possible bug in the 'redirect to" option in Set Measurements

[Md Tamjidul Hoque]

Dear All

        I was trying to use the "redirect to" option available in the "set
Measurements" to work with image file,
        but it did not.  But, when I opened the image window (i.e used
imp.show()) it worked.

I was using:

IJ.run("Set Measurements...", "area mean min shape
redirect="+imp1.getTitle()+" decimal=9");
or,
IJ.run("Set Measurements...", "area mean min shape
redirect="+imp.getTitle()+".tif decimal=9");

Even converted the image into 8 bit assuming 'Gray' min max and mean will
not work  - ... but worked once used imp.show() before calling the above
line.


Any help or update, please.

Thanks
Tamjid

[Michael Schmid]

Hi Tamjid,

you can refer to an image by name only if the WindowManager knows  
about it - that's the only place where a list of all images and their  
name is kept.

If you create a new ImagePlus and don't show it, the WindowManager  
(and no one else except your plugin) will know about its existence.  
Then, you can't access it by its name.

So it is no bug, it has to be like that.

Instead of giing the name, you have to use the following method in  
ij.plugin.filter.Analyzer:

  /** Set the "Redirect To" image. Pass 'null' as the argument to  
disable redirected sampling. */
public static void setRedirectImage(ImagePlus imp)


Michael
________________________________________________________________

On 1 Jun 2010, at 14:11, Tamjid wrote:

> Dear All
>
>         I was trying to use the "redirect to" option available in  
> the "set
> Measurements" to work with image file,
>         but it did not.  But, when I opened the image window (i.e used
> imp.show()) it worked.
>
> I was using:
>
> IJ.run("Set Measurements...", "area mean min shape
> redirect="+imp1.getTitle()+" decimal=9");
> or,
> IJ.run("Set Measurements...", "area mean min shape
> redirect="+imp.getTitle()+".tif decimal=9");
>
> Even converted the image into 8 bit assuming 'Gray' min max and  
> mean will
> not work  - ... but worked once used imp.show() before calling the  
> above
> line.
>
>
> Any help or update, please.
>
> Thanks
> Tamjid

[Md Tamjidul Hoque]

Thanks Michael for the info. But, do you mean

I have to use

"IJ.run("Set Measurements...", "area mean min shape redirect=None
decimal=9");"

instead? I mean "redirect=None" or equivalent by passing null through the
method?

If so, then I think the philosophy behind the "redirect to" was to get some
information

from image A when you are working on image B, when B can be a modified
version of A.

I am getting outlined image from image B and need to get the intensity from
the original image A

for the corresponding outlined area.

I am using batch mode java-application and can't open window. So, what to do
in such case?

Thanks
Tamjid




On Tue, Jun 1, 2010 at 11:20 PM, Michael Schmid <[hidden email]>wrote:

> Hi Tamjid,
>
> you can refer to an image by name only if the WindowManager knows about it
> - that's the only place where a list of all images and their name is kept.
>
> If you create a new ImagePlus and don't show it, the WindowManager (and no
> one else except your plugin) will know about its existence. Then, you can't
> access it by its name.
>
> So it is no bug, it has to be like that.
>
> Instead of giing the name, you have to use the following method in
> ij.plugin.filter.Analyzer:
>
>  /** Set the "Redirect To" image. Pass 'null' as the argument to disable
> redirected sampling. */
> public static void setRedirectImage(ImagePlus imp)
>
>
> Michael
> ________________________________________________________________
>
>
> On 1 Jun 2010, at 14:11, Tamjid wrote:
>
>  Dear All
>>
>>        I was trying to use the "redirect to" option available in the "set
>> Measurements" to work with image file,
>>        but it did not.  But, when I opened the image window (i.e used
>> imp.show()) it worked.
>>
>> I was using:
>>
>> IJ.run("Set Measurements...", "area mean min shape
>> redirect="+imp1.getTitle()+" decimal=9");
>> or,
>> IJ.run("Set Measurements...", "area mean min shape
>> redirect="+imp.getTitle()+".tif decimal=9");
>>
>> Even converted the image into 8 bit assuming 'Gray' min max and mean will
>> not work  - ... but worked once used imp.show() before calling the above
>> line.
>>
>>
>> Any help or update, please.
>>
>> Thanks
>> Tamjid
>>
>

[Michael Schmid]

Hi Tamjid,

set the other measurement options, then the redirect:

