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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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=''):
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 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 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 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 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)
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)
def run():
print "===== Batch Convert Scan Image 4 ====="
# 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 '/'
destFolder = sourceFolder + "scanimage4/"
destMaxFolder = destFolder + "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(" ====== Starting Batch Convert Scan Image 4 ======")
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)
#source .tif output (after conversion)
outPath = destFolder + filename
#max projection output
outMaxPath = destMaxFolder + "max_" + filename
#before we open, check if eventual dest exists
if os.path.exists(outPath):
msgStr = " 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
msgStr = " Original Image is: " + str(imp.width) + " X " + str(imp.height) + " X " + str(imp.getNSlices())
print msgStr
IJ.log(msgStr)
if 1:
msgStr = " Removing Calibration From ScanImage 4 .tif"
print msgStr
IJ.log(msgStr)
#20140810, I CAN'T BELIEVE I FINALLY FOUND THIS !!!
infoStr = imp.getProperty("Info")
#print infoStr
#scanimage4 has a linear Calibration Function: y = a+bx
# a: -32768.000000
# b: 1.000000
# Unit: "Gray Value"
#for some reason scanimage4 is setting a linear image calibration, we see negative values but there are NOT there
cal = imp.getCalibration()
calCoeff = cal.getCoefficients()
msgStr = ' calibration is y=ax+b' + ' a=' + str(calCoeff[0]) + ' b=' + str(calCoeff[1])
print msgStr
IJ.log(msgStr)
#append calibration to info string
imp.setCalibration(None)
infoStr += 'calibCoeff_a = ' + str(calCoeff[0]) + '\n'
infoStr += 'calibCoeff_b = ' + str(calCoeff[1]) + '\n'
#i have appended to Info, update it
#found this burried here: http://code.google.com/p/fiji-bi/source/browse/ij/ImagePlus.java?repo=imageja&name=imagej
imp.setProperty("Info", infoStr);
#get and print out min/max
theMin = StackStatistics(imp).min
theMax = StackStatistics(imp).max
msgStr = ' min=' + str(theMin) + ' max=' + str(theMax)
print msgStr
IJ.log(msgStr)
#subtract the linear calibration slope 'a' (what about intercept 'b' ?)
#coefficient 'a' is normally negative, this is what we are using 'Add'
#run("Subtract...", "value=32768 stack");
subArgVal = 'value=%s stack' % (calCoeff[0],)
IJ.run('Add...', subArgVal)
#save file
fs = FileSaver(imp)
msgStr = " Saving 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 Max File to", outMaxPath
fs.saveAsTiff(outMaxPath)
#close max
impMax.changes = 0
impMax.close()
#close original
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 = " Batch Convert Scan Image 4 is Done, Number Opened " + str(numOpened) + ", Number Saved " + str(numSaved)
print " ==="
print msgStr
print " ==="
IJ.log(msgStr)
elif i < 1000: digit = str(i) imagePath = sourceFolder + digit + appendix outputPath = outputFolder + digit + '.tif' # open image file print 'Opening image', imagePath imp = IJ.openImage( imagePath ) slices = imp.getNSlices() stack1 = imp.getStack() stack2 = IMGS( imp.getWidth(), imp.getHeight() ) print 'Normalizing image...' for s in range( 0, slices ): ip = stack1.getProcessor(s+1) for x in range( 0, imp.getWidth() ): for y in range( 0, imp.getHeight() ): oldI = ip.get( x, y ) newI = 65535 * (oldI - minI)/(maxI - minI) newI = int(newI) ip.set( x, y, newI ) label = stack1.getSliceLabel(s+1) ip.resetMinAndMax() stack2.addSlice( label, ip ) IJ.showProgress(s+1, slices) imp.setStack( stack2 ) fs = FileSaver( imp ) print "Saving to", outputPath fs.saveAsTiff( outputPath )
# 파일 이름 지정해서 저장 from ij import IJ from ij.io import FileSaver imp = IJ.getImage() fs = FileSaver(imp) # image가 파일로 지정될 폴더 folder = "C:\Arbeitplatz\03_ImageJ_script_learning\sample_code\images" # \ 가 에러 유발 filepath = folder + "\" + "boats.tif" print filepath fs.saveAsTiff(filepath)
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)
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 ) slices = impM.getNSlices()
def run():
print "===== bBatchConvertTo8Bitv3 ====="
# 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(" ====== Startin bBatchConvertTo8Bitv3 ======")
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"
#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
#i can't get properties as long list of {key=value}
#how do i then set each property in new imp1/imp2? Do IJ.openImagehave ot loop?
#infoProperty = imp.getInfoProperty() #Returns the "Info" property string, java.lang.String
#print 'infoProperty'
#print infoProperty
#.getProp(key) #Returns the value from the "Info" property string associated with 'key'
#myProp = imp.getProperties() #returns java.util.Properties
#print 'myProp (really long)'
#print myProp
#print 'patrick'
#myList = str(myProp).split('\r')
#I want' to strip out 'Info=ImageDescription: '
#myList = re.sub('Info=ImageDescription: ', '', str(myList))
#for i in range (0,len(myList)):
# myList[i] = myList[i].split('=')
#print myList[0]
#print myList[1]
#print myList[2]
#print myList[3]
#imp.setProperty('myStr', 1)
#try usinf ImageStack
#myImageStack = imp.getImageStack()
#eventuallly just call imp.getProp(str) which Returns the value from the "Info"
#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");
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()
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()
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
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, Number Opened " + str(numOpened) + ", Number Saved " + str(numSaved)
print " ==="
