[ome-devel] ScanR importer

[Rubén Muñoz]

Hi Melissa,

I have tested the current LSM Importer and it is doing fine with multi-position scans.
That will be incredibly useful here to create OME.TIFs, in combination with bfconvert.

I found some possible improvement for the ScanR importer.
We have always provided with sets that have all the wells, but one of our users skipped some wells with the microscope.

That was not converting because of two things:
	- The loops iterated only until the number of real acquired wells nWells.
	- The tiff array was filled sequentially.

Therefore the imageName is calculated always sequentially.

I have introduced some changes that work for us, but might be not adecuated. You will see that:
	- The wellRows has to be set, otherwise the uniqueRows may not be a good count in these cases. 
	- "timeloop count" is used to prevent the execution of nTimepoints = list.length / (nChannels * nWells * nPos * nSlices); 
	- next variable is always increased even when an image is not found

With all this I get lots of black images during conversion to multiple file OME-TIF. That's not perfect but they can be deleted afterwards.

Please permit me to upload one of these to the FTP with name "scanRskippedWells.zip", and let me know if I can help with something else.

Best regards

Rubén


diff bioformats/components/bio-formats/src/loci/formats/in/ScanrReader.java bioformats.ruben/components/bio-formats/src/loci/formats/in/ScanrReader.java 
300,301c300,306
<     if (wellRows * wellColumns == 0) {
<       if (wellCount <= 96) {
---
>     //if (wellRows * wellColumns == 0) {
>     // FIXME: Three only formats are enforced
>       if (wellCount <= 8) {
>         wellColumns = 2;
>         wellRows = 4;
>       }
>       else if (wellCount <= 96) {
302a308
>         wellRows = 8;
305a312
>         wellRows = 8;
307,309c314,316
<       wellRows = wellCount / wellColumns;
<       if (wellRows * wellColumns < wellCount) wellRows++;
<     }
---
>       //wellRows = wellCount / wellColumns;
>       //if (wellRows * wellColumns < wellCount) wellRows++;
>     //}
318a326
> 
365a374
> 	else next++;
522a532,534
>         else if (key.equals("timeloop count")) {
>           core[0].sizeT = Integer.parseInt(value) + 1;
>         }