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 makeStack(stackDir, stackName = "stack"):
IJ.run("Image Sequence...", "open="+stackDir+" file = (\"img_.*\") sort")
imp = IJ.getImage()
#IJ.run("8-bit")
fs = FileSaver(imp)
print "Saving stack"
fs.saveAsTiff(stackDir + "/" +stackName+".tif")
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 run():
printLog("=====ZY_CreatTemp_V2====", 0)
#Prompt user to open a image
od = OpenDialog("Choose image file", None)
if od is None:
msgStr = "User Cancled"
printLog(msgStr, 1)
else:
sourceFolder = od.getDirectory()
fileName = od.getFileName()
imp = IJ.openImage(sourceFolder + fileName)
imp.show()
n = imp.getNSlices()
printLog("Processing source file: " + fileName, 1)
imp2 = pickSlice(imp)
if imp2:
destFolder = os.path.join(sourceFolder, 'Temps')
#outName = os.path.join(destFolder,fileName[:-4]+'_temp.tif') #remove the .tif in filename
outName = os.path.join(destFolder, 'temp.tif')
# check or make the folder
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
#make temp
dupNSlice(imp2, n - 1)
printLog("Saving to: " + outName, 1)
fs = FileSaver(imp2)
fs.saveAsTiffStack(outName)
imp2.close()
imp.close()
msgStr = "ZY_CraetTemp_V2.py is Done."
printLog(msgStr, 0)
def run():
printLog("=====ZY_CreatTemp_V2====",0)
#Prompt user to open a image
od = OpenDialog("Choose image file", None)
if od is None:
msgStr = "User Cancled"
printLog(msgStr,1)
else:
sourceFolder = od.getDirectory()
fileName = od.getFileName()
imp = IJ.openImage(sourceFolder+fileName)
imp.show()
n = imp.getNSlices()
printLog("Processing source file: " + fileName,1)
imp2= pickSlice(imp)
if imp2:
destFolder = os.path.join(sourceFolder, 'Temps')
#outName = os.path.join(destFolder,fileName[:-4]+'_temp.tif') #remove the .tif in filename
outName = os.path.join(destFolder,'temp.tif')
# check or make the folder
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
#make temp
dupNSlice(imp2,n-1)
printLog("Saving to: " + outName,1)
fs = FileSaver(imp2)
fs.saveAsTiffStack(outName)
imp2.close()
imp.close()
msgStr = "ZY_CraetTemp_V2.py is Done."
printLog(msgStr,0)
def resizeAndSave(filePaths, l):
while l.get() < min(len(filePaths), currentWrittenLayer + nTilesAtATime + 1) :
k = l.getAndIncrement()
if k < min(len(filePaths), currentWrittenLayer + nTilesAtATime):
filePath = filePaths[k]
imageName = os.path.basename(filePath)
resizedImageName = os.path.splitext(imageName)[0] + '_resized_' + factorString + os.path.splitext(imageName)[1]
imageFolderName = os.path.basename(os.path.dirname(filePath))
resizedFilePath = fc.cleanLinuxPath(os.path.join(downSampledEMFolder, imageFolderName, resizedImageName))
im = Opener().openImage(filePath)
IJ.log('Am I going to process the image: im.height = ' + str(im.height) + ' - tileHeight = ' + str(tileHeight) + ' tile number ' + str(k))
if im.height == tileHeight: # crop a few lines at the top only if it has not already been done (sometimes the pipeline gets rerun)
im = fc.crop(im,cropRoi)
im = fc.normLocalContrast(im, normLocalContrastSize, normLocalContrastSize, 3, True, True)
# IJ.run(im, 'Replace value', 'pattern=0 replacement=1') # only for final waferOverview
FileSaver(im).saveAsTiff(filePath)
if not os.path.isfile(resizedFilePath):
im = fc.resize(im, scaleFactor)
FileSaver(im).saveAsTiff(resizedFilePath)
IJ.log('Image resized to ' + resizedFilePath)
im.close()
def makeStack(stackDir, stackName="stack"):
IJ.run("Image Sequence...",
"open=" + stackDir + " file = (\"img_.*\") sort")
imp = IJ.getImage()
#IJ.run("8-bit")
fs = FileSaver(imp)
print "Saving stack"
fs.saveAsTiff(stackDir + "/" + stackName + ".tif")
def bSaveStack(imp, fullPath):
fs = FileSaver(imp)
#print 'bSaveStack()', fullPath, 'nslices=', imp.getNSlices()
bPrintLog('bSaveStack():' + fullPath + ' slices=' + str(imp.getNSlices()), 1)
if imp.getNSlices()>1:
fs.saveAsTiffStack(fullPath)
else:
fs.saveAsTiff(fullPath)
def straighten(stackName):
'''
IJ.run("Set Measurements...", "area mean min center redirect=None decimal=3")
IJ.open(stackName)
imp = IJ.getImage()
stack = imp.getImageStack()
for i in xrange(1, imp.getNSlices()+1):
image = ImagePlus(str(i), stack.getProcessor(i))
xvals = []
yvals = []
maxvals = []
j = 0
for k in xrange(0, 512, 2):
IJ.makeRectangle(k, 0, 4, 512)
IJ.run("Measure")
table = RT.getResultsTable()
x = table.getValue("XM", 0)
y = table.getValue("YM", 0)
#maxi = IJ.getResult("Max")
table = []
xvals.append(k)
yvals.append(y)
#maxvals.append(maxi)
#if maxvals[j] == 0 and j > 0:
#yvals[j] = yvals[j-1]
j += 1
print "xvals:", xvals
print "yvals:", yvals
mr = MR()
IJ.run("Make Selection...", "freeline, "+str(xvals)+" ,"+ str(yvals))
#IJ.runMacro("makeSelection...", "freeline, "+str(xvals)+" ,"+ str(yvals));
#IJ.run("makeSelection(\"freeline\", xvals, yvals);")
#IJ.run("Straighten...", "line = 80")
'''
IJ.open(stackName)
imp = IJ.getImage()
stack = imp.getImageStack()
print imp.getNSlices()
for i in range(1, imp.getNSlices() + 1):
image = ImagePlus(str(i), stack.getProcessor(i))
IJ.runMacroFile(
"/Users/juliansegert/repos/Bio119_root_tracking/straightenOneImage.ijm"
)
newImp = WM.getCurrentImage()
fs = FileSaver(newImp)
fs.saveAsTiff(
"/Users/juliansegert/Documents/Roots/Four_root_image_stacks/Pos01/"
+ str(i) + ".tif")
newImp.close()
def straighten(stackName):
'''
IJ.run("Set Measurements...", "area mean min center redirect=None decimal=3")
IJ.open(stackName)
imp = IJ.getImage()
stack = imp.getImageStack()
for i in xrange(1, imp.getNSlices()+1):
image = ImagePlus(str(i), stack.getProcessor(i))
xvals = []
yvals = []
maxvals = []
j = 0
for k in xrange(0, 512, 2):
IJ.makeRectangle(k, 0, 4, 512)
IJ.run("Measure")
table = RT.getResultsTable()
x = table.getValue("XM", 0)
y = table.getValue("YM", 0)
#maxi = IJ.getResult("Max")
table = []
xvals.append(k)
yvals.append(y)
#maxvals.append(maxi)
#if maxvals[j] == 0 and j > 0:
#yvals[j] = yvals[j-1]
j += 1
print "xvals:", xvals
print "yvals:", yvals
mr = MR()
IJ.run("Make Selection...", "freeline, "+str(xvals)+" ,"+ str(yvals))
#IJ.runMacro("makeSelection...", "freeline, "+str(xvals)+" ,"+ str(yvals));
#IJ.run("makeSelection(\"freeline\", xvals, yvals);")
#IJ.run("Straighten...", "line = 80")
'''
IJ.open(stackName)
imp = IJ.getImage()
stack = imp.getImageStack()
print imp.getNSlices()
for i in range(1, imp.getNSlices()+1):
image = ImagePlus(str(i), stack.getProcessor(i))
IJ.runMacroFile("/Users/juliansegert/repos/Bio119_root_tracking/straightenOneImage.ijm")
newImp = WM.getCurrentImage()
fs = FileSaver(newImp)
fs.saveAsTiff("/Users/juliansegert/Documents/Roots/Four_root_image_stacks/Pos01/"+str(i)+".tif")
newImp.close()
def covertTo8bitsBatch(folder_in,folder_out): for folder in os.listdir(folder_in): infolderpath = folder_in+folder outfolderpath = folder_out + folder os.mkdir(outfolderpath) for filename in os.listdir(infolderpath): imp = IJ.openImage(os.path.join(infolderpath, filename)) IJ.run(imp, "8-bit", "") fs = FileSaver(imp) filepath = os.path.join(outfolderpath, filename) fs.saveAsTiff(filepath)
def save_tif(imps, new_name, new_dir):
"""
takes imps object and name string, saves as tif
"""
new_name = os.path.join(new_dir, new_name)
if os.path.exists(new_name):
print("File " + new_name + " exists, continuing")
return
else:
fs = FileSaver(imps)
fs.saveAsTiff(new_name)
def saveStack(destFolder,file_name,imp):
#rename the result and save it to subfolder
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
