ij.gui.Plot enhancement request...

[Jeffrey B. Woodward]

ImageJ'ers/Wayne,

I am trying to use the ij.gui.Plot class to create a scatter plot.
Actually, the Plot contains both a scatter plot and a simple curve
(diagonal line with points at [0,0] and [max,max]). The diagonal line is
just for a visual reference; the real data points are what make up the
scatter plot. The issue is that in doing this, I can't find a way for
the user to use the List button (or the Save button) to get a listing of
the data points. This is because the List/Save buttons seem only appear
to operate on the points used in the constructor (in my case the
endpoints of the reference diagonal), but my data points for the scatter
plot are added after construction using the addPoints() method.

My first thought was to supply my scatter plot points in the constructor
and add the reference line with the addPoints() method; however, I don't
see any way to avoid drawing them as a polyline doing it this way -- I
want a scatter plot of those points, not a polyline!

Hopefully I am missing something obvious in the API/source code, but in
case if I am not, is this an enhancement that the ImageJ community is
interested in? Should I take a crack at this myself, or is somebody else
interested enough to do it?

BTW: I suppose that there may be a hack/workaround for my specific
case...perhaps I could supply my points in the constructor drawn with a
fully transparent color/invisible-ink, then add the points for my
reference diagonal using the addPoints() method with a LINE shape and
appropriate color, and lastly, add the scatter plot points [again] with
the addPoints() method with a DOT shape and appropriate color. Seems
ugly -- probably doomed to failure -- other
suggestions/hacks/workarounds/free-therapy-sessions are welcome.

Many thanks,

-Woody

[jmutterer]

Unintuitively, the last serie added to a plot is drawn first. Add the line
reference after your data points, and the list button will list your points.

Jerome.

Plot.add("dots", x, y);
Plot.add("line", newArray(0,x.length),newArray(0,y.length));

On Thu, Nov 13, 2008 at 7:32 AM, Jeffrey B. Woodward <
[hidden email]> wrote:

> ImageJ'ers/Wayne,
>
> I am trying to use the ij.gui.Plot class to create a scatter plot.
> Actually, the Plot contains both a scatter plot and a simple curve (diagonal
> line with points at [0,0] and [max,max]). The diagonal line is just for a
> visual reference; the real data points are what make up the scatter plot.
> The issue is that in doing this, I can't find a way for the user to use the
> List button (or the Save button) to get a listing of the data points. This
> is because the List/Save buttons seem only appear to operate on the points
> used in the constructor (in my case the endpoints of the reference
> diagonal), but my data points for the scatter plot are added after
> construction using the addPoints() method.
>
> My first thought was to supply my scatter plot points in the constructor
> and add the reference line with the addPoints() method; however, I don't see
> any way to avoid drawing them as a polyline doing it this way -- I want a
> scatter plot of those points, not a polyline!
>
> Hopefully I am missing something obvious in the API/source code, but in
> case if I am not, is this an enhancement that the ImageJ community is
> interested in? Should I take a crack at this myself, or is somebody else
> interested enough to do it?
>
> BTW: I suppose that there may be a hack/workaround for my specific
> case...perhaps I could supply my points in the constructor drawn with a
> fully transparent color/invisible-ink, then add the points for my reference
> diagonal using the addPoints() method with a LINE shape and appropriate
> color, and lastly, add the scatter plot points [again] with the addPoints()
> method with a DOT shape and appropriate color. Seems ugly -- probably doomed
> to failure -- other suggestions/hacks/workarounds/free-therapy-sessions are
> welcome.
>
> Many thanks,
>
> -Woody
>

[Michael Schmid]

Hi Woody,

yes, I agree, the Plot class stores only one set of data, it is the  
data that you submit with the constructor. Everything that you add  
later is plotted (in the sequence that you add it) but not stored as  
data. Finally, with Plot.show() [or in a java program, plot.show()]  
the data submitted with the constructor are plotted with the current  
color and line type settings, but always as a line.
Plot.draw calls drawPolyline, not addPoints, so there is no way out  
with the current version of ImageJ (sorry, Jerome, your version won't  
let you list the data)

It is not so clear what could be a good solution.

