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Re: Renaming files 1-99

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Jeff Hardin

Re: Renaming files 1-99

Dear Grant,

I had to write a plugin for this for Perkin-Elmer confocal stack
files. There's no other way I could figure out how to do this. I
should release this on the ImageJ web site, but need to clean it up
and comment the code. It involves (a) knowing your naming structure;
and (b) adding "0"s to pad the file name. The problem is that where
these zeroes have to go depends on the naming structure, so there is
no universal renamer that can realistically work.

Hope that helps...

Cheers,

Jeff
----------------------------------------------
Jeff Hardin
Professor, Department of Zoology
Director, Biology Core Curriculum
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: (608) 262-9634
fax: (608) 262-7319
email: [hidden email]

On Jan 4, 2007, at 11:00 PM, IMAGEJ automatic digest system wrote:

> Date: Thu, 4 Jan 2007 12:38:15 -0800
> From: "McAuley, Grant (LLU)" <[hidden email]>
> Subject: Raw Image Stacks: Image Ordering/Reordering
>
> Sorry if this has been asked before (searched list archives - maybe
> not right combination of words?).
>
> I need to import stacks of raw images using File->Import->Raw and
> selecting 'Open All Files in Folder'. The images have filenames
> that contain letters and numbers: zz-1, zz-2, ... , zz-10,
> zz-11, ..., zz-48.
>
> When the stack gets created the order becomes: zz-1, zz-10,
> zz-11, ... , zz-2, zz-21, ... instead of what I want: zz-1,
> zz-2, ..., zz-10, zz-11, ...
>
> 1) Can I tell ImageJ to do a numeric instead of alpha sort on the
> filename numbers when the stack is created?
> 2) If not, is there a better way to resort the stack than the
> 'Stack Sorter' plugin (nice, but tedious for 48 images/stack)?

Joel Sheffield

Re: Renaming files 1-99

Dear Grant,

Here's a real kludge that will only work if your files were generated
in sequential order.

It is possible to use the old DOS "DIR" command to generate a list of
files that are sorted by time/date, either by "created", "modified"
or by "accessed", and redirect this to a file. You can then use the
ImageJ List Opener plugin to open the list.

Assuming that you are running a windows machine:
1. Start>Run>CMD
2. DIR drive:/directory /OD >>drive:/directory/listfile.txt
3. In ImageJ, Plugins>List Opener

for slightly more information about the DOS DIR command, type DIR/?
in the CMD window.

This will not work if, as in the Leica SP1, all files are saved at
the same time. On the other hand, you may be lucky.

Date sent: Wed, 10 Jan 2007 11:46:08 -0600
Send reply to: ImageJ Interest Group <[hidden email]>
From: Jeff Hardin <[hidden email]>
Subject: Re: Renaming files 1-99
To: [hidden email]

> Dear Grant,
>
> I had to write a plugin for this for Perkin-Elmer confocal stack
> files. There's no other way I could figure out how to do this. I
> should release this on the ImageJ web site, but need to clean it up
> and comment the code. It involves (a) knowing your naming structure;
> and (b) adding "0"s to pad the file name. The problem is that where
> these zeroes have to go depends on the naming structure, so there is
> no universal renamer that can realistically work.
>
> Hope that helps...
>
> Cheers,
>
> Jeff
> ----------------------------------------------
> Jeff Hardin
> Professor, Department of Zoology
> Director, Biology Core Curriculum
> University of Wisconsin
> 1117 W. Johnson St.
> Madison, WI 53706
> voice: (608) 262-9634
> fax: (608) 262-7319
> email: [hidden email]
>
>
> On Jan 4, 2007, at 11:00 PM, IMAGEJ automatic digest system wrote:
>
> > Date: Thu, 4 Jan 2007 12:38:15 -0800
> > From: "McAuley, Grant (LLU)" <[hidden email]>
> > Subject: Raw Image Stacks: Image Ordering/Reordering
> >
> > Sorry if this has been asked before (searched list archives - maybe
> > not right combination of words?).
> >
> > I need to import stacks of raw images using File->Import->Raw and
> > selecting 'Open All Files in Folder'. The images have filenames
> > that contain letters and numbers: zz-1, zz-2, ... , zz-10,
> > zz-11, ..., zz-48.
> >
> > When the stack gets created the order becomes: zz-1, zz-10,
> > zz-11, ... , zz-2, zz-21, ... instead of what I want: zz-1,
> > zz-2, ..., zz-10, zz-11, ...
> >
> > 1) Can I tell ImageJ to do a numeric instead of alpha sort on the
> > filename numbers when the stack is created?
> > 2) If not, is there a better way to resort the stack than the
> > 'Stack Sorter' plugin (nice, but tedious for 48 images/stack)?