fullname=os.path.join(destFolder,file_name)
#print (fullname)
fs = FileSaver(imp)
#print 'bSaveStack()', fullPath, 'nslices=', sr_imp.getNSlices()
msgStr = "Dimension:" + str(imp.width) + " X " + str(imp.height) + " X " + str(imp.getNSlices())
printLog("-Save "+file_name+" to "+destFolder,1)
printLog("-"+msgStr,2)
fs.saveAsTiffStack(fullname)
def saveStack(destFolder,file_name,imp):
#rename the result and save it to subfolder
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
fullname=os.path.join(destFolder,file_name)
#print (fullname)
fs = FileSaver(imp)
#print 'bSaveStack()', fullPath, 'nslices=', sr_imp.getNSlices()
msgStr = "Dimension:" + str(imp.width) + " X " + str(imp.height) + " X " + str(imp.getNSlices())
printLog("-Save "+file_name+" to "+destFolder,1)
printLog("-"+msgStr,2)
fs.saveAsTiffStack(fullname)
def applyFilter(stackName):
imp = IJ.openImage(stackName)
stack = imp.getImageStack()
for i in xrange(1, imp.getNSlices()+1):
image = ImagePlus(str(i), stack.getProcessor(i))
IJ.run(image, "Auto Threshold", "method=Li white")
#IJ.run(image, "Analyze Particles...", "size= 1000-Infinity circularity=0.00-1.00 show=Masks in_situ")
imp2 = ImagePlus("Threshold", stack)
fs = FileSaver(imp2)
print "Saving filtered stack"
fs.saveAsTiff(stackName[:-4] + "-filtered(Li).tif")
def save_tif(imps, name, new_dir):
"""
takes imps object and name string, saves as tif
"""
new_name = os.path.join(new_dir, name+".tif")
if os.path.exists(new_name):
message = ">> *File:* \n -->"+ new_name + "\n exists, continuing"
IJ.log(message)
print("File "+ new_name + " exists, continuing")
return
else:
fs = FileSaver(imps[0])
fs.saveAsTiff(new_name)
def applyFilter(stackName):
imp = IJ.openImage(stackName)
stack = imp.getImageStack()
for i in xrange(1, imp.getNSlices() + 1):
image = ImagePlus(str(i), stack.getProcessor(i))
IJ.run(image, "Auto Threshold", "method=Li white")
#IJ.run(image, "Analyze Particles...", "size= 1000-Infinity circularity=0.00-1.00 show=Masks in_situ")
imp2 = ImagePlus("Threshold", stack)
fs = FileSaver(imp2)
print "Saving filtered stack"
fs.saveAsTiff(stackName[:-4] + "-filtered(Li).tif")
def stackToSlices(folder_in,folder_out,folder_num):
for filename in os.listdir(folder_in):
imp = IJ.openImage(os.path.join(folder_in, filename))
stack = imp.getImageStack()
output=folder_out+str(folder_num)
folder_num = folder_num+1
os.makedirs(output)
for i in xrange(1, imp.getNSlices()+1):
ip = stack.getProcessor(i)
imp = ImagePlus("imp", ip)
fs= FileSaver(imp)
filepath = os.path.join(output,str(i))
fs.saveAsTiff(filepath)
def saveImage(imp, out_file):
if overwritePref == overwriteChoices[0]:
if not os.path.exists(out_file):
FileSaver(imp).saveAsTiff(out_file)
else:
overwriteList.append(out_file)
elif overwritePref == overwriteChoices[1]:
if not os.path.exists(out_file):
FileSaver(imp).saveAsTiff(out_file)
else:
overwriteList.append(out_file)
FileSaver(imp).saveAsTiff(out_file)
def generate_limit_labels(imp, limits, cb_fraction, params):
"""generate text ROIs in correct positions to label colorbar"""
rois = []
w = imp.getWidth()
h = imp.getHeight()
txt_h_px = float(h) / 15
txt_sz_pt = int(round((18.0 / 24.0) * txt_h_px))
for limit in limits:
roi = TextRoi(1, 1, str(round(limit, 3)),
Font("SansSerif", Font.ITALIC, txt_sz_pt))
roi.setJustification(TextRoi.RIGHT)
roi.setFillColor(Color.BLACK)
roi.setStrokeColor(Color.WHITE)
rois.append(roi)
roim = RoiManager(False)
roim.reset()
imp.show()
mbui.autoset_zoom(imp)
for fridx in range(1, imp.getNSlices() + 1):
imp.setPosition(fridx)
roi_uu = rois[1].clone()
xpos = w - cb_fraction * w - float(w) / 100 - rois[1].getFloatWidth()
roi_uu.setLocation(xpos, 1)
imp.setRoi(roi_uu)
roim.addRoi(roi_uu)
roi_ll = rois[0].clone()
roi_ll.setLocation(xpos, h - rois[0].getFloatHeight())
imp.setRoi(roi_ll)
roim.addRoi(roi_ll)
roim.runCommand("Show All")
FileSaver(imp).saveAsTiff(
os.path.join(params.output_path,
"overlaid curvature nudged labels.tif"))
# nudge positions
roim.reset()
imp.killRoi()
for fridx in range(1, imp.getNSlices() + 1):
imp.setPosition(fridx)
roi_uu = rois[1].clone()
xpos = w - cb_fraction * w - float(w) / 100
roi_uu.setLocation(xpos, 1)
imp.setRoi(roi_uu)
roim.addRoi(roi_uu)
roi_ll = rois[0].clone()
roi_ll.setLocation(xpos, h - rois[0].getFloatHeight())
imp.setRoi(roi_ll)
roim.addRoi(roi_ll)
roim.runCommand("Show All")
FileSaver(imp).saveAsTiff(
os.path.join(params.output_path, "overlaid curvature.tif"))
return imp
def scaleandfilter(infile,outfile,scalex,scaley):
print ("infile is: "+infile)
imp = Opener().openImage(infile)
print imp
print "scalex = %f; scaley = %f" % (scalex,scaley)
# Rescale
ip = imp.getProcessor()
ip.setInterpolate(True)
sp = StackProcessor(imp.getStack(),ip);
sp2=sp.resize(int(round(ip.width * scalex)), int(round(ip.height *scaley)));
imp.setStack(imp.getTitle(),sp2);
cal = imp.getCalibration()
cal.pixelWidth /= scalex
cal.pixelHeight /= scaley
IJ.run(imp, "8-bit","")
intif=infile+".tif"
outtif=infile+"-filtered.tif"
print("saving input file as "+intif)
f=FileSaver(imp)
f.saveAsTiffStack(intif)
imp.close()
# anisotropic filtering
anisopts="-scanrange:10 -tau:2 -nsteps:2 -lambda:0.1 -ipflag:0 -anicoeff1:1 -anicoeff2:0 -anicoeff3:0"
anisopts=anisopts+" -dx:%f -dy:%f -dz:%f" % (cal.pixelWidth,cal.pixelHeight,cal.pixelDepth)
if sys.version_info > (2, 4):
#for testing
# subprocess.check_call(["cp",intif,outtif])
subprocess.check_call(["anisofilter"]+anisopts.split(' ')+[intif,outtif])
else:
os.system(" ".join(["anisofilter"]+anisopts.split(' ')+[intif,outtif]))
# Hessian (tubeness)
print("Opening output tif: "+outtif)
imp = Opener().openImage(outtif)
imp.setCalibration(cal)
print("Running tubeness on tif: "+outtif)
IJ.run(imp,"Tubeness", "sigma=1")
IJ.run(imp, "8-bit","")
# Save to PIC
print("Saving as PIC: "+outfile)
# IJ.saveAs("tiff","outtif")
IJ.run(imp,"Biorad ...", "biorad="+outfile)
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 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 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 run(self):
try:
bounds = self.layer.getMinimalBoundingBox(Patch, True)
filepath = os.path.join(
self.target_dir, "section-" + str(self.i).zfill(5) + "-[x=" +
str(bounds.x) + "-y=" + str(bounds.y) + "-width=" +
str(bounds.width) + "-height=" + str(bounds.height) + "].zip")
if os.path.exists(filepath):
System.out.println("Skipping: " + filepath)
return
# Export
System.out.println("Preparing: " + os.path.split(filepath)[1])
img = self.layer.getProject().getLoader().getFlatAWTImage(
self.layer, bounds, 1.0, -1, ImagePlus.GRAY8, Patch, None,
False, Color.black)
bi = BufferedImage(img.getWidth(None), img.getHeight(None),
BufferedImage.TYPE_BYTE_GRAY)
g = bi.createGraphics()
g.drawImage(img, 0, 0, None)
g.dispose()
g = None
imp = ImagePlus(str(self.layer.getZ()), ByteProcessor(bi))
FileSaver(imp).saveAsZip(filepath)
bi.flush()
bi = None
imp.flush()
imp = None
ip = None
System.out.println("Saved: " + os.path.split(filepath)[1])
except:
import sys
e = sys.exc_info()
System.out.println("Error:" + str(e[0]) + "\n" + str(e[1]) + "\n" +
str(e[2]))
def saveCroppedROIs(self, event):
""" Duplicates cropped ROIs and saves """
# Create export dir, if not already present
current_export_dir = self.createExportDir("Cropped_ROI")
for Image in self.Images.values(): # for all Image instances
# save image
cropped_copy = Image.imp.crop() # returns cropped image as an imp
