[ome-devel] Scanr patch

[Rubén Muñoz]

Hi Melissa,
I have tried just it with two different sets that do not form a square. 
Wow. These last changes are brilliant. The names and the conversion are precise.

Just a minor thing, in line 520, the item "loop count" is the number of cycles but " 1" should be added.

core[0].sizeT = Integer.parseInt(value) + 1;

Actually sometimes: 
I have noticed that, when the acquisition was aborted and 'core[0].sizeT' is parsed, missing frames of one serie are taken from next serie.
Of course the code expects the coherency with the descriptor, so I update it manually in those cases.

Best regards,
Rubén


On Sep 20, 2010, at 6:36 PM, Melissa Linkert wrote:

> Hi Rubén,
> 
>> That's a good point, actually we still need it.
>> I certainly forgot to recalculate this value.
> 
> OK, no problem.
> 
> With r6959 (which closes ticket #550), non-acquired wells should no
> longer be included in the series list.  As far as I can tell, acquired
> wells are also being properly labelled now, but if you could confirm that I
> would greatly appreciate it.
> 
> Regards,
> -Melissa
> 
> On Fri, Sep 17, 2010 at 09:08:44AM +0200, Rubén Muñoz wrote:
>> Hi Melissa,
>> 
>> That's a good point, actually we still need it. 
>> I certainly forgot to recalculate this value. What about?:
>> 
>> int nSpot = well * nPos + pos + 1;
>> names[realPosCount] = "Well " + (well + 1) + ", Field " + (pos +1) + " (Spot " + nSpot + ")";
>> 
>> The code doesn't label non-acquired wells.
>> 
>> Best,
>> Rubén
>> 
>> On Sep 16, 2010, at 11:58 PM, Melissa Linkert wrote:
>> 
>>> Hi Rubén,
>>> 
>>> Applying this patch is not a problem, but I just want to verify that the
>>> format of the Image names is correct.
>>> 
>>> In a previous thread, you had asked to have the spot number included in
>>> the Image name (as is currently being done).  See:
>>> 
>>> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2009-December/001536.html
>>> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2009-December/001538.html
>>> 
>>> Are you sure that the spot number should be removed from the Image name?
>>> 
>>> Regards,
>>> -Melissa
>>> 
>>> On Thu, Sep 16, 2010 at 09:47:45AM +0200, Rubén Muñoz wrote:
>>>> Hi Melissa, 
>>>> 
>>>> After using the ScanR importer with some non-captured wells, I realized that the names were incorrect.
>>>> I did the following patch to fix the problem. 
>>>> 
>>>> This is not preventing the converter to create more metadata and images than actually needed, but is already a help.
>>>> 
>>>> Thanks!
>>>> 
>>>> Rubén
>>>> 
>>>> 337a338,339
>>>>>   String [] names = new String [nWells * nPos];
>>>>> 
>>>> 361a364
>>>>>                 names[realPosCount] = "Well " + (well + 1) + ", Field " + (pos +1);
>>>> 468,470c471
>>>> <       String name = "Well " + (well + 1) + ", Field " + (field +1) + " (Spot " +
>>>> <         (i + 1) + ")";
>>>> <       store.setImageName(name, i);
>>>> ---
>>>>>     store.setImageName(names[i], i);
>>