def run():
printLog("=====ZY_CreatTemp_V2====", 0)
#Prompt user to open a image
od = OpenDialog("Choose image file", None)
if od is None:
msgStr = "User Cancled"
printLog(msgStr, 1)
else:
sourceFolder = od.getDirectory()
fileName = od.getFileName()
imp = IJ.openImage(sourceFolder + fileName)
imp.show()
n = imp.getNSlices()
printLog("Processing source file: " + fileName, 1)
imp2 = pickSlice(imp)
if imp2:
destFolder = os.path.join(sourceFolder, 'Temps')
#outName = os.path.join(destFolder,fileName[:-4]+'_temp.tif') #remove the .tif in filename
outName = os.path.join(destFolder, 'temp.tif')
# check or make the folder
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
#make temp
dupNSlice(imp2, n - 1)
printLog("Saving to: " + outName, 1)
fs = FileSaver(imp2)
fs.saveAsTiffStack(outName)
imp2.close()
imp.close()
msgStr = "ZY_CraetTemp_V2.py is Done."
printLog(msgStr, 0)
def run():
printLog("=====ZY_CreatTemp_V2====",0)
#Prompt user to open a image
od = OpenDialog("Choose image file", None)
if od is None:
msgStr = "User Cancled"
printLog(msgStr,1)
else:
sourceFolder = od.getDirectory()
fileName = od.getFileName()
imp = IJ.openImage(sourceFolder+fileName)
imp.show()
n = imp.getNSlices()
printLog("Processing source file: " + fileName,1)
imp2= pickSlice(imp)
if imp2:
destFolder = os.path.join(sourceFolder, 'Temps')
#outName = os.path.join(destFolder,fileName[:-4]+'_temp.tif') #remove the .tif in filename
outName = os.path.join(destFolder,'temp.tif')
# check or make the folder
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
#make temp
dupNSlice(imp2,n-1)
printLog("Saving to: " + outName,1)
fs = FileSaver(imp2)
fs.saveAsTiffStack(outName)
imp2.close()
imp.close()
msgStr = "ZY_CraetTemp_V2.py is Done."
printLog(msgStr,0)
def 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 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 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 saveStack(destFolder,file_name,imp):
#rename the result and save it to subfolder
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
fullname=os.path.join(destFolder,file_name)
#print (fullname)
fs = FileSaver(imp)
#print 'bSaveStack()', fullPath, 'nslices=', sr_imp.getNSlices()
msgStr = "Dimension:" + str(imp.width) + " X " + str(imp.height) + " X " + str(imp.getNSlices())
printLog("-Save "+file_name+" to "+destFolder,1)
printLog("-"+msgStr,2)
fs.saveAsTiffStack(fullname)
def saveStack(destFolder,file_name,imp):
#rename the result and save it to subfolder
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
fullname=os.path.join(destFolder,file_name)
#print (fullname)
fs = FileSaver(imp)
#print 'bSaveStack()', fullPath, 'nslices=', sr_imp.getNSlices()
msgStr = "Dimension:" + str(imp.width) + " X " + str(imp.height) + " X " + str(imp.getNSlices())
printLog("-Save "+file_name+" to "+destFolder,1)
printLog("-"+msgStr,2)
fs.saveAsTiffStack(fullname)
def scaleandfilter(infile,outfile,scalex,scaley):
print ("infile is: "+infile)
imp = Opener().openImage(infile)
print imp
print "scalex = %f; scaley = %f" % (scalex,scaley)
# Rescale
ip = imp.getProcessor()
ip.setInterpolate(True)
sp = StackProcessor(imp.getStack(),ip);
sp2=sp.resize(int(round(ip.width * scalex)), int(round(ip.height *scaley)));
imp.setStack(imp.getTitle(),sp2);
cal = imp.getCalibration()
cal.pixelWidth /= scalex
cal.pixelHeight /= scaley
IJ.run(imp, "8-bit","")
intif=infile+".tif"
outtif=infile+"-filtered.tif"
print("saving input file as "+intif)
f=FileSaver(imp)
f.saveAsTiffStack(intif)
imp.close()
# anisotropic filtering
anisopts="-scanrange:10 -tau:2 -nsteps:2 -lambda:0.1 -ipflag:0 -anicoeff1:1 -anicoeff2:0 -anicoeff3:0"
anisopts=anisopts+" -dx:%f -dy:%f -dz:%f" % (cal.pixelWidth,cal.pixelHeight,cal.pixelDepth)
if sys.version_info > (2, 4):
#for testing
# subprocess.check_call(["cp",intif,outtif])
subprocess.check_call(["anisofilter"]+anisopts.split(' ')+[intif,outtif])
else:
os.system(" ".join(["anisofilter"]+anisopts.split(' ')+[intif,outtif]))
# Hessian (tubeness)
print("Opening output tif: "+outtif)
imp = Opener().openImage(outtif)
imp.setCalibration(cal)
print("Running tubeness on tif: "+outtif)
IJ.run(imp,"Tubeness", "sigma=1")
IJ.run(imp, "8-bit","")
# Save to PIC
print("Saving as PIC: "+outfile)
# IJ.saveAs("tiff","outtif")
IJ.run(imp,"Biorad ...", "biorad="+outfile)
def savedata(imp, savepath, extension='ome.tiff', replace=False):
# general function for saving image data in different formats
# check if file already exists and delete if replace is true
if os.path.exists(savepath):