print msgStr
print " ==="
IJ.log(msgStr)
for fn in ['0', '1']:
filename = os.environ['HOME'] + '/' + basename + '_' + fn + '.pgm'
imp = IJ.openImage(filename)
if imp is None:
print "Could not open image from file:", filename
frame.append(imp)
print 'loaded frames'
width = frame[0].width
height = frame[0].height
bpix = zeros('h', (width + height)**2)
for fn in [0, 1]:
pix = frame[fn].getProcessor().getPixels()
for i in range(len(pix)):
x = i % width + i / width + fn # the second frame (fn == 1) is shifted 1px to the right
y = (width - i % width - 1) + (i / width)
bpix[y * (width + height) + x] = pix[i]
print 'wrote frame %s' % fn
ip = ShortProcessor(width + height, width + height, bpix, None)
bayer = ImagePlus("Sensor", ip)
fs = FileSaver(bayer)
fs.saveAsTiff(os.path.dirname(filename) + '/' + 'raw.tiff')
print '/opt/local/bin/tiffset' + ' -s' + ' 270' + ' width = ' + str(width) + ', height = ' + str(height) + ' ' + os.environ['HOME'] + '/test/' + 'raw.tiff'
subprocess.call(['/opt/local/bin/tiffset', '-s', '270', 'width = ' + str(width) + ', height = ' + str(height), os.environ['HOME'] + '/test/' + 'raw.tiff'])
bayer.show()
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
if infoStr is None:
infoStr = ''
infoStr += 'bMaxProject=v0.1\n'
imp.setProperty("Info", infoStr)
imp.show()
impWin = imp.getTitle()
# BODY
madeMax = 0
if numSlices == 1:
# don;t make max
madeMax = 0
maxSlices = numSlices
maxImp = imp
else:
madeMax = 1
# take max project
#IJ.run(imp, "Z Project...", "projection=[Max Intensity]");
maxProjectArgs = 'projection=[Max Intensity]'
IJ.run(imp, "Z Project...", maxProjectArgs); # makes a new window MAX_
maxWindow = 'MAX_' + impWin
maxImp = WindowManager.getImage(maxWindow)
maxImp.setProperty("Info", infoStr)
maxSlices = maxImp.getNSlices() # should be 1
# save
bPrintLog('Saving stack with ' + str(maxSlices) + ' slices:' + dstTifPath, 3)
fs = FileSaver(maxImp)
if maxSlices>1:
fs.saveAsTiffStack(dstTifPath)
else:
fs.saveAsTiff(dstTifPath)
if madeMax:
maxImp.changes = 0
maxImp.close()
# END BODY
# close original
imp.changes = 0
imp.close()
def loadStacks():
IJ.log(" ")
IJ.log(
"oib concatenator v0.5.1; 2012; [email protected]; [email protected]; revised by [email protected]"
)
IJ.log("tested with: ImageJ 1.47a; FIJI update on July 20th 2012")
srcDir = DirectoryChooser("Choose directory").getDirectory()
if not srcDir:
return
sId = ".oib"
#stackType = getChoice("", ["normal stack", "virtual stack"])
stackType = "normal stack" # Concatenate seems not to work with virtual
#filepath = srcDir +"tiff"
#print(filepath)
iStack = 0
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
path = os.path.join(root, filename)
if not (sId in filename):
continue
IJ.log("opening " + filename)
if stackType == "virtual stack":
IJ.run(
"Bio-Formats Importer", "open=" + path +
" color_mode=Default view=[Standard ImageJ] stack_order=Default use_virtual_stack"
)
else:
IJ.run(
"Bio-Formats Importer", "open=" + path +
" color_mode=Default view=[Standard ImageJ] stack_order=Default"
)
# first stack
if iStack == 0:
imp = IJ.getImage()
imp.setTitle(
filename +
".tiff") # in order of the combining to work additive
nSlices = imp.getNSlices()
nChannels = imp.getNChannels()
nTimeFrames = imp.getNFrames()
#IJ.run("Stack to Hyperstack...", "order=xyczt(default) channels="+str(nChannels)+" slices="+str(nSlices)+" frames="+str(nTimeFrames)+" display=Color");
#IJ.log("convert back to normal stack: Image...Hyperstacks...Hyperstack to Stack")
fs = FileSaver(imp)
fs.saveAsTiff(srcDir + filename + ".tiff")
else:
imp = IJ.getImage()
imp.setTitle(
filename +
".tiff") # in order of the combining to work additive
#IJ.run(imp,"Concatenate...", "image1=stack image2=st2 title=[stack]");
#IJ.run("Stack to Hyperstack...", "order=xyczt(default) channels="+str(nChannels)+" slices="+str(nSlices)+" frames="+str(nTimeFrames)+" display=Color");
#IJ.log("convert back to normal stack: Image...Hyperstacks...Hyperstack to Stack")
fs = FileSaver(imp)
fs.saveAsTiff(srcDir + filename + ".tiff")
iStack = iStack + 1
print(iStack)
IJ.log("nChannels = " + str(nChannels))
IJ.log("nSlices = " + str(nSlices))
IJ.log("nFrames = " + str(nTimeFrames * iStack))
#IJ.run("Stack to Hyperstack...", "order=xyczt(default) channels="+str(nChannels)+" slices="+str(nSlices)+" frames="+str(nTimeFrames)+" display=Color");
IJ.log(
"convert back to normal stack: Image...Hyperstacks...Hyperstack to Stack"
)
IJ.log(
"if you got an error message from the hyperstack you probably ran out of memory and it did not load all files!"
)
def import_and_straighten(imgDir):
"""
Core function. Opens images in given directory in series and calls a straightening function.
Thresholds using weka if stddev of pixel intensities is too high (bright field), otherwise uses
histogram based segmentation.
"""
targetWidth = 800 #adjustable
make_directory(imgDir)
index = "000000000"
filename = imgDir + "/img_" + index + "__000.tif"
if path.exists(filename):
weka = Weka_segmentor(IJ.openImage(filename))
while path.exists(filename):
IJ.run("Set Measurements...",
"mean standard min center redirect=None decimal=3")
IJ.run("Clear Results")
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("Measure")
table = RT.getResultsTable()
stddev = RT.getValue(table, "StdDev", 0)
if stddev < 20:
segmented = weka.getThreshold(imp)
segmented.show()
IJ.run("8-bit")
IJ.run("Invert")
imp.close()
imp = segmented
else:
IJ.run(imp, "Auto Threshold", "method=Li white") #threshold
imp = preProcess_(imp)
#straighten_roi_rotation()
coords = run_straighten()
newImp = IJ.getImage()
"""
fs = FileSaver(newImp)
fs.saveAsTiff(imgDir + "/straightened" + "/img_" + index + "__000-straight.tif")
"""
IJ.run("Image Padder",
"pad_right=" + str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/binary" + "/img_" + index +
"__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