- Storing all data and listing them in separate columns?
This has the disadvantage that auxiliary lines such as your diagonal  
or a horizontal line plotted to show the x axis (at y=0 for plots  
with positive and negative values) would generate extra data in the  
list.
Also, it might break existing macros or procedures relying on getting  
only one y column of data.

- Adding a Plot.setShape(shape) method and calling addPoints instead  
of drawPolyline in Plot.draw?
This would perpetuate the counterintuitive problem that you have to  
set the shape, line width and color for the data passed in the  
constructor after all the other addPoints methods.

- Passing shape, size/lineWidth and color of the initial data with  
the constructor?
This would add at least two very long constructors (for float and  
double arrays).

    public Plot(String title, String xLabel, String yLabel, double[]  
xValues, double[] yValues, int flags, int shape, int lineWidth, Color  
color)

Also not extremely elegant...

Any better idea?

Michael
________________________________________________________________

On 13 Nov 2008, at 08:14, Jerome Mutterer wrote:

> Unintuitively, the last serie added to a plot is drawn first. Add  
> the line
> reference after your data points, and the list button will list  
> your points.
>
> Jerome.
>
> Plot.add("dots", x, y);
> Plot.add("line", newArray(0,x.length),newArray(0,y.length));
>
> On Thu, Nov 13, 2008 at 7:32 AM, Jeffrey B. Woodward <
> [hidden email]> wrote:
>
>> ImageJ'ers/Wayne,
>>
>> I am trying to use the ij.gui.Plot class to create a scatter plot.
>> Actually, the Plot contains both a scatter plot and a simple curve  
>> (diagonal
>> line with points at [0,0] and [max,max]). The diagonal line is  
>> just for a
>> visual reference; the real data points are what make up the  
>> scatter plot.
>> The issue is that in doing this, I can't find a way for the user  
>> to use the
>> List button (or the Save button) to get a listing of the data  
>> points. This
>> is because the List/Save buttons seem only appear to operate on  
>> the points
>> used in the constructor (in my case the endpoints of the reference
>> diagonal), but my data points for the scatter plot are added after
>> construction using the addPoints() method.
>>
>> My first thought was to supply my scatter plot points in the  
>> constructor
>> and add the reference line with the addPoints() method; however, I  
>> don't see
>> any way to avoid drawing them as a polyline doing it this way -- I  
>> want a
>> scatter plot of those points, not a polyline!
>>
>> Hopefully I am missing something obvious in the API/source code,  
>> but in
>> case if I am not, is this an enhancement that the ImageJ community is
>> interested in? Should I take a crack at this myself, or is  
>> somebody else
>> interested enough to do it?
>>
>> BTW: I suppose that there may be a hack/workaround for my specific
>> case...perhaps I could supply my points in the constructor drawn  
>> with a
>> fully transparent color/invisible-ink, then add the points for my  
>> reference
>> diagonal using the addPoints() method with a LINE shape and  
>> appropriate
>> color, and lastly, add the scatter plot points [again] with the  
>> addPoints()
>> method with a DOT shape and appropriate color. Seems ugly --  
>> probably doomed
>> to failure -- other suggestions/hacks/workarounds/free-therapy-
>> sessions are
>> welcome.
>>
>> Many thanks,
>>
>> -Woody
>>

[jmutterer]

The trick is to call the contructor with two null double arrays. The
following plugin allows listing of the data points.

public class plot_test implements PlugIn {

    public void run(String arg) {
        if (IJ.versionLessThan("1.30c"))
            return;

        float[] x = {0.1f, 0.25f, 0.35f, 0.5f,
0.61f,0.7f,0.85f,0.89f,0.95f}; // x-coordinates
        float[] y = {2f,5.6f,7.4f,9f,9.4f,8.7f,6.3f,4.5f,1f}; //
x-coordinates

        float[] x2 = {0f,1f};
        float[] y2 = {0f,1f};

        double[] a = null;
        double [] b =null;

        Plot plot = new Plot("Example Plot","X Axis","Y Axis",a,b);
        plot.setLimits(0, 1, 0, 10);
        plot.setLineWidth(2);
        plot.addPoints(x,y,PlotWindow.X);
        plot.addPoints(x2,y2,PlotWindow.LINE);
        plot.show();
    }
}