if replace:
os.remove(savepath)
if not replace:
return None
# general safety check
# if not extension:
# extension = 'ome.tiff'
# check extension
if extension in ['tiff', 'tif', 'ome.tiff', 'ome.tif', 'png', 'jpeg']:
fs = FileSaver(imp)
nslices = imp.getStack().getSize() # get the number of slices
# in case of TIFF
if extension == ('tiff' or 'tif' or 'TIFF' or 'TIF'):
if nslices > 1:
fs.saveAsTiffStack(savepath)
if nslices == 1:
fs.saveAsTiff(savepath)
# in case of OME-TIFF
elif extension == 'ome.tiff' or extension == 'ome.tif':
pstr = ExportTools.bfexporter(imp, savepath, useLOCI=True)
print('BioFormats Paramstring : ', pstr)
# in case of PNG
elif extension == ('png' or 'PNG'):
fs.saveAsPng(savepath)
# in case
elif extension == ('jpeg' or 'jpg' or 'JPEG' or 'JPG'):
fs.saveAsJpeg(savepath)
else:
extension = 'ome.tiff'
print("save as OME-TIFF: ") # savepath
pstr = ExportTools.bfexporter(imp, savepath, useLOCI=True)
print('BioFormats Paramstring : ', pstr)
return savepath
def run():
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 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()
def run():
print "===== bBatchConvertTo8Bitv3 ====="
# Expecting one argument: the file path
if len(sys.argv) < 2:
print " We need at least one folder as input"
print " Usage: ./fiji-macosx bBatchConvertTo8Bitv3 <folder-path>/"
# Prompt user for a folder
sourceFolder = DirectoryChooser("Please Choose A Directory Of .tif Files").getDirectory()
if not sourceFolder:
return
else:
sourceFolder = sys.argv[1] #assuming it ends in '/'
#get user options
okGo = getOptions() # creates {numberOfChannels, replaceExisting}
if okGo == -1:
return 0
destFolder = sourceFolder + "channels8_256/"
#make destination directory
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
print " Processing source folder: ", sourceFolder
print " Saving to destination folder: ", destFolder
numOpened = 0
numSaved = 0
for filename in os.listdir(sourceFolder):
startWithDot = filename.startswith(".")
isMax = filename.endswith("max.tif")
isTif = filename.endswith(".tif")
if (not startWithDot) and (not isMax) and (isTif):
shortName, fileExtension = os.path.splitext(filename)
outPath = destFolder + "/" + filename
outPath1 = destFolder + "/" + shortName + "_ch1" + ".tif"
outPath2 = destFolder + "/" + shortName + "_ch2" + ".tif"
#before we open, check if eventual dest exists
if not replaceExisting:
if numberOfChannels == 2 and os.path.exists(outPath1) and os.path.exists(outPath2):
print " 512 Destination file exists, not saving the image.", filename
continue #with next iteration
if numberOfChannels == 1 and os.path.exists(outPath):
print " 512 Destination file exists, not saving the image.", filename
continue #with next iteration
print " ===================================="
print " -> Opening", sourceFolder+filename
imp = IJ.openImage(sourceFolder + filename)
if imp is None:
print " Could not open image from file:", filename
continue #with next iteration
imp.show()
numOpened +=1
#i can get properties as long list of {key=value}
#how do i then set each property in new imp1/imp2? Do IJ.openImagehave ot loop?
#print imp.getProperties()
#in the future IJ.openImagehavewant to have option to scale down to 512X512
#run("Scale...", "x=- y=- z=1.0 width=512 height=512 depth=196 interpolation=Bilinear average process create title=20131007_a144_008_ch1-1.tif");
print " Image is: " + str(imp.width) + " X " + str(imp.height) + " X " + str(imp.getNSlices())
#if imp.getBitDepth() == 16:
if imp.width>512 and imp.height>512:
print " Converting to 512X512 with 'Scale'"
#IJ.run("8-bit")
theTitle = "tmpOutput"
IJ.run(imp, "Scale...", "x=- y=- z=1.0 width=512 height=512 depth=" + str(imp.getNSlices()) + " interpolate=Bilinear average process create title=" + theTitle)
imp = IJ.getImage()
#bug: original window is left open
if numberOfChannels == 2:
print " deinterleaving"
IJ.run("Deinterleave", "how=2"); #makes 2 window
#ch2
imp2 = IJ.getImage()
fs = FileSaver(imp2)
print " Saving 8bit File to", outPath2
fs.saveAsTiffStack(outPath2)
numSaved += 1
imp2.changes = 0
imp2.close()
#ch1
imp1 = IJ.getImage()
fs = FileSaver(imp1)
print " Saving 8bit File to", outPath2
fs.saveAsTiffStack(outPath1)
numSaved += 1
imp1.changes = 0
imp1.close()
elif numberOfChannels == 1: #single channel
fs = FileSaver(imp)
print " Saving 8bit File to", outPath
fs.saveAsTiffStack(outPath)
numSaved += 1
imp.changes = 0
imp.close()
else:
print " File was not larger than 512X512???"
