Hi Chris-
Glad you figured it out. Sorry I didn't have time to look into this and
get back to you. Here are some quick thoughts:
Just as with the annotations, you need to have something that will map
your raw height values to the logrithmic vertical dimension. One way
would be to add a CoordinateSystem to the pointTupleType so you would
have the logHeightType in the domain (through the CS) and the mapping
would be picked up. You don't want to change retentionTimeType or
mzType, so you want to have IdentityCoordinateSystems for those values.
So, you could have IdentityCS's for retentionTimeType and mzType and
then have a CartesianProductCoordinateSystem of those and the
LogCoordinateSystem for the height and attach that to your pointTupleType.
Alternatively, you could create the LogCoordinateSystem for LogHeight
and call the toReference method on that, transforming your height values
to logHeight and pass those into the GriddedSet:
LogCoordinateSystem logCS = new LogCoordinateSystem(new
RealTupleType(logHeightType));
float[][] logValues = logCS.toReference({{heightMin, heightMax}});
lheightMin = logValues[0][0];
lheightMax = logValues[0][1];
pointTupletype = new RealTupleType(retentionTimeType, mzType,
logHeightType);
// Create the box set.
return GriddedSet.create(
pointTupleType,
new float[][]{
{rtMin, rtMax, rtMin, rtMax, rtMin, rtMax, rtMin, rtMax,
rtMin, rtMin, rtMin, rtMin, rtMax, rtMax, rtMax, rtMax,},
{mzMin, mzMin, mzMin, mzMin, mzMax, mzMax, mzMax, mzMax,
mzMin, mzMax, mzMin, mzMax, mzMin, mzMax, mzMin, mzMax},
{lheightMin, lheightMin, lheightMax, lheightMax, lheightMax,
lheightMax, lheightMin, lheightMin, lheightMin, lheightMin,
lheightMax, lheightMax, lheightMax, lheightMax, lheightMin,
lheightMin}},
new int[]{2, 8});
(code above not tested at all).
Good luck!
Don
On 11/1/11 3:16 AM, Pudney Chris (ext) GBJH wrote:
G'day,
> I am struggling to define a FunctionType that will correctly position
the
> labels when logarithmic scaling is applied.
I managed to solve this using the following code to include a
LogCoordinateSystem in the range of the annotation function:
// Height Types.
final RealType heightType = RealType.getRealType("Height");
final RealType logHeightType = RealType.getRealType("LogHeight",
CommonUnit.promiscuous);
heightTupleType = new RealTupleType(
heightType, new LogCoordinateSystem(new RealTupleType(logHeightType)),
null);
annotationType = TextType.getTextType("Annotation");
annotationTupleType = new TupleType(new MathType[]{heightTupleType,
annotationType});
// Create a function from domain (retention time and m/z) to text
annotation.
annotationFunction = new FunctionType(domainTuple, annotationTupleType);
The full code is in the project svn repository:
http://mzmine.svn.sourceforge.net/viewvc/mzmine/branches/syngenta_normalize_slider/src/net/sf/mzmine/modules/visualization/threed/ThreeDDisplay.java?revision=2566&view=markup
The final piece of the puzzle is applying logarithmic scaling to the
heights of bounding boxes that are used to highlight individual surface
peaks. The box heights match the peak heights and are created using
GriddedSets:
pointTupletype = new RealTupleType(retentionTimeType, mzType, heightType);
// Create the box set.
return GriddedSet.create(
pointTupleType,
new float[][]{
{rtMin, rtMax, rtMin, rtMax, rtMin, rtMax, rtMin, rtMax,
rtMin, rtMin, rtMin, rtMin, rtMax, rtMax, rtMax, rtMax,},
{mzMin, mzMin, mzMin, mzMin, mzMax, mzMax, mzMax, mzMax,
mzMin, mzMax, mzMin, mzMax, mzMin, mzMax, mzMin, mzMax},
{heightMin, heightMin, heightMax, heightMax, heightMax,
heightMax, heightMin, heightMin, heightMin, heightMin,
heightMax, heightMax, heightMax, heightMax, heightMin,
heightMin}},
new int[]{2, 8});
The boxes are rendered correctly for linear scaling of the height axis
but not for logarithmic scaling. Presumably to get this working the
GriddedSet (or similar) must reference the LogCoordinateSystem defined
earlier but how?
I'd be grateful for any suggestions.
Code for this class is here:
http://mzmine.svn.sourceforge.net/viewvc/mzmine/branches/syngenta_normalize_slider/src/net/sf/mzmine/modules/visualization/threed/ThreeDPeakCells.java?revision=2566&view=markup
Thanks,
Chris.
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