Jerome


On Thu, Nov 13, 2008 at 11:41 AM, Michael Schmid <[hidden email]>wrote:

> Hi Woody,
>
> yes, I agree, the Plot class stores only one set of data, it is the data
> that you submit with the constructor. Everything that you add later is
> plotted (in the sequence that you add it) but not stored as data. Finally,
> with Plot.show() [or in a java program, plot.show()] the data submitted with
> the constructor are plotted with the current color and line type settings,
> but always as a line.
> Plot.draw calls drawPolyline, not addPoints, so there is no way out with
> the current version of ImageJ (sorry, Jerome, your version won't let you
> list the data)
>
> It is not so clear what could be a good solution.
>
> - Storing all data and listing them in separate columns?
> This has the disadvantage that auxiliary lines such as your diagonal or a
> horizontal line plotted to show the x axis (at y=0 for plots with positive
> and negative values) would generate extra data in the list.
> Also, it might break existing macros or procedures relying on getting only
> one y column of data.
>
> - Adding a Plot.setShape(shape) method and calling addPoints instead of
> drawPolyline in Plot.draw?
> This would perpetuate the counterintuitive problem that you have to set the
> shape, line width and color for the data passed in the constructor after all
> the other addPoints methods.
>
> - Passing shape, size/lineWidth and color of the initial data with the
> constructor?
> This would add at least two very long constructors (for float and double
> arrays).
>
>   public Plot(String title, String xLabel, String yLabel, double[] xValues,
> double[] yValues, int flags, int shape, int lineWidth, Color color)
>
> Also not extremely elegant...
>
> Any better idea?
>
> Michael
> ________________________________________________________________
>
>
> On 13 Nov 2008, at 08:14, Jerome Mutterer wrote:
>
>  Unintuitively, the last serie added to a plot is drawn first. Add the line
>> reference after your data points, and the list button will list your
>> points.
>>
>> Jerome.
>>
>> Plot.add("dots", x, y);
>> Plot.add("line", newArray(0,x.length),newArray(0,y.length));
>>
>> On Thu, Nov 13, 2008 at 7:32 AM, Jeffrey B. Woodward <
>> [hidden email]> wrote:
>>
>>  ImageJ'ers/Wayne,
>>>
>>> I am trying to use the ij.gui.Plot class to create a scatter plot.
>>> Actually, the Plot contains both a scatter plot and a simple curve
>>> (diagonal
>>> line with points at [0,0] and [max,max]). The diagonal line is just for a
>>> visual reference; the real data points are what make up the scatter plot.
>>> The issue is that in doing this, I can't find a way for the user to use
>>> the
>>> List button (or the Save button) to get a listing of the data points.
>>> This
>>> is because the List/Save buttons seem only appear to operate on the
>>> points
>>> used in the constructor (in my case the endpoints of the reference
>>> diagonal), but my data points for the scatter plot are added after
>>> construction using the addPoints() method.
>>>
>>> My first thought was to supply my scatter plot points in the constructor
>>> and add the reference line with the addPoints() method; however, I don't
>>> see
>>> any way to avoid drawing them as a polyline doing it this way -- I want a
>>> scatter plot of those points, not a polyline!
>>>
>>> Hopefully I am missing something obvious in the API/source code, but in
>>> case if I am not, is this an enhancement that the ImageJ community is
>>> interested in? Should I take a crack at this myself, or is somebody else
>>> interested enough to do it?
>>>
>>> BTW: I suppose that there may be a hack/workaround for my specific
>>> case...perhaps I could supply my points in the constructor drawn with a
>>> fully transparent color/invisible-ink, then add the points for my
>>> reference
>>> diagonal using the addPoints() method with a LINE shape and appropriate
>>> color, and lastly, add the scatter plot points [again] with the
>>> addPoints()
>>> method with a DOT shape and appropriate color. Seems ugly -- probably
>>> doomed
>>> to failure -- other suggestions/hacks/workarounds/free-therapy-sessions
>>> are
>>> welcome.
>>>
>>> Many thanks,
>>>
>>> -Woody
>>>
>>>

[Michael Schmid]

Hi Jerome,

you are right!