imp.close() #close original
else:
if isTif:
#print " ===================================="
print " -> Ignoring .tif:", filename
print " ==="
print " bBatchConvertTo8Bitv3.py is Done, Number Opened " + str(numOpened) + ", Number Saved ", str(numSaved)
print " ==="
def save(self, image, outputName): saver = FileSaver(image) saver.saveAsTiffStack(self.outputDir + self.subDir + outputName + ".tif") print "Saved " + self.outputDir + self.subDir + outputName + ".tif"
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 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)
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)
def saveMultichannelImage(self, title, channels, luts): tmp = RGBStackMerge.mergeChannels(channels, False) tmp.luts = luts saver = FileSaver(tmp) saver.saveAsTiffStack(self.outputDir + title + ".tif") tmp.close()
def 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()
projectR.doProjection()
projectionR = projectR.getProjection()
impR2 = ImageCalculator().run("Subtract create stack", impR1, projectionR)
IJ.run(impR2, "Enhance Contrast", "saturated=0.4 process_all")
IJ.run(impR2, "Set Scale...",
"distance=" + str(CamRScale) + " known=1 unit=cm")
IJ.run(impR2, "Grid...",
"grid=Lines area=" + str(GridSize) + " color=Cyan")
IJ.run(impR2, "Translate...",
"x=" + str(TranslateR) + " y=0 interpolation=None stack")
savepath = path.join(folder, UID + "_CR.tif")
print savepath
fs = FileSaver(impR2)
if fs.saveAsTiffStack(savepath):
print("Files saved succesfully")
else:
print "No CamR Images to Open"
if runCamL:
impL1 = FolderOpener.open(folder, "file=CamL sort")
UID = impL1.title
filepath = folder.strip(UID + '/')
projectL = ZProjector(impL1)
projectL.setMethod(ZProjector.AVG_METHOD)
projectL.setImage(impL1)
projectL.setStartSlice(int(BackgroundWindowStart))
projectL.setStopSlice(int(BackgroundWindowEnd))
projectL.doProjection()
def run():
print "=====ZY_Resizetif_V1===="
#expecting one argument: the file path (choose the folder first)
if len(sys.argv) < 2:
print "We need at least one folder as input"
print "Please choose the input folder"
#prompt user to choose a folder"
sourceFolder = DirectoryChooser(
"Please choose a directory of .tif files").getDirectory()
if not sourceFolder:
return
else:
sourceFolder = sys.argv[1] #assuming it ends in '/'
#get user options
okGo = getOptions()
if okGo == -1:
return 0
destFolder = os.path.join(sourceFolder, 'resized')
print destFolder
# check or make the folder
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
print "Processing souce folder", sourceFolder
print "Saving to destination folder", destFolder
IJ.log(" ====== Startin ZY_resize_V1 ======")
IJ.log(" Processing source folder: " + sourceFolder)
IJ.log(" Saving to destination folder: " + destFolder)
numOpened = 0
numSaved = 0
for filename in os.listdir(sourceFolder):
startWithDot = filename.startswith(".")
isMax = filename.endswith("max.tif")
isTif = filename.endswith(".tif")
if (not startWithDot) and (not isMax) and isTif:
shortname, fileExtension = os.path.splitext(filename)
outPath = destFolder + "/" + filename
outPath1 = destFolder + "/" + shortname + "_ch1" + ".tif"
outPath2 = destFolder + "/" + shortname + "_ch2" + ".tif"
# before processing, check if eventual dest exists
if not replaceExisting:
if numberOfChannels == 2 and os.path.exists(
outPath1) and os.path.exists(outPath2):
msgStr = " -->The file==" + filename + "== has been resized, not processing again"
print msgStr
IJ.log(msgStr)
continue #with next iteration
if numberOfChannels == 1 and os.path.exists(outPath):
msgStr = " -->The file==" + filename + "== has been resized, not processing again"
print msgStr
IJ.log(msgStr)
continue #with next iteration
print "================================"
msgStr = str(numOpened +
1) + ". opening>> " + sourceFolder + filename
print msgStr
IJ.log(msgStr)
imp = IJ.openImage(sourceFolder + filename)
if imp is None:
msgStr = " -->>Error: could not open image file:" + filename
print msgStr
IJ.log(msgStr)
continue #with next iteration
imp.show()
numOpened += 1
msgStr = " -->Original size is:" + str(
imp.width) + "x" + str(imp.height) + "x" + str(
imp.getNSlices())
print msgStr
IJ.log(msgStr)
if imp.width < reWidth or imp.height < reHeight:
IJ.run(
imp, "Size...", "width=" + str(reWidth) + " height=" +
str(reHeight) + " depth=" + str(imp.getNSlices()) +
" interpolation=Bilinear")
msgStr = " -> Changing size to:" + str(
imp.width) + "x" + str(imp.height) + "x" + str(
imp.getNSlices())
print msgStr
IJ.log(msgStr)
imp = IJ.getImage()
if numberOfChannels == 2:
print "deinterleaving"
IJ.run("Deinterleaving", "how = 2") #make 2 windows
#ch2
imp2 = IJ.getImage()
fs = FileSaver(imp2)
print "saving channel 2 file to", outPath2
fs.saveAsTiffStack(outPath2)
numSaved += 1
imp2.changes = 0
imp2.close()
#ch1
imp1 = IJ.getImage()
fs = FileSaver(imp1)
print "saving channel 1 file to", outPath1
fs.saveAsTiffStack(outPath1)
numSaved += 1
imp1.changes = 0
imp1.close()
elif numberOfChannels == 1:
fs = FileSaver(imp)
print "saving file to", outPath
fs.saveAsTiffStack(outPath)
numSaved += 1
imp.changes = 0
else:
msgStr = " --> The file == " + filename + "== was ignored,because the size is bigger than setting"
print msgStr
IJ.log(msgStr)
imp.close() #close original
else: # showing that we ignoring the max
if (not startWithDot) and isTif:
#print " ===================================="
print filename
msgStr = " --> Ignoring .tif:" + filename
print msgStr
IJ.log(msgStr)
msgStr = " ZY_Resized_V1.py is Done, Number Opened " + str(
numOpened) + ", Number Saved " + str(numSaved)
print " ==="
print msgStr
print " ==="
IJ.log("==========")
IJ.log(msgStr)
# return filedir
return target_folder
filedir = getArg()
filedir = os.path.join(filedir)
filelist = os.listdir(filedir)
for afile in filelist:
if afile.lower().endswith('.lif'):
print filedir
print "..." + afile
filebase = splitext(afile)[0]
imps = getImps(os.path.join(filedir, afile))
printInfo(imps)
for (counter, item) in enumerate(imps):
outimp = zproj(item)
#outname = filedir + filebase + "/" + "s" + str(counter) + ".tif"
subname = ijtool.split(item.getTitle(), " - ")[1]
#outname = filedir + filebase + "/" + subname + "_ZP.tif"
outname = os.path.join(filedir, filebase, subname + "_ZP.tif")
print outname
outdir = os.path.join(filedir, filebase)
print outdir
if not os.path.isdir(outdir):
os.mkdir(outdir)
fs = FileSaver(outimp)
fs.saveAsTiffStack(outname)
#outimp = zproject(filepath)
#outimp.show()
def PrepareDatabase(minw, maxw, baseDir, aspectRatio, majorWidth, majorHeight):
outputpath = baseDir + "/" + str(majorWidth) + "_" + str(
majorHeight) + "_orig.tif"
#initialize stacks and labels
stackScaled = []
stackOrig = ImageStack(majorWidth, majorHeight)
imageNames = []
for i in range(minw, maxw + 1):
stackScaled.append(ImageStack(i, int(round(i / aspectRatio, 0))))
imageNames.append('')
counter = 0
# initialize zip file for originals
zf = zipfile.ZipFile(baseDir + "/originals.zip",
mode='w',
compression=zipfile.ZIP_DEFLATED,
allowZip64=1)
zf.writestr('from_string.txt', 'hello')
zf.close()
zf = zipfile.ZipFile(baseDir + "/originals.zip",
mode='a',
compression=zipfile.ZIP_DEFLATED,
allowZip64=1)
for root, dirs, files in os.walk(str(baseDir)):
for f1 in files:
if f1.endswith(".jpg") or f1.endswith(".jpe") or f1.endswith(
".jpeg"):
id = root + "/" + f1
IJ.redirectErrorMessages()
IJ.redirectErrorMessages(1)
imp = IJ.openImage(id)
if imp is None:
print "Couldn\'t open image from file:", id
continue
# skip non RGBimages
if imp.getProcessor().getNChannels() != 3:
print "Converting non RGB image:", id
if imp.getStackSize() > 1:
StackConverter(imp).convertToRGB()
else:
ImageConverter(imp).convertToRGB()
#skip images with different aspect ratio
width = imp.getWidth()
height = imp.getHeight()
ratio = round(
float(width) / float(height), 2
) # this makes the ratio filering approximate, minor variations in image dimensions will be ignored
if ratio != aspectRatio:
IJ.log("Skipping image of size: " + str(width) + "," +
str(height))
continue
# now scale the image within a given range
scale = Scale(imp.getProcessor())
IJ.log("Scaling image " + str(counter) + " " + str(id))
for i in range(minw, maxw + 1):
stackScaled[i - minw].addSlice(
None,
ScaleImageToSize(scale, i,
int(round(i / aspectRatio, 0))))
imageNames[i - minw] += str(id) + ";"
# save the originals to a temp directory
scaledOrig = ImagePlus(
None, ScaleImageToSize(scale, majorWidth, majorHeight))
SaveToZip(zf, scaledOrig, baseDir, counter)
counter += 1
zf.close()
# save the stacks
for i in range(minw, maxw + 1):
impScaled = ImagePlus(
str(minw) + "_" + str(int(round(i / aspectRatio, 0))),
stackScaled[i - minw])
impScaled.show()
#print imageNames
impScaled.setProperty('Info', imageNames[i - minw][:-1])
fs = FileSaver(impScaled)
filepath = baseDir + "/" + str(i) + "_" + str(
int(round(i / aspectRatio, 0))) + ".tif"
IJ.log("Saving output stack" + str(filepath))
fs.saveAsTiffStack(filepath)
#IJ.save(impScaled, filepath);
IJ.log("Done")
def run():
print "=====ZY_Resizetif_V1===="
#expecting one argument: the file path (choose the folder first)
if len(sys.argv) < 2:
print "We need at least one folder as input"
print "Please choose the input folder"
#prompt user to choose a folder"
sourceFolder = DirectoryChooser("Please choose a directory of .tif files").getDirectory()
if not sourceFolder:
return
else:
sourceFolder = sys.argv[1] #assuming it ends in '/'
#get user options
okGo = getOptions()
if okGo == -1:
return 0
destFolder = os.path.join(sourceFolder, 'resized')
print destFolder
# check or make the folder
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
print "Processing souce folder", sourceFolder
print "Saving to destination folder", destFolder
IJ.log(" ====== Startin ZY_resize_V1 ======")
IJ.log(" Processing source folder: " + sourceFolder)
IJ.log(" Saving to destination folder: " + destFolder)
numOpened = 0
numSaved = 0
for filename in os.listdir(sourceFolder):
startWithDot = filename.startswith(".")