#use same centerline for original greyscale image
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("8-bit")
IJ.runMacro("makeLine(" + coords + ")")
IJ.run("Straighten...", "line = 80")
newImp = IJ.getImage()
IJ.run("Image Padder",
"pad_right=" + str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
IJ.run("8-bit")
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/greyscale" + "/img_" + index +
"__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
index = to_9_Digits(str(int(index) + 1))
filename = filename = imgDir + "/img_" + index + "__000.tif"
def call(self, save_images=False): self.thread_used = threading.currentThread().getName() self.started = time.time() try: filenames = os.listdir(self.params.input_folder) filenames.sort() imp1 = IJ.openImage(os.path.join(self.params.input_folder, filenames[self.imgA])) imp2 = IJ.openImage(os.path.join(self.params.input_folder, filenames[self.imgB])) IJ.log(time.asctime()) IJ.log(str(self.imgA) + ": " + str(imp1)) IJ.log(str(self.imgB) + ": " + str(imp2)) print str(self.imgA) + ": " + str(imp1) print str(self.imgB) + ": " + str(imp2) mesh_resolution = int(imp1.getWidth() / self.params.point_distance) effective_point_distance = imp1.getWidth() / mesh_resolution mesh = SpringMesh(mesh_resolution, imp1.getWidth(), imp1.getHeight(), 1, 1000, 0.9) vertices = mesh.getVertices() maskSamples = RealPointSampleList(2) for vertex in vertices: maskSamples.add(RealPoint(vertex.getL()), ARGBType(-1)) # equivalent of 0xffffffff pm12 = ArrayList() v1 = mesh.getVertices() ip1 = imp1.getProcessor().convertToFloat().duplicate() ip2 = imp2.getProcessor().convertToFloat().duplicate() ip1Mask = self.createMask(imp1.getProcessor().convertToRGB()) ip2Mask = self.createMask(imp2.getProcessor().convertToRGB()) ct = TranslationModel2D() BlockMatching.matchByMaximalPMCC( ip1, ip2, ip1Mask, ip2Mask, self.params.scale, ct, self.params.block_radius, self.params.block_radius, self.params.search_radius, self.params.search_radius, self.params.min_R, self.params.rod_R, self.params.max_curvature_R, v1, pm12, ErrorStatistic(1)) pre_smooth_block_matches = len(pm12) if self.params.save_data: pre_smooth_filename = self.params.output_folder + str(imp2.getTitle())[:-4] + "_" + str(imp1.getTitle())[:-4] + "_pre_smooth_pts.txt" self.writePointsFile(pm12, pre_smooth_filename) if self.params.use_local_smoothness_filter: model = Util.createModel(self.params.local_model_index) try: model.localSmoothnessFilter(pm12, pm12, self.params.local_region_sigma, self.params.max_local_epsilon, self.params.max_local_trust) if self.params.save_data: post_smooth_filename = self.params.output_folder + str(imp2.getTitle())[:-4] + "_" + str(imp1.getTitle())[:-4] + "_post_smooth_pts.txt" self.writePointsFile(pm12, post_smooth_filename) except: pm12.clear() color_samples, max_displacement = self.matches2ColorSamples(pm12) post_smooth_block_matches = len(pm12) print time.asctime() print str(self.imgB) + "_" + str(self.imgA) + "\tblock_matches\t" + str(pre_smooth_block_matches) + "\tsmooth_filtered\t" + str(pre_smooth_block_matches - post_smooth_block_matches) + "\tmax_displacement\t" + str(max_displacement) + "\trelaxed_length\t" + str(effective_point_distance) + "\tsigma\t" + str(self.params.local_region_sigma) IJ.log(time.asctime()) IJ.log(str(self.imgB) + "_" + str(self.imgA) + ": block_matches " + str(pre_smooth_block_matches) + ", smooth_filtered " + str(pre_smooth_block_matches - post_smooth_block_matches) + ", max_displacement " + str(max_displacement) + ", relaxed_length " + str(effective_point_distance) + ", sigma " + str(self.params.local_region_sigma)) if self.params.save_data and self.wf: self.wf.write(str(self.imgB) + "\t" + str(self.imgA) + "\t" + str(imp2.getTitle())[:-4] + "\t" + str(imp1.getTitle())[:-4] + "\t" + str(pre_smooth_block_matches) + "\t" + str(pre_smooth_block_matches - post_smooth_block_matches) + "\t" + str(max_displacement) + "\t" + str(effective_point_distance) + "\t" + str(self.params.local_region_sigma) + "\t" + str(mesh_resolution) + "\n") if self.params.export_point_roi: pm12Sources = ArrayList() pm12Targets = ArrayList() PointMatch.sourcePoints(pm12, pm12Sources) PointMatch.targetPoints(pm12, pm12Targets) roi1 = pointsToPointRoi(pm12Sources) roi2 = pointsToPointRoi(pm12Targets) imp1.setRoi(roi1) imp2.setRoi(roi2) if self.params.export_displacement_vectors: pm12Targets = ArrayList() PointMatch.targetPoints(pm12, pm12Targets) maskSamples2 = RealPointSampleList(2) for point in pm12Targets: maskSamples2.add(RealPoint(point.getW()), ARGBType(-1)) factory = ImagePlusImgFactory() kdtreeMatches = KDTree(color_samples) kdtreeMask = KDTree(maskSamples) img = factory.create([imp1.getWidth(), imp1.getHeight()], ARGBType()) self.drawNearestNeighbor( img, NearestNeighborSearchOnKDTree(kdtreeMatches), NearestNeighborSearchOnKDTree(kdtreeMask)) scaled_img = self.scaleIntImagePlus(img, 0.1) if self.params.save_data: fs = FileSaver(scaled_img) fs.saveAsTiff(self.params.output_folder + str(imp2.getTitle())[:-4] + "_" + str(imp1.getTitle())) else: scaled_img.show() print time.asctime() print str(self.imgB) + "_" + str(self.imgA) + "\tsaved\t" + filenames[self.imgB] IJ.log(time.asctime()) IJ.log(str(self.imgB) + "_" + str(self.imgA) + ": saved " + filenames[self.imgB]) except Exception, ex: self.exception = ex print str(ex) IJ.log(str(ex)) if self.params.save_data and self.wf: self.wf.write(str(ex) + "\n")
def run_script():
print('Print Script Parameter')
print('path: {}'.format(path_j))
print('dir_output: {}'.format(dir_output))
print('ippath: {}'.format(ippath_j))
print('op_bi_path: {}'.format(op_bi_path_j))
print('op_data_path: {}'.format(op_data_path_j))
print(batchmodeop)
path = str(path_j)
ippath = str(ippath_j)
op_bi_path = str(op_bi_path_j)
op_data_path = str(op_data_path_j)
print('Preparing ...')