Sorry, I had overlooked the last few lines of Plot.addPoints  
responsible for this feature so I thought it was impossible.

Michael
________________________________________________________________

On 13 Nov 2008, at 14:44, Jerome Mutterer wrote:

> The trick is to call the contructor with two null double arrays. The
> following plugin allows listing of the data points.
>
> public class plot_test implements PlugIn {
>
>     public void run(String arg) {
>         if (IJ.versionLessThan("1.30c"))
>             return;
>
>         float[] x = {0.1f, 0.25f, 0.35f, 0.5f,
> 0.61f,0.7f,0.85f,0.89f,0.95f}; // x-coordinates
>         float[] y = {2f,5.6f,7.4f,9f,9.4f,8.7f,6.3f,4.5f,1f}; //
> x-coordinates
>
>         float[] x2 = {0f,1f};
>         float[] y2 = {0f,1f};
>
>         double[] a = null;
>         double [] b =null;
>
>         Plot plot = new Plot("Example Plot","X Axis","Y Axis",a,b);
>         plot.setLimits(0, 1, 0, 10);
>         plot.setLineWidth(2);
>         plot.addPoints(x,y,PlotWindow.X);
>         plot.addPoints(x2,y2,PlotWindow.LINE);
>         plot.show();
>     }
> }
>
>
> Jerome
>
>
> On Thu, Nov 13, 2008 at 11:41 AM, Michael Schmid  
> <[hidden email]>wrote:
>
>> Hi Woody,
>>
>> yes, I agree, the Plot class stores only one set of data, it is  
>> the data
>> that you submit with the constructor. Everything that you add  
>> later is
>> plotted (in the sequence that you add it) but not stored as data.  
>> Finally,
>> with Plot.show() [or in a java program, plot.show()] the data  
>> submitted with
>> the constructor are plotted with the current color and line type  
>> settings,
>> but always as a line.
>> Plot.draw calls drawPolyline, not addPoints, so there is no way  
>> out with
>> the current version of ImageJ (sorry, Jerome, your version won't  
>> let you
>> list the data)
>>
>> It is not so clear what could be a good solution.
>>
>> - Storing all data and listing them in separate columns?
>> This has the disadvantage that auxiliary lines such as your  
>> diagonal or a
>> horizontal line plotted to show the x axis (at y=0 for plots with  
>> positive
>> and negative values) would generate extra data in the list.
>> Also, it might break existing macros or procedures relying on  
>> getting only
>> one y column of data.
>>
>> - Adding a Plot.setShape(shape) method and calling addPoints  
>> instead of
>> drawPolyline in Plot.draw?
>> This would perpetuate the counterintuitive problem that you have  
>> to set the
>> shape, line width and color for the data passed in the constructor  
>> after all
>> the other addPoints methods.
>>
>> - Passing shape, size/lineWidth and color of the initial data with  
>> the
>> constructor?
>> This would add at least two very long constructors (for float and  
>> double
>> arrays).
>>
>>   public Plot(String title, String xLabel, String yLabel, double[]  
>> xValues,
>> double[] yValues, int flags, int shape, int lineWidth, Color color)
>>
>> Also not extremely elegant...
>>
>> Any better idea?
>>
>> Michael
>> ________________________________________________________________
>>
>>
>> On 13 Nov 2008, at 08:14, Jerome Mutterer wrote:
>>
>>  Unintuitively, the last serie added to a plot is drawn first. Add  
>> the line
>>> reference after your data points, and the list button will list your
>>> points.
>>>
>>> Jerome.
>>>
>>> Plot.add("dots", x, y);
>>> Plot.add("line", newArray(0,x.length),newArray(0,y.length));
>>>
>>> On Thu, Nov 13, 2008 at 7:32 AM, Jeffrey B. Woodward <
>>> [hidden email]> wrote:
>>>
>>>  ImageJ'ers/Wayne,
>>>>
>>>> I am trying to use the ij.gui.Plot class to create a scatter plot.
>>>> Actually, the Plot contains both a scatter plot and a simple curve
>>>> (diagonal
>>>> line with points at [0,0] and [max,max]). The diagonal line is  
>>>> just for a
>>>> visual reference; the real data points are what make up the  
>>>> scatter plot.
>>>> The issue is that in doing this, I can't find a way for the user  
>>>> to use
>>>> the
>>>> List button (or the Save button) to get a listing of the data  
>>>> points.
>>>> This
>>>> is because the List/Save buttons seem only appear to operate on the
>>>> points
>>>> used in the constructor (in my case the endpoints of the reference
>>>> diagonal), but my data points for the scatter plot are added after
>>>> construction using the addPoints() method.
>>>>
>>>> My first thought was to supply my scatter plot points in the  
>>>> constructor
>>>> and add the reference line with the addPoints() method; however,  
>>>> I don't
>>>> see
>>>> any way to avoid drawing them as a polyline doing it this way --  
>>>> I want a
>>>> scatter plot of those points, not a polyline!
>>>>
>>>> Hopefully I am missing something obvious in the API/source code,  
>>>> but in
>>>> case if I am not, is this an enhancement that the ImageJ  
>>>> community is
>>>> interested in? Should I take a crack at this myself, or is  
>>>> somebody else
>>>> interested enough to do it?
>>>>
>>>> BTW: I suppose that there may be a hack/workaround for my specific
>>>> case...perhaps I could supply my points in the constructor drawn  
>>>> with a
>>>> fully transparent color/invisible-ink, then add the points for my
>>>> reference
>>>> diagonal using the addPoints() method with a LINE shape and  
>>>> appropriate
>>>> color, and lastly, add the scatter plot points [again] with the
>>>> addPoints()
>>>> method with a DOT shape and appropriate color. Seems ugly --  
>>>> probably
>>>> doomed
>>>> to failure -- other suggestions/hacks/workarounds/free-therapy-
>>>> sessions
>>>> are
>>>> welcome.
>>>>
>>>> Many thanks,
>>>>
>>>> -Woody
>>>>
>>>>