img_filename = os.path.join(current_export_dir, Image.title)
if os.path.splitext(img_filename)[1] != ".tif":
os.path.join(img_filename, ".tif")
FileSaver(cropped_copy).saveAsTiff(img_filename)
# save roi
roi_filename = os.path.splitext(img_filename)[0] + "_roi.roi"
roi = Image.imp.getRoi()
if roi != None:
rm = RM.getInstance()
if rm == None:
rm = RM()
rm.addRoi(roi)
rm.runCommand("Save", roi_filename) # which one does it save
rm.runCommand("Delete")
IJ.log("Cropped ROI saved: " +
os.path.join(current_export_dir, Image.title))
def save_qc_image(imp, rois, output_path):
"""save rois overlaid on imp to output_path"""
imp.killRoi()
if len(rois) > 0:
roim = RoiManager(False)
for roi in rois:
roim.addRoi(roi)
roim.runCommand("Show All with labels")
RGBStackConverter.convertToRGB(imp)
roim.moveRoisToOverlay(imp)
FileSaver(imp).saveAsTiff(output_path)
roim.runCommand("Show None")
roim.close()
else:
FileSaver(imp).saveAsTiff(output_path)
return
def run():
srcDir = DirectoryChooser("Choose directory").getDirectory()
if not srcDir:
return
targetDir = DirectoryChooser("Choose target directory").getDirectory()
if targetDir is None:
# User canceled the dialog
return
sId = ".tiff"
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
path = os.path.join(root, filename)
if not (sId in filename):
continue
cs = ChannelSeparator()
cs.setId(path)
print "cs", cs
bf = BFVirtualStack(path, cs, False, False, False)
for sliceIndex in xrange(1, bf.getSize() + 1):
print "Processing slice", sliceIndex
ip = bf.getProcessor(sliceIndex)
sliceFileName = os.path.join(targetDir + filename + "_" +
str(sliceIndex) + ".tiff")
print "writing ", sliceFileName
FileSaver(ImagePlus(str(sliceIndex),
ip)).saveAsTiff(sliceFileName)
def run(self):
try:
filepath = self.makeFilePath()
if os.path.exists(filepath):
return
x, y, k = self.coords
width, height, n_layers = self.dimensions
# Cube's field of view in XY
fov = Rectangle(x, y, width, height)
# Join the bounds of the layers
r = None
for b in self.bounds[k:min(k + n_layers, len(bounds))]:
if r is None:
r = Rectangle(b.x, b.y, b.width, b.height)
else:
r.add(b)
if not fov.intersects(r):
# Would be empty
return
drawImage = Graphics2D.getDeclaredMethod(
"drawImage", [Image, AffineTransform, ImageObserver])
drawImage.setAccessible(True)
dispose = Graphics.getDeclaredMethod("dispose", [])
dispose.setAccessible(True)
# Populate and write cube
stack = ImageStack(width, height)
for layer in self.layers[k:min(k + n_layers, len(self.layers))]:
img = layer.getProject().getLoader().getFlatAWTImage(
layer, fov, 1.0, -1, ImagePlus.GRAY8, Patch, None, False,
Color.black)
bi = BufferedImage(img.getWidth(None), img.getHeight(None),
BufferedImage.TYPE_BYTE_GRAY)
g = bi.createGraphics()
aff = AffineTransform(1, 0, 0, 1, 0, 0)
#g.drawImage(img, aff, None) # Necessary to bypass issues that result in only using 7-bits and with the ByteProcessor constructor
drawImage.invoke(g, [img, aff, None])
#g.dispose()
dispose.invoke(g, [])
g = None
img = None
stack.addSlice("", ByteProcessor(bi))
bi.flush()
bi = None
imp = ImagePlus("x=%s y=%s k=%s" % (x, y, k), stack)
Utils.ensure(filepath)
FileSaver(imp).saveAsZip(filepath)
imp.flush()
imp = None
except:
e = sys.exc_info()
System.out.println("Error:" + str(e[0]) + "\n" + str(e[1]) + "\n" +
str(e[2]))
System.out.println(traceback.format_exception(e[0], e[1], e[2]))
def run():
msg = "<html>"
wm = WindowManager
wcount = wm.getWindowCount()
if wcount == 0:
msg += "No windows open, nothing to do.<br/>"
IJ.showMessage(PluginTitle, msg)
return
msg += "Number of open windows: " + str(wcount) + "<br/>"
# let the User choose a directory to store the files
target = DirectoryChooser("Choose target directory").getDirectory()
if target is None:
# User canceled the dialog
msg += "<br/>No directory chosen, aborting.<br/>"
IJ.showMessage(PluginTitle, msg)
return
msg += "Selected '" + target + "'as destination folder.<br/>"
# determine padding width for filenames
pad = len(str(wcount))
for i in range(wcount):
# image ID lists start with 1 instead of 0, so for convenience:
wid = i + 1
imp = wm.getImage(wid)
imgid = wm.getNthImageID(wid)
#print "window id:", wid, ", imageID:", wm.getNthImageID(wid)
# Construct filename
filename = 'tile_' + str(wid).zfill(pad) + '.tif'
filepath = target + '/' + filename
fs = FileSaver(imp)
if imp.getImageStackSize() > 1:
if not fs.saveAsTiffStack(filepath):
IJ.error("<html>Error saving current image, stopping.")
return
else:
if not fs.saveAsTiff(filepath):
IJ.error("<html>Error saving current image, stopping.")
return
msg += "<br/>Successfully saved " + str(wcount) + " files.<br/>"
IJ.showMessage(PluginTitle, msg)
def stackToSlices(folder_in,folder_out,folder_num):
"""Convert a 3D nrrd image to a tiff series"""
for x in range(14):
fnum = folder_num+x
print(fnum)
filename = str(fnum)+".nrrd"
imp = IJ.openImage(os.path.join(folder_in, filename))
print(os.path.join(folder_in, filename))
stack = imp.getImageStack()
output=folder_out+str(fnum)
os.makedirs(output)
for i in xrange(1, imp.getNSlices()+1):
ip = stack.getProcessor(i)
imp = ImagePlus("imp", ip)
IJ.run(imp, "8-bit", "")
fs= FileSaver(imp)
filepath = os.path.join(output,str(i)+".tif")
fs.saveAsTiff(filepath)
def run(FolderName, SaveFolder):
# Find tiffiles in folder
onlyfiles = [f for f in os.listdir(FolderName) if
os.path.isfile(os.path.join(FolderName, f)) and f.lower().endswith('.tif')]
for ii in xrange(0, len(onlyfiles)):
path = os.path.join(FolderName, onlyfiles[ii])
print "Processing file..", path
# Find stimulus, Block, regions from filename for sorting
# Get all underscores
underscores = [m.start() for m in re.finditer('_', onlyfiles[ii])]
# Fish Name
findfish = onlyfiles[ii].find('Fish')
findunderscore = [i for i in underscores if i > findfish][0]
fishnum = onlyfiles[ii][findfish:findunderscore]
print 'Fish Number..', fishnum
# Block
findblock = onlyfiles[ii].find('Block')
findunderscore = [i for i in underscores if i > findblock][0]
blocknum = onlyfiles[ii][findblock:findunderscore]
print 'Block Number..', blocknum
# Stimulus
findstimulus = onlyfiles[ii].find('Blue')
findunderscore = [i for i in underscores if i > findstimulus][0]
stimulustype = onlyfiles[ii][findstimulus:findunderscore]
print 'Stimulus type..', stimulustype
# Region
findregion = onlyfiles[ii].find('Hb')
findunderscore = [i for i in underscores if i > findregion][0]
region = onlyfiles[ii][findregion-1:findunderscore]
print 'Region..', region
targetDir = os.path.join(SaveFolder, fishnum, region) + filesep
print 'Images will be saved in .....', targetDir
if not os.path.exists(targetDir):
os.makedirs(targetDir)
cs = ChannelSeparator()
cs.setId(path)
bf = BFVirtualStack(path, cs, False, False, False)
for sliceIndex in xrange(1,bf.getSize() + 1):
print "Processing slice", sliceIndex
ip = bf.getProcessor(sliceIndex)
sliceFileName = os.path.join(targetDir, "T=" + str(sliceIndex) + ".tif")
FileSaver(ImagePlus(str(sliceIndex), ip)).saveAsTiff(sliceFileName)
def saveFileImage(imagePlus, dumpSaveFilePath, dumpFileName):
fileSaver = FileSaver(imagePlus)
imageName = imagePlus.getTitle()
#File.makeDirectory(dumpDirectory)
dumpFileString = str(dumpSaveFilePath)+"/"+str(imageName)+"_"+str(dumpFileName)
#filestring=File.openAsString(dumpFileString);
#dumpFileString = str(dumpDirectory)
#fileSaver.saveAsTiff(dumpFileString)
#IJ.saveAsTiff(imagePlus,dumpFileString)
IJ.saveAs(imagePlus, "Tiff", dumpFileString);
