> After successfully cropping 8 wells from a folder (in the first post I just
> aimed to crop 4 wells in first row, now I add another variant j to include
> second row), I moved on to make it easier for batch process:
> select a folder with raw data, pattern crop, create 8 subfolders in the
> same folder with raw data, the cropped images are saved in these 8
> subfolders.
>
> This is what I did:
>
> *sdir = getDirectory("choose source directory ");
> run("Image Sequence...", "open=sdir number=20 starting=1 increment=1
>
> scale=100 file=[] or=[] sort");
> for (i=0; i<4; i++) {
> for (j=0; j<2; j++) {
> makeRectangle(78+251*i, 349+303*j, 216, 216);
> well ="well-"+i+j + File.separator;
> ddir = sdir+well;
> File.makeDirectory(ddir);
> run("Duplicate...", "title="+j+1+"_"+i+1+" duplicate range=6-
>
> 20");
> run("Image Sequence... ", "format=TIFF name= ["+well+"]
> start=0 digits=4 save=["+ddir+"]");
> run("Close");
> }
> }*
>
> The problem is there are 5 subfolders created, with name such as "well-0" to
> "well-4", inside the cropped images respond to 0-0,1-0,2-0,3-0,3-1, if I
> name the 8 wells by "i-j" format:
>
> 0-0 1-0 2-0 3-0
> 0-1 1-1 2-1 3-1
>
> My guess is imageJ read my macro "+i+j" in "*well ="well-"+i+j +
> File.separator;*" as a math addition, so 0-0 go into fldler well-0, 1-0 go
> into folder well-1, and so on, because 1-0 and 0-1' addition result are the
> same (0+1=1+0), somehow imageJ skip 0-1, the same for 1-1 and 2-1 were
> skipped.
>
> How can I fix this? Thanks again for the gracious help!
>
> Zheng
>
> 2011/7/27 Peter Haub <
[hidden email]>
>
>> Hi Zheng,
>>
>> correct the last 'saveAs' statement
>>
>> saveAs("tiff", "C:\\Documents and Settings\\WangLab\\Desktop\\**
>> TRYZZ\\"+i+");
>>
>> to
>>
>> saveAs("tiff", "C:\\Documents and Settings\\WangLab\\Desktop\\**
>> TRYZZ\\"+i+"");
>>
>> or
>>
>> saveAs("tiff", "C:\\Documents and Settings\\WangLab\\Desktop\\**
>> TRYZZ\\"+i);
>>
>> peter
>>
>>
>>
>> On 28.07.2011 05:33, zezh1112 wrote:
>>
>>> Hi everyone,
>>>
>>> This is my first time to try to write a ImageJ micro, so sorry for the
>>> easy
>>> question I will ask,
>>>
>>> The situation is that I have a plate within which there are 8 wells （4
>>> wells
>>> in one row, 2 rows together, in the attachment you can find one pic
>>> showing
>>> this pattern）, one fruit fly is moving around in each well. I recorded
>>> these
>>> 8 flies at a certain frequency within observation time, so I got a bunch
>>> of
>>> images in the end (the only thing moving is flies) . I want to crop each
>>> well from the whole plate picture, then run the object tracking plugin to
>>> check locomotion of this fly. Since the pattern of 8 wells is constant,
>>> instead of manually cropping each well, I hope I can write a macro to
>>> "pattern crop" the 8 wells at the same time.
>>>
>>> My main logic is by changing the x and y value of "makeRectangle" to crop
>>> consequential wells. (below is two trials hoping to crop the 4 wells in
>>> the
>>> first row, after success I would go on to add the second row)
>>>
>>> *I tried first the most straight-forward way, and it works:*
>>>
>>> run("Image Sequence...", "open=[C:\\Documents and
>>> Settings\\WangLab\\Desktop\\**20110628D\\ZZ20100628D100] number=20
>>> starting=1 increment=1 scale=100 file=[] or=[] sort");
>>>
>>>
>>>
>>> makeRectangle(60+100*0, 120, 200, 200);
>>>
>>> run("Duplicate...", "title=0 duplicate range=3-20");
>>>
>>> saveAs("tiff", "C:\\Documents and Settings\\Wang Lab\\Desktop\\TRY
>>> ZZ\\0");
>>>
>>> run("Close");
>>>
>>> makeRectangle(60+100*1, 120, 200, 200);
>>>
>>> run("Duplicate...", "title=1 duplicate range=3-20");
>>>
>>> saveAs("tiff", "C:\\Documents and Settings\\Wang Lab\\Desktop\\TRY
>>> ZZ\\1");
>>>
>>> run("Close");
>>>
>>> makeRectangle(60+100*2, 120, 200, 200);
>>>
>>> run("Duplicate...", "title=2 duplicate range=3-20");
>>>
>>> saveAs("tiff", "C:\\Documents and Settings\\Wang Lab\\Desktop\\TRY
>>> ZZ\\2");
>>>
>>> run("Close");
>>>
>>> makeRectangle(60+100*3, 120, 200, 200);
>>>
>>> run("Duplicate...", "title=3 duplicate range=3-20");
>>>
>>> saveAs("tiff", "C:\\Documents and Settings\\Wang Lab\\Desktop\\TRY
>>> ZZ\\3");
>>>
>>> run("Close");
>>>
>>>
>>> *Then I used "for" loop as follows:*
>>>
>>> run("Image Sequence...", "open=[C:\\Documents and
>>> Settings\\WangLab\\Desktop\\**20110628D\\ZZ20100628D100] number=20
>>> starting=1 increment=1
>>>
>>> scale=100 file=[] or=[] sort");
>>> for (i=0; i<4; i++) {
>>> makeRectangle(60+100*i, 120, 200, 200);
>>> run("Duplicate...", "title="+i+" duplicate range=3-20");
>>> saveAs("tiff", "C:\\Documents and Settings\\WangLab\\Desktop\\**
>>> TRYZZ\\"+i+");
>>>
>>> run("close");
>>> }
>>>
>>> After I run this macro, an error pop out:
>>> ")" expected in line 6
>>> <run>("close");
>>>
>>> How can I correct this? Anyone can help me? Thanks a lot in advance!
>>>
>>> Zheng
>>>
>>>
>>> --
>>> View this message in context:
http://imagej.588099.n2.**>>> nabble.com/pattern-cropping-**tp6628531p6628531.html<
http://imagej.588099.n2.nabble.com/pattern-cropping-tp6628531p6628531.html>
>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>
>>>