[ome-users] Problems with Ext.getPlanePositionX(positionX[no], no);

Antonio Trabalza a.trabalza at csc.mrc.ac.uk
Thu Apr 30 23:15:21 BST 2015

Dear OME users,

Sorry if I double posted this.

I am trying to write a IJ macro to organize several stacks taken by prairie
2 photon microscope in a format nice for the stitching plugin to process

I am having serious problems with the IJ macro external commands
Ext.getPlanePositionX, Y and Z. I can't get them to work.

I wrote (just to set up the concept, it will be a part of a longer macro):

id = File.openDialog("Choose a file");
run("Bio-Formats Macro Extensions")
run("Bio-Formats Importer", "open=[" + id + "] color_mode=Default
open_all_series view=[Standard ImageJ] stack_order=Default");
positionX = newArray(imageCount);
positionY = newArray(imageCount);
positionZ = newArray(imageCount);
for (no=0; no<imageCount; no++) {
  Ext.getPlanePositionX(positionX[no], no);
  Ext.getPlanePositionY(positionY[no], no);
  Ext.getPlanePositionZ(positionZ[no], no);

ideally I would like to print the data to a tile configuration file (CSV).

I am getting this error:

')' expected in line ...
Ext.getPlanePositionX( <positionX> [no], no);

this should work similarly to
but it complains about positionX....

Maybe I am doing something very stupid, but please can anybody help me? I
am getting mad....

Thank you in advance for your time and kind regards.

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