def loadProcessAndSave(sourcepath, fn):
try:
imp = IJ.openImage(sourcepath)
norm_imp = fn(imp) # invoke function 'fn', in this case 'normalizeContrast'
targetpath = os.path.join(targetDir, os.path.basename(sourcepath))
if not targetpath.endswith(".tif"):
targetpath += ".tif"
FileSaver(norm_imp).saveAsTiff(targetpath)
except:
print "Could not load or process file:", filepath
print sys.exc_info()
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 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 exportTifStack(self, destFolder=''):
channelNumber = 1
for imp in self.channelImp:
if not destFolder:
destFolder = os.path.join(self.enclosingPath, self.enclosingfolder + '_tif')
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
if not imp:
bPrintLog("ERROR: exportTifStack() did not find an imp at channel number '" + str(channelNumber) + "'", 0)
return -1
self.updateInfoStr()
imp.setProperty("Info", self.infoStr);
saveFile = os.path.splitext(self.filename)[0] + '_ch' + str(channelNumber) + '.tif'
savePath = os.path.join(destFolder, saveFile)
# save
fs = FileSaver(imp)
bPrintLog('saveTifStack():' + savePath, 3)
if imp.getNSlices()>1:
fs.saveAsTiffStack(savePath)
else:
fs.saveAsTiff(savePath)
channelNumber += 1
def writeZip(img, path, title=""):
if isinstance(img, RandomAccessibleInterval):
imp = IL.wrap(img, title)
elif isinstance(img, ImagePlus):
imp = img
if title:
imp.setTitle(title)
else:
syncPrint("Cannot writeZip to %s:\n Unsupported image type %s" % (path, str(type(img))))
return None
#
FileSaver(imp).saveAsZip(path)
return imp
def saveMaxProject(self, destFolder=''):
channelNumber = 1
for imp in self.channelImp:
if not destFolder:
destFolder = os.path.join(self.enclosingPath, self.enclosingfolder + '_tif', 'max')
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
# make max project
zp = ZProjector(imp)
zp.setMethod(ZProjector.MAX_METHOD)
zp.doProjection()
zimp = zp.getProjection()
# save
saveFile = 'max_' + os.path.splitext(self.filename)[0] + '_ch' + str(channelNumber) + '.tif'
savePath = os.path.join(destFolder, saveFile)
fs = FileSaver(zimp)
bPrintLog('saveMaxProject():' + savePath, 3)
fs.saveAsTiff(savePath)
channelNumber += 1
def tstormanlysis(inputfile, csvdatapath, hppath):
'''
TSTORMANALYSIS will use predefined parameter for storm analysis in "ThunderSTORM"
'''
# set camera
IJ.run(
inputfile, "Camera setup",
"offset=166.0 isemgain=true photons2adu=8.8 gainem=300.0 pixelsize=160.0"
)
# run STORM analysis
IJ.run(inputfile, "Run analysis", (
"filter=[Wavelet filter (B-Spline)] "
"scale=2.0 order=3 detector=[Local maximum] connectivity=8-neighbourhood "
"threshold=std(Wave.F1) estimator=[PSF: Integrated Gaussian] sigma=1.6 "
"fitradius=3 method=[Weighted Least squares] full_image_fitting=false "
"mfaenabled=false renderer=[No Renderer]"))
resultwd = wm.getWindow('ThunderSTORM: results')
# run drift correction
IJ.run(
inputfile, "Show results table",
("action=drift magnification=5.0 "
"method=[Cross correlation] save=false steps=5 showcorrelations=false"
))
driftwd = wm.getWindow('Drift')
IJ.run(inputfile, "Show results table",
"action=density neighbors=5 radius=50.0 dimensions=2D")
IJ.run(inputfile, "Export results",
("filepath=[" + csvdatapath + "] "
"fileformat=[CSV (comma separated)] "
"sigma=true intensity=true chi2=true "
"offset=true saveprotocol=true "
"x=true y=true bkgstd=true "
"id=true uncertainty=true frame=true"))
IJ.run(
inputfile, "Visualization", "imleft=0.0 imtop=0.0 "
"imwidth=128.0 imheight=128.0 "
"renderer=[Averaged shifted histograms] "
"magnification=5.0 colorizez=false threed=false shifts=2")
imp_histogram = IJ.getImage()
fs = FileSaver(imp_histogram)
FileSaverCheck(fs, os.path.dirname(hppath), os.path.basename(hppath))
# close windows --------------------------------------------------------
inputfile.close()
imp_histogram.close()
driftwd.close()
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
def saveMaxProject(self, destFolder=''):
# ch1
if self.imp_ch1:
# make max project
zp = ZProjector(self.imp_ch1)
zp.setMethod(ZProjector.MAX_METHOD)
zp.doProjection()
zimp = zp.getProjection()
# save
fs = FileSaver(zimp)
bPrintLog('saveMaxProject():' + self.savePathMax_ch1, 3)
fs.saveAsTiff(self.savePathMax_ch1)
# ch2
if self.imp_ch2:
# make max project
zp = ZProjector(self.imp_ch2)
zp.setMethod(ZProjector.MAX_METHOD)
zp.doProjection()
zimp = zp.getProjection()
# save
fs = FileSaver(zimp)
bPrintLog('saveMaxProject():' + self.savePathMax_ch2, 3)
fs.saveAsTiff(self.savePathMax_ch2)
# ch1
if self.imp_ch3:
# make max project
zp = ZProjector(self.imp_ch3)
zp.setMethod(ZProjector.MAX_METHOD)
zp.doProjection()
zimp = zp.getProjection()
# save
fs = FileSaver(zimp)
bPrintLog('saveMaxProject():' + self.savePathMax_ch3, 3)
fs.saveAsTiff(self.savePathMax_ch3)
if chosenData < 9 and applyNucleiCropping == 1: imageNPath = nucleiFolder + digit + appendix imageNCroppedPath = cropNucleiOutput + digit + appendix print 'Opening image', imageNPath impN = IJ.openImage( imageNPath ) impN.setRoi( ROI_xStart, ROI_yStart, ROI_xSize, ROI_ySize ) slices = impN.getNSlices() if ROI_zSize == 0: ROI_zSize = slices stack = impN.getStack() # crop(int x, int y, int z, int width, int height, int depth) impN.setStack( stack.crop( ROI_xStart, ROI_yStart, ROI_zStart, ROI_xSize, ROI_ySize, ROI_zSize ) ) #impN.setStack( stack.crop( ROI_xStart, ROI_yStart, 130, ROI_xSize, ROI_ySize, 220 ) ) #impN.setStack( stack.crop( ROI_xStart, ROI_yStart, 275, ROI_xSize, ROI_ySize, 1 ) ) fs = FileSaver( impN ) fs.saveAsTiff( imageNCroppedPath ) zp = ZProjector(impN) zp.setMethod( ZProjector.MAX_METHOD ) zp.doProjection() MIPimpN = zp.getProjection() #MIPimpN.show() if applyMembraneCropping == 1: imageMPath = membraneFolder + digit + appendix imageMCroppedPath = cropMembraneOutput + digit + appendix print 'Opening image', imageMPath impM = IJ.openImage( imageMPath ) impM.setRoi( ROI_xStart, ROI_yStart, ROI_xSize, ROI_ySize )
def save(self, image, outputName): saver = FileSaver(image) saver.saveAsTiffStack(self.outputDir + self.subDir + outputName + ".tif") print "Saved " + self.outputDir + self.subDir + outputName + ".tif"
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")
def saveMultichannelImage(self, title, channels, luts): tmp = RGBStackMerge.mergeChannels(channels, False) tmp.luts = luts saver = FileSaver(tmp) saver.saveAsTiffStack(self.outputDir + title + ".tif") tmp.close()
def run():
print "=====ZY_Resizetif_V1===="
#expecting one argument: the file path (choose the folder first)
if len(sys.argv) < 2:
print "We need at least one folder as input"
print "Please choose the input folder"
#prompt user to choose a folder"
sourceFolder = DirectoryChooser("Please choose a directory of .tif files").getDirectory()
if not sourceFolder:
return
else:
sourceFolder = sys.argv[1] #assuming it ends in '/'
#get user options
okGo = getOptions()
if okGo == -1:
return 0
destFolder = os.path.join(sourceFolder, 'resized')
print destFolder
# check or make the folder
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
print "Processing souce folder", sourceFolder
print "Saving to destination folder", destFolder
IJ.log(" ====== Startin ZY_resize_V1 ======")
IJ.log(" Processing source folder: " + sourceFolder)
IJ.log(" Saving to destination folder: " + destFolder)
numOpened = 0
numSaved = 0
for filename in os.listdir(sourceFolder):
startWithDot = filename.startswith(".")
