Wand and XStart,YStart

[BenTupper]

Hi All,

I am still experiencing some bad magic using the new Wand -  
specifically, I wonder if the inputs to the doWand(x,y) macro command  
have changed with the version.  I am 99% sure that in the past (at  
least in version 1.42) I provided doWand(x,y) with unscaled pixel  
coordinates even if the image had a scale.  In general I used pixel  
coordinates taken from the Results Table when the XStart and YStart  
coordinates were available.  However, it doesn't seem to me that this  
behavior is the same in version 1.43b even if I am using the wand in  
legacy mode.

Below is a short macro that loads a small scaled binary image from my  
web space (yeah for run("URL..."))  The macro loads for me with the  
following scale info...


Title: calROI-3.tif
Width:  75.06 µm (88)
Height:  65.68 µm (77)
Resolution:  1.172 pixels per µm
ID: -17
Coordinate origin:  0,0
Bits per pixel: 8 (inverting grayscale LUT)
Display range: 0-255
No Threshold
Uncalibrated
Path: calROI.tif

- Running in version 1.43b, you can see that the entire image is  
selected which is not what I expected.

- Running in version 1.42q, you can see that the particle in the upper  
left is highlighted which is what I expected.

Have I missed something in the change of Wand?  My first guess is that  
Wand is getting coords that have been changed into "real" world units,  
but a quick peek at Macro.Functions.doWand() and IJ.doWand() don't  
reveal anything funny to my eyes.  My second guess is that the  
[XStart, YStart] pixel values [16,4] are converted to a pixel just  
outside the masked pixels as [13.652  3.413].  Zooming into that  
location shows it is indeed a background pixel.

If it is the latter, then it seems I can't use XStart, YStart with  
Wand.  Ouch.

Perhaps it is because XStart, YStart appear to be on the right hand  
side of the object and Wand looks at the seed location and to its  
right for an initial boundary pixel?


// START HERE
if (startsWith(getVersion(), "1.43")){
        run("Wand Tool...", "mode=Legacy tolerance=0");
}
run("URL...", "url=http://www.tidewater.net/~pemaquid/calROI.tif");
run("Set Measurements...", "area bounding shape redirect=None  
decimal=3");
run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00  
show=Nothing display clear record");
x = getResult("XStart", 0);
y = getResult("YStart", 0);
print("Start [x,y]=", x, ", ", y);
doWand(x,y);
// END HERE

Thanks and cheers,
Ben

Ben Tupper


P.S. I sure hope you all are getting the sun that we here in Maine are  
not getting this summer. In fact, we are huddled around the fireplace  
today as it only hit 53F.  Brrr.  The only good thing about it is that  
I don't have to paint the house!

[Wayne Rasband]

This bug, introduced in v1.43a, is fixed in the v1.43c daily build.  
The XStart and YStart values saved by the particle analyzer were not  
correct.

-wayne


On Jul 7, 2009, at 7:04 PM, Ben Tupper wrote:

> Hi All,
>
> I am still experiencing some bad magic using the new Wand -  
> specifically, I wonder if the inputs to the doWand(x,y) macro  
> command have changed with the version.  I am 99% sure that in the  
> past (at least in version 1.42) I provided doWand(x,y) with  
> unscaled pixel coordinates even if the image had a scale.  In  
> general I used pixel coordinates taken from the Results Table when  
> the XStart and YStart coordinates were available.  However, it  
> doesn't seem to me that this behavior is the same in version 1.43b  
> even if I am using the wand in legacy mode.
>
> Below is a short macro that loads a small scaled binary image from  
> my web space (yeah for run("URL..."))  The macro loads for me with  
> the following scale info...
>
>
> Title: calROI-3.tif
> Width:  75.06 µm (88)
> Height:  65.68 µm (77)
> Resolution:  1.172 pixels per µm
> ID: -17
> Coordinate origin:  0,0
> Bits per pixel: 8 (inverting grayscale LUT)
> Display range: 0-255
> No Threshold
> Uncalibrated
> Path: calROI.tif
>
> - Running in version 1.43b, you can see that the entire image is  
> selected which is not what I expected.
>
> - Running in version 1.42q, you can see that the particle in the  
> upper left is highlighted which is what I expected.
>
> Have I missed something in the change of Wand?  My first guess is  
> that Wand is getting coords that have been changed into "real"  
> world units, but a quick peek at Macro.Functions.doWand() and  
> IJ.doWand() don't reveal anything funny to my eyes.  My second  
> guess is that the [XStart, YStart] pixel values [16,4] are  
> converted to a pixel just outside the masked pixels as [13.652  
> 3.413].  Zooming into that location shows it is indeed a background  
> pixel.
>
> If it is the latter, then it seems I can't use XStart, YStart with  
> Wand.  Ouch.
>
> Perhaps it is because XStart, YStart appear to be on the right hand  
> side of the object and Wand looks at the seed location and to its  
> right for an initial boundary pixel?
>
>
> // START HERE
> if (startsWith(getVersion(), "1.43")){
> run("Wand Tool...", "mode=Legacy tolerance=0");
> }
> run("URL...", "url=http://www.tidewater.net/~pemaquid/calROI.tif");
> run("Set Measurements...", "area bounding shape redirect=None  
> decimal=3");
> run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00  
> show=Nothing display clear record");
> x = getResult("XStart", 0);
> y = getResult("YStart", 0);
> print("Start [x,y]=", x, ", ", y);
> doWand(x,y);
> // END HERE
>
> Thanks and cheers,
> Ben
>
> Ben Tupper
>
>
> P.S. I sure hope you all are getting the sun that we here in Maine  
> are not getting this summer. In fact, we are huddled around the  
> fireplace today as it only hit 53F.  Brrr.  The only good thing  
> about it is that I don't have to paint the house!

