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Plot bug?

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Rotella, Anthony M. (GRC)[]

Plot bug?

Hello all,

I am working on plotting some data using the Plot commands, and
I noticed something interesting. I have been plotting arrays, and been
getting confusing results using the setLimits function. My code looks
like this:

Plot.create("Total Area vs. Slice Number","Slice", "Total Area",
totalArea);
Plot.setColor("orange");
Plot.setLimits(1, totalArea.length, 0, 50000);
Plot.show();

The array has a 0 value at 0 (I wanted the data to correlate with slice
number, so the array really starts at 1, hence the 1-totalArea.length
for x-values.) and then at 1 it jumps up to about 17000. Now, in the
plot, there are several problems:

1. It displays totalArea[1] somewhere around (0, 6000), optically, on
the plot. If I hover my mouse over that point though, it says (1,
17250). Interesting....

2. Despite setting the y-scale to be (0, 50000), the last axis label on
the plot only goes up to 15000, so it probably goes up to about 17500.

Thanks,

Tony Rotella

Justin McGrath

Re: Plot bug?

From the definition page at
http://rsb.info.nih.gov/ij/developer/macro/functions.html.

Plot.setLimits(xMin, xMax, yMin, yMax)
Sets the range of the x-axis and y-axis of plots created using
Plot.create(). Must be called immediately after Plot.create().

Move Plot.setLimits() after Plot.create().

Also, nothing in your code says 1-totalArea.length. Anyhow, I don't
know why you would want the maximum x value of the graph to be the
length of the array holding the x values. I would imagine that you
want it to be the maximum (or slightly larger than maximum ) value of
the values in the x array. Likewise, you want the minimum x value to
be the minimum (or sligtly less than minimum) of the values in the x
array, which may or may not be anywhere near 1, as you have coded.

Having the array index match the slice number is odd. Just use
slice_number-1 when you access values in the array.

Justin

On 8/17/07, Rotella, Anthony M. (GRC)[] <[hidden email]> wrote:

> Hello all,
>
> I am working on plotting some data using the Plot commands, and
> I noticed something interesting. I have been plotting arrays, and been
> getting confusing results using the setLimits function. My code looks
> like this:
>
> Plot.create("Total Area vs. Slice Number","Slice", "Total Area",
> totalArea);
> Plot.setColor("orange");
> Plot.setLimits(1, totalArea.length, 0, 50000);
> Plot.show();
>
> The array has a 0 value at 0 (I wanted the data to correlate with slice
> number, so the array really starts at 1, hence the 1-totalArea.length
> for x-values.) and then at 1 it jumps up to about 17000. Now, in the
> plot, there are several problems:
>
> 1. It displays totalArea[1] somewhere around (0, 6000), optically, on
> the plot. If I hover my mouse over that point though, it says (1,
> 17250). Interesting....
>
> 2. Despite setting the y-scale to be (0, 50000), the last axis label on
> the plot only goes up to 15000, so it probably goes up to about 17500.
>
> Thanks,
>
> Tony Rotella
>

Rotella, Anthony M. (GRC)[]

Re: Plot bug?

If you look at my code, the plot is of an area vs. slice number. That means that the x-values would start at 1, and go till the end of the array, increasing by 1. And it would be nice to start at 0 like normal, but then when you plot them, you would have data at the wrong slice number, since they would start at zero, not 1. I think if you look at my code a second time, this should be clear.

________________________________

From: ImageJ Interest Group on behalf of Justin McGrath
Sent: Fri 8/17/2007 9:11 PM
To: [hidden email]
Subject: Re: Plot bug?

From the definition page at
http://rsb.info.nih.gov/ij/developer/macro/functions.html.

Plot.setLimits(xMin, xMax, yMin, yMax)
Sets the range of the x-axis and y-axis of plots created using
Plot.create(). Must be called immediately after Plot.create().

Move Plot.setLimits() after Plot.create().

