Is it possible to change numLabels manually when using labelvolshow?

Hi,

I adopted labelvolshow into custom function to show 3D time series data, but encountered a problem about colormap.

My data are these size

V = 483x496x5 double;

multiple same size and class Ln = 483x496x5 uint16;

the values in a L are given according to appearance time,

this makes my total numLabels is more than 2000 but only some of them in the same L.

(e.g: L346 is 483x496x5 uint16, the values for (x= 163:224, y= 120:189, z= 2:3) is 1966 )

The documentation said LabelColor accept numLabels-by-3, where numLabels represents the number of labels in the labeled volume

but I still give it a try

cmap = colormap(jet(numLabels));
hImage=labelvolshow(L, V,'Parent',P1, ...
            'BackgroundColor',backgroundcolor, 'ScaleFactors', scalefact,...
            'VolumeOpacity', volopacity, 'VolumeThreshold', volthreshold, 'LabelColor',cmap);

as expected, I got error message:

Error using labelvolshow

Expected LabelColor to be of size 8x3, but it is of size 2806x3.

So I want to know is there any suggestion/solution for my purpose?

[Wu Yu-Wei]

I found myself not so clear in the original post that

I forgot to mention the shape of one label might change but the ID remains the same before disappearing.

So I don't want the colour for same labels change and I want different IDs with different colours in a short time period.

e.g: the orange, red and purple labels exist around t18 -> t19 -> tn

The biggest problem is the ID easily exceed the limit of colours for labelvolshow (recently I found it is 128) after t30.

All the labels become same colour.

I guess reusing colours is ok as long as these different labels can be distinguished by time

But I'm not sure how to do it.

Thanks

Answer 1

[Walter Roberson]

background_label = 0;
cmap = colormap(jet(numLabels));

%then for any particular L, V:
usedL = setdiff(unique(L), background_label);
hImage=labelvolshow(L, V,'Parent',P1, ...
            'BackgroundColor',backgroundcolor, 'ScaleFactors', scalefact,...
            'VolumeOpacity', volopacity, 'VolumeThreshold', volthreshold, 'LabelColor',cmap(usedL,:));

This assumes that there is a background label 0 that is to be ignored.

[Wu Yu-Wei]

Dear Walter,

Thank you for your answer!

But this part makes the total colours are not enough for all labels.

usedL = setdiff(unique(L), background_label);

So I received error below:

Error using labelvolshow

Expected LabelColor to be of size 7x3, but it is of size 6x3.

Error in labelvolshow/set.LabelColor

I tried this

usedL = setdiff(unique(L)+1, background_label);

but I found all the labels become (almost) the same colour when the numLabels is very large so the difference in colormap is very little due to my cmap is

cmap = colormap(jet(numLabels));

Your solution gave me a hint but it is still not so clear for me so I haven't find out how to solve it. ha.

[Walter Roberson]

Okay, it appears that the background is handled as-if it is a "label" with its own color, but marked as transparent. So

usedL = unique(L);
colormap(jet(numel(usedL)))
hImage=labelvolshow(L, V,'Parent',P1, ...
            'BackgroundColor',backgroundcolor, 'ScaleFactors', scalefact,...
            'VolumeOpacity', volopacity, 'VolumeThreshold', volthreshold, 'LabelColor',cmap);

[Wu Yu-Wei]

Dear Walter,

Thanks for your answer,

It seems the labelvolshow uses the real value in the L array.

e.g, 36th L array (which is also t36), there are 10 labels and their IDs are in the pic.

Although the cmap is set for 10 elements.

cmap = colormap(jet(numel(usedL)))

But the real value in L array exceed the limit of colours for labelvolshow (recently I found it is 128) and all labels become same colour.

[Wu Yu-Wei]

By the way,

The volumeViewer cannot set different colours.

Even when I want to manually set colour for individual label, they change together.

I'll suggest MATHWORKS to improve 3D view