[BenTupper]

Thanks, Wayne!



On Jul 7, 2009, at 10:34 PM, Rasband Wayne wrote:

> This bug, introduced in v1.43a, is fixed in the v1.43c daily build.  
> The XStart and YStart values saved by the particle analyzer were not  
> correct.
>
> -wayne
>
>
> On Jul 7, 2009, at 7:04 PM, Ben Tupper wrote:
>
>> Hi All,
>>
>> I am still experiencing some bad magic using the new Wand -  
>> specifically, I wonder if the inputs to the doWand(x,y) macro  
>> command have changed with the version.  I am 99% sure that in the  
>> past (at least in version 1.42) I provided doWand(x,y) with  
>> unscaled pixel coordinates even if the image had a scale.  In  
>> general I used pixel coordinates taken from the Results Table when  
>> the XStart and YStart coordinates were available.  However, it  
>> doesn't seem to me that this behavior is the same in version 1.43b  
>> even if I am using the wand in legacy mode.
>>
>> Below is a short macro that loads a small scaled binary image from  
>> my web space (yeah for run("URL..."))  The macro loads for me with  
>> the following scale info...
>>
>>
>> Title: calROI-3.tif
>> Width:  75.06 µm (88)
>> Height:  65.68 µm (77)
>> Resolution:  1.172 pixels per µm
>> ID: -17
>> Coordinate origin:  0,0
>> Bits per pixel: 8 (inverting grayscale LUT)
>> Display range: 0-255
>> No Threshold
>> Uncalibrated
>> Path: calROI.tif
>>
>> - Running in version 1.43b, you can see that the entire image is  
>> selected which is not what I expected.
>>
>> - Running in version 1.42q, you can see that the particle in the  
>> upper left is highlighted which is what I expected.
>>
>> Have I missed something in the change of Wand?  My first guess is  
>> that Wand is getting coords that have been changed into "real"  
>> world units, but a quick peek at Macro.Functions.doWand() and  
>> IJ.doWand() don't reveal anything funny to my eyes.  My second  
>> guess is that the [XStart, YStart] pixel values [16,4] are  
>> converted to a pixel just outside the masked pixels as [13.652  
>> 3.413].  Zooming into that location shows it is indeed a background  
>> pixel.
>>
>> If it is the latter, then it seems I can't use XStart, YStart with  
>> Wand.  Ouch.
>>
>> Perhaps it is because XStart, YStart appear to be on the right hand  
>> side of the object and Wand looks at the seed location and to its  
>> right for an initial boundary pixel?
>>
>>
>> // START HERE
>> if (startsWith(getVersion(), "1.43")){
>> run("Wand Tool...", "mode=Legacy tolerance=0");
>> }
>> run("URL...", "url=http://www.tidewater.net/~pemaquid/calROI.tif");
>> run("Set Measurements...", "area bounding shape redirect=None  
>> decimal=3");
>> run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00  
>> show=Nothing display clear record");
>> x = getResult("XStart", 0);
>> y = getResult("YStart", 0);
>> print("Start [x,y]=", x, ", ", y);
>> doWand(x,y);
>> // END HERE
>>
>> Thanks and cheers,
>> Ben
>>
>> Ben Tupper
>>
>>
>> P.S. I sure hope you all are getting the sun that we here in Maine  
>> are not getting this summer. In fact, we are huddled around the  
>> fireplace today as it only hit 53F.  Brrr.  The only good thing  
>> about it is that I don't have to paint the house!

Ben Tupper