def SaveToZip(zf, ip, baseDir, counter):
fs = FileSaver(ip)
fs.setJpegQuality(75)
fs.saveAsJpeg(baseDir + "/tmp.jpeg")
zipName = str(counter) + ".jpeg"
zf.write(baseDir + "/tmp.jpeg", arcname=zipName)
os.remove(baseDir + "/tmp.jpeg")
def SaveToZip(zf, ip, baseDir, counter): fs = FileSaver(ip) fs.setJpegQuality(75) fs.saveAsJpeg(baseDir + "/tmp.jpeg") zipName = str(counter) + ".jpeg" zf.write(baseDir + "/tmp.jpeg", arcname=zipName) os.remove(baseDir + "/tmp.jpeg")
def split_channels_blue(imp):
#Create blue channel
original_blue = ChannelSplitter.getChannel(imp, 3)
original_blue_IP = ImagePlus(filename, original_blue)
fs = FileSaver(original_blue_IP)
folder = "/Users/gceleste/Desktop/test/channels"
filepath = folder + "/" + "{}_bluechannel.tif".format(filename)
fs.saveAsTiff(filepath)
#Open blue channel image.
blue = IJ.open(filepath)
#blue_IP = ImagePlus(filename, blue)
IJ.run(
"3D Objects Counter",
"threshold=100 slice=1 min.=50 max.=1447680 exclude_objects_on_edges objects summary"
)
#Save blue object map
blue_map = IJ.getImage()
fs = FileSaver(blue_map)
folder = "/Users/gceleste/Desktop/test/object maps"
filepath = folder + "/" + "{}_objectmap(blue).jpg".format(filename)
fs.saveAsJpeg(filepath)
#Close blue channel image.
blue_map.close()
blue = IJ.getImage()
blue.close()
def split_channels_red(imp):
#Create red channel
original_red = ChannelSplitter.getChannel(imp, 1)
original_red_IP = ImagePlus(filename, original_red)
fs = FileSaver(original_red_IP)
folder = "/Users/gceleste/Desktop/test/channels"
filepath = folder + "/" + "{}_redchannel.tif".format(filename)
fs.saveAsTiff(filepath)
#Open red channel image.
red = IJ.open(filepath)
#red_IP = ImagePlus(filename, red)
IJ.run(
"3D Objects Counter",
"threshold=130 slice=1 min.=50 max.=1447680 exclude_objects_on_edges objects summary"
)
#Save red object map.
red_map = IJ.getImage()
fs = FileSaver(red_map)
folder = "/Users/gceleste/Desktop/test/object maps"
filepath = folder + "/" + "{}_objectmap(red).jpg".format(filename)
fs.saveAsJpeg(filepath)
#Close red channel images.
red_map.close()
red = IJ.getImage()
red.close()
def savedata(imp, savepath, extension='ome.tiff', replace=False):
# general function for saving image data in different formats
# check if file already exists and delete if replace is true
if os.path.exists(savepath):
if replace:
os.remove(savepath)
if not replace:
return None
# general safety check
# if not extension:
# extension = 'ome.tiff'
# check extension
if extension in ['tiff', 'tif', 'ome.tiff', 'ome.tif', 'png', 'jpeg']:
fs = FileSaver(imp)
nslices = imp.getStack().getSize() # get the number of slices
# in case of TIFF
if extension == ('tiff' or 'tif' or 'TIFF' or 'TIF'):
if nslices > 1:
fs.saveAsTiffStack(savepath)
if nslices == 1:
fs.saveAsTiff(savepath)
# in case of OME-TIFF
elif extension == 'ome.tiff' or extension == 'ome.tif':
pstr = ExportTools.bfexporter(imp, savepath, useLOCI=True)
print('BioFormats Paramstring : ', pstr)
# in case of PNG
elif extension == ('png' or 'PNG'):
fs.saveAsPng(savepath)
# in case
elif extension == ('jpeg' or 'jpg' or 'JPEG' or 'JPG'):
fs.saveAsJpeg(savepath)
else:
extension = 'ome.tiff'
print("save as OME-TIFF: ") # savepath
pstr = ExportTools.bfexporter(imp, savepath, useLOCI=True)
print('BioFormats Paramstring : ', pstr)
return savepath
def process(srcDir, dstDir, nameContains, currentDir, fileName, keepDirectories, anneBoleyn, overOut):
print "Opening", fileName
saveDir = currentDir.replace(srcDir, dstDir) if keepDirectories else dstDir
head, tail = os.path.splitext(fileName)
imps = BF.openImagePlus(os.path.join(currentDir, fileName))
for imp in imps:
if not anneBoleyn:
print "Now showing image..."
imp.show()
IJ.run(imp, "Blue", "")
fs = FileSaver(imp)
if not os.path.exists(saveDir):
os.makedirs(saveDir)
if not overOut:
if os.path.exists(saveDir + "\\" + head + ".jpg"):
print "This JPG exists already and will not be overwritten. Moving on..."
