def _get_args_as_java_array(*args):
"""
Convert the Python args list into a Java array of strings.
:param args: the args list
:return: the Java array of strings
"""
result = JArrayList()
if args is not None and len(args) > 0:
for arg in args:
result.add(str(arg))
return result.toArray()
def _get_args_as_java_array(*args):
"""
Convert the Python args list into a Java array of strings.
:param args: the args list
:return: the Java array of strings
"""
result = JArrayList()
if args is not None and len(args) > 0:
for arg in args:
if arg is not None:
if isinstance(arg, unicode) or isinstance(arg, str):
result.add(arg)
elif isinstance(arg, JObject):
result.add(arg.toString())
else:
result.add(unicode(arg))
else:
result.add(str(arg))
return result.toArray()
# 1 corresponds to the second mass image (e.g. mass 13.0)
ratioProps1 = RatioProps(1, 0)
mp1 = MimsPlus(ui, ratioProps1)
imageArray.add(mp1)
IJ.log("Opening ratio: " + mp1.getTitle())
# Ratio images
# 2 corresponds to the first mass image (e.g. mass 26.0)
# 3 corresponds to the second mass image (e.g. mass 27.0)
ratioProps2 = RatioProps(3, 2)
mp2 = MimsPlus(ui, ratioProps2)
imageArray.add(mp2)
IJ.log("Opening ratio: " + mp2.getTitle())
images = jarray.zeros(imageArray.size(), MimsPlus)
images = imageArray.toArray(images)
#////////////////////////////
# Create and display table.
#////////////////////////////
table = MimsJTable(ui)
table.setStats(stats)
table.setRois(rois)
table.setImages(images)
table.setPlanes(planes)
#append=false
nPlanes = ui.getOpener().getNImages()
if nPlanes > 1:
table.createTable(False)
else:
table.createSumTable(False)
# 1 corresponds to the second mass image (e.g. mass 13.0)
ratioProps1 = RatioProps(1, 0)
mp1 = MimsPlus(ui, ratioProps1)
imageArray.add(mp1)
IJ.log("Opening ratio: "+mp1.getTitle())
# Ratio images
# 2 corresponds to the first mass image (e.g. mass 26.0)
# 3 corresponds to the second mass image (e.g. mass 27.0)
ratioProps2 = RatioProps(3, 2)
mp2 = MimsPlus(ui, ratioProps2)
imageArray.add(mp2)
IJ.log("Opening ratio: "+mp2.getTitle())
images = jarray.zeros(imageArray.size(), MimsPlus)
images = imageArray.toArray(images)
#////////////////////////////
# Create and display table.
#////////////////////////////
table = MimsJTable(ui)
table.setStats(stats)
table.setRois(rois)
table.setImages(images)
table.setPlanes(planes)
#append=false
nPlanes = ui.getOpener().getNImages()
if nPlanes > 1:
table.createTable(False)
else:
table.createSumTable(False)
mimStack = ui.getmimsStackEditing()
imp = ArrayList()
images = ui.getOpenMassImages()
#compress the planes
blockSize = images[0].getNSlices()
done = mimStack.compressPlanes(blockSize)
#force to 32bit
massCorrection = nrimsData.massCorrection(ui)
massCorrection.forceFloatImages(images)
if done:
nw = nrimsData.Nrrd_Writer(ui)
dataFile = nw.save(images, System.getProperty("java.io.tmpdir"), "comp_" + name)
tempFiles.add(dataFile)
tempFileArray = tempFiles.toArray()
#all work is done in first file
ui.openFile(tempFileArray[0])
for i in range(len(tempFileArray)):
if i != 0:
IJ.log("Concating file " + str(i));
directory = tempFileArray[i].getParent()
name = tempFileArray[i].getName()
tempUi = nrims.UI()
tempUi.openFile(tempFileArray[i])
tempImage = tempUi.getOpener()
image = ui.getOpener()
images = ui.getOpenMassImages()
mimStack = ui.getmimsStackEditing()
for j in range(len(images)):
images[j].setTitle(name)