import gc
if batchmodeop:
Interpreter.batchMode = True
nchannels = 2
dir_check = []
# create output path
for c in range(nchannels):
dir_check.append(os.path.join(op_bi_path, str(c+1)))
dir_check.append(os.path.join(op_data_path, str(c+1)))
dircheck(dir_check)
# create the pending file list ------------------------------------------ #
pendingfllist = []
pendingpathlist_ip = []
pendingpathlist_op_data = []
pendingpathlist_op_bi = []
# return the pending files ------------------------------------------ #
filelist = {}
filenamelist = listfiles(os.path.join(ippath, '1'), '.tif')['filelist']
filedir = ['ip_filename', 'ip_path', 'op_data', 'op_bi']
treatment = ['wildtype', 'knockout']
# group the data by the treatment ------------------------------------------ #
for c in range(nchannels):
filelist[str(c+1)] = {}
for group in treatment:
filelist[str(c+1)][group] = {}
# create list
filelist_temp = []
for l in filenamelist:
if group == 'wildtype':
x = re.search('(.*)_w{1}[0-9]{1}_(.*)', l)
else:
x = re.search('(.*)_k{1}[0-9]{1}_(.*)', l)
try:
found = x.group(0)
filelist_temp.append(found)
except AttributeError:
found = ''
ip_filepath = []
op_bi_filepath = []
op_data_filepath = []
for f in filelist_temp:
ip_filepath_tmp = os.path.join(ippath, str(c+1), f)
ip_filepath.append(ip_filepath_tmp)
op_data_filepath_temp = os.path.join(op_data_path, str(c+1), f.replace('.tif', '.csv'))
op_data_filepath.append(op_data_filepath_temp)
op_bi_filepath_temp = os.path.join(op_bi_path, str(c+1), f)
op_bi_filepath.append(op_bi_filepath_temp)
filelist[str(c+1)][group][filedir[0]] = filelist_temp
filelist[str(c+1)][group][filedir[1]] = ip_filepath
filelist[str(c+1)][group][filedir[2]] = op_bi_filepath
filelist[str(c+1)][group][filedir[3]] = op_data_filepath
pprint.pprint(filelist)
# image processing ------------------------------------------ #
threshold_c = {'1': 300, '2': 100}
for c in range(nchannels):
for group in treatment:
for i in range(len(filelist[str(c+1)][group][filedir[0]])):
# open image
ipfilepath_tmp = filelist[str(c+1)][group][filedir[1]][i]
op_bi_filepath_tmp = filelist[str(c+1)][group][filedir[2]][i]
op_data_filepath_tmp = filelist[str(c+1)][group][filedir[3]][i]
print(ipfilepath_tmp)
print(op_bi_filepath_tmp)
print(op_data_filepath_tmp)
imp = IJ.openImage(ipfilepath_tmp)
imp.show()
IJ.setThreshold(threshold_c[str(c+1)], 5000)
IJ.run(imp, "Convert to Mask", "")
IJ.run(imp, "Set Measurements...", "area mean standard modal min centroid center perimeter bounding fit shape feret's integrated median skewness kurtosis area_fraction stack redirect=None decimal=9")
IJ.run(imp, "Analyze Particles...", "size=0-Infinity show=Masks display exclude clear")
# save binary
imp_bi = IJ.getImage()
fs = FileSaver(imp_bi)
fs.saveAsTiff(op_bi_filepath_tmp)
imp_bi.close()
# save results
biresults = wm.getWindow("Results")
wm.setWindow(biresults)
IJ.saveAs("Results", op_data_filepath_tmp)
if not biresults is None:
biresults.close()
imp.close()
if batchmodeop:
Interpreter.batchMode = False
return
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)
def loadStacks():
IJ.log(" ")
IJ.log("oib_tiff_converter_ver1.0; 08/24/2018; [email protected]")
IJ.log("tested with: ImageJ2; FIJI update on 8/24/2018")
srcDir = DirectoryChooser("Choose directory").getDirectory()
if not srcDir:
return
sId = ".oib"
#stackType = getChoice("", ["normal stack", "virtual stack"])
stackType = "normal stack" # Concatenate seems not to work with virtual
#filepath = srcDir +"tiff"
#print(filepath)
iStack = 0
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
path = os.path.join(root, filename)
if not (sId in filename):
continue
IJ.log("opening " + filename)
if stackType == "virtual stack":
IJ.run(
"Bio-Formats Importer", "open=" + path +
" color_mode=Default view=[Standard ImageJ] stack_order=Default use_virtual_stack"
)
else:
IJ.run(
"Bio-Formats Importer", "open=" + path +
" color_mode=Default view=[Standard ImageJ] stack_order=Default"
)
# first stack
if iStack == 0:
imp = IJ.getImage()
imp.setTitle(
filename +
".tiff") # in order of the combining to work additive
nSlices = imp.getNSlices()
nChannels = imp.getNChannels()
nTimeFrames = imp.getNFrames()
imp.setDimensions(nChannels, nSlices, nTimeFrames)
comp = CompositeImage(imp, CompositeImage.COLOR)
comp.show()
fs = FileSaver(comp)
fs.saveAsTiff(srcDir + filename + "_hyperstack" + ".tiff")
else:
imp = IJ.getImage()
comp = CompositeImage(imp, CompositeImage.COLOR)
comp.show()
fs = FileSaver(comp)
fs.saveAsTiff(srcDir + filename + "_hyperstack" + ".tiff")
iStack = iStack + 1
print(iStack)
#IJ.log("nChannels = "+str(nChannels))
#IJ.log("nSlices = "+str(nSlices))
#IJ.log("nFrames = "+str(nTimeFrames*iStack))
#IJ.run("Stack to Hyperstack...", "order=xyczt(default) channels="+str(nChannels)+" slices="+str(nSlices)+" frames="+str(nTimeFrames)+" display=Color");
IJ.log(
"convert back to normal stack: Image...Hyperstacks...Hyperstack to Stack"
)
def run():
print "===== Batch Convert Scan Image 4 ====="
# 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 '/'
destFolder = sourceFolder + "scanimage4/"
destMaxFolder = destFolder + "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(" ====== Starting Batch Convert Scan Image 4 ======")
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)
#source .tif output (after conversion)
outPath = destFolder + filename
#max projection output
outMaxPath = destMaxFolder + "max_" + filename
#before we open, check if eventual dest exists
if os.path.exists(outPath):
msgStr = " 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
msgStr = " Original Image is: " + str(
imp.width) + " X " + str(imp.height) + " X " + str(
imp.getNSlices())
print msgStr
IJ.log(msgStr)
if 1:
msgStr = " Removing Calibration From ScanImage 4 .tif"
print msgStr
IJ.log(msgStr)
#20140810, I CAN'T BELIEVE I FINALLY FOUND THIS !!!
infoStr = imp.getProperty("Info")
#print infoStr
#scanimage4 has a linear Calibration Function: y = a+bx
# a: -32768.000000
# b: 1.000000
# Unit: "Gray Value"
#for some reason scanimage4 is setting a linear image calibration, we see negative values but there are NOT there
cal = imp.getCalibration()
calCoeff = cal.getCoefficients()
msgStr = ' calibration is y=ax+b' + ' a=' + str(
calCoeff[0]) + ' b=' + str(calCoeff[1])
print msgStr
IJ.log(msgStr)
#append calibration to info string
imp.setCalibration(None)
infoStr += 'calibCoeff_a = ' + str(calCoeff[0]) + '\n'
infoStr += 'calibCoeff_b = ' + str(calCoeff[1]) + '\n'
#i have appended to Info, update it
#found this burried here: http://code.google.com/p/fiji-bi/source/browse/ij/ImagePlus.java?repo=imageja&name=imagej
imp.setProperty("Info", infoStr)
#get and print out min/max
theMin = StackStatistics(imp).min
theMax = StackStatistics(imp).max
msgStr = ' min=' + str(theMin) + ' max=' + str(theMax)
print msgStr
IJ.log(msgStr)
#subtract the linear calibration slope 'a' (what about intercept 'b' ?)