--
Joel B. Sheffield, Ph.D.
Biology Department, Temple University
1900 North 12th Street
Philadelphia, PA 19122
[hidden email]
(215) 204 8839, fax (215) 204 0486
http://astro.temple.edu/~jbs

Daniel Glen

Re: Renaming files 1-99

In reply to this post by Jeff Hardin

For another kludge, there was this posting in October:
https://list.nih.gov/cgi-bin/wa?A2=ind0610&L=imagej&H=1&P=12039

On Jan 10, 2007, at 12:46 PM, Jeff Hardin wrote:

> Dear Grant,
>
> I had to write a plugin for this for Perkin-Elmer confocal stack
> files. There's no other way I could figure out how to do this. I
> should release this on the ImageJ web site, but need to clean it up
> and comment the code. It involves (a) knowing your naming
> structure; and (b) adding "0"s to pad the file name. The problem is
> that where these zeroes have to go depends on the naming structure,
> so there is no universal renamer that can realistically work.
>
> Hope that helps...
>
> Cheers,
>
> Jeff
> ----------------------------------------------
> Jeff Hardin
> Professor, Department of Zoology
> Director, Biology Core Curriculum
> University of Wisconsin
> 1117 W. Johnson St.
> Madison, WI 53706
> voice: (608) 262-9634
> fax: (608) 262-7319
> email: [hidden email]
>
>
> On Jan 4, 2007, at 11:00 PM, IMAGEJ automatic digest system wrote:
>
>> Date: Thu, 4 Jan 2007 12:38:15 -0800
>> From: "McAuley, Grant (LLU)" <[hidden email]>
>> Subject: Raw Image Stacks: Image Ordering/Reordering
>>
>> Sorry if this has been asked before (searched list archives -
>> maybe not right combination of words?).
>>
>> I need to import stacks of raw images using File->Import->Raw and
>> selecting 'Open All Files in Folder'. The images have filenames
>> that contain letters and numbers: zz-1, zz-2, ... , zz-10,
>> zz-11, ..., zz-48.
>>
>> When the stack gets created the order becomes: zz-1, zz-10,
>> zz-11, ... , zz-2, zz-21, ... instead of what I want: zz-1,
>> zz-2, ..., zz-10, zz-11, ...
>>
>> 1) Can I tell ImageJ to do a numeric instead of alpha sort on the
>> filename numbers when the stack is created?
>> 2) If not, is there a better way to resort the stack than the
>> 'Stack Sorter' plugin (nice, but tedious for 48 images/stack)?

Kyle E. Miller

Re: Renaming files 1-99

Dear Grant,

There is a program called "A better finder rename" that is very useful for
renaming files. Just google the name of the program to find the site to
download. It costs ~$20, but works very well on both macs and pcs.

Best,

Kyle

On 1/12/07 12:33 PM, "Daniel Glen" <[hidden email]> wrote:

> For another kludge, there was this posting in October:
> https://list.nih.gov/cgi-bin/wa?A2=ind0610&L=imagej&H=1&P=12039
>
> On Jan 10, 2007, at 12:46 PM, Jeff Hardin wrote:
>
>> Dear Grant,
>>
>> I had to write a plugin for this for Perkin-Elmer confocal stack
>> files. There's no other way I could figure out how to do this. I
>> should release this on the ImageJ web site, but need to clean it up
>> and comment the code. It involves (a) knowing your naming
>> structure; and (b) adding "0"s to pad the file name. The problem is
>> that where these zeroes have to go depends on the naming structure,
>> so there is no universal renamer that can realistically work.
>>
>> Hope that helps...
>>
>> Cheers,
>>
>> Jeff
>> ----------------------------------------------
>> Jeff Hardin
>> Professor, Department of Zoology
>> Director, Biology Core Curriculum
>> University of Wisconsin
>> 1117 W. Johnson St.
>> Madison, WI 53706
>> voice: (608) 262-9634
>> fax: (608) 262-7319
>> email: [hidden email]
>>
>>
>> On Jan 4, 2007, at 11:00 PM, IMAGEJ automatic digest system wrote:
>>
>>> Date: Thu, 4 Jan 2007 12:38:15 -0800
>>> From: "McAuley, Grant (LLU)" <[hidden email]>
>>> Subject: Raw Image Stacks: Image Ordering/Reordering
>>>
>>> Sorry if this has been asked before (searched list archives -
>>> maybe not right combination of words?).
>>>
>>> I need to import stacks of raw images using File->Import->Raw and
>>> selecting 'Open All Files in Folder'. The images have filenames
>>> that contain letters and numbers: zz-1, zz-2, ... , zz-10,
>>> zz-11, ..., zz-48.
>>>
>>> When the stack gets created the order becomes: zz-1, zz-10,
>>> zz-11, ... , zz-2, zz-21, ... instead of what I want: zz-1,
>>> zz-2, ..., zz-10, zz-11, ...
>>>
>>> 1) Can I tell ImageJ to do a numeric instead of alpha sort on the
>>> filename numbers when the stack is created?
>>> 2) If not, is there a better way to resort the stack than the
>>> 'Stack Sorter' plugin (nice, but tedious for 48 images/stack)?
>
>

Divakar Ramachandran

Re: Renaming files 1-99

In reply to this post by Jeff Hardin

Grant,

I had asked a similar question some time ago. Two solutions are possible. As Kyle suggested you could rename the files with zero padding so that the alphabetical and numerical sort orders coincide. I have used a free program XnView (not sure if it works on Mac) for this. The other is to use the virtual stack opener plugin available from the ImageJ plugins page. Wayne Rasband has updated this to get the correct sort order.

HTH,
Divakar

Divakar Ramachandran
Minneapolis.

----- Original Message ----
From: Kyle Miller <[hidden email]>
To: [hidden email]
Sent: Friday, 12 January, 2007 2:05:32 PM
Subject: Re: Renaming files 1-99

Dear Grant,

There is a program called "A better finder rename" that is very useful for
renaming files. Just google the name of the program to find the site to
download. It costs ~$20, but works very well on both macs and pcs.

Best,

Kyle

On 1/12/07 12:33 PM, "Daniel Glen" <[hidden email]> wrote:

Ahmed Khwaja

Re: Renaming files 1-99

In reply to this post by Kyle E. Miller

This is a free program and just amazing.
http://www.fauland.com/af5.htm

Also there is a file splitter and merger, useful as well.

Best,
Ahmed

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Kyle
Miller
Sent: Friday, 12 January, 2007 4:06 PM
To: [hidden email]
Subject: Re: Renaming files 1-99

Dear Grant,

There is a program called "A better finder rename" that is very useful for
renaming files. Just google the name of the program to find the site to
download. It costs ~$20, but works very well on both macs and pcs.

Best,

Kyle

On 1/12/07 12:33 PM, "Daniel Glen" <[hidden email]> wrote:

> For another kludge, there was this posting in October:
> https://list.nih.gov/cgi-bin/wa?A2=ind0610&L=imagej&H=1&P=12039
>
> On Jan 10, 2007, at 12:46 PM, Jeff Hardin wrote:
>
>> Dear Grant,
>>
>> I had to write a plugin for this for Perkin-Elmer confocal stack
>> files. There's no other way I could figure out how to do this. I
>> should release this on the ImageJ web site, but need to clean it up
>> and comment the code. It involves (a) knowing your naming structure;
>> and (b) adding "0"s to pad the file name. The problem is that where
>> these zeroes have to go depends on the naming structure, so there is
>> no universal renamer that can realistically work.
>>
>> Hope that helps...
>>
>> Cheers,
>>
>> Jeff
>> ----------------------------------------------
>> Jeff Hardin
>> Professor, Department of Zoology
>> Director, Biology Core Curriculum
>> University of Wisconsin
>> 1117 W. Johnson St.
>> Madison, WI 53706
>> voice: (608) 262-9634
>> fax: (608) 262-7319
>> email: [hidden email]
>>
>>
>> On Jan 4, 2007, at 11:00 PM, IMAGEJ automatic digest system wrote:
>>
>>> Date: Thu, 4 Jan 2007 12:38:15 -0800
>>> From: "McAuley, Grant (LLU)" <[hidden email]>
>>> Subject: Raw Image Stacks: Image Ordering/Reordering
>>>
>>> Sorry if this has been asked before (searched list archives - maybe
>>> not right combination of words?).
>>>
>>> I need to import stacks of raw images using File->Import->Raw and
>>> selecting 'Open All Files in Folder'. The images have filenames
>>> that contain letters and numbers: zz-1, zz-2, ... , zz-10, zz-11,
>>> ..., zz-48.
>>>
>>> When the stack gets created the order becomes: zz-1, zz-10, zz-11,
>>> ... , zz-2, zz-21, ... instead of what I want: zz-1, zz-2, ...,
>>> zz-10, zz-11, ...
>>>
>>> 1) Can I tell ImageJ to do a numeric instead of alpha sort on the
>>> filename numbers when the stack is created?
>>> 2) If not, is there a better way to resort the stack than the 'Stack
>>> Sorter' plugin (nice, but tedious for 48 images/stack)?
>
>