isMax = filename.endswith("max.tif")
isTif = filename.endswith(".tif")
if (not startWithDot) and (not isMax) and isTif:
shortname, fileExtension = os.path.splitext(filename)
outPath = destFolder + "/" + filename
outPath1 = destFolder + "/" + shortname + "_ch1" + ".tif"
outPath2 = destFolder + "/" + shortname + "_ch2" + ".tif"
# before processing, check if eventual dest exists
if not replaceExisting:
if numberOfChannels == 2 and os.path.exists(outPath1) and os.path.exists(outPath2):
msgStr = " -->The file==" + filename + "== has been resized, not processing again"
print msgStr
IJ.log(msgStr)
continue #with next iteration
if numberOfChannels == 1 and os.path.exists(outPath):
msgStr = " -->The file==" + filename + "== has been resized, not processing again"
print msgStr
IJ.log(msgStr)
continue #with next iteration
print "================================"
msgStr = str(numOpened+1) + ". opening>> " + sourceFolder + filename
print msgStr
IJ.log(msgStr)
imp = IJ.openImage(sourceFolder+filename)
if imp is None:
msgStr = " -->>Error: could not open image file:" + filename
print msgStr
IJ.log(msgStr)
continue #with next iteration
imp.show()
numOpened +=1
msgStr = " -->Original size is:" + str(imp.width) + "x" + str(imp.height) + "x" + str(imp.getNSlices())
print msgStr
IJ.log(msgStr)
if imp.width < reWidth or imp.height < reHeight:
IJ.run(imp, "Size...", "width=" + str(reWidth) + " height=" + str(reHeight) + " depth=" + str(imp.getNSlices()) + " interpolation=Bilinear")
msgStr = " -> Changing size to:" + str(imp.width) + "x" + str(imp.height)+ "x" + str(imp.getNSlices())
print msgStr
IJ.log(msgStr)
imp = IJ.getImage()
if numberOfChannels == 2:
print "deinterleaving"
IJ.run("Deinterleaving", "how = 2") #make 2 windows
#ch2
imp2=IJ.getImage()
fs = FileSaver(imp2)
print "saving channel 2 file to", outPath2
fs.saveAsTiffStack(outPath2)
numSaved += 1
imp2.changes = 0
imp2.close()
#ch1
imp1 = IJ.getImage()
fs= FileSaver(imp1)
print "saving channel 1 file to", outPath1
fs.saveAsTiffStack(outPath1)
numSaved += 1
imp1.changes = 0
imp1.close()
elif numberOfChannels == 1:
fs= FileSaver(imp)
print "saving file to", outPath
fs.saveAsTiffStack(outPath)
numSaved += 1
imp.changes = 0
else:
msgStr = " --> The file == " + filename + "== was ignored,because the size is bigger than setting"
print msgStr
IJ.log(msgStr)
imp.close() #close original
else: # showing that we ignoring the max
if (not startWithDot) and isTif:
#print " ===================================="
print filename
msgStr = " --> Ignoring .tif:" + filename
print msgStr
IJ.log(msgStr)
msgStr = " ZY_Resized_V1.py is Done, Number Opened " + str(numOpened) + ", Number Saved " + str(numSaved)
print " ==="
print msgStr
print " ==="
IJ.log("==========")
IJ.log(msgStr)
thr1, thrimp1 = calculateThreshold(imp1, roi, methods[0])
thr2, thrimp2 = calculateThreshold(imp2, roi, methods[1])
cursor = TwinCursor(img1.randomAccess(), img2.randomAccess(), Views.iterable(mask).localizingCursor())
rtype = img1.randomAccess().get().createVariable()
raw = manders.calculateMandersCorrelation(cursor, rtype)
rthr1 = rtype.copy()
rthr2 = rtype.copy()
rthr1.set(thr1)
rthr2.set(thr2)
cursor.reset()
thrd = manders.calculateMandersCorrelation(cursor, rthr1, rthr2, ThresholdMode.Above)
print "Results are: %f %f %f %f" % (raw.m1, raw.m2, thrd.m1, thrd.m2)
results.incrementCounter()
rowno = results.getCounter() - 1
results.setValue("Cell", rowno, int(rowno))
results.setValue("Threshold 1", rowno, int(thr1))
results.setValue("Threshold 2", rowno, int(thr2))
results.setValue("M1 raw", rowno, float(raw.m1))
results.setValue("M2 raw", rowno, float(raw.m2))
results.setValue("M1 thrd", rowno, float(thrd.m1))
results.setValue("M2 thrd", rowno, float(thrd.m2))
thrimp = RGBStackMerge.mergeChannels([thrimp1, thrimp2], False)
saver = FileSaver(thrimp)
saver.saveAsTiffStack(outputDir + "Cell_%i-" % results.getCounter() + title + ".tif")
thrimp.close()
results.show("Colocalization results")
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()
#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()
labId = "qm-04513"
smpId = "RAD-2015-0148Y-HCl-xs"
datDir = edsDir + "/Oxford/" + ePrjDir + "/reports/" + labId + "-" + smpId
sTifPath = datDir + "/tif/"
bSetMinMax = False
gMin = 1000
gMax = 11400
fwUnits = 28.9
units = IJ.micronSymbol + "m"
imp = IJ.getImage()
imp = jmg.calibImage(imp, fwUnits, units=-6)
if(bSetMinMax == True):
IJ.setMinAndMax(gMin, gMax)
imp.updateAndRepaintWindow()
ti = imp.getShortTitle()
fi = sTifPath + ti + ".tif"
fs = FileSaver(imp)
imp.changes = False
print(fi)
if fs.saveAsTiff(fi):
print "Tif saved successfully at ", fi
print("done")
def run():
print "===== bBatchConvertTo8Bitv3 ====="
global numberOfChannels
global replaceExisting
global gVersion
gVersion = 3.1
# Expecting one argument: the file path
if len(sys.argv) < 2:
print " We need a hard-drive folder with .tif stacks as input"
print " Usage: ./fiji-macosx bBatchConvertTo8Bitv3 <folder-path>/"
# Prompt user for a folder
sourceFolder = DirectoryChooser("Please Choose A Directory Of .tif Files").getDirectory()
if not sourceFolder:
return
else:
sourceFolder = sys.argv[1] #assuming it ends in '/'
#get user options
okGo = getOptions() # creates {numberOfChannels, replaceExisting}
if okGo == -1:
return 0
destFolder = sourceFolder + "channels8/"
destMaxFolder = sourceFolder + "max/"
#make destination directory
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
#make max destination directory
if not os.path.isdir(destMaxFolder):
os.makedirs(destMaxFolder)
print " Processing source folder: ", sourceFolder
print " Saving to destination folder: ", destFolder
IJ.log(" ")
IJ.log(" ====== Starting bBatchConvertTo8Bit_v3 ======")
IJ.log(" Processing from source folder: " + sourceFolder)
IJ.log(" Saving to destination folder: " + destFolder)
IJ.log(" gVersion=" + str(gVersion))
IJ.log(" numberOfChannels=" + str(numberOfChannels))
IJ.log(" replaceExisting=" + str(replaceExisting))
numOpened = 0
numSaved = 0
for filename in os.listdir(sourceFolder):
startWithDot = filename.startswith(".")
