[ome-devel] ScanR Reader
Rubén Muñoz
ruben.munoz at embl.de
Fri May 14 13:23:52 BST 2010
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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