outDir = homDir + relOut
outPth = outDir + "/" + outNamFull
if bTestPaths == True:
# print the directories and try loading the ROI image
print(inDir)
strImg = inDir + "/ROI.png"
imp = IJ.openImage(strImg)
if imp == None:
print("Error loading ROI.png")
else:
if bHeadless != True:
imp.show()
print(outPth)
else:
jmg.ensureDir(outDir)
impMontFull = jmg.makeMontage(lName, nCol, nRow, inDir, lCal=lCal, sca=1.0, lCr=None, bDebug=False, bHeadless=bHeadless)
if bScale:
newW = round(scaFac * impMontFull.getWidth())
newH = round(scaFac * impMontFull.getHeight())
newN = sampID + "-" + mapID
# strSca = "x=%g y=%g width=%d height=%d interpolation=Bicubic average create title=%s" % (scaFac, scaFac, newW, newH, newN)
impOut = jmg.scaleImg(impMontFull, scaFac)
# IJ.run(impMontFull, "Scale...", strSca )
impMontFull.changes=False
impMontFull.close()
# impOut = IJ.getImage()
else:
impOut = impMontFull
inImg = impOut
sampID = "qm-03965-KJL-027" nmPerPx = 1.213 minCirc = 0.5 minSize = 1.0e1 maxSize = 1.0e6 barW = 100 # bar width, nm barH = 6 # bar height, pts barF = 28 # bar font, pts barC = "Black" # bar color strBar = "width=%g height=%g font=%g color=%s location=[Lower Right] bold" % (barW, barH, barF, barC) sImgPath = imgDir + relImg + "/" + sampID + "/dm3/" sRptPath = rptDir + "/" + sampID + "/" jmg.ensureDir(sRptPath) sRptCsvPath = sRptPath + sampID + ".csv" sRptImgPath = sRptPath + "png/" jmg.ensureDir(sRptImgPath) # create empty output vectors for results imgOut = [] parOut = [] ecdOut = [] conOut = [] cirOut = [] rndOut = [] solOut = [] arOut = [] query = sImgPath + "*.dm3"
import jmFijiGen as jmg
tic = time.time()
sFac = 0.0
barW = 5 # bar width, microns
barH = 6 # bar height, pts
barF = 24 # bar font, pts
barC = "White" # bar color
barL= "Lower Right" # bar location
dc = DirectoryChooser("Choose directory")
basePath = dc.getDirectory()
sPngPath = basePath + os.sep + "png" + os.sep
jmg.ensureDir(sPngPath)
names = []
for file in os.listdir(basePath):
if file.endswith(".tif"):
name = os.path.splitext(file)[0]
names.append(name)
names.sort()
sSat = "saturated=%.2f" % sFac
strBar = "width=%g height=%g font=%g color=%s location=[%s] bold" % (barW, barH, barF, barC, barL)
for name in names:
from ij import IJ
from ij import ImagePlus
import jmFijiGen as jmg
tic = time.time()
imgRt = os.environ['IMG_ROOT']
relPrj = "/Kateeva-15-01"
labId = "qm-04309"
smpId = "R31"
sDm3Path = imgRt + relPrj + "/" + labId + "-" + smpId + "/dm3/"
sTifPath = imgRt + relPrj + "/" + labId + "-" + smpId + "/tif/"
jmg.ensureDir(sTifPath)
query = sDm3Path + "*.dm3"
print(query)
lFiles = glob.glob(query)
i = 0
for fi in lFiles:
i += 1
orig = ImagePlus(fi)
strName = os.path.basename(fi)
strName = strName.split('.')[0]
lStr = strName.split('-')
l = len(lStr)
strNum = lStr[l-1]
iNum = int(strNum)
orig.setTitle(strNum)
Prefs.set("Last.Image.Dir", basePath)
names = []
for file in os.listdir(basePath):
if file.endswith(".tif"):
name = os.path.splitext(file)[0]
names.append(name)
names.sort()
# basePath = '/Users/jrminter/dat/images/test/qm-04570-1421DJD-04-C03/'
iniPath = basePath + os.sep + 'ImageMetadata.ini'
os.chdir(basePath)
mu = IJ.micronSymbol
calibDir = basePath + "calib" + os.sep
jmg.ensureDir(calibDir)
config = ConfigParser.RawConfigParser()
config.read(iniPath)
for name in names:
path = basePath + os.sep + name + ".tif"
print(name, path)
fMag = config.getfloat(name, "Mag")
fScaleX = config.getfloat(name, "ScaleX")
fScaleY = config.getfloat(name, "ScaleY")
sUnits = config.get(name, "Units")
if (bConvertNmToUm == True):
if(sUnits == "nm"):
fScaleX /= 1000.
fScaleY /= 1000.
sUnits = mu + "m"