IJ.run("Set Measurements...", "area mean min shape redirect=None  
decimal=9"); //clears any redirect
Analyzer.setRedirectImage(imp); //sets the redirect

Michael
________________________________________________________________

On 1 Jun 2010, at 16:10, Tamjid wrote:

> Thanks Michael for the info. But, do you mean
>
> I have to use
>
> "IJ.run("Set Measurements...", "area mean min shape redirect=None
> decimal=9");"
>
> instead? I mean "redirect=None" or equivalent by passing null  
> through the
> method?
>
> If so, then I think the philosophy behind the "redirect to" was to  
> get some
> information
>
> from image A when you are working on image B, when B can be a modified
> version of A.
>
> I am getting outlined image from image B and need to get the  
> intensity from
> the original image A
>
> for the corresponding outlined area.
>
> I am using batch mode java-application and can't open window. So,  
> what to do
> in such case?
>
> Thanks
> Tamjid
>
>
>
>
> On Tue, Jun 1, 2010 at 11:20 PM, Michael Schmid  
> <[hidden email]>wrote:
>
>> Hi Tamjid,
>>
>> you can refer to an image by name only if the WindowManager knows  
>> about it
>> - that's the only place where a list of all images and their name  
>> is kept.
>>
>> If you create a new ImagePlus and don't show it, the WindowManager  
>> (and no
>> one else except your plugin) will know about its existence. Then,  
>> you can't
>> access it by its name.
>>
>> So it is no bug, it has to be like that.
>>
>> Instead of giing the name, you have to use the following method in
>> ij.plugin.filter.Analyzer:
>>
>>  /** Set the "Redirect To" image. Pass 'null' as the argument to  
>> disable
>> redirected sampling. */
>> public static void setRedirectImage(ImagePlus imp)
>>
>>
>> Michael
>> ________________________________________________________________
>>
>>
>> On 1 Jun 2010, at 14:11, Tamjid wrote:
>>
>>  Dear All
>>>
>>>        I was trying to use the "redirect to" option available in  
>>> the "set
>>> Measurements" to work with image file,
>>>        but it did not.  But, when I opened the image window (i.e  
>>> used
>>> imp.show()) it worked.
>>>
>>> I was using:
>>>
>>> IJ.run("Set Measurements...", "area mean min shape
>>> redirect="+imp1.getTitle()+" decimal=9");
>>> or,
>>> IJ.run("Set Measurements...", "area mean min shape
>>> redirect="+imp.getTitle()+".tif decimal=9");
>>>
>>> Even converted the image into 8 bit assuming 'Gray' min max and  
>>> mean will
>>> not work  - ... but worked once used imp.show() before calling  
>>> the above
>>> line.
>>>
>>>
>>> Any help or update, please.
>>>
>>> Thanks
>>> Tamjid
>>>
>>

[Md Tamjidul Hoque]

Dear Michael

thanks and apology for mis-understanding your previous explanation. But,
the problem is still there.

Here is the part of the code sample and the problem:
===================================
Line #1: String anaStr = "...........";
Line #2: Prefs.blackBackground = false;
Line #3:
Line #4: IJ.run("Set Measurements...", "area mean min shape
redirect=None decimal=9"); //clears any redirect
Line #5:
Line #6: Analyzer.setRedirectImage(impA); //sets the redirect
Line #7:
Line #8: IJ.run(impB, "Analyze Particles...", anaStr); //
========================================

The above code does not work unless I place "impA.show();" at line #3or
# 5(but not at line #7);
It may be either to do something with "setRedirectImage()" or I am
missing something else.

And the most surprising thing to me was, by placing "impA.show();" at
line #3or # 5 it works but
it works alternatively! like if it works 1st time then it will work 3rd,
5th, 7th ...time ... and will not work
2nd, 4th, 6th ... time - ... but certainly
"Analyzer.setRedirectImage(impA);" without calling "impA.show();" before
is not working.
When it does not work it shows message, "Redirect image("ImageA") not
found." ... hope all these information will help.

Any help is much appreciated.