isMax = filename.endswith("max.tif")
isTif = filename.endswith(".tif")
if (not startWithDot) and (not isMax) and (isTif):
shortName, fileExtension = os.path.splitext(filename)
outPath = destFolder + "/" + filename
outPath1 = destFolder + "/" + shortName + "_ch1" + ".tif"
outPath2 = destFolder + "/" + shortName + "_ch2" + ".tif"
#max projection output
outMaxPath = destMaxFolder + "/" + "max_" + filename
outMaxPath1 = destMaxFolder + "/" + "max_" + shortName + "_ch1" + ".tif"
outMaxPath2 = destMaxFolder + "/" + "max_" + shortName + "_ch2" + ".tif"
#before we open, check if eventual dest exists
if not replaceExisting:
if numberOfChannels == 2 and os.path.exists(outPath1) and os.path.exists(outPath2):
msgStr = " 8-Bit Destination file exists, not processing the image:" + filename
print msgStr
IJ.log(msgStr)
continue #with next iteration
if numberOfChannels == 1 and os.path.exists(outPath):
msgStr = " 8-Bit Destination file exists, not processing the image:" + filename
print msgStr
IJ.log(msgStr)
continue #with next iteration
print " ===================================="
msgStr = " -->> Opening " + sourceFolder+filename
print msgStr
IJ.log(msgStr)
imp = IJ.openImage(sourceFolder + filename)
if imp is None:
msgStr = " ERROR: Could not open image from file: " + filename
print msgStr
IJ.log(msgStr)
continue #with next iteration
imp.show()
numOpened +=1
infoStr = imp.getProperty("Info") #get all .tif tags
if not infoStr:
infoStr = ''
infoStr += 'bBatchConvertTo8Bit_Version=' + str(gVersion) + '\n'
infoStr += 'bBatchConvertTo8Bit_Time=' + time.strftime("%Y%m%d") + '_' + time.strftime("%H%M%S") + '\n'
msgStr = " Original Image is: " + str(imp.width) + " X " + str(imp.height) + " X " + str(imp.getNSlices())
print msgStr
IJ.log(msgStr)
if imp.getBitDepth() == 16:
msgStr = " Converting to 8-bit..."
print msgStr
IJ.log(msgStr)
IJ.run("8-bit")
if numberOfChannels == 2:
msgStr = " deinterleaving"
print msgStr
IJ.run("Deinterleave", "how=2"); #makes 2 window
#
#ch2
imp2 = IJ.getImage()
imp2.setProperty("Info", infoStr);
fs = FileSaver(imp2)
msgStr = " ch2: Saving deinterleaved 8bit File to: " + outPath2
print msgStr
IJ.log(msgStr)
numSlices = imp2.getNSlices()
if (numSlices>1):
fs.saveAsTiffStack(outPath2)
else:
fs.saveAsTiff(outPath2)
#max, ch2
if (numSlices>1):
maxCmdParams = 'start=1' + ' stop=' + str(numSlices) + ' projection=[Max Intensity]'
IJ.run("Z Project...", maxCmdParams)
#impMax2 = IJ.getImage()
print " Saving 8bit Max File to", outMaxPath2
impMax2 = IJ.getImage()
fs = FileSaver(impMax2)
fs.saveAsTiff(outMaxPath2)
impMax2.changes = 0
impMax2.close()
numSaved += 1
imp2.changes = 0
imp2.close()
#
#ch1
imp1 = IJ.getImage()
imp1.setProperty("Info", infoStr);
fs = FileSaver(imp1)
msgStr = " ch1: Saving deinterleaved 8bit File to" + outPath1
print msgStr
numSlices = imp1.getNSlices()
if (numSlices>1):
fs.saveAsTiffStack(outPath1)
else:
fs.saveAsTiff(outPath1)
#max, ch1
if (numSlices>1):
maxCmdParams = 'start=1' + ' stop=' + str(numSlices) + ' projection=[Max Intensity]'
IJ.run("Z Project...", maxCmdParams)
impMax1 = IJ.getImage()
fs = FileSaver(impMax1)
msgStr = " Saving 8bit Max File to" + outMaxPath1
print msgStr
IJ.log(msgStr)
fs.saveAsTiff(outMaxPath1)
impMax1.changes = 0
impMax1.close()
numSaved += 1
imp1.changes = 0
imp1.close()
elif numberOfChannels == 1: #single channel
imp.setProperty("Info", infoStr);
fs = FileSaver(imp)
msgStr = " Saving 8bit File to" + outPath
print msgStr
IJ.log(msgStr)
numSlices = imp.getNSlices()
if (numSlices>1):
fs.saveAsTiffStack(outPath)
else:
fs.saveAsTiff(outPath)
numSaved += 1
#max
if (numSlices>1):
maxCmdParams = 'start=1' + ' stop=' + str(numSlices) + ' projection=[Max Intensity]'
IJ.run("Z Project...", maxCmdParams)
impMax = IJ.getImage()
fs = FileSaver(impMax)
print " Saving 8bit Max File to", outMaxPath
fs.saveAsTiff(outMaxPath)
impMax.changes = 0
impMax.close()
imp.changes = 0
imp.close()
else:
print " File was not 16 bit???"
imp.close() #close original
else:
if (not startWithDot) and isTif:
#print " ===================================="
print filename
msgStr = " -> Ignoring .tif:" + filename
print msgStr
IJ.log(msgStr)
msgStr = " ====== bBatchConvertTo8Bitv3.py is Done ======"
print msgStr
IJ.log(msgStr)
msgStr = " Total Number Opened " + str(numOpened) + ", Total Number Saved " + str(numSaved)
print msgStr
IJ.log(msgStr)
mu = IJ.micronSymbol
strUnits = mu + "m"
fScaleX /= 1000.
fScaleY /= 1000.
imp = IJ.openImage(strPath)
cal = imp.getCalibration()
cal.setXUnit(strUnits)
cal.setYUnit(strUnits)
cal.pixelWidth = fScaleX
cal.pixelHeight = fScaleY
imp.show()
time.sleep(1)
imp.changes = False
fs = FileSaver(imp)
if fs.saveAsTiff(strPath):
print "Tif saved successfully at ", strPath
imp.close()
print(strUnits)
# print(row[3])
print("done")
def scaleandfilter(infile,outfile,scalex,scaley,scalez,anisofilter,runtube):
print ("infile is: "+infile)
imp = Opener().openImage(infile)
print imp
print "scalex = %f; scaley = %f ; scalez = %f" % (scalex,scaley,scalez)
# Rescale
cal = imp.getCalibration()
iml = ImgLib.wrap(imp)
scaledimg = Scale3D(iml, scalex, scaley, scalez)
imp2=ImgLib.wrap(scaledimg)
# find range of pixel values for scaled image
from mpicbg.imglib.algorithm.math import ComputeMinMax
# (for imglib2 will be: net.imglib2.algorithm.stats)
minmax=ComputeMinMax(scaledimg)
minmax.process()
(min,max)=(minmax.getMin().get(),minmax.getMax().get())
# Make a copy of the stack (converting to 8 bit as we go)
stack = ImageStack(imp2.width, imp2.height)
print "min = %e, max =%e" % (min,max)
for i in xrange(1, imp2.getNSlices()+1):
imp2.setSliceWithoutUpdate(i)
ip=imp2.getProcessor()
# set range
ip.setMinAndMax(min,max)
stack.addSlice(str(i), ip.convertToByte(True))
# save copy of calibration info
cal=imp.getCalibration()
# close original image
imp.close()
# make an image plus with the copy
scaled = ImagePlus(imp2.title, stack)
# Deal with calibration info which didn't seem to come along for the ride
cal.pixelWidth/=scalex
cal.pixelHeight/=scaley
cal.pixelDepth/=scalez
scaled.setCalibration(cal)
print "dx = %f; dy=%f; dz=%f" % (cal.pixelWidth,cal.pixelHeight,cal.pixelDepth)
intif=infile+".tif"
outtif=infile+"-filtered.tif"
if anisofilter.upper() != 'FALSE':
print("saving input file as "+intif)
f=FileSaver(scaled)
f.saveAsTiffStack(intif)
scaled.close()
# anisotropic filtering
anisopts="-scanrange:10 -tau:2 -nsteps:2 -lambda:0.1 -ipflag:0 -anicoeff1:1 -anicoeff2:0 -anicoeff3:0"
anisopts=anisopts+" -dx:%f -dy:%f -dz:%f" % (cal.pixelWidth,cal.pixelHeight,cal.pixelDepth)
if sys.version_info > (2, 4):
#for testing
# subprocess.check_call(["cp",intif,outtif])
subprocess.check_call([anisofilter]+anisopts.split(' ')+[intif,outtif])
else:
os.system(" ".join([anisofilter]+anisopts.split(' ')+[intif,outtif]))
# Open anisofilter output back into Fiji
print("Opening output tif: "+outtif)
scaled = Opener().openImage(outtif)
scaled.setCalibration(cal)
# Hessian (tubeness)
print("Running tubeness")
if(runtube):
tp=TubenessProcessor(1.0,False)
result = tp.generateImage(scaled)
IJ.run(result, "8-bit","")
else:
result=scaled
# Save out file
fileName, fileExtension = os.path.splitext(outfile)
print("Saving as "+fileExtension+": "+outfile)
if fileExtension.lower()=='.nrrd':
nw=Nrrd_Writer()
nw.setNrrdEncoding("gzip")
nw.save(result,outfile)
else:
# Save to PIC
IJ.run(result,"Biorad ...", "biorad=["+outfile+"]")
scaled.close()
result.close()
# testHeadlessCrop_.py
#
# load and crop an image in headless mode
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
import os
from ij import IJ
from ij.io import FileSaver
gitDir = os.environ['GIT_HOME']
relImg = "/OSImageAnalysis/images"
imgPath = gitDir + relImg + "/latex.tif"
delta = 32
imp = IJ.openImage(imgPath)
name = imp.getShortTitle()
w = imp.getWidth()
h = imp.getHeight()
imp.setRoi(delta,delta,w-(2*delta),h-(2*delta))