[Jeffrey B. Woodward]

Thank you Jerome and Michael for your help on this one. I missed those
lines in the source as well!

-Woody


Michael Schmid wrote:

> Hi Jerome,
>
> you are right!
>
> Sorry, I had overlooked the last few lines of Plot.addPoints
> responsible for this feature so I thought it was impossible.
>
> Michael
> ________________________________________________________________
>
> On 13 Nov 2008, at 14:44, Jerome Mutterer wrote:
>
>> The trick is to call the contructor with two null double arrays. The
>> following plugin allows listing of the data points.
>>
>> public class plot_test implements PlugIn {
>>
>>     public void run(String arg) {
>>         if (IJ.versionLessThan("1.30c"))
>>             return;
>>
>>         float[] x = {0.1f, 0.25f, 0.35f, 0.5f,
>> 0.61f,0.7f,0.85f,0.89f,0.95f}; // x-coordinates
>>         float[] y = {2f,5.6f,7.4f,9f,9.4f,8.7f,6.3f,4.5f,1f}; //
>> x-coordinates
>>
>>         float[] x2 = {0f,1f};
>>         float[] y2 = {0f,1f};
>>
>>         double[] a = null;
>>         double [] b =null;
>>
>>         Plot plot = new Plot("Example Plot","X Axis","Y Axis",a,b);
>>         plot.setLimits(0, 1, 0, 10);
>>         plot.setLineWidth(2);
>>         plot.addPoints(x,y,PlotWindow.X);
>>         plot.addPoints(x2,y2,PlotWindow.LINE);
>>         plot.show();
>>     }
>> }
>>
>>
>> Jerome
>>
>>
>> On Thu, Nov 13, 2008 at 11:41 AM, Michael Schmid
>> <[hidden email]>wrote:
>>
>>> Hi Woody,
>>>
>>> yes, I agree, the Plot class stores only one set of data, it is the
>>> data
>>> that you submit with the constructor. Everything that you add later is
>>> plotted (in the sequence that you add it) but not stored as data.
>>> Finally,
>>> with Plot.show() [or in a java program, plot.show()] the data
>>> submitted with
>>> the constructor are plotted with the current color and line type
>>> settings,
>>> but always as a line.
>>> Plot.draw calls drawPolyline, not addPoints, so there is no way out
>>> with
>>> the current version of ImageJ (sorry, Jerome, your version won't let
>>> you
>>> list the data)
>>>
>>> It is not so clear what could be a good solution.
>>>
>>> - Storing all data and listing them in separate columns?
>>> This has the disadvantage that auxiliary lines such as your diagonal
>>> or a
>>> horizontal line plotted to show the x axis (at y=0 for plots with
>>> positive
>>> and negative values) would generate extra data in the list.
>>> Also, it might break existing macros or procedures relying on
>>> getting only
>>> one y column of data.
>>>
>>> - Adding a Plot.setShape(shape) method and calling addPoints instead of
>>> drawPolyline in Plot.draw?
>>> This would perpetuate the counterintuitive problem that you have to
>>> set the
>>> shape, line width and color for the data passed in the constructor
>>> after all
>>> the other addPoints methods.
>>>
>>> - Passing shape, size/lineWidth and color of the initial data with the
>>> constructor?