Thanks
Tamjid




Michael Schmid wrote:

> Hi Tamjid,
>
> set the other measurement options, then the redirect:
>
> IJ.run("Set Measurements...", "area mean min shape redirect=None
> decimal=9"); //clears any redirect
> Analyzer.setRedirectImage(imp); //sets the redirect
>
> Michael
> ________________________________________________________________
>
> On 1 Jun 2010, at 16:10, Tamjid wrote:
>
>> Thanks Michael for the info. But, do you mean
>>
>> I have to use
>>
>> "IJ.run("Set Measurements...", "area mean min shape redirect=None
>> decimal=9");"
>>
>> instead? I mean "redirect=None" or equivalent by passing null through
>> the
>> method?
>>
>> If so, then I think the philosophy behind the "redirect to" was to
>> get some
>> information
>>
>> from image A when you are working on image B, when B can be a modified
>> version of A.
>>
>> I am getting outlined image from image B and need to get the
>> intensity from
>> the original image A
>>
>> for the corresponding outlined area.
>>
>> I am using batch mode java-application and can't open window. So,
>> what to do
>> in such case?
>>
>> Thanks
>> Tamjid
>>
>>
>>
>>
>> On Tue, Jun 1, 2010 at 11:20 PM, Michael Schmid
>> <[hidden email]>wrote:
>>
>>> Hi Tamjid,
>>>
>>> you can refer to an image by name only if the WindowManager knows
>>> about it
>>> - that's the only place where a list of all images and their name is
>>> kept.
>>>
>>> If you create a new ImagePlus and don't show it, the WindowManager
>>> (and no
>>> one else except your plugin) will know about its existence. Then,
>>> you can't
>>> access it by its name.
>>>
>>> So it is no bug, it has to be like that.
>>>
>>> Instead of giing the name, you have to use the following method in
>>> ij.plugin.filter.Analyzer:
>>>
>>>  /** Set the "Redirect To" image. Pass 'null' as the argument to
>>> disable
>>> redirected sampling. */
>>> public static void setRedirectImage(ImagePlus imp)
>>>
>>>
>>> Michael
>>> ________________________________________________________________
>>>
>>>
>>> On 1 Jun 2010, at 14:11, Tamjid wrote:
>>>
>>>  Dear All
>>>>
>>>>        I was trying to use the "redirect to" option available in
>>>> the "set
>>>> Measurements" to work with image file,
>>>>        but it did not.  But, when I opened the image window (i.e used
>>>> imp.show()) it worked.
>>>>
>>>> I was using:
>>>>
>>>> IJ.run("Set Measurements...", "area mean min shape
>>>> redirect="+imp1.getTitle()+" decimal=9");
>>>> or,
>>>> IJ.run("Set Measurements...", "area mean min shape
>>>> redirect="+imp.getTitle()+".tif decimal=9");
>>>>
>>>> Even converted the image into 8 bit assuming 'Gray' min max and
>>>> mean will
>>>> not work  - ... but worked once used imp.show() before calling the
>>>> above
>>>> line.
>>>>
>>>>
>>>> Any help or update, please.
>>>>
>>>> Thanks
>>>> Tamjid
>>>>
>>>

[Rasband, Wayne (NIH/NIMH) [E]]

ImageJ 1.44b fixes a bug that caused redirected measurement of non-displayed images to fail.

-wayne

On Jun 1, 2010, at 8:12 PM, Md Tamjidul Hoque wrote:

> Dear Michael
>
> thanks and apology for mis-understanding your previous explanation. But,
> the problem is still there.
>
> Here is the part of the code sample and the problem:
> ===================================
> Line #1: String anaStr = "...........";
> Line #2: Prefs.blackBackground = false;
> Line #3:
> Line #4: IJ.run("Set Measurements...", "area mean min shape
> redirect=None decimal=9"); //clears any redirect
> Line #5:
> Line #6: Analyzer.setRedirectImage(impA); //sets the redirect
> Line #7:
> Line #8: IJ.run(impB, "Analyze Particles...", anaStr); //
> ========================================
>
> The above code does not work unless I place "impA.show();" at line #3or
> # 5(but not at line #7);
> It may be either to do something with "setRedirectImage()" or I am
> missing something else.
>
> And the most surprising thing to me was, by placing "impA.show();" at
> line #3or # 5 it works but
> it works alternatively! like if it works 1st time then it will work 3rd,
> 5th, 7th ...time ... and will not work
> 2nd, 4th, 6th ... time - ... but certainly
> "Analyzer.setRedirectImage(impA);" without calling "impA.show();" before
> is not working.
> When it does not work it shows message, "Redirect image("ImageA") not
> found." ... hope all these information will help.
>
> Any help is much appreciated.
>
> Thanks
> Tamjid
>
>
>
>
> Michael Schmid wrote:
>> Hi Tamjid,
>>
>> set the other measurement options, then the redirect:
>>
>> IJ.run("Set Measurements...", "area mean min shape redirect=None
>> decimal=9"); //clears any redirect
>> Analyzer.setRedirectImage(imp); //sets the redirect
>>
>> Michael
>> ________________________________________________________________
>>
>> On 1 Jun 2010, at 16:10, Tamjid wrote:
>>
>>> Thanks Michael for the info. But, do you mean
>>>
>>> I have to use
>>>
>>> "IJ.run("Set Measurements...", "area mean min shape redirect=None
>>> decimal=9");"
>>>
>>> instead? I mean "redirect=None" or equivalent by passing null through
>>> the
>>> method?
>>>
>>> If so, then I think the philosophy behind the "redirect to" was to
>>> get some
>>> information
>>>
>>> from image A when you are working on image B, when B can be a modified
>>> version of A.
>>>
>>> I am getting outlined image from image B and need to get the
>>> intensity from
>>> the original image A
>>>
>>> for the corresponding outlined area.
>>>
>>> I am using batch mode java-application and can't open window. So,
>>> what to do
>>> in such case?
>>>
>>> Thanks
>>> Tamjid
>>>
>>>
>>>
>>>
>>> On Tue, Jun 1, 2010 at 11:20 PM, Michael Schmid
>>> <[hidden email]>wrote:
>>>
>>>> Hi Tamjid,
>>>>
>>>> you can refer to an image by name only if the WindowManager knows
>>>> about it
>>>> - that's the only place where a list of all images and their name is
>>>> kept.
>>>>
>>>> If you create a new ImagePlus and don't show it, the WindowManager
>>>> (and no
>>>> one else except your plugin) will know about its existence. Then,
>>>> you can't
>>>> access it by its name.
>>>>
>>>> So it is no bug, it has to be like that.
>>>>
>>>> Instead of giing the name, you have to use the following method in
>>>> ij.plugin.filter.Analyzer:
>>>>
>>>> /** Set the "Redirect To" image. Pass 'null' as the argument to
>>>> disable
>>>> redirected sampling. */
>>>> public static void setRedirectImage(ImagePlus imp)
>>>>
>>>>
>>>> Michael
>>>> ________________________________________________________________
>>>>
>>>>
>>>> On 1 Jun 2010, at 14:11, Tamjid wrote:
>>>>
>>>> Dear All
>>>>>
>>>>>       I was trying to use the "redirect to" option available in
>>>>> the "set
>>>>> Measurements" to work with image file,
>>>>>       but it did not.  But, when I opened the image window (i.e used
>>>>> imp.show()) it worked.
>>>>>
>>>>> I was using:
>>>>>
>>>>> IJ.run("Set Measurements...", "area mean min shape
>>>>> redirect="+imp1.getTitle()+" decimal=9");
>>>>> or,
>>>>> IJ.run("Set Measurements...", "area mean min shape
>>>>> redirect="+imp.getTitle()+".tif decimal=9");
>>>>>
>>>>> Even converted the image into 8 bit assuming 'Gray' min max and
>>>>> mean will
>>>>> not work  - ... but worked once used imp.show() before calling the
>>>>> above
>>>>> line.
>>>>>
>>>>>
>>>>> Any help or update, please.
>>>>>
>>>>> Thanks
>>>>> Tamjid
>>>>>
>>>>

[Md Tamjidul Hoque]

Thanks Wayne - it is working nicely now.

- Tamjid

Rasband, Wayne (NIH/NIMH) [E] wrote:

> ImageJ 1.44b fixes a bug that caused redirected measurement of non-displayed images to fail.
>
> -wayne
>
> On Jun 1, 2010, at 8:12 PM, Md Tamjidul Hoque wrote:
>
>  
>> Dear Michael
>>
>> thanks and apology for mis-understanding your previous explanation. But,
>> the problem is still there.
>>
>> Here is the part of the code sample and the problem:
>> ===================================
>> Line #1: String anaStr = "...........";
>> Line #2: Prefs.blackBackground = false;
>> Line #3:
>> Line #4: IJ.run("Set Measurements...", "area mean min shape
>> redirect=None decimal=9"); //clears any redirect
>> Line #5:
>> Line #6: Analyzer.setRedirectImage(impA); //sets the redirect
>> Line #7:
>> Line #8: IJ.run(impB, "Analyze Particles...", anaStr); //
>> ========================================
>>
>> The above code does not work unless I place "impA.show();" at line #3or
>> # 5(but not at line #7);
>> It may be either to do something with "setRedirectImage()" or I am
>> missing something else.
>>
>> And the most surprising thing to me was, by placing "impA.show();" at
>> line #3or # 5 it works but
>> it works alternatively! like if it works 1st time then it will work 3rd,
>> 5th, 7th ...time ... and will not work
>> 2nd, 4th, 6th ... time - ... but certainly
>> "Analyzer.setRedirectImage(impA);" without calling "impA.show();" before
>> is not working.
>> When it does not work it shows message, "Redirect image("ImageA") not
>> found." ... hope all these information will help.
>>
>> Any help is much appreciated.
>>
>> Thanks
>> Tamjid
>>
>>
>>
>>
>> Michael Schmid wrote:
>>    
>>> Hi Tamjid,
>>>
>>> set the other measurement options, then the redirect:
>>>
>>> IJ.run("Set Measurements...", "area mean min shape redirect=None
>>> decimal=9"); //clears any redirect
>>> Analyzer.setRedirectImage(imp); //sets the redirect
>>>
>>> Michael
>>> ________________________________________________________________
>>>
>>> On 1 Jun 2010, at 16:10, Tamjid wrote:
>>>
>>>      
>>>> Thanks Michael for the info. But, do you mean
>>>>
>>>> I have to use
>>>>
>>>> "IJ.run("Set Measurements...", "area mean min shape redirect=None
>>>> decimal=9");"
>>>>
>>>> instead? I mean "redirect=None" or equivalent by passing null through
>>>> the
>>>> method?
>>>>
>>>> If so, then I think the philosophy behind the "redirect to" was to
>>>> get some
>>>> information
>>>>
>>>> from image A when you are working on image B, when B can be a modified
>>>> version of A.
>>>>
>>>> I am getting outlined image from image B and need to get the
>>>> intensity from
>>>> the original image A
>>>>
>>>> for the corresponding outlined area.
>>>>
>>>> I am using batch mode java-application and can't open window. So,
>>>> what to do
>>>> in such case?
>>>>
>>>> Thanks
>>>> Tamjid
>>>>
>>>>
>>>>
>>>>
>>>> On Tue, Jun 1, 2010 at 11:20 PM, Michael Schmid
>>>> <[hidden email]>wrote:
>>>>
>>>>        
>>>>> Hi Tamjid,
>>>>>
>>>>> you can refer to an image by name only if the WindowManager knows
>>>>> about it
>>>>> - that's the only place where a list of all images and their name is
>>>>> kept.
>>>>>
>>>>> If you create a new ImagePlus and don't show it, the WindowManager
>>>>> (and no
>>>>> one else except your plugin) will know about its existence. Then,
>>>>> you can't
>>>>> access it by its name.
>>>>>
>>>>> So it is no bug, it has to be like that.
>>>>>
>>>>> Instead of giing the name, you have to use the following method in
>>>>> ij.plugin.filter.Analyzer:
>>>>>
>>>>> /** Set the "Redirect To" image. Pass 'null' as the argument to
>>>>> disable
>>>>> redirected sampling. */
>>>>> public static void setRedirectImage(ImagePlus imp)
>>>>>
>>>>>
>>>>> Michael
>>>>> ________________________________________________________________
>>>>>
>>>>>
>>>>> On 1 Jun 2010, at 14:11, Tamjid wrote:
>>>>>
>>>>> Dear All
>>>>>          
>>>>>>       I was trying to use the "redirect to" option available in
>>>>>> the "set
>>>>>> Measurements" to work with image file,
>>>>>>       but it did not.  But, when I opened the image window (i.e used
>>>>>> imp.show()) it worked.
>>>>>>
>>>>>> I was using:
>>>>>>
>>>>>> IJ.run("Set Measurements...", "area mean min shape
>>>>>> redirect="+imp1.getTitle()+" decimal=9");
>>>>>> or,
>>>>>> IJ.run("Set Measurements...", "area mean min shape
>>>>>> redirect="+imp.getTitle()+".tif decimal=9");
>>>>>>
>>>>>> Even converted the image into 8 bit assuming 'Gray' min max and
>>>>>> mean will
>>>>>> not work  - ... but worked once used imp.show() before calling the
>>>>>> above
>>>>>> line.
>>>>>>
>>>>>>
>>>>>> Any help or update, please.
>>>>>>
>>>>>> Thanks
>>>>>> Tamjid
>>>>>>
>>>>>>