[ome-devel] ScanR Reader
Melissa Linkert
melissa at glencoesoftware.com
Fri May 14 17:21:11 BST 2010
Hi Rubén,
> Mmm. I think that some users configure the microscope to 99 loops and then
> interrupt the acquisition, must be a bad practice from their side. In those
> cases probably the Olympus software "alert us" setting "timeloop real". This
> is only a guess but again the code works as it was. You are right to leave
> this modification out but the lower value of "timeloop real" and "timeloop
> count +1 " should work also.
That does seem like a strange practice, but at least it explains the
discrepancy. The datasets where I noticed this problem do not seem to
have a "timeloop real" value (for reference, they are the
161009test2/151009_001 and 161009test2/151009_002 plates).
> As I said, recently I received new datasets... What a surprise when some
> didn't have labels "A1", "A2", ... Well those are not importing. Please
> permit me again to show my small corrections that did the trick:
As always, thank you for providing a patch and uploading a test
dataset. Your patch looks fine and works well with the other datasets
that I have, so has been committed in SVN r6317.
Regards,
-Melissa
On Fri, May 14, 2010 at 7:23 AM, Rubén Muñoz <ruben.munoz at embl.de> wrote:
> Hi Melissa,
> I am glad to hear from you and hope that the successful changes are of use
> to your purpose.
> I have identified my current sets slightly different to the examples
> provided before that's why I will upload one more.
>
> Regarding your latest changes in ScanrReader.java:
>
> 1) Setting nPos = realPosCount and after you core = new
> CoreMetadata[nWells * nPos];
>
> you're getting too many positions in the core array.
>
> This is certainly the case if realPosCount is greater than the
> original value of nPos. The approach taken in r6313 is to set nPos to
> the lesser of nPos and realPosCount; does that work for your test
> cases?
>
> Only recently I started getting multiple positions in a well, and I have
> just tried with old and new datasets. Your guess is correct and now this
> works again.
>
> 3) In newer acquisitions "timeloop real" was replaced by "timeloop count"
> and it is 0 for only
>
> 1 timepoint acquisitions, so I had to add one (+ 1) to the parsed value.
>
> My concern is that the value of "timeloop count" appears to be
> unreliable. I have a few datasets that are as you describe -
> "timeloop count" is equal to the number of timepoints minus 1.
>
> Mmm. I think that some users configure the microscope to 99 loops and then
> interrupt the acquisition, must be a bad practice from their side. In those
> cases probably the Olympus software "alert us" setting "timeloop real". This
> is only a guess but again the code works as it was. You are right to leave
> this modification out but the lower value of "timeloop real" and "timeloop
> count +1 " should work also.
> As I said, recently I received new datasets... What a surprise when some
> didn't have labels "A1", "A2", ... Well those are not importing. Please
> permit me again to show my small corrections that did the trick:
> My best regards,
> --- ScanrReader.java (revision 6315)
> +++ ScanrReader.java (working copy)
> @@ -70,6 +70,7 @@
> private Vector<String> metadataFiles = new Vector<String>();
> private int wellRows, wellColumns;
> private int fieldRows, fieldColumns;
> + private int wellCount = 0;
> private Vector<String> channelNames = new Vector<String>();
> private Hashtable<String, Integer> wellLabels =
> new Hashtable<String, Integer>();
> @@ -260,13 +261,13 @@
> wellColumns = uniqueColumns.size();
>
> if (wellRows * wellColumns == 0) {
> - if (wellLabels.size() <= 96) {
> + if (wellCount <= 96) {
> wellColumns = 12;
> }
> - else if (wellLabels.size() <= 384) {
> + else if (wellCount <= 384) {
> wellColumns = 24;
> }
> - wellRows = wellLabels.size() / wellColumns;
> + wellRows = wellCount / wellColumns;
> if (wellRows * wellColumns < wellLabels.size()) wellRows++;
> }
>
> @@ -298,7 +299,8 @@
> String[] keys = wellLabels.keySet().toArray(new
> String[wellLabels.size()]);
> int realPosCount = 0;
> for (int well=0; well<nWells; well++) {
> - Integer w = wellLabels.get(keys[well]);
> + Integer w = keys.length > 0 ? wellLabels.get(keys[well]) : null;
> +
> int wellIndex = w == null ? well + 1 : w.intValue();
>
> String wellPos = getBlock(wellIndex, "W");
> @@ -334,7 +336,7 @@
> }
> }
>
> - if (wellLabels.size() != nWells) {
> + if (wellLabels.size() > 0 && wellLabels.size() != nWells) {
> uniqueRows.clear();
> uniqueColumns.clear();
> for (String well : wellLabels.keySet()) {
> @@ -501,6 +503,7 @@
> else if (key.equals("well selection table + cDNA")) {
> if (Character.isDigit(value.charAt(0))) {
> wellIndex = value;
> + wellCount++;
> }
> else {
> wellLabels.put(value, new Integer(wellIndex));
>
>
> Regards,
> -Melissa
>
> On Wed, May 5, 2010 at 9:59 AM, Rubén Muñoz <ruben.munoz at embl.de> wrote:
>
> Dear Melissa,
>
> Bioformats has incorporated many changes lately, it works for me when I
> compile loci_tools.jar directly from the SVN. As of yesterday the
> pre-compiled .jar from your page didn't open the ScanR datasets, please let
> me know if I can give more details on this.