>>> This would add at least two very long constructors (for float and
>>> double
>>> arrays).
>>>
>>>   public Plot(String title, String xLabel, String yLabel, double[]
>>> xValues,
>>> double[] yValues, int flags, int shape, int lineWidth, Color color)
>>>
>>> Also not extremely elegant...
>>>
>>> Any better idea?
>>>
>>> Michael
>>> ________________________________________________________________
>>>
>>>
>>> On 13 Nov 2008, at 08:14, Jerome Mutterer wrote:
>>>
>>>  Unintuitively, the last serie added to a plot is drawn first. Add
>>> the line
>>>> reference after your data points, and the list button will list your
>>>> points.
>>>>
>>>> Jerome.
>>>>
>>>> Plot.add("dots", x, y);
>>>> Plot.add("line", newArray(0,x.length),newArray(0,y.length));
>>>>
>>>> On Thu, Nov 13, 2008 at 7:32 AM, Jeffrey B. Woodward <
>>>> [hidden email]> wrote:
>>>>
>>>>  ImageJ'ers/Wayne,
>>>>>
>>>>> I am trying to use the ij.gui.Plot class to create a scatter plot.
>>>>> Actually, the Plot contains both a scatter plot and a simple curve
>>>>> (diagonal
>>>>> line with points at [0,0] and [max,max]). The diagonal line is
>>>>> just for a
>>>>> visual reference; the real data points are what make up the
>>>>> scatter plot.
>>>>> The issue is that in doing this, I can't find a way for the user
>>>>> to use
>>>>> the
>>>>> List button (or the Save button) to get a listing of the data points.
>>>>> This
>>>>> is because the List/Save buttons seem only appear to operate on the
>>>>> points
>>>>> used in the constructor (in my case the endpoints of the reference
>>>>> diagonal), but my data points for the scatter plot are added after
>>>>> construction using the addPoints() method.
>>>>>
>>>>> My first thought was to supply my scatter plot points in the
>>>>> constructor
>>>>> and add the reference line with the addPoints() method; however, I
>>>>> don't
>>>>> see
>>>>> any way to avoid drawing them as a polyline doing it this way -- I
>>>>> want a
>>>>> scatter plot of those points, not a polyline!
>>>>>
>>>>> Hopefully I am missing something obvious in the API/source code,
>>>>> but in
>>>>> case if I am not, is this an enhancement that the ImageJ community is
>>>>> interested in? Should I take a crack at this myself, or is
>>>>> somebody else
>>>>> interested enough to do it?
>>>>>
>>>>> BTW: I suppose that there may be a hack/workaround for my specific
>>>>> case...perhaps I could supply my points in the constructor drawn
>>>>> with a
>>>>> fully transparent color/invisible-ink, then add the points for my
>>>>> reference
>>>>> diagonal using the addPoints() method with a LINE shape and
>>>>> appropriate
>>>>> color, and lastly, add the scatter plot points [again] with the
>>>>> addPoints()
>>>>> method with a DOT shape and appropriate color. Seems ugly -- probably
>>>>> doomed
>>>>> to failure -- other
>>>>> suggestions/hacks/workarounds/free-therapy-sessions
>>>>> are
>>>>> welcome.
>>>>>
>>>>> Many thanks,
>>>>>
>>>>> -Woody
>>>>>
>>>>>
>
>