Thomas Sadowski

Re: Renaming files 1-99

In reply to this post by Jeff Hardin

Hello all,This is the best file renamer program that I have foundhttp://www.den4b.com/downloads.php?project=ReNamer-Tom> Date: Sun, 14 Jan 2007 14:10:43 -0400> From: [hidden email]> Subject: Re: Renaming files 1-99> To: [hidden email]> > This is a free program and just amazing.> http://www.fauland.com/af5.htm > > Also there is a file splitter and merger, useful as well.> > Best,> Ahmed> > -----Original Message-----> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Kyle> Miller> Sent: Friday, 12 January, 2007 4:06 PM> To: [hidden email]> Subject: Re: Renaming files 1-99> > Dear Grant,> > There is a program called "A better finder rename" that is very useful for> renaming files. Just google the name of the program to find the site to> download. It costs ~$20, but works very well on both macs and pcs.> > Best,> > Kyle> > On 1/12/07 12:33 PM, "Daniel Glen" <[hidden email]> wrote:> > > For another kludge, there was this posting in October:> > https://list.nih.gov/cgi-bin/wa?A2=ind0610&L=imagej&H=1&P=12039> > > > On Jan 10, 2007, at 12:46 PM, Jeff Hardin wrote:> > > >> Dear Grant,> >> > >> I had to write a plugin for this for Perkin-Elmer confocal stack > >> files. There's no other way I could figure out how to do this. I > >> should release this on the ImageJ web site, but need to clean it up > >> and comment the code. It involves (a) knowing your naming structure; > >> and (b) adding "0"s to pad the file name. The problem is that where > >> these zeroes have to go depends on the naming structure, so there is > >> no universal renamer that can realistically work.> >> > >> Hope that helps...> >> > >> Cheers,> >> > >> Jeff> >> ----------------------------------------------> >> Jeff Hardin> >> Professor, Department of Zoology> >> Director, Biology Core Curriculum> >> University of Wisconsin> >> 1117 W. Johnson St.> >> Madison, WI 53706> >> voice: (608) 262-9634> >> fax: (608) 262-7319> >> email: [hidden email]> >> > >> > >> On Jan 4, 2007, at 11:00 PM, IMAGEJ automatic digest system wrote:> >> > >>> Date: Thu, 4 Jan 2007 12:38:15 -0800> >>> From: "McAuley, Grant (LLU)" <[hidden email]>> >>> Subject: Raw Image Stacks: Image Ordering/Reordering> >>> > >>> Sorry if this has been asked before (searched list archives - maybe > >>> not right combination of words?).> >>> > >>> I need to import stacks of raw images using File->Import->Raw and > >>> selecting 'Open All Files in Folder'. The images have filenames > >>> that contain letters and numbers: zz-1, zz-2, ... , zz-10, zz-11, > >>> ..., zz-48.> >>> > >>> When the stack gets created the order becomes: zz-1, zz-10, zz-11, > >>> ... , zz-2, zz-21, ... instead of what I want: zz-1, zz-2, ..., > >>> zz-10, zz-11, ...> >>> > >>> 1) Can I tell ImageJ to do a numeric instead of alpha sort on the > >>> filename numbers when the stack is created?> >>> 2) If not, is there a better way to resort the stack than the 'Stack > >>> Sorter' plugin (nice, but tedious for 48 images/stack)?> > > > > > > ---------------------------------------> Kyle E. Miller> Dept. of Zoology> Michigan State University> 337 Natural Sciences Bldg.> E. Lansing, MI 48824> > Office Phone: 517-353-9283> Lab Phone: 517-353-8476> Cell Phone: 917-509-0227
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vbindokas

