from ij import ImagePlus
from ij import IJ
import os
imgDir = os.environ['IMG_ROOT']
relImg = "/test/suite/"
# n.b. 17.56 and 17.57 - this gets it wrong both 24.3889
fName = 'fib620.tif'
# fName = 'anaFiveDM.tif'
# fName = 'sirionSisBSE.tif'
# fName = 'sirionXHD.tif'
# fName = 'clumpedAgX.dm3'
filePath = imgDir + relImg + fName
r = ImageProcessorReader(ChannelSeparator(LociPrefs.makeImageReader()))
# print(dir(r))
r.setId(filePath)
num = r.getImageCount()
width = r.getSizeX()
height = r.getSizeY()
md = r.getGlobalMetadata()
# print(type(md))
# print(num, width, height)
stack = ImageStack(width, height)
i = 0
ip = r.openProcessors(i)[0]
stack.addSlice("1", ip);
imp = ImagePlus("foo", stack);
r.close()
imp.show()
import os
from loci.plugins.util import BFVirtualStack, ImageProcessorReader
print '---------------------------------------------------------------------------------------'
base = '/scratch/imageproc/data/paolo/FluoView_stitching/oib_format/TVA4vglut2_n2_4X_20140126_234209'
infile = 'Slide1sec001/Slide1sec001_01.oib'
path = os.path.join(base, infile)
#print 'file: %s' % path
irdr = ImageProcessorReader()
irdr.setId(path)
bf = BFVirtualStack(path, irdr, False, False, False)
print 'Successfully created virtual stack.'
width = bf.getWidth()
height = bf.getHeight()
size = bf.getSize()
procreader = bf.getReader()
# meta = procreader.getMetadata()
# print meta
absposx = procreader.getMetadataValue('AbsPositionValueX')
absposy = procreader.getMetadataValue('AbsPositionValueY')
print 'Dimensions (x, y, size): %s, %s, %s' % (width, height, size)
print 'Absolute positions: %s, %s' % (absposx, absposy)