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()