else:
print "Saving to", os.path.join(saveDir, head + ".jpg")
fs.saveAsJpeg(os.path.join(saveDir, head + ".jpg"))
imp.close()
def writeThumbnail(self):
plateID, row, col, x, y = self.currentCoordinate
imName = "_".join([ str(plateID), str(row), str(col) ] ) + ".jpg"
imName = os.path.join(self.thumbDir, imName)
fs = FileSaver(self.openImage)
fs.saveAsJpeg( imName )
#filelist = os.listdir(filedir)
for root, directories, filenames in os.walk(filedir):
print directories
for filename in filenames:
if filename.lower().endswith('.lif'):
print filedir
print "..." + filename
filebase = splitext(filename)[0]
imps = getImps(os.path.join(filedir, filename))
printInfo(imps)
for (counter, item) in enumerate(imps):
#outimp = zproj(item)
outimp = makeComposite(item)
#outimp.show()
#outname = filedir + filebase + "/" + "s" + str(counter) + ".tif"
subname = ijtool.split(item.getTitle(), " - ")[1]
#outname = filedir + filebase + "/" + subname + "_ZP.tif"
outdir = os.path.join(filedir, "processed")
outname = os.path.join(outdir, filebase + "_" + subname + "_" + str(counter) + "_Composite")
print outname
if not os.path.isdir(outdir):
os.mkdir(outdir)
fs = FileSaver(outimp)
fs.saveAsTiffStack(outname+".tif")
fs.saveAsJpeg(outname+".jpg")
#outimp = zproject(filepath)
#outimp.show()
from ij.plugin import ImageCalculator as IC
from ij.process import ImageStatistics as IS
from ij.io import FileSaver
from ij import WindowManager
import os
xpoints = [954, 708, 3156, 2760]
ypoints = [1290, 2112, 1920, 1158]
folderds = "F:\\MSc Misis\\4 Semestre\\Tesis 1\\DS Prueba"
folderdsf = "F:\\MSc Misis\\4 Semestre\\Tesis 1\\DS Duplicado"
i = 0
for filename in os.listdir(folderds):
#Establecer Path
Pathfile = ("F:\\MSc Misis\\4 Semestre\\Tesis 1\\DS Prueba\\" + filename)
#Extraer imagen del Path
dsimage = IJ.openImage(Pathfile)
#Creación del área de interés
roi = PolygonRoi(xpoints, ypoints, 4, Roi.POLYGON)
#Creación de la imagen
dsimage.setRoi(roi)
#Duplicación de la imagen
imp2 = dsimage.duplicate()
#conversion a recipiente FileSaver
fs = FileSaver(imp2)
#Nombrar archivo
filename = folderdsf + "\\" + str(i) + ".jpg"
#Guardar archivo como JPEG
fs.saveAsJpeg(filename)
#impresion en consola del proceso
print "Proccessing FinalFile", filename
i = i + 1
rt4 = ResultsTable()
ta_coloc2=Analyzer(green_coloc,Measurements.INTEGRATED_DENSITY ,rt4);
ta_coloc2.measure();
greenIntensity=(rt4.getColumnAsDoubles(rt4.getColumnIndex("IntDen")))[0];
ic_coloc =ImageCalculator();
coloc_img=ic_coloc.run("Multiply create",red_coloc,green_coloc);
rt5 = ResultsTable()
ta_coloc3=Analyzer(coloc_img,Measurements.INTEGRATED_DENSITY ,rt5);
ta_coloc3.measure();
totalIntensity=(rt5.getColumnAsDoubles(rt5.getColumnIndex("IntDen")))[0];
rgb=RGBStackMerge();
composite=rgb.mergeChannels([red_coloc,green_coloc],False);
composite.show();
fs=FileSaver(composite);
fs.saveAsJpeg(outputDirectory + '/' + "coloc_"+filename);
composite.close();
if redIntensity == 0:
summary["Red-Green-Coloc-%"]= "NaN"
else:
summary["Red-Green-Coloc-%"]= float (totalIntensity*100/redIntensity)
if greenIntensity == 0:
summary["Green-Green-Coloc-%"]= "NaN"
else:
summary["Green-Red-Coloc-%"]= float (totalIntensity*100/greenIntensity)
# Writes everything in the output file
fieldnames=[]
# fieldnames.append("Directory")
elif chosenData == 8: #sourceFolder = 'I:\\NewDatasets\\Zeiss\\20160426\\red\\partiallyNormalized\\cropped_spim_TL' sourceFolder = 'I:\\NewDatasets\\Zeiss\\20160426\\red\\test_cropped_spim_TL' outputFolder = 'I:\\SegmentationResults\\MIPsRawData\\20160426\\MIP_small_cropped_t' startT = 3 endT = 23 appendix = '_Angle1.tif' for i in range(startT, endT+1): if i < 10: digit = '00' + str(i) elif i < 100: digit = '0' + str(i) elif i < 1000: digit = str(i) imagePath = sourceFolder + digit + appendix outputPath = outputFolder + digit + '.jpg' # open image file print 'Opening image', imagePath imp = IJ.openImage( imagePath ) zp = ZProjector(imp) zp.setMethod( ZProjector.MAX_METHOD ) zp.doProjection() MIPimp = zp.getProjection() fs = FileSaver( MIPimp ) fs.saveAsJpeg( outputPath ) print 'Done'
y1 = (float(bounds.y) + float(bounds.y + bounds.height)) / 2.
fileh.write("\t".join([
roi.getName(),
str(x1),
str(y1),
str(bounds.width),
str(bounds.height)
]) + "\n")
fileh.close()
#Export overlay
IJ.doCommand("Flatten")
time.sleep(1)
ids = WindowManager.getIDList()
imp_overlay = None
print ids
for id_img in ids:
if imp.getID() != id_img:
imp_overlay = WindowManager.getImage(id_img)
break
if imp_overlay is None:
sys.exit(1)
fs = FileSaver(imp_overlay)
fs.saveAsJpeg(dirToSave + imp.getShortTitle() + "_cells.jpg")
imp_overlay.hide()
imp_overlay.flush()
IJ.freeMemory()
