http://imagej.273.s1.nabble.com/Image-Thresholding-for-Binary-workflow-tp5007850p5007876.html
oops, there is one more macro function that I overlooked, probably the method of choice:
Changes pixels in the image or selection that have a value in the range v1-v2 to v3. For example, changeValues(0,5,5) changes all pixels less than 5 to 5.
is slower than Java code: The code is executed not in Java but in the ImageJ macro interpreter. For each pixel, it reads you macro code again and then decides what to do, based on that code. Of course, this takes additional time, even though the ImageJ macro interpreter is programmed very efficiently.
On May 23, 2014, at 16:03, Rainer M. Engel wrote:
> Thank you Michael and Jan,
>
> good advice which will work in most cases. Very good.
>
> Then, what would be the best (fastest) method to filter for a distinct
> color value. The Macro Expression did not seem to be very fast on that.
>
> Someting like "Replace value" (Plugin, FIJI) for 32bit images would be
> great, although I did not test it for speed so far.
>
> Speed:
> run("Macro...", "code=[if (v==127) v=0;]"); -> 12547ms
> run("Replace value", "pattern=127 replacement=0"); -> 125ms
>
> But the plugin does not care about ROIs ...
>
> I'm not sure if I can modify the plugins code, anyway, maybe I'll have a
> look some time. Should be feasible ;-)
>
> Best regards,
> Rainer
>
>
> Am 23.05.2014 14:59, schrieb Michael Schmid:
>> Hi Rainer,
>>
>>> Process > Binary > Make Binary
>>> sometimes caused plausible black/white dominance switches.
>>
>> If you have this problem, it is most likely caused by different settings of 'Black Background' in Process>Binary>Options. You should also check whether the image has an inverted LUT.
>>
>>> I tried ..
>>> setMinAndMax(173, 173);
>>> .. but this does no clamping like I thought it might..
>>
>> The setMinAndMax changes only the display, not the image data. For 8-bit images, this is done via the LUT, so you can apply the LUT afterwards, and the image will be converted to 0 (values less or equal 173) and 255 (values higher than 173). The mapping will be independent on LUT and Black background settings:
>>
>> setMinAndMax(173, 173);
>> run("Apply LUT");
>>
>>
>> Michael
>> ________________________________________________________________
>> On May 22, 2014, at 11:23, Rainer M. Engel wrote:
>>
>>> Hello together,
>>>
>>> I'm looking for way to threshold an image and in the same process making
>>> it binary.
>>>
>>> Process > Binary > Make Binary
>>> sometimes caused plausible black/white dominance switches.
>>>
>>> Process > Math > Macro
>>> works better for my purposes (i.e.| if (v<=25) v=0; else v=255)
>>>
>>> The later Expression is very slow compared even to an Gaussian Blur or
>>> similar. Are there other, hopefully faster ways (for high resolution) to
>>> threshold and make binary (8bit)?
>>>
>>> I tried ..
>>> setMinAndMax(173, 173);
>>> .. but this does no clamping like I thought it might..
>>>
>>> Any help is much appreciated.
>>>
>>> Best regards,
>>> Rainer
>>
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