Remove Blocks of Slices from Stack

[kev0153]

Hi,

I have a stack of 1000 slices.  I would like to remove a block of 6 slices.  For example  Slice 1 keep, slice 1-6 remove, slice 8 keep, slice 8-14 remove, slice 15 keep etc..

I could do this by hand but with 1000 slices it would take awhile.  I don't really know java so any help would be appreciated thanks

Kevin Clark

[dscho]

Hi,

On Wed, 3 Mar 2010, kev0153 wrote:

> I have a stack of 1000 slices.  I would like to remove a block of 6
> slices. For example Slice 1 keep, slice 1-6 remove, slice 8 keep, slice
> 8-14 remove, slice 15 keep etc..
>
> I could do this by hand but with 1000 slices it would take awhile.  I
> don't really know java so any help would be appreciated thanks

If you are using Fiji, you can use Image>Stacks>Manipulation>Substack
Maker. Otherwise, you might want to run a macro like this:

        Dialog.create("Delete slice range");
        Dialog.addNumber("first_slice", 1);
        Dialog.addNumber("last_slice", 1);
        Dialog.show();

        first = Dialog.getNumber();
        count = Dialog.getNumber() + 1 - first;

        setSlice(first);
        for (i = 0; i < count; i++)
                run("Delete Slice");

(Note: this is completely untested, so you might need to fix a typo or
two.)

This macro only allows deleting one consecutive slice range, though, so
you have to start it 6 times.

Ciao,
Johannes

[kev0153]

Excellent Thanks, I'll give it a try. Plus I was unaware of Fiji until now.
 Checking it out.

Thanks

KEvin

On Wed, Mar 3, 2010 at 10:24 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Wed, 3 Mar 2010, kev0153 wrote:
>
> > I have a stack of 1000 slices.  I would like to remove a block of 6
> > slices. For example Slice 1 keep, slice 1-6 remove, slice 8 keep, slice
> > 8-14 remove, slice 15 keep etc..
> >
> > I could do this by hand but with 1000 slices it would take awhile.  I
> > don't really know java so any help would be appreciated thanks
>
> If you are using Fiji, you can use Image>Stacks>Manipulation>Substack
> Maker. Otherwise, you might want to run a macro like this:
>
>        Dialog.create("Delete slice range");
>        Dialog.addNumber("first_slice", 1);
>        Dialog.addNumber("last_slice", 1);
>        Dialog.show();
>
>        first = Dialog.getNumber();
>        count = Dialog.getNumber() + 1 - first;
>
>        setSlice(first);
>        for (i = 0; i < count; i++)
>                run("Delete Slice");
>
> (Note: this is completely untested, so you might need to fix a typo or
> two.)
>
> This macro only allows deleting one consecutive slice range, though, so
> you have to start it 6 times.
>
> Ciao,
> Johannes
>
>

[John Oreopoulos]

Hi Kevin. I had a similar need a couple years ago and someone on the  
ImageJ list helped me put together a small macro that does what you  
described you wanted it to do:

a=0;
n=getNumber("Frame reduction ratio (1/n)", 5);
for (i=1;i<=nSlices;)
{
        run("Set Slice...", "slice="+i);
        if(a!=0)
                run("Delete Slice");
        else
                i++;
        a++;
        if(a==n)
                a=0;
}

John Oreopoulos


On 3-Mar-10, at 1:23 PM, Kevin Clark wrote:

