF file
A Leica LIF file can contain multiple series. By default this code opens only the last series. I wonder if there is a way to access (in a controlled way) the other series in the file.

29 Jan 2013 imread for multiple life science image file formats imports images and metadata using the LOCI Bioformats package Author: Christoph Moehl

To use this we need loci_tools.jar here: http://www.loci.wisc.edu/bio-formats/downloads

I am wondering how you know the syntax to access the methods in this jar file.

For example, how do you know to use

arr = loci.common.DataTools.makeDataArray2D(plane, bpp, fp, little, height);

??

I could not find any documentation on this.

29 Jan 2013 imread for multiple life science image file formats imports images and metadata using the LOCI Bioformats package Author: Christoph Moehl

To use this we need loci_tools.jar here: http://www.loci.wisc.edu/bio-formats/downloads

I am wondering how you know the syntax to access the methods in this jar file.

For example, how do you know to use

arr = loci.common.DataTools.makeDataArray2D(plane, bpp, fp, little, height);

??

I could not find any documentation on this.

26 Nov 2010 SCATTERCLOUD Scatterplot over a density cloud. Author: Steve Simon

Hi, Ruello.
I haven't looked at this recently, but I believe that the point ended up being plotted at the 'bottom left' of each rectangular region over which the data points were summed.
—DIV

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