IJ.run(imp,"Crop","")
imgPath = gitDir + relImg + "/%s-cr.tif" % name
fs = FileSaver(imp)
fs.saveAsTiff(imgPath)
def saveTif(self, allowOverwrite=1):
#make output folder
if not os.path.isdir(self.dstFolder):
os.makedirs(self.dstFolder)
#ch1
if self.imp_ch1:
#savePath = self.dstFolder + self.enclosingFolderName + '_ch1.tif' #save into new folder
if os.path.isfile(self.savePath_ch1) and not allowOverwrite:
print bPrintLog('File Exists NOT Saving: ' + savePath, 3)
else:
fs = FileSaver(self.imp_ch1)
bPrintLog('Saving: ' + self.savePath_ch1, 3)
if self.imp_ch1.getNSlices()>1:
fs.saveAsTiffStack(self.savePath_ch1)
else:
fs.saveAsTiff(self.savePath_ch1)
#ch2
if self.imp_ch2:
#save into new folder
#savePath = self.dstFolder + self.enclosingFolderName + '_ch2.tif' #save into new folder
if os.path.isfile(self.savePath_ch2) and not allowOverwrite:
bPrintLog('File Exists NOT Saving: ' + self.savePath_ch2, 3)
else:
fs = FileSaver(self.imp_ch2)
bPrintLog('Saving: ' + self.savePath_ch2, 3)
if self.imp_ch2.getNSlices()>1:
fs.saveAsTiffStack(self.savePath_ch2)
else:
fs.saveAsTiff(self.savePath_ch2)
#ch3
if self.imp_ch3:
#save into new folder
#savePath = self.dstFolder + self.enclosingFolderName + '_ch3.tif' #save into new folder
if os.path.isfile(self.savePath_ch3) and not allowOverwrite:
bPrintLog('File Exists NOT Saving: ' + self.savePath_ch3, 3)
else:
fs = FileSaver(self.imp_ch3)
bPrintLog('Saving: ' + self.savePath_ch3, 3)
if self.imp_ch3.getNSlices()>1:
fs.saveAsTiffStack(self.savePath_ch3)
else:
fs.saveAsTiff(self.savePath_ch3)
def runOneTif(tifPath, dstTifPath):
bPrintLog('=== runOneTif processing tif:' + tifPath, 3)
bPrintLog('Loading file...', 3)
imp = IJ.openImage(tifPath)
if imp is None:
bPrintLog('ERROR: could not open image from file:' + tifPath, 3)
return 0
logStr = 'done loading file: ' + str(imp.width) + ' ' + str(imp.height) + ' ' + str(imp.getNSlices())
bPrintLog(logStr, 3)
numSlices = imp.getNSlices()
if numSlices>1:
pass
else:
bPrintLog('ERROR: number of slices must be more than one, file: ' + tifPath)
return 0
bPrintLog('numSlices: ' + str(numSlices), 3)
infoStr = imp.getProperty("Info") #get all tags
#print infoStr
if infoStr is None:
infoStr = ''
infoStr += 'bAverageFrames=v0.1\n'
imp.setProperty("Info", infoStr)
imp.show()
impWin = imp.getTitle()
#
# start body
#infer type of file from
# get the actual bit depth used (e.g. ScanImage is 11 bit, Prairie is 13 bit)
header = bParseHeader(imp)
b_sequence = ''
if 'b_sequence' in header:
b_sequence = str(header['b_sequence'])
bPrintLog('b_sequence: ' + b_sequence, 3)
madeAverage = 0
# if numSlices is not divisable by gNumToAverage then chop a few slices off bottom/end
if b_sequence.startswith('TSeries'):
if globalOptions['gNumToAverage'] > 1:
numToRemove = numSlices % globalOptions['gNumToAverage']
if numToRemove > 0:
bPrintLog('Removing bottom slices: ' + str(numToRemove), 3)
# run("Slice Remover", "first=3 last=5 increment=1");
removeArgs = 'first=' + str(numSlices-numToRemove+1) + ' last=' + str(numSlices) + ' increment=1'
IJ.run('Slice Remover', removeArgs)
numSlices = imp.getNSlices()
bPrintLog('numSlices: ' + str(numSlices), 3)
#fix this: if stack is really short this will not be taken
if (numSlices > globalOptions['gNumToAverage']):
bPrintLog('Taking average of ' + str(globalOptions['gNumToAverage']) + ' slices from ' + str(numSlices), 3)
stackRegParams = 'projection=[Average Intensity] group=' + str(globalOptions['gNumToAverage'])
IJ.run('Grouped Z Project...', stackRegParams) # makes window AVG_
madeAverage = 1
avgWindow = 'AVG_' + impWin
avgImp = WindowManager.getImage(avgWindow)
avgSlices = avgImp.getNSlices()
# Grouped Z PRoject swaps slices for frames?
tmpSlices = avgImp.getNSlices()
tmpFrames = avgImp.getNFrames()
if tmpFrames > 1:
newSlices = tmpFrames
newFrames = tmpSlices
nChannels = 1
bPrintLog('Swaping frames for slices after grouped z',3)
bPrintLog('newSlices=' + str(newSlices) + ' newFrames='+str(newFrames), 4)
avgImp.setDimensions(nChannels, newSlices, newFrames)
infoStr += 'gNumToAverage=' + str(globalOptions['gNumToAverage']) + '\n'
# I want to adjust the framePeriod, prairie would be 'b_framePeriod'
avgImp.setProperty("Info", infoStr)
else:
avgImp = imp
avgSlices = numSlices
else:
bPrintLog('Not taking average of sequence: ' + b_sequence,3)
avgImp = imp
avgSlices = numSlices
if globalOptions['medianFilter']>0:
bPrintLog('Running median filter: ' + str(globalOptions['medianFilter']), 3)
medianArgs = 'radius=' + str(globalOptions['medianFilter']) + ' stack'
IJ.run(avgImp, "Median...", medianArgs);
infoStr += 'bMedianFilter=' + str(globalOptions['medianFilter']) + '\n'
avgImp.setProperty("Info", infoStr)
# convert to 8 bit
# 1) read bit depth from header (e.g. 2^13)
# 2) do math on image and convert to 8-bit
# run("Divide...", "value=32 stack");
if globalOptions['gConvertToEightBit']:
bPrintLog('converting to 8-bit by dividing image down and then convert to 8-bit with ImageConverter.setDoScaling(False)', 3)
bitDepth = 2^13
divideBy = bitDepth / 2^8
# divide the 13 bit image down to 8 bit
#run("Divide...", "value=32 stack");
bPrintLog('divideBy:' + str(divideBy), 3)
divideArgs = 'value=' + str(divideBy) + ' stack'
IJ.run(avgImp, "Divide...", divideArgs);
# convert to 8-bit will automatically scale, to turn this off use
# eval("script", "ImageConverter.setDoScaling(false)");
ImageConverter.setDoScaling(False)
# run("8-bit");
bPrintLog('converting to 8-bit with setDoScaling False', 3)
IJ.run(avgImp, "8-bit", '');
bPrintLog('Saving stack with ' + str(avgSlices) + ' slices:' + dstTifPath, 3)
fs = FileSaver(avgImp)
if avgSlices>1:
fs.saveAsTiffStack(dstTifPath)
else:
fs.saveAsTiff(dstTifPath)
if madeAverage:
avgImp.changes = 0
avgImp.close()
imp.changes = 0
imp.close()
# end body
#
# why was this here
#imp.changes = 0
#imp.close()
return 1
def run():
print "===== bBatchConvertTo8Bitv3 ====="
# Expecting one argument: the file path
if len(sys.argv) < 2:
print " We need at least one folder as input"
print " Usage: ./fiji-macosx bBatchConvertTo8Bitv3 <folder-path>/"
# Prompt user for a folder
sourceFolder = DirectoryChooser("Please Choose A Directory Of .tif Files").getDirectory()
if not sourceFolder:
return
else:
sourceFolder = sys.argv[1] #assuming it ends in '/'
#get user options
okGo = getOptions() # creates {numberOfChannels, replaceExisting}
if okGo == -1:
return 0
destFolder = sourceFolder + "channels8_256/"
#make destination directory
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
print " Processing source folder: ", sourceFolder
print " Saving to destination folder: ", destFolder
numOpened = 0
numSaved = 0
for filename in os.listdir(sourceFolder):
startWithDot = filename.startswith(".")
isMax = filename.endswith("max.tif")
isTif = filename.endswith(".tif")
if (not startWithDot) and (not isMax) and (isTif):
shortName, fileExtension = os.path.splitext(filename)
outPath = destFolder + "/" + filename
outPath1 = destFolder + "/" + shortName + "_ch1" + ".tif"
outPath2 = destFolder + "/" + shortName + "_ch2" + ".tif"
#before we open, check if eventual dest exists
if not replaceExisting:
if numberOfChannels == 2 and os.path.exists(outPath1) and os.path.exists(outPath2):
print " 512 Destination file exists, not saving the image.", filename
continue #with next iteration
if numberOfChannels == 1 and os.path.exists(outPath):
print " 512 Destination file exists, not saving the image.", filename
continue #with next iteration
print " ===================================="
print " -> Opening", sourceFolder+filename
imp = IJ.openImage(sourceFolder + filename)
if imp is None:
print " Could not open image from file:", filename
continue #with next iteration
imp.show()
numOpened +=1
#i can get properties as long list of {key=value}
#how do i then set each property in new imp1/imp2? Do IJ.openImagehave ot loop?