#coefficient 'a' is normally negative, this is what we are using 'Add'
#run("Subtract...", "value=32768 stack");
subArgVal = 'value=%s stack' % (calCoeff[0], )
IJ.run('Add...', subArgVal)
#save file
fs = FileSaver(imp)
msgStr = " Saving 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 Max File to", outMaxPath
fs.saveAsTiff(outMaxPath)
#close max
impMax.changes = 0
impMax.close()
#close original
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 = " Batch Convert Scan Image 4 is Done, Number Opened " + str(
numOpened) + ", Number Saved " + str(numSaved)
print " ==="
print msgStr
print " ==="
IJ.log(msgStr)
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()
bPrintLog('numSlices: ' + str(numSlices), 3)
infoStr = imp.getProperty("Info") #get all tags
if infoStr is None:
infoStr = ''
infoStr += 'bMaxProject=v0.1\n'
imp.setProperty("Info", infoStr)
imp.show()
impWin = imp.getTitle()
# BODY
# get the bit depth form opened imp
impBitDepth = imp.getBitDepth()
bPrintLog('image bit depth:' + str(impBitDepth), 3)
# get the actual bit depth used (e.g. ScanImage is 11 bit, Prairie is 13 bit)
header = bParseHeader(imp)
actualBitDepth = impBitDepth
if 'b_bitDepth' in header:
actualBitDepth = int(header['b_bitDepth'])
bPrintLog('actual bit depth:' + str(actualBitDepth), 3)
made8bit = 0
if impBitDepth == 8:
made8bit = 1
else:
made8bit = 1
if 0:
divideBy = math.pow(2, actualBitDepth) / math.pow(
2, 8) # divide the 13 bit or 11 bit image down to 8 bit
bPrintLog('diving by:' + str(divideBy), 3)
bPrintLog(
'converting to 8-bit by dividing image by ' + str(divideBy) +
' and then convert to 8-bit with ImageConverter.setDoScaling(False)',
3)
#run("Divide...", "value=32 stack");
divideArgs = 'value=' + str(divideBy) + ' stack'
IJ.run(imp, "Divide...", divideArgs)
# convert to 8-bit will automatically scale, to turn this off use
# eval("script", "ImageConverter.setDoScaling(false)");
# 20170810 was this
#ImageConverter.setDoScaling(False)
ImageConverter.setDoScaling(True)
# run("8-bit");
bPrintLog('converting to 8-bit with setDoScaling False', 3)
IJ.run(imp, "8-bit", '')
#does this in place, no new window
# save
bPrintLog('Saving stack with ' + str(numSlices) + ' slices:' + dstTifPath,
3)
fs = FileSaver(imp)
if numSlices > 1:
fs.saveAsTiffStack(dstTifPath)
else:
fs.saveAsTiff(dstTifPath)
# END BODY
# close original
imp.changes = 0
imp.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)
ip = EM.getProcessor()
width = ip.getWidth()
height = ip.getHeight()
EM.setProcessor(EM.getTitle(), EM.getProcessor().resize(256, 256))
ImageConverter(EM).convertToGray8()
# create stack z=2
EMstack = ImageStack(EM.getWidth(), EM.getHeight())
EMstack.addSlice(str(1), EM.getProcessor())
EMstack.addSlice(str(2), EM.getProcessor())
EM = ImagePlus(EM.getTitle(), EMstack)
# save EM image
saveEMfilepath = os.path.join(workdir, "EM.tif")
fs = FileSaver(EM)
fs.saveAsTiff(saveEMfilepath)
print("(- )preprocessing done")
############################################ predict image
# use plugin CSBDeep (https://github.com/CSBDeep/CSBDeep_fiji/blob/master/script/CARE_generic.py)
# create path to save pLM image
savepLMfilepath = os.path.join(workdir, "registration_input", "pLM.tif")
# define some parameters
nTiles = 16
overlap = 32
normalizeInput = True
percentileBottom = 0.5
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
files.sort() 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)
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")
from sys import argv
stackDir = argv[1]
#IJ.run("Image Sequence...", "open="+stackDir+" sort")
imp = IJ.openImage(stackDir + "/stack.tif")
stack = imp.getImageStack()
print "Number of slices:", imp.getNSlices()
for i in xrange(1, imp.getNSlices()):
print i
image = stack.getProcessor(i)
IJ.run(ImagePlus(str(i), image), "Auto Threshold", "method=Default white")
imp2 = ImagePlus("Threshold", stack)
fs = FileSaver(imp2)
fs.saveAsTiff(stackDir + "/Filtered.tif")
"""
#in case you want to make a stack from a folder
imp = IJ.getImage()
#stack = imp.getImageStack()
fs = FileSaver(imp)
fs.saveAsTiff(stackDir + "/stack.tif")
#print "Number of slices:", stack.getNSlices()
#imp = IJ.openImage(argv[1]) #first command line arg is file directory
#print imp.title
"""
print("order=xyczt(default) channels=2 slices="+ str(z_slices) + " frames=1 display=Color", image.getDimensions())
image_two = HyperStackConverter.toHyperStack(image,2,z_slices,1)
image = CompositeImage(image_two)
image.show()
rt = run_comdet(image)
rt.save(directory+"/"+filename+"_results.csv" )
image = IJ.getImage()
if auto_cell:
mask = generate_mask(image_green, auto_cell_thresh)
fs = FileSaver(mask)
filepath = directory + "/" + filename + "_mask.tiff"
fs.saveAsTiff(filepath)
rest = ResultsTable.open(directory+"/"+filename+"_results.csv")
#print(rest.getColumnHeadings())
remove_outside_cell(rest,mask)
rest.save(directory+"/"+filename+"_results.csv" )
else:
rest = rt
image.setDimensions(2, z_slices, 1)
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 run():
print "===== bBatchConvertTo8Bitv3 ====="
global numberOfChannels
global replaceExisting
# 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(" ====== Startin bBatchConvertTo8Bitv3 ======")
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"
#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
#i can't get properties as long list of {key=value}
#how do i then set each property in new imp1/imp2? Do IJ.openImagehave ot loop?
