[kepler-users] Help understanding Kepler paradigm for batch processing images

[Jeremy Douglass]

Ustun,

Thanks. Because I'm just trying to batch process the files, I need to
produce a series of whatever Image Converter will consume -- which I
assume (?) based on the 03 example that ships with Kepler is just a
plain file path e.g. "/User/test/file1.PNG". Essentially, I want Image
Converter receive 5 file path strings and run 5 times.

What OS are you running Kepler on? If the Directory Listing returns a
different data structure depending on the OS, perhaps I should be file
this as a bug?

Right now I'm trying to adding a "name" column to the array before
feeding it to Record Disassembler by using the Concatenate Arrays
actor, but no luck so far....

-- Jeremy


On Sun, Jul 12, 2009 at 10:07 PM, Ustun Yildiz<yildiz at cs.ucdavis.edu> wrote:
> Hi:
>
> I am sorry but I guess I gave you a wrong advise in my previous message.
> I have the impression that Directory Listing-->Array to Sequence give
> you the elements as separate tokens. Your number 1) guess is correct
> below.
>
> I tried to put Display after Array to Sequence, I have a name tag to
> filter with Record Dissasemler. I guess different computers generate
> different listings. Looking at your output, you just need the name of
> the files right? and not complete directory/file_name elements ?
>
> -Ustun.
>
> On Sun, Jul 12, 2009 at 9:52 PM, Jeremy
> Douglass<jeremydouglass at gmail.com> wrote:
>> Thank you Ustun -- I'm trying a Record Dissasembler with an added
>> "name" output port now, but it isn't working.
>>
>> When I add just a Record Disassembler where you suggested (Directory
>> Listing ---> Array to Sequence ---> Record Disassembler), I'm getting
>> "Exception: ptolemy.data.stringToken." Once I use the GUI to add an
>> output port named "name" to the Disassembler I get the more verbose
>> error "Type resolution failed because of an error during type
>> inference in .test, because: Invalid type for input port in
>> .test.Record Disassembler." Adding the Disassembler directly to the
>> Directory Listing gives me similar errors, only the exception is
>> arrayToken instead of stringToken.
>>
>> Right now I'm wildly guessing that the problem is either:
>> 1) perhaps my directory listing results don't actually come with a
>> "name" element column, and so there is no name element for the
>> Disassembler to filter on -- as this apparently works for you, perhaps
>> returning a single column array is OS X specific behavior of Directory
>> listing, and perhaps there is a way to add this column myself through
>> an array operation? ...or
>> 2) Perhaps you didn't mean I should use Array to Sequence, but rather
>> Array to Elements in some fashion?
>>
>> Any advice greatly appreciated. For your ref, here is what I'm seeing
>> if I run Directory Listing -> Display:
>>
>> {"/Users/test/Picture 1.PNG", "/Users/test/Picture 2.PNG",
>> "/Users/test/Picture 3.PNG", "/Users/test/Picture 4.PNG",
>> "/Users/test/Picture 5.PNG"}
>>
>> ...and if I run Directory Listing -> Array to Sequence -> Display:
>>
>> /Users/test/Picture 1.PNG
>> /Users/test/Picture 2.PNG
>> /Users/test/Picture 3.PNG
>> /Users/test/Picture 4.PNG
>> /Users/test/Picture 5.PNG
>>
>> -- Jeremy
>>
>>
>> On Sat, Jul 11, 2009 at 1:06 PM, Ustun Yildiz<yildiz at cs.ucdavis.edu> wrote:
>>> I have the impression that you try to apply an operation (actor) to
>>> the elements in a directory. In order to capture the names of such
>>> elements and pipeline them into subsequent actors, I use
>>>
>>> Directory Listing ---> Array to Sequence ---> Record Dissasembler
>>>
>>> The first takes a directory name and the last outputs single names (as
>>> many as the elements). The purpose of the Record Dissasembler is to
>>> capture "name" element in the output of Array to Sequence actor. You
>>> have to change the output port of Record Dissasembler to "name".
>>>
>>> Ustun.
>>>
>>>
>>>
>>>
>>> On Sat, Jul 11, 2009 at 12:51 PM, Jeremy
>>> Douglass<jeremydouglass at gmail.com> wrote:
>>>> I'm a new Kepler and struggling to apply a single actor (e.g. Image
>>>> Converter) to a batch of objects (e.g. a directory of images, as
>>>> represented by the array generated by Directory Listing).
>>>>
>>>> I've read the documentation and searched the forums, and tried
>>>> modifying examples, but I'm not understanding something paradigmatic,
>>>> and would appreciate a tip: how do you pipe an array of files through
>>>> single-file actors?
>>>>
>>>> EXAMPLE:
>>>>
>>>> In Kepler 1.0.0, 03-ImageDisplay.xml uses an SDC director, and specifies:
>>>>   Constant Image Filename --> Image Converter --> ImageJ
>>>>
>>>> In an attempt to converter a *directory* of images, I tried adding a
>>>> Directory Listing actor:
>>>>   Constant Dirname --> Directory Listing --> Image Converter --> ImageJ
>>>>
>>>> ...however this generates an error, as Image Converter will only act
>>>> on a string, not an array. So I tried
>>>>   Constant Dirname --> Directory Listing --> Array to Sequence -->
>>>> Image Converter --> ImageJ
>>>>
>>>> ...which almost works if I hand-specified the number of Array elements
>>>> in the directory ahead of time), but still only processed the first
>>>> file listed in the string (Picture 1.png) -- I'm assuming it just
>>>> throws the rest of the string away.
>>>>
>>>> I'm not understanding something about how one processes a list in a
>>>> Kepler workflow -- I've looked through Array Operation and Iterative
>>>> Operation actors, and none of them seem to be analogous to an
>>>> imperative programming loop. Am I using the wrong kind of director?
>>>> Something else?
>>>>
>>>> Thanks for your help.
>>>>
>>>> BACKGROUND: My larger goal is to adapt a frame based image processing
>>>> workflow into Kepler (it is currently a combination of python,
>>>> javascript, and bash scripts). To illustrate, one part of the workflow
>>>> takes a heterogeneous collection of images (all file types and sizes)
>>>> and copies them to a new directory as a collection of standardized
>>>> collection jpegs. Another part of the workflow dumps a movie to a
>>>> frame directory of jpegs, then runs multiple image measurement and
>>>> image processing operations (e.g. ImageJ, MATLAB) on each frame and
>>>> saves the results to a text file.
>>>> _______________________________________________
>>>> Kepler-users mailing list
>>>> Kepler-users at kepler-project.org
>>>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>>
>>>
>>
>