>
> The reason of my e-mail are some code improvements in ScanrReader.java,
>
> 1) Setting nPos = realPosCount and after you core = new
> CoreMetadata[nWells * nPos]; you're getting too many positions in the core
> array.
>
> 2) row + col gives a concatenation of strings but for small layouts (some
> people uses small 8-well plates) this results 651?. I introduced here the
> Well number (different to the Spot number), you may want to change this but
> just the Well number is of help here.
>
> 3) In newer acquisitions "timeloop real" was replaced by "timeloop count"
> and it is 0 for only 1 timepoint acquisitions, so I had to add one (+ 1) to
> the parsed value.
>
> Please let me know any comment regarding the previous changes, they all
> might be of help.
>
> Thanks and regards,
>
> Rubén
>
>
>
> Index: ScanrReader.java
>
> ===================================================================
>
> --- ScanrReader.java (revision 6224)
>
> +++ ScanrReader.java (working copy)
>
> @@ -347,7 +347,7 @@
>
> wellColumns = uniqueColumns.size();
>
> nWells = wellRows * wellColumns;
>
> }
>
> - nPos = realPosCount;
>
> + //nPos = realPosCount;
>
> reader = new MinimalTiffReader();
>
> reader.setId(tiffs[0]);
>
> @@ -420,11 +420,14 @@
>
> store.setWellSampleImageRef(imageID, 0, well, field);
>
> store.setImageID(imageID, i);
>
> - String row =
>
> - String.valueOf(wellRows > 26 ? wellRow + 1 : (char) ('A' +
> wellRow));
>
> - String col =
>
> - String.valueOf(wellRows > 26 ? (char) ('A' + wellCol) : wellCol +
> 1);
>
> - String name = "Well " + row + col + ", Field " + (field + 1) +
>
> + //String row =
>
> + // String.valueOf(wellRows > 26 ? wellRow + 1 : (char) ('A' +
> wellRow));
>
> + //String col =
>
> + // String.valueOf(wellRows > 26 ? (char) ('A' + wellCol) : wellCol +
> 1);
>
> +
>
> + int wellIndex = wellRow*wellColumns + wellCol + 1;
>
> +
>
> + String name = "Well " + wellIndex + ", Field " + (field + 1) +
>
> " (Spot " + (i + 1) + ")";
>
> store.setImageName(name, i);
>
> }
>
> @@ -479,8 +482,8 @@
>
> else if (key.equals("# slices")) {
>
> core[0].sizeZ = Integer.parseInt(value);
>
> }
>
> - else if (key.equals("timeloop real")) {
>
> - core[0].sizeT = Integer.parseInt(value);
>
> + else if (key.equals("timeloop count") || key.equals("timeloop
> real")) {
>
> + core[0].sizeT = Integer.parseInt(value) + 1;
>
> }
>
> else if (key.equals("name")) {
>
> channelNames.add(value);
>
>
>
>
>
>
>
>
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