#infoProperty = imp.getInfoProperty() #Returns the "Info" property string, java.lang.String
#print 'infoProperty'
#print infoProperty
#.getProp(key) #Returns the value from the "Info" property string associated with 'key'
#myProp = imp.getProperties() #returns java.util.Properties
#print 'myProp (really long)'
#print myProp
#print 'patrick'
#myList = str(myProp).split('\r')
#I want' to strip out 'Info=ImageDescription: '
#myList = re.sub('Info=ImageDescription: ', '', str(myList))
#for i in range (0,len(myList)):
# myList[i] = myList[i].split('=')
#print myList[0]
#print myList[1]
#print myList[2]
#print myList[3]
#imp.setProperty('myStr', 1)
#try usinf ImageStack
#myImageStack = imp.getImageStack()
#eventuallly just call imp.getProp(str) which Returns the value from the "Info"
#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");
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()
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()
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
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, Number Opened " + str(numOpened) + ", Number Saved " + str(numSaved)
print " ==="
print msgStr
print " ==="
IJ.log(msgStr)
def call(self, save_images=False):
self.thread_used = threading.currentThread().getName()
self.started = time.time()
try:
IJ.log(time.asctime())
IJ.log(str(self.patchA))
IJ.log(str(self.patchB))
print str(self.patchA)
print str(self.patchB)
# Adapted from ElasticMontage.java
# https://github.com/trakem2/TrakEM2/blob/master/TrakEM2_/src/main/java/mpicbg/trakem2/align/ElasticMontage.java
pi1 = self.patchA.createTransformedImage()
pi2 = self.patchB.createTransformedImage()
fp1 = pi1.target.convertToFloat()
mask1 = pi1.getMask()
if mask1 is None:
fpMask1 = None
else:
fpMask1 = scaleByte(mask1)
fp2 = pi2.target.convertToFloat()
mask2 = pi2.getMask()
if mask2 is None:
fpMask2 = None
else:
fpMask2 = scaleByte(mask1)
w = self.tileA.getWidth()
h = self.tileA.getHeight()
num_x = Math.max(2, int(Math.ceil(w / self.params.spring_length) + 1))
num_y = Math.max(2, int(Math.ceil(h / self.params.spring_triangle_height_twice) + 1))
w_mesh = (num_x - 1) * self.params.spring_length
h_mesh = (num_y - 1) * self.params.spring_triangle_height_twice
mesh = SpringMesh(num_x,
num_y,
w_mesh,
h_mesh,
self.params.stiffness,
self.params.max_stretch * self.params.scale,
self.params.damp)
vertices = mesh.getVertices()
maskSamples = RealPointSampleList(2)
for vertex in vertices:
maskSamples.add(RealPoint(vertex.getL()), ARGBType(-1)) # equivalent of 0xffffffff
pm12 = ArrayList()
v1 = mesh.getVertices()
t = self.tileB.getModel().createInverse()
t.concatenate(self.tileA.getModel())
BlockMatching.matchByMaximalPMCC(
fp1,
fp2,
fpMask1,
fpMask2,
self.params.scale,
t,
self.params.block_radius,
self.params.block_radius,
self.params.search_radius,
self.params.search_radius,
self.params.min_R,
self.params.rod_R,
self.params.max_curvature_R,
v1,
pm12,
ErrorStatistic(1))
pre_smooth_block_matches = len(pm12)
if self.params.save_data:
pre_smooth_filename = self.params.output_folder + str(self.patchB) + "_" + str(self.patchA) + "_pre_smooth_pts.txt"
self.writePointsFile(pm12, pre_smooth_filename)
if self.params.use_local_smoothness_filter:
model = Util.createModel(self.params.local_model_index)
try:
model.localSmoothnessFilter(pm12, pm12, self.params.local_region_sigma, self.params.max_local_epsilon, self.params.max_local_trust)
if self.params.save_data:
post_smooth_filename = self.params.output_folder + str(self.patchB) + "_" + str(self.patchA) + "_post_smooth_pts.txt"
self.writePointsFile(pm12, post_smooth_filename)
except:
pm12.clear()
color_samples, max_displacement = self.matches2ColorSamples(pm12)
post_smooth_block_matches = len(pm12)
print time.asctime()
print str(self.patchB) + "_" + str(self.patchA) + "\tblock_matches\t" + str(pre_smooth_block_matches) + "\tsmooth_filtered\t" + str(pre_smooth_block_matches - post_smooth_block_matches) + "\tmax_displacement\t" + str(max_displacement) + "\trelaxed_length\t" + str(self.params.spring_length) + "\tsigma\t" + str(self.params.local_region_sigma)
IJ.log(time.asctime())
IJ.log(str(self.patchB) + "_" + str(self.patchA) + ": block_matches " + str(pre_smooth_block_matches) + ", smooth_filtered " + str(pre_smooth_block_matches - post_smooth_block_matches) + ", max_displacement " + str(max_displacement) + ", relaxed_length " + str(self.params.spring_length) + ", sigma " + str(self.params.local_region_sigma))
if self.params.save_data and self.wf:
self.wf.write(str(self.patchB) +
"\t" + str(self.patchA) +
"\t" + str(pre_smooth_block_matches) +
"\t" + str(pre_smooth_block_matches - post_smooth_block_matches) +
"\t" + str(max_displacement) +
"\t" + str(self.params.spring_length) +
"\t" + str(self.params.local_region_sigma) +
"\t" + str(num_x) + "\n")
if self.params.export_point_roi:
pm12Sources = ArrayList()
pm12Targets = ArrayList()
PointMatch.sourcePoints(pm12, pm12Sources)
PointMatch.targetPoints(pm12, pm12Targets)
roi1 = pointsToPointRoi(pm12Sources)
roi2 = pointsToPointRoi(pm12Targets)
# # Adapted from BlockMatching.java
# # https://github.com/axtimwalde/mpicbg/blob/master/mpicbg/src/main/java/mpicbg/ij/blockmatching/BlockMatching.java
# tTarget = TranslationModel2D()
# sTarget = SimilarityModel2D()
# tTarget.set(-self.params.search_radius, -self.params.search_radius)
# sTarget.set(1.0/self.params.scale, 0, 0, 0)
# lTarget = CoordinateTransformList()
# lTarget.add(sTarget)
# lTarget.add(tTarget)
# lTarget.add(t)
# targetMapping = TransformMapping(lTarget)
# mappedScaledTarget = FloatProcessor(fp1.getWidth() + 2*search_radius, fp1.getHeight() + 2*search_radius)
# targetMapping.mapInverseInterpolated(fp2, mappedScaledTarget)
# imp1 = tileImagePlus("imp1", fp1)
# imp1.show()
# imp2 = ImagePlus("imp2", mappedScaledTarget)
# imp2.show()
imp1 = ImagePlus("imp1", fp1)
imp1.show()
imp2 = ImagePlus("imp2", fp2)
imp2.show()
imp1.setRoi(roi1)
imp2.setRoi(roi2)
if self.params.export_displacement_vectors:
pm12Targets = ArrayList()
PointMatch.targetPoints(pm12, pm12Targets)
maskSamples2 = RealPointSampleList(2)
for point in pm12Targets:
maskSamples2.add(RealPoint(point.getW()), ARGBType(-1))
factory = ImagePlusImgFactory()
kdtreeMatches = KDTree(color_samples)
kdtreeMask = KDTree(maskSamples)
img = factory.create([fp1.getWidth(), fp1.getHeight()], ARGBType())
self.drawNearestNeighbor(
img,
NearestNeighborSearchOnKDTree(kdtreeMatches),
NearestNeighborSearchOnKDTree(kdtreeMask))
scaled_img = self.scaleIntImagePlus(img, 0.03)
if self.params.save_data:
fs = FileSaver(scaled_img)
fs.saveAsTiff(self.params.output_folder + str(self.patchB) + "_" + str(self.patchA) + ".tif")
else:
scaled_img.show()
print time.asctime()
print str(self.patchB) + "_" + str(self.patchA) + "\tsaved"
IJ.log(time.asctime())
IJ.log(str(self.patchB) + "_" + str(self.patchA) + ": saved")
except Exception, ex:
self.exception = ex
print str(ex)
IJ.log(str(ex))
if self.params.save_data and self.wf:
self.wf.write(str(ex) + "\n")
def import_and_straighten(imgDir):
"""
Core function. Opens images in given directory in series and calls a straightening function.