Re: Renaming files 1-99

In reply to this post by Divakar Ramachandran

This macro that can left pad the numbers. The macro determines
the number-field width and pads to 5 places (default; modify as needed).
This is designed to run on only tiffs as written, and will fail if
multiple number fields are present in the names. It is a brute force
approach since the current IJ restriction of renaming disk files
(limited to certain directories)- it opens the files, renames each, then
does a save-as (leaving originals). Sorting the directory by time of
creation allows the old copies to deleted easily.
Macro text follows
___snip___
// macro to fix numbering scheme
//macro extracts SEQ number and left-pads so files import right, good
//directory order; a work in progress...
// July'06 Vytas Bindokas, University of Chicago
//
function leftPad(n, width) { // pad code from example macros
s =""+n;
while (lengthOf(s)<width)
s = "0"+s;
return s;
}
dex1=0;
dex2=0;
nums=newArray("0","1","2","3","4","5","6","7","8","9");
dir = getDirectory("Choose a Directory ");
list = getFileList(dir);
print(list.length);
setBatchMode(true); // runs up to 6 times faster
for (f=0; f<list.length; f++) { //main files loop
path = dir+list[f];
print(path);
showProgress(f, list.length);
if (!endsWith(path,"/")) open(path);
// MAIN LOOP
if (nImages>=1) {
if (endsWith(path,"f")) { //do only tiff files,(names that end in
"f")
start = getTime();
t=getTitle();
for (i=0; i<=9; i++) {
a=indexOf(t,toString(i));
z=lastIndexOf(t,toString(i));
if (a>-1 ){
if (dex1==0) dex1=a;
if (a<dex1) dex1=a;
}
if (z>-1 ){
if(dex2==0) {dex2=z; }
else if (z>dex2) {dex2=z; }
}
}
m=leftPad(parseInt(substring(t,dex1,dex2+1)),5); // pad to 5 places
b=substring(t,0,dex1);
e=substring(t,dex2+1,lengthOf(t));
m2=toString(m);
t2=b+m2+e;
rename(t2);
saveAs("tif", path);
run("Close");
}
print((getTime()-start)/1000);

_________snip________________

Vytas Bindokas, Ph.D.
Research Assoc. / Assoc. Prof.,
Director, BSD Light Microscopy Core Facility
Dept Neurobiol Pharmacol Physiol MC0926
947 E 58th Street
The University of Chicago
Chicago IL 60637
Room Abbott 120
773-702-4875

email [hidden email]
web site for LMCF:
http://digital.bsd.uchicago.edu/index.html

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Divakar Ramachandran
Sent: Friday, January 12, 2007 11:14 PM
To: [hidden email]
Subject: Re: Renaming files 1-99

Grant,

I had asked a similar question some time ago. Two solutions are
possible. As Kyle suggested you could rename the files with zero padding
so that the alphabetical and numerical sort orders coincide. I have used
a free program XnView (not sure if it works on Mac) for this. The other
is to use the virtual stack opener plugin available from the ImageJ
plugins page. Wayne Rasband has updated this to get the correct sort
order.

HTH,
Divakar

Divakar Ramachandran
Minneapolis.

----- Original Message ----
From: Kyle Miller <[hidden email]>
To: [hidden email]
Sent: Friday, 12 January, 2007 2:05:32 PM
Subject: Re: Renaming files 1-99

Dear Grant,

There is a program called "A better finder rename" that is very useful
for
renaming files. Just google the name of the program to find the site to
download. It costs ~$20, but works very well on both macs and pcs.

Best,

Kyle

On 1/12/07 12:33 PM, "Daniel Glen" <[hidden email]> wrote:

---------------------------------------
Kyle E. Miller
Dept. of Zoology
Michigan State University
337 Natural Sciences Bldg.
E. Lansing, MI 48824

Office Phone: 517-353-9283
Lab Phone: 517-353-8476
Cell Phone: 917-509-0227

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