isMax = filename.endswith("max.tif")
isTif = filename.endswith(".tif")
if (not startWithDot) and (not isMax) and isTif:
shortname, fileExtension = os.path.splitext(filename)
outPath = destFolder + "/" + filename
outPath1 = destFolder + "/" + shortname + "_ch1" + ".tif"
outPath2 = destFolder + "/" + shortname + "_ch2" + ".tif"
# before processing, check if eventual dest exists
if not replaceExisting:
if numberOfChannels == 2 and os.path.exists(outPath1) and os.path.exists(outPath2):
msgStr = " -->The file==" + filename + "== has been resized, not processing again"
print msgStr
IJ.log(msgStr)
continue #with next iteration
if numberOfChannels == 1 and os.path.exists(outPath):
msgStr = " -->The file==" + filename + "== has been resized, not processing again"
print msgStr
IJ.log(msgStr)
continue #with next iteration
print "================================"
msgStr = str(numOpened+1) + ". opening>> " + sourceFolder + filename
print msgStr
IJ.log(msgStr)
imp = IJ.openImage(sourceFolder+filename)
if imp is None:
msgStr = " -->>Error: could not open image file:" + filename
print msgStr
IJ.log(msgStr)
continue #with next iteration
imp.show()
numOpened +=1
msgStr = " -->Original size is:" + str(imp.width) + "x" + str(imp.height) + "x" + str(imp.getNSlices())
print msgStr
IJ.log(msgStr)
if imp.width < reWidth or imp.height < reHeight:
IJ.run(imp, "Size...", "width=" + str(reWidth) + " height=" + str(reHeight) + " depth=" + str(imp.getNSlices()) + " interpolation=Bilinear")
msgStr = " -> Changing size to:" + str(imp.width) + "x" + str(imp.height)+ "x" + str(imp.getNSlices())
print msgStr
IJ.log(msgStr)
imp = IJ.getImage()
if numberOfChannels == 2:
print "deinterleaving"
IJ.run("Deinterleaving", "how = 2") #make 2 windows
#ch2
imp2=IJ.getImage()
fs = FileSaver(imp2)
print "saving channel 2 file to", outPath2
fs.saveAsTiffStack(outPath2)
numSaved += 1
imp2.changes = 0
imp2.close()
#ch1
imp1 = IJ.getImage()
fs= FileSaver(imp1)
print "saving channel 1 file to", outPath1
fs.saveAsTiffStack(outPath1)
numSaved += 1
imp1.changes = 0
imp1.close()
elif numberOfChannels == 1:
fs= FileSaver(imp)
print "saving file to", outPath
fs.saveAsTiffStack(outPath)
numSaved += 1
imp.changes = 0
else:
msgStr = " --> The file == " + filename + "== was ignored,because the size is bigger than setting"
print msgStr
IJ.log(msgStr)
imp.close() #close original
else: # showing that we ignoring the max
if (not startWithDot) and isTif:
#print " ===================================="
print filename
msgStr = " --> Ignoring .tif:" + filename
print msgStr
IJ.log(msgStr)
msgStr = " ZY_Resized_V1.py is Done, Number Opened " + str(numOpened) + ", Number Saved " + str(numSaved)
print " ==="
print msgStr
print " ==="
IJ.log("==========")
IJ.log(msgStr)
def scaleandfilter(infile,outfile,scalex,scaley,scalez,anisofilter,runtube):
print ("infile is: "+infile)
imp = Opener().openImage(infile)
print imp
print "scalex = %f; scaley = %f ; scalez = %f" % (scalex,scaley,scalez)
# Rescale
cal = imp.getCalibration()
iml = ImgLib.wrap(imp)
scaledimg = Scale3D(iml, scalex, scaley, scalez)
imp2=ImgLib.wrap(scaledimg)
# find range of pixel values for scaled image
from mpicbg.imglib.algorithm.math import ComputeMinMax
# (for imglib2 will be: net.imglib2.algorithm.stats)
minmax=ComputeMinMax(scaledimg)
minmax.process()
(min,max)=(minmax.getMin().get(),minmax.getMax().get())
# Make a copy of the stack (converting to 8 bit as we go)
stack = ImageStack(imp2.width, imp2.height)
print "min = %e, max =%e" % (min,max)
for i in xrange(1, imp2.getNSlices()+1):
imp2.setSliceWithoutUpdate(i)
ip=imp2.getProcessor()
# set range
ip.setMinAndMax(min,max)
stack.addSlice(str(i), ip.convertToByte(True))
# save copy of calibration info
cal=imp.getCalibration()
# close original image
imp.close()
# make an image plus with the copy
scaled = ImagePlus(imp2.title, stack)
# Deal with calibration info which didn't seem to come along for the ride
cal.pixelWidth/=scalex
cal.pixelHeight/=scaley
cal.pixelDepth/=scalez
scaled.setCalibration(cal)
print "dx = %f; dy=%f; dz=%f" % (cal.pixelWidth,cal.pixelHeight,cal.pixelDepth)
intif=infile+".tif"
outtif=infile+"-filtered.tif"
if anisofilter.upper() != 'FALSE':
print("saving input file as "+intif)
f=FileSaver(scaled)
f.saveAsTiffStack(intif)
scaled.close()
# anisotropic filtering
anisopts="-scanrange:10 -tau:2 -nsteps:2 -lambda:0.1 -ipflag:0 -anicoeff1:1 -anicoeff2:0 -anicoeff3:0"
anisopts=anisopts+" -dx:%f -dy:%f -dz:%f" % (cal.pixelWidth,cal.pixelHeight,cal.pixelDepth)
if sys.version_info > (2, 4):
#for testing
# subprocess.check_call(["cp",intif,outtif])
subprocess.check_call([anisofilter]+anisopts.split(' ')+[intif,outtif])
else:
os.system(" ".join([anisofilter]+anisopts.split(' ')+[intif,outtif]))
# Open anisofilter output back into Fiji
print("Opening output tif: "+outtif)
scaled = Opener().openImage(outtif)
scaled.setCalibration(cal)
# Hessian (tubeness)
print("Running tubeness")
if(runtube):
tp=TubenessProcessor(1.0,False)
result = tp.generateImage(scaled)
IJ.run(result, "8-bit","")
else:
result=scaled
# Save out file
fileName, fileExtension = os.path.splitext(outfile)
print("Saving as "+fileExtension+": "+outfile)
if fileExtension.lower()=='.nrrd':
nw=Nrrd_Writer()
nw.setNrrdEncoding("gzip")
nw.save(result,outfile)
else:
# Save to PIC
IJ.run(result,"Biorad ...", "biorad=["+outfile+"]")
scaled.close()
result.close()
for i in range(0, channels):
imageProcessor = ShortProcessor(width, height)
imageStack = ImageStack(width, height)
for sphere in spheres:
fnorm = int(round((sphere['f'][i] - fmin[i]) / (fmax[i] - fmin[i]) * 65536.0))
x = sphere['cx']
y = sphere['cy']
d = sphere['r'] * 2
imageProcessor.putPixel(x, y, fnorm)
imageStack.addSlice(imageProcessor)
channelImages.append(ImagePlus("Rendering C" + "%i" % (i + 1), imageStack))
imageO = RGBStackMerge.mergeChannels(channelImages, False)
else:
for i in range(0, channels):
objectImage = ObjectCreator3D(sx, sy, sz)
for sphere in spheres:
fnorm = int(round((sphere['f'][i] - fmin[i]) / (fmax[i] - fmin[i]) * 65536.0))
objectImage.createEllipsoid(
sphere['cx'], sphere['cy'], sphere['cz'],
sphere['r'], sphere['r'], round(sphere['r'] / zscale),
fnorm, False)
channelImages.append(ImagePlus("Rendering C" + "%i" % (i + 1), objectImage.getStack()))
imageO = RGBStackMerge.mergeChannels(channelImages, False)
# Save result
saver = FileSaver(imageO)
saver.saveAsTiffStack(outputFile)
print "Saved " + outputFile
#filelist = os.listdir(filedir)
for root, directories, filenames in os.walk(filedir):
print directories
for filename in filenames:
if filename.lower().endswith('.lif'):
print filedir
print "..." + filename
filebase = splitext(filename)[0]
imps = getImps(os.path.join(filedir, filename))
printInfo(imps)
for (counter, item) in enumerate(imps):
#outimp = zproj(item)
outimp = makeComposite(item)
#outimp.show()
#outname = filedir + filebase + "/" + "s" + str(counter) + ".tif"
subname = ijtool.split(item.getTitle(), " - ")[1]
#outname = filedir + filebase + "/" + subname + "_ZP.tif"
outdir = os.path.join(filedir, "processed")
outname = os.path.join(outdir, filebase + "_" + subname + "_" + str(counter) + "_Composite")
print outname
if not os.path.isdir(outdir):
os.mkdir(outdir)
fs = FileSaver(outimp)
fs.saveAsTiffStack(outname+".tif")
fs.saveAsJpeg(outname+".jpg")
#outimp = zproject(filepath)
#outimp.show()
def run():
print "===== bBatchConvertTo8Bitv3 ====="
# Expecting one argument: the file path
if len(sys.argv) < 2:
print " We need at least one folder as input"
print " Usage: ./fiji-macosx bBatchConvertTo8Bitv3 <folder-path>/"
# Prompt user for a folder
sourceFolder = DirectoryChooser(
"Please Choose A Directory Of .tif Files").getDirectory()
if not sourceFolder:
return
else:
sourceFolder = sys.argv[1] #assuming it ends in '/'
#get user options
okGo = getOptions() # creates {numberOfChannels, replaceExisting}
if okGo == -1:
return 0
destFolder = sourceFolder + "channels8/"
#make destination directory
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
print " Processing source folder: ", sourceFolder
print " Saving to destination folder: ", destFolder
numOpened = 0
numSaved = 0
for filename in os.listdir(sourceFolder):
startWithDot = filename.startswith(".")
isMax = filename.endswith("max.tif")
isTif = filename.endswith(".tif")
if (not startWithDot) and (not isMax) and (isTif):
shortName, fileExtension = os.path.splitext(filename)
outPath = destFolder + "/" + filename
outPath1 = destFolder + "/" + shortName + "_ch1" + ".tif"
outPath2 = destFolder + "/" + shortName + "_ch2" + ".tif"
#before we open, check if eventual dest exists
if not replaceExisting:
if numberOfChannels == 2 and os.path.exists(
outPath1) and os.path.exists(outPath2):
print " 8-Bit Destination file exists, not saving the image.", filename
continue #with next iteration
if numberOfChannels == 1 and os.path.exists(outPath):
print " 8-Bit Destination file exists, not saving the image.", filename
continue #with next iteration
print " ===================================="
print " -> Opening", sourceFolder + filename
imp = IJ.openImage(sourceFolder + filename)
if imp is None:
print " Could not open image from file:", filename
continue #with next iteration
imp.show()
numOpened += 1
#i can get properties as long list of {key=value}
#how do i then set each property in new imp1/imp2? Do IJ.openImagehave ot loop?