> Excellent Thanks, I'll give it a try. Plus I was unaware of Fiji  
> until now.
>  Checking it out.
>
> Thanks
>
> KEvin
>
> On Wed, Mar 3, 2010 at 10:24 AM, Johannes Schindelin <
> [hidden email]> wrote:
>
>> Hi,
>>
>> On Wed, 3 Mar 2010, kev0153 wrote:
>>
>>> I have a stack of 1000 slices.  I would like to remove a block of 6
>>> slices. For example Slice 1 keep, slice 1-6 remove, slice 8 keep,  
>>> slice
>>> 8-14 remove, slice 15 keep etc..
>>>
>>> I could do this by hand but with 1000 slices it would take  
>>> awhile.  I
>>> don't really know java so any help would be appreciated thanks
>>
>> If you are using Fiji, you can use Image>Stacks>Manipulation>Substack
>> Maker. Otherwise, you might want to run a macro like this:
>>
>>        Dialog.create("Delete slice range");
>>        Dialog.addNumber("first_slice", 1);
>>        Dialog.addNumber("last_slice", 1);
>>        Dialog.show();
>>
>>        first = Dialog.getNumber();
>>        count = Dialog.getNumber() + 1 - first;
>>
>>        setSlice(first);
>>        for (i = 0; i < count; i++)
>>                run("Delete Slice");
>>
>> (Note: this is completely untested, so you might need to fix a  
>> typo or
>> two.)
>>
>> This macro only allows deleting one consecutive slice range,  
>> though, so
>> you have to start it 6 times.
>>
>> Ciao,
>> Johannes
>>
>>

[Philip Ershler]

Here is substack maker that will do what you what  (except sort of  
backwards)

Phil

Substack Maker

Author: Anthony Padua (padua001 at mc.duke.edu)
Daniel Barboriak, MD (barbo013 at mc.duke.edu)
Neuroradiology
Duke University Medical Center
History: 2003/06/26: First version
2004/12/10: Calibration is carried over to the substack
2005/11/02: Macro recordable
Requires: ImageJ 1.30m or newer
Source: Substack_Maker.java
Installation: Download Substack_Maker.class to the plugins folder and  
restart ImageJ.
Description: The purpose of this plugin is to extract selected images  
from a stack to make a new substack. It would take one of two types of  
input: either a range of images (e.g. 2-14) or a list of images (e.g.  
7,9,25,27,34,132) and copy those images from the active stack to a new  
stack in the order of listing or ranging.

On Mar 3, 2010, at 11:57 AM, John Oreopoulos wrote:

> Hi Kevin. I had a similar need a couple years ago and someone on the  
> ImageJ list helped me put together a small macro that does what you  
> described you wanted it to do:
>
> a=0;
> n=getNumber("Frame reduction ratio (1/n)", 5);
> for (i=1;i<=nSlices;)
> {
> run("Set Slice...", "slice="+i);
> if(a!=0)
> run("Delete Slice");
> else
> i++;
> a++;
> if(a==n)
> a=0;
> }
>
> John Oreopoulos
>
>
> On 3-Mar-10, at 1:23 PM, Kevin Clark wrote:
>
>> Excellent Thanks, I'll give it a try. Plus I was unaware of Fiji  
>> until now.
>> Checking it out.
>>
>> Thanks
>>
>> KEvin
>>
>> On Wed, Mar 3, 2010 at 10:24 AM, Johannes Schindelin <
>> [hidden email]> wrote:
>>
>>> Hi,
>>>
>>> On Wed, 3 Mar 2010, kev0153 wrote:
>>>
>>>> I have a stack of 1000 slices.  I would like to remove a block of 6
>>>> slices. For example Slice 1 keep, slice 1-6 remove, slice 8 keep,  
>>>> slice
>>>> 8-14 remove, slice 15 keep etc..
>>>>
>>>> I could do this by hand but with 1000 slices it would take  
>>>> awhile.  I
>>>> don't really know java so any help would be appreciated thanks
>>>
>>> If you are using Fiji, you can use  
>>> Image>Stacks>Manipulation>Substack
>>> Maker. Otherwise, you might want to run a macro like this:
>>>
>>>       Dialog.create("Delete slice range");
>>>       Dialog.addNumber("first_slice", 1);
>>>       Dialog.addNumber("last_slice", 1);
>>>       Dialog.show();
>>>
>>>       first = Dialog.getNumber();
>>>       count = Dialog.getNumber() + 1 - first;
>>>
>>>       setSlice(first);
>>>       for (i = 0; i < count; i++)
>>>               run("Delete Slice");
>>>
>>> (Note: this is completely untested, so you might need to fix a  
>>> typo or
>>> two.)
>>>
>>> This macro only allows deleting one consecutive slice range,  
>>> though, so
>>> you have to start it 6 times.
>>>
>>> Ciao,
>>> Johannes
>>>
>>>