macro for automatic import of image sequences

[Oliver Bannach]

Hi folks

I'd like to have a macro for automatic opening of image sequences. This
is what the macro should do:
1) The main directory (dirX) needs to be specified by a popup dialog
2) The .tif files are located in subdirectories named ch0/ and ch1/,
respectively. The files (*.tif) in these two directories should be
imported as two image sequences
3) The two sequences should be colored red and green

I wrote this macro, but it doesn't seem to work:

dirX = getDirectory("Choose Source Directory ");
run("Image Sequence...", "open=[dirX\\ch0\\*.tif] number=6 starting=1
increment=1 scale=100 file=[] or=[] convert sort");
run("Green");
run("Image Sequence...", "open=[dirX\\ch1\\*.tif] number=6 starting=1
increment=1 scale=100 file=[] or=[] convert sort");
run("Red");

Maybe somebody can fix it? Any help is greatly appreciated. Many thanks
in advance!

regards
Oliver

[Michael Schmid]

Hi Oliver,

you can't specify a file with a "*" in run("Image Sequence...
You should specify one of the files there.
If you don't know the name of one file in advance, get one.
E.g., if there are only .tifs in the directory, you can write:

list = getFileList(dirX+"/ch0/");
file0 = list[0];

otherwise you have to loop through the list to find a tiff that
you can use as a starting point.

To specify that you want to import tiffs only, you can write
file=[.tif] in the run("Image Sequence... arguments.


Also, make sure that you have no variable names inside the
quotes. The argument should be, e.g.,
"open=["+dirX+"/"+ch1+"/"file0] number=..."

The plus sign is the string concatenation operator.

Michael
________________________________________________________________

On 25 Mar 2008, at 17:53, Oliver Bannach wrote:

> Hi folks
>
> I'd like to have a macro for automatic opening of image sequences.  
> This
> is what the macro should do:
> 1) The main directory (dirX) needs to be specified by a popup dialog
> 2) The .tif files are located in subdirectories named ch0/ and ch1/,
> respectively. The files (*.tif) in these two directories should be
> imported as two image sequences
> 3) The two sequences should be colored red and green
>
> I wrote this macro, but it doesn't seem to work:
>
> dirX = getDirectory("Choose Source Directory ");
> run("Image Sequence...", "open=[dirX\\ch0\\*.tif] number=6 starting=1
> increment=1 scale=100 file=[] or=[] convert sort");
> run("Green");
> run("Image Sequence...", "open=[dirX\\ch1\\*.tif] number=6 starting=1
> increment=1 scale=100 file=[] or=[] convert sort");
> run("Red");
>
> Maybe somebody can fix it? Any help is greatly appreciated. Many  
> thanks
> in advance!
>
> regards
> Oliver

[Oliver Bannach]

Dear Michael,

thank you very much for your support. I changed my macro according to
your suggestions:

dirX = getDirectory("Choose Source Directory ");
list = getFileList(dirX+"/ch0/");
file0 = list [0];
run("Image Sequence...", "open=["+dirX+"/"+ch0+"/"+file0"] number=6
starting increment=1 scale=100 file=[] or=[] convert sort file=[.tif]");
run("Green");
list = getFileList(dirX+"/ch1/");
file0 = list [0];
run("Image Sequence...", "open=["+dirX+"/"+ch1+"/"+file0"] number=6
starting increment=1 scale=100 file=[] or=[] convert sort file=[.tif]");
run("Red");

When I run the macro, I can choose a directory. But next an error
message is displayed "Undefined variable in line 4". What is still wrong?

Thank you!
Oliver

Michael Schmid schrieb:

> Hi Oliver,
>
> you can't specify a file with a "*" in run("Image Sequence...
> You should specify one of the files there.
> If you don't know the name of one file in advance, get one.
> E.g., if there are only .tifs in the directory, you can write:
>
> list = getFileList(dirX+"/ch0/");
> file0 = list[0];
>
> otherwise you have to loop through the list to find a tiff that
> you can use as a starting point.
>
> To specify that you want to import tiffs only, you can write
> file=[.tif] in the run("Image Sequence... arguments.
>
>
> Also, make sure that you have no variable names inside the
> quotes. The argument should be, e.g.,
> "open=["+dirX+"/"+ch1+"/"file0] number=..."
>
> The plus sign is the string concatenation operator.
>
> Michael
> ________________________________________________________________
>
> On 25 Mar 2008, at 17:53, Oliver Bannach wrote:
>
>> Hi folks
>>
>> I'd like to have a macro for automatic opening of image sequences. This
>> is what the macro should do:
>> 1) The main directory (dirX) needs to be specified by a popup dialog
>> 2) The .tif files are located in subdirectories named ch0/ and ch1/,
>> respectively. The files (*.tif) in these two directories should be
>> imported as two image sequences
>> 3) The two sequences should be colored red and green
>>
>> I wrote this macro, but it doesn't seem to work:
>>
>> dirX = getDirectory("Choose Source Directory ");
>> run("Image Sequence...", "open=[dirX\\ch0\\*.tif] number=6 starting=1
>> increment=1 scale=100 file=[] or=[] convert sort");
>> run("Green");
>> run("Image Sequence...", "open=[dirX\\ch1\\*.tif] number=6 starting=1
>> increment=1 scale=100 file=[] or=[] convert sort");
>> run("Red");
>>
>> Maybe somebody can fix it? Any help is greatly appreciated. Many thanks
>> in advance!
>>
>> regards
>> Oliver

[Michael Schmid]

Hi Oliver,

sorry, I see, ch0 is not a variable but part of the file name.
I did not read you mail carefully.
So it should be something like

   run("Image Sequence...", "open=["+dirX+"/ch0/"+file0"] number=6  
starting increment=1 scale=100 or=[] convert sort file=[.tif]");

Also not that you should have only one "file=" entry in the list
of arguments.

Michael
________________________________________________________________

On 25 Mar 2008, at 18:57, Oliver Bannach wrote:

> Dear Michael,
>
> thank you very much for your support. I changed my macro according  
> to your suggestions:
>
> dirX = getDirectory("Choose Source Directory ");
> list = getFileList(dirX+"/ch0/");
> file0 = list [0];
> run("Image Sequence...", "open=["+dirX+"/"+ch0+"/"+file0"] number=6  
> starting increment=1 scale=100 file=[] or=[] convert sort file=
> [.tif]");
> run("Green");
> list = getFileList(dirX+"/ch1/");
> file0 = list [0];
> run("Image Sequence...", "open=["+dirX+"/"+ch1+"/"+file0"] number=6  
> starting increment=1 scale=100 file=[] or=[] convert sort file=
> [.tif]");
> run("Red");
>
> When I run the macro, I can choose a directory. But next an error  
> message is displayed "Undefined variable in line 4". What is still  
> wrong?
>
> Thank you!
> Oliver
>
> Michael Schmid schrieb:
>> Hi Oliver,
>>
>> you can't specify a file with a "*" in run("Image Sequence...
>> You should specify one of the files there.
>> If you don't know the name of one file in advance, get one.
>> E.g., if there are only .tifs in the directory, you can write:
>>
>> list = getFileList(dirX+"/ch0/");
>> file0 = list[0];
>>
>> otherwise you have to loop through the list to find a tiff that
>> you can use as a starting point.
>>
>> To specify that you want to import tiffs only, you can write
>> file=[.tif] in the run("Image Sequence... arguments.
>>
>>
>> Also, make sure that you have no variable names inside the
>> quotes. The argument should be, e.g.,
>> "open=["+dirX+"/"+ch1+"/"file0] number=..."
>>
>> The plus sign is the string concatenation operator.
>>
>> Michael
>> ________________________________________________________________
>>
>> On 25 Mar 2008, at 17:53, Oliver Bannach wrote:
>>
>>> Hi folks
>>>
>>> I'd like to have a macro for automatic opening of image  
>>> sequences. This
>>> is what the macro should do:
>>> 1) The main directory (dirX) needs to be specified by a popup dialog
>>> 2) The .tif files are located in subdirectories named ch0/ and ch1/,
>>> respectively. The files (*.tif) in these two directories should be
>>> imported as two image sequences
>>> 3) The two sequences should be colored red and green
>>>
>>> I wrote this macro, but it doesn't seem to work:
>>>
>>> dirX = getDirectory("Choose Source Directory ");
>>> run("Image Sequence...", "open=[dirX\\ch0\\*.tif] number=6  
>>> starting=1
>>> increment=1 scale=100 file=[] or=[] convert sort");
>>> run("Green");
>>> run("Image Sequence...", "open=[dirX\\ch1\\*.tif] number=6  
>>> starting=1
>>> increment=1 scale=100 file=[] or=[] convert sort");
>>> run("Red");
>>>
>>> Maybe somebody can fix it? Any help is greatly appreciated. Many  
>>> thanks
>>> in advance!
>>>
>>> regards
>>> Oliver