#print imp.getProperties()
#in the future IJ.openImagehavewant to have option to scale down to 512X512
#run("Scale...", "x=- y=- z=1.0 width=512 height=512 depth=196 interpolation=Bilinear average process create title=20131007_a144_008_ch1-1.tif");
print " Image is: " + str(imp.width) + " X " + str(
imp.height) + " X " + str(imp.getNSlices())
if imp.getBitDepth() == 16:
print " Converting to 8-bit..."
IJ.run("8-bit")
if numberOfChannels == 2:
print " deinterleaving"
IJ.run("Deinterleave", "how=2")
#makes 2 window
#ch2
imp2 = IJ.getImage()
fs = FileSaver(imp2)
print " Saving 8bit File to", outPath2
fs.saveAsTiffStack(outPath2)
numSaved += 1
imp2.changes = 0
imp2.close()
#ch1
imp1 = IJ.getImage()
fs = FileSaver(imp1)
print " Saving 8bit File to", outPath2
fs.saveAsTiffStack(outPath1)
numSaved += 1
imp1.changes = 0
imp1.close()
elif numberOfChannels == 1: #single channel
fs = FileSaver(imp)
print " Saving 8bit File to", outPath
fs.saveAsTiffStack(outPath)
numSaved += 1
imp.changes = 0
imp.close()
else:
print " File was not 16 bit???"
imp.close() #close original
else:
if isTif:
#print " ===================================="
print " -> Ignoring .tif:", filename
print " ==="
print " bBatchConvertTo8Bitv3.py is Done, Number Opened " + str(
numOpened) + ", Number Saved ", str(numSaved)
print " ==="
def analyze(tempFile):
# Get currently selected image
#imp = WindowManager.getCurrentImage()
imp = IJ.openImage(tempFile)
imp.show()
dims = imp.getDimensions();
imp.setDimensions(dims[2], dims[4], dims[3]);
#----------------------------
# Create the model object now
#----------------------------
# Some of the parameters we configure below need to have
# a reference to the model at creation. So we create an
# empty model now.
model = Model()
# Send all messages to ImageJ log window.
model.setLogger(Logger.IJ_LOGGER)
#------------------------
# Prepare settings object
#------------------------
settings = Settings()
settings.setFrom(imp)
print(settings.imageFileName)
# Configure detector - We use the Strings for the keys
settings.detectorFactory = LogDetectorFactory()
settings.detectorSettings = {
'DO_SUBPIXEL_LOCALIZATION' : False,
'RADIUS' : 20.,
'TARGET_CHANNEL' : 1,
'THRESHOLD' : 0.95,
'DO_MEDIAN_FILTERING' : True,
}
# Configure spot filters - Classical filter on quality
#filter1 = FeatureFilter('QUALITY', 0.5, True)
#settings.addSpotFilter(filter1)
# Configure tracker - We want to allow merges and fusions
settings.trackerFactory = SimpleSparseLAPTrackerFactory()
settings.trackerSettings = LAPUtils.getDefaultLAPSettingsMap() #probably good enough
#settings.trackerSettings['ALLOW_TRACK_SPLITTING'] = False
#settings.trackerSettings['ALLOW_TRACK_MERGING'] = False
settings.trackerSettings['LINKING_MAX_DISTANCE'] = 35.0
settings.trackerSettings['GAP_CLOSING_MAX_DISTANCE']= 60.0
settings.trackerSettings['MAX_FRAME_GAP']= 2
# Configure track analyzers - Later on we want to filter out tracks
# based on their displacement, so we need to state that we want
# track displacement to be calculated. By default, out of the GUI,
# not features are calculated.
# The displacement feature is provided by the TrackDurationAnalyzer.
settings.addTrackAnalyzer(TrackDurationAnalyzer())
#-------------------
# Instantiate plugin
#-------------------
trackmate = TrackMate(model, settings)
ok = trackmate.process()
if not ok:
sys.exit(str(trackmate.getErrorMessage()))
#----------------
# Display results
#----------------
selectionModel = SelectionModel(model)
displayer = HyperStackDisplayer(model, selectionModel, imp)
displayer.render()
displayer.refresh()
# Echo results with the logger we set at start:
model.getLogger().log(str(model))
print(str(settings))
filename = os.path.splitext(settings.imageFileName)
pathname = settings.imageFolder + "" + filename[0] + "tracks.xml"
guicontroller = TrackMateGUIController(trackmate)
newFile = File(pathname)
ExportTracksToXML(guicontroller).export(model, settings, newFile)
actionObject = CaptureOverlayAction()
actionObject.execute(trackmate)
imp = WindowManager.getCurrentImage()
fileSaver = FileSaver(imp)
fileSaver.saveAsTiffStack(settings.imageFolder + "" + filename[0] + "overlay.tif")
WindowManager.closeAllWindows()
guicontroller.quit()
selectionModel.clearSelection();
model.clearTracks(1)
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
thr1, thrimp1 = calculateThreshold(imp1, roi, methods[0])
thr2, thrimp2 = calculateThreshold(imp2, roi, methods[1])
cursor = TwinCursor(img1.randomAccess(), img2.randomAccess(), Views.iterable(mask).localizingCursor())
rtype = img1.randomAccess().get().createVariable()
raw = manders.calculateMandersCorrelation(cursor, rtype)
rthr1 = rtype.copy()
rthr2 = rtype.copy()
rthr1.set(thr1)
rthr2.set(thr2)
cursor.reset()
thrd = manders.calculateMandersCorrelation(cursor, rthr1, rthr2, ThresholdMode.Above)
print "Results are: %f %f %f %f" % (raw.m1, raw.m2, thrd.m1, thrd.m2)
results.incrementCounter()
rowno = results.getCounter() - 1
results.setValue("Cell", rowno, int(rowno))
results.setValue("Threshold 1", rowno, int(thr1))
results.setValue("Threshold 2", rowno, int(thr2))
results.setValue("M1 raw", rowno, float(raw.m1))
results.setValue("M2 raw", rowno, float(raw.m2))
results.setValue("M1 thrd", rowno, float(thrd.m1))
results.setValue("M2 thrd", rowno, float(thrd.m2))
thrimp = RGBStackMerge.mergeChannels([thrimp1, thrimp2], False)
saver = FileSaver(thrimp)
saver.saveAsTiffStack(outputDir + "Cell_%i-" % results.getCounter() + title + ".tif")
thrimp.close()
results.show("Colocalization results")
wcount = wm.getWindowCount()
if wcount == 0:
log.warn("No windows open, nothing to do.")
