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 autoProcAZtecImage(fwMicrons, wrkDir, barWid=0.1, barHt=9, barFnt=24, barCol="Black", barLoc="Lower Right"): imp = IJ.getImage() fName = imp.getShortTitle() wid = imp.getWidth() argThree = "distance=%g known=%f pixel=1 unit=um" % (wid, fwMicrons) IJ.run(imp, "Set Scale...", argThree) IJ.run(imp, "Enhance Contrast", "saturated=0.35") fs = FileSaver(imp) if path.exists(wrkDir) and path.isdir(wrkDir): print "folder exists:", wrkDir tifName = fName + ".tif" tifPath = path.join(wrkDir, tifName) print(tifPath) if fs.saveAsTiff(tifPath): print "Tif saved successfully at ", tifPath IJ.run(imp, "RGB Color", "") # dummy to get things set foo = imp.duplicate() s2 = "width=%g height=%g font=%g color=%s location=[%s] bold" % (barWid, barHt, barFnt, barCol, barLoc) IJ.run(foo, "Add Scale Bar", s2) # explicitly save preferences Prefs.savePreferences() foo.changes = False foo.close() IJ.run(imp, "Add Scale Bar", s2) fs = FileSaver(imp) pngName = fName + ".png" pngPath = path.join(wrkDir, pngName) if fs.saveAsPng(pngPath): print "png saved successfully at ", pngPath
def saveFile(imp, format, outputDirPath): fs = FileSaver(imp) saveDict = { 'tif': lambda: fs.saveAsTiff(outputDirPath + imp.getTitle() + ".tif"), 'zip': lambda: fs.saveAsZip(outputDirPath + imp.getTitle() + ".zip"), 'png': lambda: fs.saveAsPng(outputDirPath + imp.getTitle() + '.png'), 'txt': lambda: fs.saveAsTxt(outputDirPath + imp.getTitle() + '.txt'), 'jpg': lambda: fs.saveAsJpg(outputDirPath + imp.getTitle() + '.jpg') } saveDict[format]() return
import sys sys.path.append("/Users/berthola/Desktop/Fiji Scripts") from matrixoperator import Matrix from javax.media.j3d import Transform3D from javax.vecmath import Point3d from ij.io import FileSaver from profilingFixedCoordinates import getDendriticProfiles from profilingFixedCoordinates import getNodeCoordinates from machine_ import featureVector good = featureVector(72481, 99481, 50) bad = featureVector(83160, 99481, 50) plot = Plot("histogram", "y-coordinates", "count",range(0, 50), good) plot.setLimits(0.0, 50.0, 0, 60000000.0) plot.show() fs=FileSaver(plot.getImagePlus()) fs.saveAsPng(System.getProperty("user.home") + "/Desktop/Histotest/y" + "good.png") plot = Plot("histogram", "y-coordinates", "count",range(0, 50), bad) plot.setLimits(0.0, 50.0, 0, 60000000.0) plot.show() fs=FileSaver(plot.getImagePlus()) fs.saveAsPng(System.getProperty("user.home") + "/Desktop/Histotest/y" + "bad.png")
IJ.open(imgPath); IJ.run("Properties...", "channels=1 slices=1 frames=1 unit=um pixel_width=0.03143555 pixel_height=0.03144531 voxel_depth=1.0000000"); orig = IJ.getImage(); ti = orig.getShortTitle(); pngPath = homDir + relDir + "/" + ti + ".png" 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 IJ.run(orig, "RGB Color", "") # dummy to get things set foo = orig.duplicate() IJ.run(foo, "Add Scale Bar", strBar) # explicitly save preferences Prefs.savePreferences() foo.changes = False foo.close() IJ.run(orig, "Add Scale Bar", strBar) print(pngPath) fs = FileSaver(orig) if fs.saveAsPng(pngPath): print "png saved successfully at ", pngPath time.sleep(sleepTime) orig.close()
for i in range(0, len(pca)): if pca[i] <= binright and pca[i] >= binleft: counter += 1 histovector.append(counter) counter=0 binleft+=length binright+=length #histomirror=histovector.reverse() print "The histogram vector is:", histovector """ #Plot center from java.awt import Color from ini.trakem2.display import Display3D Display3D.addFatPoint("eigen center", tree.getLayerSet(), center.get(0, 0), center.get(0, 1), center.get(0, 2), 10, Color.red) """ plot = Plot("histogram", "bins", "count", range(iterations), histovector) plot.show() fs=FileSaver(plot.getImagePlus()) fs.saveAsPng(System.getProperty("user.home") + "/Desktop/Histotest/pcaleft" + str(ID) + ".png") histovector.reverse() plot = Plot("histogram", "bins", "count", range(iterations), histovector) plot.show() fs=FileSaver(plot.getImagePlus()) fs.saveAsPng(System.getProperty("user.home") + "/Desktop/Histotest/pcaright" + str(ID) + ".png")
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): orig = jmg.correctForeshortening(orig, tiltDeg) IJ.run(orig, "RGB Color", "") IJ.run(orig, "Add Scale Bar", strBar) orig.show() outPth = sPngPath + strWrk + ".png" fs = FileSaver(orig) if fs.saveAsPng(outPth): print "png saved successfully at ", outPth time.sleep(1) # orig.close() IJ.run("Close All") toc = time.time() elapsed = toc - tic print("analyzed %g images" % i) print("completed in %g sec" % elapsed )
from ij import IJ import os from ij import WindowManager as WM import re from ij.io import FileSaver path1 = 'I:\\image_process_msi\\KR_data\\CRC_KR_TEST_MSIMUT\\MSIMUT' save_path = 'I:\\image_process_msi\\KR_data\\KR_adjust\\KR_test_msi' for filename in os.listdir(path1)[0:2]: if filename.endswith(".png"): imp = IJ.openImage(os.path.join(path1, filename)) #这里就可以用插件啦 IJ.run(imp, "Colour Deconvolution", "vectors=H&E") images = map(WM.getImage, WM.getIDList()) for img in images: print('title is ', img.title) if (re.search(r'Colour\_1', img.title) is not None): fs = FileSaver(img) fs.saveAsPng(os.path.join(save_path, filename)) print(img.title, 'have saved') img.close()