profile = roi.getPixels()
c.assign("prof", profile)
# pks = c.eval("SpectrumSearch(prof, sigma=3, threshold=25, background=TRUE, iterations=20, markov=TRUE, window=5)").asList()
pks = c.eval("SpectrumSearch(prof, sigma=2, threshold=10, background=TRUE, iterations=20, markov=TRUE, window=2)").asList()
pksY = pks[0].asIntegers()
#for i in pksX:
# print roi.x1, i
# rois.append(PointRoi(roi.x1, roi.y1 + i))
#ol = Overlay()
#for aroi in rois:
# ol.add(aroi)
#imp.setOverlay(ol)
return pksY
c = RConnection()
x = c.eval("R.version.string")
print x.asString()
print c.eval("library(Peaks)").asString()
imp = IJ.getImage()
roi = imp.getRoi()
alldata = []
maxlen = 0
totallen = 0
if roi.getType() == Roi.LINE:
#print "a line roi"
for i in range(imp.getStackSize()):
imp.setSlice(i+1)
peakYs = getPeaks(roi, c)
peakTs = [i+1 for j in range(len(peakYs))]
from org.rosuda.REngine.Rserve import RConnection
from ij.gui import Roi, Overlay
c = RConnection()
x = c.eval("R.version.string")
print x.asString()
print "Loaded Package:", c.eval("library(Peaks)").asString()
imp = IJ.getImage()
roi = imp.getRoi()
if roi.getType() == Roi.LINE:
print "a line roi found"
profile = roi.getPixels()
c.assign("prof", profile)
# pks = c.eval("SpectrumSearch(prof, sigma=1, threshold=25, background=TRUE, iterations=20, markov=TRUE, window=5)").asList()
# pks = c.eval("SpectrumSearch(prof, sigma=3, threshold=25, background=TRUE, iterations=20, markov=TRUE, window=5)").asList()
# pks = c.eval("SpectrumSearch(prof, sigma=3, threshold=2, background=TRUE, iterations=20, markov=TRUE, window=2)").asList()
pks = c.eval("SpectrumSearch(prof, sigma=2, threshold=2, background=TRUE, iterations=20, markov=FALSE, window=2)").asList()
pksX = pks[0].asIntegers()
rois = []
print "Number of Peaks:", len(pksX)
for i in pksX:
#print "\t", roi.x1, i
rois.append(PointRoi(roi.x1, roi.y1 + i))
ol = Overlay()
for aroi in rois:
ol.add(aroi)
imp.setOverlay(ol)
c.close()
# RServeExample.py
# Try out RServe
# examples available here: http://www.rforge.net/Rserve/example.html
# get needed files here: http://rforge.net/Rserve/files/
#
# Modifications
# Date Who Ver What
# ---------- --- ------ -------------------------------------------------
# 2014-11-20 JRM 0.1.00 A test
from org.rosuda.REngine.Rserve import RConnection
from ij import IJ
from ij.gui import Roi, Overlay, Line
c = RConnection()
x = c.eval("R.version.string")
print x.asString()
imp = IJ.openImage("C:/Data/images/test/blobs.gif")
if imp == None:
print("Error getting image")
else:
myLine = Line(116, 204, 91, 226)
imp.setRoi(myLine)
imp.show()
print c.eval("library(Peaks)").asString()
roi = imp.getRoi()
if roi.getType() == Roi.LINE:
print("a line roi")
profile = roi.getPixels()
c.assign("prof", profile)
lMin = c.eval("min(prof)").asDouble()
print(lMin)