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()
