labId = "qm-04513"
smpId = "RAD-2015-0148Y-HCl-xs"
datDir = edsDir + "/Oxford/" + ePrjDir + "/reports/" + labId + "-" + smpId
sTifPath = datDir + "/tif/"
bSetMinMax = False
gMin = 1000
gMax = 11400
fwUnits = 28.9
units = IJ.micronSymbol + "m"
imp = IJ.getImage()
imp = jmg.calibImage(imp, fwUnits, units=-6)
if(bSetMinMax == True):
IJ.setMinAndMax(gMin, gMax)
imp.updateAndRepaintWindow()
ti = imp.getShortTitle()
fi = sTifPath + ti + ".tif"
fs = FileSaver(imp)
imp.changes = False
print(fi)
if fs.saveAsTiff(fi):
print "Tif saved successfully at ", fi
print("done")
query = sTifPath + "*.tif"
lFiles = glob.glob(query)
i = 0
for fi in lFiles:
i += 1
fi = fi.replace("\\", "/")
orig = ImagePlus(fi)
strName = os.path.basename(fi)
print(strName)
orig.setTitle(strName)
strWrk = strName.split('.')[0]
lStr = strWrk.split('-')
l = len(lStr)
if (i <= nLo):
jmg.calibImage(orig, fwLo, units=-6)
else:
jmg.calibImage(orig, fwHi, units=-6)
strBar = "width=%g height=%g font=%g color=%s location=[%s] bold" % (barW, barH, barF, barC, barL)
# a hack to get the scale bars to work reliably
foo = orig.duplicate()
if lStr[l-1][0:2] == "an":
IJ.run(orig, "Enhance Contrast", sSat)
IJ.run(orig, "RGB Color", "")
IJ.run(orig, "Add Scale Bar", strBar)
orig.show()
else:
IJ.run(orig, "Gamma...", sGamma)
IJ.run(orig, "Enhance Contrast", sSat)
IJ.run(orig, "RGB Color", "")
IJ.run(orig, "Add Scale Bar", strBar)
# calibImage_.py
#
# Apply a calibration to an image from the full width
#
# Modifications
# Date Who Ver What
# ---------- --- ------ -------------------------------------------------
# 2014-10-15 JRM 0.1.00 Get'er done
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
import os
import jmFijiGen as jmg
from ij import IJ
from ij import WindowManager
# full width in microns
fw = 57.9
impCal = WindowManager.getCurrentImage()
impCal = jmg.calibImage(impCal, fw, units=-6)
impCal.show()
query = sTifPath + "*.tif"
lFiles = glob.glob(query)
i = 0
for fi in lFiles:
i += 1
fi = fi.replace("\\", "/")
orig = ImagePlus(fi)
strName = os.path.basename(fi)
print(strName)
orig.setTitle(strName)
strWrk = strName.split('.')[0]
lStr = strWrk.split('-')
l = len(lStr)
jmg.calibImage(orig, fwImg, units=-6)
# save the calibrated image
fs = FileSaver(orig)
print(fi)
if fs.saveAsTiff(fi):
print "Tif saved successfully at ", fi
strBar = "width=%g height=%g font=%g color=%s location=[%s] bold" % (barW, barH, barF, barC, barL)
# a hack to get the scale bars to work reliably
if (bSetMinMax==True):
orig.show()
IJ.setMinAndMax(gMin, gMax)
else:
IJ.run(orig, "Enhance Contrast", sSat)
if(bDoTiltCorrect == True):
# testCalibImage_.py
#
# Test calibration of the image using calibImage in jmFijiGen.py
# Modifications
# Date Who Ver What
# ---------- --- ------ -------------------------------------------------
# 2014-10-10 JRM 0.1.00 initial prototype development using bugs
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
import os
import glob
import time
from ij import IJ
from ij import ImagePlus
from ij import WindowManager
import jmFijiGen as jmg
gitDir = os.environ['GIT_HOME']
relImg = "/OSImageAnalysis/images/EC-bse-10kV.png"
fw = 4.45 # microns. Can read this from AZtec details dialog for image.
imgPath = gitDir + relImg
print(imgPath)
raw = IJ.openImage(imgPath)
raw = jmg.calibImage(raw, fw, units=-6)
raw.show()