#print imp.getProperties()
#in the future IJ.openImagehavewant to have option to scale down to 512X512
#run("Scale...", "x=- y=- z=1.0 width=512 height=512 depth=196 interpolation=Bilinear average process create title=20131007_a144_008_ch1-1.tif");
print " Image is: " + str(imp.width) + " X " + str(imp.height) + " X " + str(imp.getNSlices())
#if imp.getBitDepth() == 16:
if imp.width>512 and imp.height>512:
print " Converting to 512X512 with 'Scale'"
#IJ.run("8-bit")
theTitle = "tmpOutput"
IJ.run(imp, "Scale...", "x=- y=- z=1.0 width=512 height=512 depth=" + str(imp.getNSlices()) + " interpolate=Bilinear average process create title=" + theTitle)
imp = IJ.getImage()
#bug: original window is left open
if numberOfChannels == 2:
print " deinterleaving"
IJ.run("Deinterleave", "how=2"); #makes 2 window
#ch2
imp2 = IJ.getImage()
fs = FileSaver(imp2)
print " Saving 8bit File to", outPath2
fs.saveAsTiffStack(outPath2)
numSaved += 1
imp2.changes = 0
imp2.close()
#ch1
imp1 = IJ.getImage()
fs = FileSaver(imp1)
print " Saving 8bit File to", outPath2
fs.saveAsTiffStack(outPath1)
numSaved += 1
imp1.changes = 0
imp1.close()
elif numberOfChannels == 1: #single channel
fs = FileSaver(imp)
print " Saving 8bit File to", outPath
fs.saveAsTiffStack(outPath)
numSaved += 1
imp.changes = 0
imp.close()
else:
print " File was not larger than 512X512???"
imp.close() #close original
else:
if isTif:
#print " ===================================="
print " -> Ignoring .tif:", filename
print " ==="
print " bBatchConvertTo8Bitv3.py is Done, Number Opened " + str(numOpened) + ", Number Saved ", str(numSaved)
print " ==="
def run (self):
# make output folder
if not os.path.isdir(self.dstFolder):
os.makedirs(self.dstFolder)
tifFileName = os.path.split(self.tifFilePath)[1]
isCh1 = self.tifFilePath.endswith('_ch1.tif')
isCh2 = self.tifFilePath.endswith('_ch2.tif')
doThisFilePath = ''
if self.alignmentChannel==1 and isCh1:
doThisFilePath = self.tifFilePath
elif self.alignmentChannel==2 and isCh2:
doThisFilePath = self.tifFilePath
if (doThisFilePath):
###
###
bPrintLog('Loading file: ' + doThisFilePath, 3)
imp = IJ.openImage(doThisFilePath)
if imp is None:
print "ERROR: could not open image from file:", doThisFilePath
return -1
d = imp.getDimensions() # Returns the dimensions of this image (width, height, nChannels, nSlices, nFrames) as a 5 element int array.
logStr = 'dimensions are w:' + str(d[0]) + ' h:' + str(d[1]) + ' channels:' + str(d[2]) + ' slices:' + str(d[3]) + ' frames:' + str(d[4])
bPrintLog(logStr, 3)
'''
this is not designed to handle stacks that have frames !!!
'''
##
numSlices = imp.getNSlices()
if numSlices>1:
pass
else:
numFrames = imp.getNFrames()
if numFrames > 1:
# swap nFrames with nSLices
numSlices = numFrames
numFrames = 1
nChannels = 1
bPrintLog('Swapping frames for slices. numSlices=' + str(numSlices) + ' numFrames=' + str(numFrames), 3)
imp.setDimensions(nChannels, numSlices, numFrames)
else:
bPrintLog('ERROR: number of slices must be more than one, file: ' + tifFileName)
return -1
##
# get the stack header (e.g. infoStr)
infoStr = imp.getProperty("Info") #get all tags
if infoStr is None:
infoStr = ''
## median filter
if self.medianFilter > 0:
bPrintLog('Running median filter: ' + str(self.medianFilter), 3)
medianArgs = 'radius=' + str(self.medianFilter) + ' stack'
IJ.run(imp, "Median...", medianArgs);
infoStr += 'bMedianFilter=' + str(self.medianFilter) + '\n'
imp.setProperty("Info", infoStr)
#add to stack header
infoStr += 'b_AlignFolder=v0.0\n'
imp.setProperty("Info", infoStr)
imp.show()
impWin = imp.getTitle()
#show the slice we start alignment on
middleSlice = int(math.floor(numSlices / 2))
imp.setSlice(middleSlice)
transformationFile = self.dstFolder + tifFileName + '.txt'
if run_alignment:
bPrintLog('Running MultiStackReg for: ' + tifFileName, 3)
stackRegParams = 'stack_1=[%s] action_1=Align file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body] save' %(impWin,transformationFile)
IJ.run('MultiStackReg', stackRegParams)
else:
bPrintLog('DEBUG: NOT running MultiStackReg for: ' + tifFileName, 3)
# save alignment
bPrintLog('Saving aligned stack():' + self.dstFolder + tifFileName, 3)
fs = FileSaver(imp)
if numSlices>1:
fs.saveAsTiffStack(self.dstFolder + tifFileName)
else:
fs.saveAsTiff(self.dstFolder + tifFileName)
imp.changes = 0
imp.close()
###
###
#open and run alignment on other channel
if isCh1:
otherFilePath = self.tifFilePath.strip('_ch1.tif') + '_ch2.tif'
elif isCh2:
otherFilePath = self.tifFilePath.strip('_ch2.tif') + '_ch1.tif'
if os.path.isfile(otherFilePath):
otherFileName = os.path.split(otherFilePath)[1]
bPrintLog('Loading [OTHER] file: ' + doThisFilePath, 3)
imp = IJ.openImage(otherFilePath)
if imp is None:
print "ERROR: could not open other image from file:", otherFilePath
return -1
##
numSlices = imp.getNSlices()
if numSlices>1:
pass
else:
numFrames = imp.getNFrames()
if numFrames > 1:
# swap nFrames with nSLices
numSlices = numFrames
numFrames = 1
nChannels = 1
bPrintLog('Swapping frames for slices. numSlices=' + str(numSlices) + ' numFrames=' + str(numFrames), 3)
imp.setDimensions(nChannels, numSlices, numFrames)
else:
bPrintLog('ERROR: number of slices must be more than one, file: ' + tifFileName)
return -1
##
#add to stack header
infoStr = imp.getProperty("Info") #get all tags
if infoStr is None:
infoStr = ''
infoStr += 'b_AlignFolder=v0.0' + '\n'
imp.setProperty("Info", infoStr)
imp.show()
impWin = imp.getTitle()
if run_alignment:
bPrintLog('Running MultiStackReg for: ' + otherFileName, 3)
stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' %(impWin,transformationFile)
IJ.run('MultiStackReg', stackRegParams)
else:
bPrintLog('DEBUG: Not running MultiStackReg for: ' + otherFileName, 3)
#save alignment
bPrintLog('Saving aligned stack():' + self.dstFolder + otherFileName, 3)
fs = FileSaver(imp)
if numSlices>1:
fs.saveAsTiffStack(self.dstFolder + otherFileName)
else:
fs.saveAsTiff(self.dstFolder + otherFileName)
imp.changes = 0
imp.close()
files = [f for f in files if ".tif" in f]
for f in files:
imp = IJ.openImage(rootdir + f)
ip = imp.getProcessor().convertToFloat()
pixels = ip.getPixels()
thresh = 800 # reduce(max,pixels)
def ffun(x):
if (x * 4000 / thresh) > 3000:
return 3000
else:
return x * 4000 / thresh
newpixels = map(ffun, pixels)
ip2 = FloatProcessor(ip.width, ip.height, newpixels, None)
print f
ip2.setInterpolationMethod(2)
ip2 = ip2.resize(ip.width / 2, ip.height / 2, True)
imp2 = ip2.createImage()
imp2 = ImagePlus(imp.title, imp2)
fs = FileSaver(imp2)
fs.saveAsTiff(outroot + f[:-3] + "down.tif")
imp.close()
imp2.close()
del (imp)
del (imp2)
del (ip2)
del (newpixels)
del (pixels)
del (ip)