Thresholds using weka if stddev of pixel intensities is too high (bright field), otherwise uses
histogram based segmentation.
"""
targetWidth = 800 #adjustable
make_directory(imgDir)
index = "000000000"
filename = imgDir + "/img_" + index + "__000.tif"
if path.exists(filename):
weka = Weka_segmentor(IJ.openImage(filename))
while path.exists(filename):
IJ.run("Set Measurements...", "mean standard min center redirect=None decimal=3")
IJ.run("Clear Results")
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("Measure")
table = RT.getResultsTable()
stddev = RT.getValue(table, "StdDev", 0)
if stddev < 20:
segmented = weka.getThreshold(imp)
segmented.show()
IJ.run("8-bit")
IJ.run("Invert")
imp.close()
imp = segmented
else:
IJ.run(imp, "Auto Threshold", "method=Li white") #threshold
imp = preProcess_(imp)
#straighten_roi_rotation()
coords = run_straighten()
newImp = IJ.getImage()
"""
fs = FileSaver(newImp)
fs.saveAsTiff(imgDir + "/straightened" + "/img_" + index + "__000-straight.tif")
"""
IJ.run("Image Padder", "pad_right="+str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/binary" + "/img_" + index + "__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
#use same centerline for original greyscale image
imp = IJ.openImage(filename)
imp.show()
IJ.run("Rotate 90 Degrees Left")
IJ.run("8-bit")
IJ.runMacro("makeLine("+coords+")")
IJ.run("Straighten...", "line = 80")
newImp = IJ.getImage()
IJ.run("Image Padder", "pad_right="+str(targetWidth - newImp.getWidth()))
paddedImp = IJ.getImage()
IJ.run("8-bit")
fs = FileSaver(paddedImp)
fs.saveAsTiff(imgDir + "/greyscale" + "/img_" + index + "__000-padded.tif")
IJ.runMacro("while (nImages>0) {selectImage(nImages);close();}")
index = to_9_Digits(str(int(index)+1))
filename = filename = imgDir + "/img_" + index + "__000.tif"
def run():
### Default arguments
two_sarcomere_size = 25 # determined by filter used.
rotation_angle = 0.0
### Get the image we'd like to work with.
# Don't need to ask where to save the intermediate image since it'll just be saved in the matchedmyo folder anyway
# may change this though. In case they want to keep that image around.
this_img = WindowManager.getCurrentImage()
if this_img == None:
ud = WaitForUserDialog(
"Please select the image you would like to analyze.")
ud.show()
this_img = WindowManager.getCurrentImage()
img_name = this_img.getTitle()
matchedmyo_path = "/home/AD/dfco222/scratchMarx/matchedmyo/" # this would be grabbed from the prompt
gd = GenericDialog("Preprocessing Options")
gd.addCheckbox("Automatic Resizing/Rotation", True)
gd.addCheckbox("CLAHE", True)
gd.addCheckbox("Normalization to Transverse Tubules", True)
gd.showDialog()
if gd.wasCanceled():
return
auto_resize_rotate = gd.getNextBoolean()
clahe = gd.getNextBoolean()
normalize = gd.getNextBoolean()
if auto_resize_rotate:
# Clear selection so it takes FFT of full image
rotation_angle = auto_resize_angle_measure(this_img,
two_sarcomere_size)
if clahe:
clahe_args = "blocksize={} histogram=256 maximum=3 mask=*None* fast_(less_accurate)".format(
two_sarcomere_size)
IJ.run(this_img, "Enhance Local Contrast (CLAHE)", clahe_args)
if normalize:
# Ask the user to select a subsection of the image that looks healthy-ish.
ud = WaitForUserDialog(
"Please select a subsection exhibiting a measure of healthy TT structure using the Rectangle tool.\n"
+ " Only a single cell or several are needed.\n\n" +
" Press 'OK' when finished.")
ud.show()
IJ.setTool("rectangle")
# Duplicate the selected subsection.
selection = this_img.crop()
IJ.run(selection, "Duplicate...", "title=subsection.tif")
# Grab the subsection image and rotate it.
selection = WindowManager.getImage("subsection.tif")
IJ.run(
selection, "Rotate...",
"angle={} grid=1 interpolation=Bicubic enlarge".format(
rotation_angle))
# Ask the user to select a bounding box that contains only tubules
# NOTE: Need to get rid of initial selection since it's the entire image and it's annoying to click out of
IJ.setTool("rectangle")
IJ.run(selection, "Select None", "")
ud = WaitForUserDialog(
"Select a subsection of the image that contains only tubules and no membrane."