sys.exit()
log.info("Number of open windows: %s" % wcount)
log.info("Selected [%s] as destination folder." % target)
# determine padding width for filenames
pad = len(str(wcount))
for wid in range(1, wcount + 1):
imp = wm.getImage(wid)
imgid = wm.getNthImageID(wid)
log.debug("window id: %s, imageID: %s" % (wid, wm.getNthImageID(wid)))
# Construct filename
filename = 'img_' + str(wid).zfill(pad) + '.tif'
filepath = target + '/' + filename
fs = FileSaver(imp)
if imp.getImageStackSize() > 1:
if not fs.saveAsTiffStack(filepath):
log.error("Error saving current image, stopping.")
sys.exit()
else:
if not fs.saveAsTiff(filepath):
log.error("Error saving current image, stopping.")
sys.exit()
log.info("Successfully saved %s files." % wcount)
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()
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 PrepareDatabase(minw, maxw, baseDir, aspectRatio, majorWidth, majorHeight):
outputpath = baseDir + "/" + str(majorWidth) + "_" + str(majorHeight) + "_orig.tif"
#initialize stacks and labels
stackScaled = []
stackOrig = ImageStack(majorWidth, majorHeight)
imageNames = []
for i in range(minw, maxw+1):
stackScaled.append(ImageStack(i, int(round(i/aspectRatio, 0))))
imageNames.append('')
counter = 0
# initialize zip file for originals
zf = zipfile.ZipFile(baseDir + "/originals.zip", mode='w', compression=zipfile.ZIP_DEFLATED, allowZip64=1)
zf.writestr('from_string.txt', 'hello')
zf.close()
zf = zipfile.ZipFile(baseDir + "/originals.zip", mode='a', compression=zipfile.ZIP_DEFLATED, allowZip64=1)
for root, dirs, files in os.walk(str(baseDir)):
for f1 in files:
if f1.endswith(".jpg") or f1.endswith(".jpe") or f1.endswith(".jpeg"):
id = root + "/" + f1
IJ.redirectErrorMessages()
IJ.redirectErrorMessages(1)
imp = IJ.openImage(id)
if imp is None:
print "Couldn\'t open image from file:", id
continue
# skip non RGBimages
if imp.getProcessor().getNChannels() != 3:
print "Skipping non RGB image:", id
continue
#skip images with different aspect ratio
width = imp.getWidth()
height = imp.getHeight()
ratio = round(float(width)/float(height), 2) # this makes the ratio filering approximate, minor variations in image dimensions will be ignored
if ratio != aspectRatio:
IJ.log("Skipping image of size: " + str(width) + "," + str(height))
continue
# now scale the image within a given range
scale = Scale(imp.getProcessor())
IJ.log("Scaling image " + str(counter) + " " + str(id))
for i in range(minw, maxw+1):
stackScaled[i-minw].addSlice(None, ScaleImageToSize(scale, i, int(round(i/aspectRatio, 0))))
imageNames[i-minw] += str(id) + ";"
# save the originals to a temp directory
scaledOrig = ImagePlus(None, ScaleImageToSize(scale, majorWidth, majorHeight))
SaveToZip(zf, scaledOrig, baseDir, counter)
counter += 1
zf.close()
# save the stacks
for i in range(minw, maxw+1):
impScaled = ImagePlus(str(minw) + "_" + str(int(round(i/aspectRatio, 0))), stackScaled[i-minw])
impScaled.show()
#print imageNames
impScaled.setProperty('Info', imageNames[i-minw][:-1])
fs = FileSaver(impScaled)
filepath = baseDir + "/" + str(i) + "_" + str(int(round(i/aspectRatio, 0))) + ".tif"
IJ.log("Saving output stack" + str(filepath))
fs.saveAsTiffStack(filepath)
#IJ.save(impScaled, filepath);
IJ.log("Done")
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 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()
for i in range(wcount): ### image ID lists start with 1, not 0 ## wid = id + 1 imgid = wm.getNthImageID(i+1) # print "window id ", i+1, ":", wm.getNthImageID(i+1) imp = wm.getImage(i+1) fs = FileSaver(imp) # Print image details # print " title:", imp.title # print " current window:", wm.getCurrentWindow() # Construct filename filename = 'tile_' + str(i+1).zfill(pad) + '.tif' filepath = target + '/' + filename #print "filename:", filename if fs.saveAsTiffStack(filepath): print "imageID", imgid, "saved as", filename else: print "ERROR saving imageID", imgid, "file at", filepath #print "ID list of windows:", WindowManager.getIDList() ##idlist = WindowManager.getIDList() ##for wid in idlist: ## print "window id:", wid ## ##print "front window:", WindowManager.getFrontWindow() # wm.putBehind() #print "width:", imp.width