Also, nothing in your code says 1-totalArea.length. Anyhow, I don't
know why you would want the maximum x value of the graph to be the
length of the array holding the x values. I would imagine that you
want it to be the maximum (or slightly larger than maximum ) value of
the values in the x array. Likewise, you want the minimum x value to
be the minimum (or sligtly less than minimum) of the values in the x
array, which may or may not be anywhere near 1, as you have coded.

Having the array index match the slice number is odd. Just use
slice_number-1 when you access values in the array.

Justin

On 8/17/07, Rotella, Anthony M. (GRC)[] <[hidden email]> wrote:

Justin McGrath

Re: Plot bug?

Ah, I see. Well in that case setting the plot limits will not correct
the problem. In Plot.create() it looks like you only specify the y
array, so it uses 0 to yarray.length-1 as the x array. If you just
set the x limits from 1 to array.length (without passing the right x
array), you'll cut off the first value.

You need a pass an array with the right values to Plot.create().
This should work, although there might be an easier way.

xarray = newArray(totalArea.length);
for ( i = 0 ; i < xarray.length ; i++) {
xarray[i] = i+1;
}

Then you can set your plot limits. Plot.setLimits has to come
directly after Plot.create() or the axis labels won't change.

Justin

On 8/18/07, Rotella, Anthony M. (GRC)[] <[hidden email]> wrote:

> If you look at my code, the plot is of an area vs. slice number. That means that the x-values would start at 1, and go till the end of the array, increasing by 1. And it would be nice to start at 0 like normal, but then when you plot them, you would have data at the wrong slice number, since they would start at zero, not 1. I think if you look at my code a second time, this should be clear.
>
> ________________________________
>
> From: ImageJ Interest Group on behalf of Justin McGrath
> Sent: Fri 8/17/2007 9:11 PM
> To: [hidden email]
> Subject: Re: Plot bug?
>
>
>
> From the definition page at
> http://rsb.info.nih.gov/ij/developer/macro/functions.html.
>
> Plot.setLimits(xMin, xMax, yMin, yMax)
> Sets the range of the x-axis and y-axis of plots created using
> Plot.create(). Must be called immediately after Plot.create().
>
> Move Plot.setLimits() after Plot.create().
>
> Also, nothing in your code says 1-totalArea.length. Anyhow, I don't
> know why you would want the maximum x value of the graph to be the
> length of the array holding the x values. I would imagine that you
> want it to be the maximum (or slightly larger than maximum ) value of
> the values in the x array. Likewise, you want the minimum x value to
> be the minimum (or sligtly less than minimum) of the values in the x
> array, which may or may not be anywhere near 1, as you have coded.
>
>
> Having the array index match the slice number is odd. Just use
> slice_number-1 when you access values in the array.
>
> Justin
>
> On 8/17/07, Rotella, Anthony M. (GRC)[] <[hidden email]> wrote:
> > Hello all,
> >
> > I am working on plotting some data using the Plot commands, and
> > I noticed something interesting. I have been plotting arrays, and been
> > getting confusing results using the setLimits function. My code looks
> > like this:
> >
> > Plot.create("Total Area vs. Slice Number","Slice", "Total Area",
> > totalArea);
> > Plot.setColor("orange");
> > Plot.setLimits(1, totalArea.length, 0, 50000);
> > Plot.show();
> >
> > The array has a 0 value at 0 (I wanted the data to correlate with slice
> > number, so the array really starts at 1, hence the 1-totalArea.length
> > for x-values.) and then at 1 it jumps up to about 17000. Now, in the
> > plot, there are several problems:
> >
> > 1. It displays totalArea[1] somewhere around (0, 6000), optically, on
> > the plot. If I hover my mouse over that point though, it says (1,
> > 17250). Interesting....
> >
> > 2. Despite setting the y-scale to be (0, 50000), the last axis label on
> > the plot only goes up to 15000, so it probably goes up to about 17500.
> >
> > Thanks,
> >
> > Tony Rotella
> >
>