)
ud.show()
# Grab the subsection ImagePlus
selection = WindowManager.getCurrentImage()
this_window = WindowManager.getActiveWindow()
selection_small = selection.crop()
IJ.run(selection, "Close", "")
# NOTE: May not actually display this depending on how the macros work
IJ.run(selection_small, "Duplicate...", "title=subsection_small.tif")
# Smooth the selection using the single TT filter.
# NOTE: It won't read in so we're just going to hard code it in since it's simple
tt_filt_row = "0 0 0 1 1 1 1 1 1 0 0 0 0\n"
tt_filt = ""
for i in range(21):
tt_filt += tt_filt_row
IJ.run("Convolve...", "text1=[" + tt_filt + "] normalize")
# Segment out the TTs from the 'gaps' using Gaussian Adaptive Thresholding.
selection_small = WindowManager.getImage("subsection_small.tif")
IJ.run(selection_small, "Duplicate...", "title=thresholded.tif")
threshed = WindowManager.getImage("thresholded.tif")
IJ.run(threshed, "Auto Local Threshold",
"method=Bernsen radius=7 parameter_1=1 parameter_2=0 white")
# Select the TTs from the thresholded image.
IJ.run(threshed, "Create Selection", "")
tt_selection = WindowManager.getImage("subsection_small.tif")
IJ.selectWindow("thresholded.tif")
IJ.selectWindow("subsection_small.tif")
IJ.run(tt_selection, "Restore Selection", "")
# Get TT intensity statistics.
stat_options = IS.MEAN | IS.MIN_MAX | IS.STD_DEV
stats = IS.getStatistics(tt_selection.getProcessor(), stat_options,
selection_small.getCalibration())
# Calculate pixel ceiling intensity value based on heuristic.
# TODO: Add a catch for data type overflow.
pixel_ceiling = stats.mean + 3 * stats.stdDev
print "px ceil:", pixel_ceiling
# Invert selection to get inter-sarcomeric gap intensity statistics.
IJ.run(tt_selection, "Make Inverse", "")
stat_options = IS.MEAN | IS.MIN_MAX | IS.STD_DEV
stats = IS.getStatistics(tt_selection.getProcessor(), stat_options,
selection_small.getCalibration())
# Calculate pixel floor intensity value based on heuristic.
pixel_floor = stats.mean - stats.stdDev
# TODO: Add a catch for data type underflow.
print "px floor:", pixel_floor
# Threshold original image based on these values.
IJ.selectWindow(this_img.getTitle())
IJ.run(this_img, "Select All", "")
IJ.setMinAndMax(pixel_floor, pixel_ceiling)
IJ.run(this_img, "Apply LUT", "")
## Ask if it is acceptable.
gd = GenericDialog("Acceptable?")
gd.addMessage(
"If the preprocessed image is acceptable for analysis, hit 'OK' to being analysis.\n"
+ " If the image is unacceptable or an error occurred, hit 'Cancel'")
gd.showDialog()
if gd.wasCanceled():
return
## Save the preprocessed image.
imp = IJ.getImage()
fs = FileSaver(imp)
img_save_dir = matchedmyo_path + "myoimages/" # actually get from user at some point
img_file_path = img_save_dir + img_name[:-4] + "_preprocessed.tif"
if os.path.exists(img_save_dir) and os.path.isdir(img_save_dir):
print "Saving image as:", img_file_path
if os.path.exists(img_file_path):
# use dialog box to ask if they want to overwrite
gd = GenericDialog("Overwrite?")
gd.addMessage(
"A file exists with the specified path, \"{}\". Would you like to overwrite it?"
.format(img_file_path))
gd.enableYesNoCancel()
gd.showDialog()
if gd.wasCanceled():
return
elif fs.saveAsTiff(img_file_path):
print "Preprocessed image saved successfully at:", '"' + img_file_path + '"'
else:
print "Folder does not exist or is not a folder!"
### Create the YAML file containing the parameters for classification
## Ask user for YAML input
gd = GenericDialog("YAML Input")
gd.addStringField("imageName", img_file_path, 50)
#gd.addStringField("maskName", "None")
gd.addStringField("outputParams_fileRoot", img_file_path[:-4], 50)
gd.addStringField("outputParams_fileType", "tif")
gd.addNumericField("outputParams_dpi", 300, 0)
gd.addCheckbox("outputParams_saveHitsArray", False)
gd.addStringField("outputParams_csvFile", matchedmyo_path + "results/")
gd.addCheckbox("TT Filtering", True)
gd.addToSameRow()
gd.addCheckbox("LT Filtering", True)
gd.addToSameRow()
gd.addCheckbox("TA Filtering", True)
gd.addNumericField("scopeResolutions_x", 5.0, 3)
gd.addToSameRow()
gd.addNumericField("scopeResolutions_y", 5.0, 3)
gd.addMessage("Enter in filter rotation angles separated by commas.")
gd.addStringField("", "-25, -20, -15, -10, -5, 0, 5, 10, 15, 20, 25", 50)
gd.addCheckbox("returnAngles", False)
gd.addCheckbox("returnPastedFilter", True)
gd.showDialog()
if gd.wasCanceled():
return
strings = [st.text for st in gd.getStringFields()]
#if strings[1] == "None" or "":
# strings[1] = None
nums = [float(num.text) for num in gd.getNumericFields()]
nums[0] = int(nums[0]) # Have to make sure the dpi variable is an integer
checks = [str(bool(boo.state)) for boo in gd.getCheckboxes()]
iter_argument = ','.join(
[str(float(it) - rotation_angle) for it in strings[4].split(',')])
string_block = """imageName: {0[0]}
outputParams:
fileRoot: {0[1]}
fileType: {0[2]}
dpi: {1[0]}
saveHitsArray: {2[0]}
csvFile: {0[3]}
preprocess: False
filterTypes:
TT: {2[1]}
LT: {2[2]}
TA: {2[3]}
scopeResolutions:
x: {1[1]}
y: {1[2]}
iters: [{3}]
returnAngles: {2[4]}
returnPastedFilter: {2[5]}""".format(strings, nums, checks, iter_argument)
im_title = this_img.getTitle()
with cd(matchedmyo_path):
yaml_file_path = "./YAML_files/" + im_title[:-4] + ".yml"
with open("./YAML_files/" + im_title[:-4] + ".yml", "w") as ym:
ym.write(string_block)
print "Wrote YAML file to:", matchedmyo_path + yaml_file_path[2:]
### Run the matchedmyo code on the preprocessed image
with cd(matchedmyo_path):
#os.chdir(matchedmyo_path)
#subprocess.call(["python3", matchedmyo_path+"matchedmyo.py", "fullValidation"])
subprocess.call(
["python3", "matchedmyo.py", "run", "--yamlFile", yaml_file_path])
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()
tifName = fName + ".tif" tifPath = os.path.join(fPath, tifName) print(fName) imp.changes = False wid = imp.getWidth() mu = IJ.micronSymbol scaUni = mu + "m" argThree = "distance=%g known=%f pixel=1 unit=%s" % (wid, fwMicrons, scaUni) IJ.run(imp, "Set Scale...", argThree) IJ.run(imp, "Enhance Contrast", "saturated=0.35") fs = FileSaver(imp) 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) imp.setTitle(fName) fs = FileSaver(imp) pngName = fName + ".png"
