It turns out that there is a consistency check between the actual filename and the filename recorded in the .xml
file. Once we realized that, all was well.
I have a "get it done in time for Abstract Deadline" version working smoothly - Now I have to write
a clean version. The character set caused a brief hiccup, but that was easy compared with the
(undocumented) filename consistency check.
And then there was the problem of parallel arrays containing different information - all of which had
to be the same length....or the CellSens would fold its arms and silently pout. Yet Another Undocumented Consistency Check,
where the only error message is silent refusal.
The "editor" was a java program that generates a spiral sampling pattern. My microscope jockey does photography 8-9 fields-of-view
at a time - our sampling pattern is organized as concentric rings (about 12-13) of 8 points, with each ring slightly rotated. This gives
a nice pattern which is dense at the center and sparse in the periphery, with a nice triangular grid in between. The current version
parses the XML file just enough to get the job done. I suppose I ought to implement a version that uses a real XML reader/writer.
Maybe next week...
It always amazes me that stage manufacturers seem to not realize that people need to use externally generated sampling patterns.
A little documentation (and a format slightly more user-friendly format than their XML file would have gone a long way towards making my
life easier. Either that, or they are pursuing a policy of "security through obscurity" - in which case, bring it on!
Typing in 100 x,y,z triples (each 6-8 digits long) would have driven the post-doc to drink!
Parsing and re-writing WinDoze UTF-16 XML files on a Mac is good for the soul. You don't want to see my first attempt...very ugly!
Thanks for the help - but CRLF's were the least of my problems.
--
Kenneth Sloan
[hidden email]
On Feb 9, 2013, at 09:28 , Pariksheet Nanda wrote:
> On Mon, Feb 4, 2013 at 10:16 PM, Kenneth Sloan <
[hidden email]> wrote:
>> I have looked at the .xml file generated by the CellSens and it *seems* straightforward to
>> edit the file - but so far we have been unsuccessful.
>>
>
> Perhaps the editor you are using to change the XML file may be
> changing the format of the line feeds or carriage returns (or adding
> extra such characters) and the Olympus software cannot read your
> changes properly. MetaMorph 7, has this issue with reading modified
> XML files.
>
> The Olympus software may also be holding onto some cached version of
> the stage positions and not reading back from the file- reloading the
> experiment or restarting the software may be necessary.
>
>
>> Kenneth Sloan
>
> Pariksheet
>
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