def convert32to16(fullFilePath): #overwrite the file!!!
if not os.path.isfile(fullFilePath):
bPrintLog(
'\nERROR: runOneFile() did not find file: ' + fullFilePath + '\n',
0)
return 0
elif not fullFilePath.endswith('tif'):
msg = fullFilePath + " is not a deconvoluted tif file"
bPrintLog(msg, 2)
else:
bPrintLog(
time.strftime("%H:%M:%S") +
' starting runOneFile()for overwrite: ' + fullFilePath, 1)
#open and overwrite the deconvoluted file as 16 bit
imp = Opener().openImage(fullFilePath) #deconvoluted file
if imp.getBitDepth() == 32:
imp.show()
msgStr = "Converting 32 to 16-bit..."
bPrintLog(msgStr, 3)
IJ.run("16-bit")
msgStr = "Overwriting 32-bit with 16-bit File in" + fullFilePath
bPrintLog(msgStr, 3)
IJ.run(imp, "Save", "") #save as replace without asking
imp.close()
def convert32to16(fullFilePath): #overwrite the file!!!
if not os.path.isfile(fullFilePath):
bPrintLog('\nERROR: runOneFile() did not find file: ' + fullFilePath + '\n',0)
return 0
elif not fullFilePath.endswith('tif'):
msg = fullFilePath +" is not a deconvoluted tif file"
bPrintLog(msg,2)
else:
bPrintLog(time.strftime("%H:%M:%S") + ' starting runOneFile()for overwrite: ' + fullFilePath, 1)
#open and overwrite the deconvoluted file as 16 bit
imp = Opener().openImage(fullFilePath) #deconvoluted file
if imp.getBitDepth() == 32:
imp.show()
msgStr = "Converting 32 to 16-bit..."
bPrintLog(msgStr,3)
IJ.run("16-bit")
msgStr = "Overwriting 32-bit with 16-bit File in" + fullFilePath
bPrintLog(msgStr,3)
IJ.run(imp,"Save","") #save as replace without asking
imp.close()
class bImp:
def __init__(self, filepath):
"""
Load an image or stack from filepath.
Args:
filepath (str): Full path to an image file. Can be .tif, .lsm, .czi, etc
"""
if not os.path.isfile(filepath):
bPrintLog('ERROR: bImp() did not find file: ' + filepath,0)
return 0
self.filepath = filepath
folderpath, filename = os.path.split(filepath)
self.filename = filename
self.enclosingPath = folderpath
self.enclosingfolder = os.path.split(folderpath)[1]
self.dateStr = ''
self.timeStr = ''
self.imp = None
tmpBaseName, extension = os.path.splitext(filename)
isZeiss = extension in ['.czi', '.lsm']
self.islsm = extension == '.lsm'
self.isczi = extension == '.czi'
istif = extension == '.tif'
if istif:
# scanimage3 comes in with dimensions: [512, 512, 1, 52, 1]) = [width, height, numChannels, numSlices, numFrames]
self.imp = Opener().openImage(filepath)
self.imp.show()
elif isZeiss:
#open lsm using LOCI Bio-Formats
options = ImporterOptions()
#options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE)
options.setId(filepath)
imps = BF.openImagePlus(options)
for imp in imps:
self.imp = imp #WindowManager.getImage(self.windowname)
imp.show()
if not self.imp:
bPrintLog('ERROR: bImp() was not able to open file: '+ filepath,0)
self.windowname = filename
#self.imp = WindowManager.getImage(self.windowname)
# numChannels is not correct for scanimage, corrected in readTiffHeader()
(width, height, numChannels, numSlices, numFrames) = self.imp.getDimensions()
self.width = width # pixelsPerLine
self.height = height # linesPerFrame
self.numChannels = numChannels
self.numSlices = numSlices
self.numFrames = numFrames
self.infoStr = self.imp.getProperty("Info") #get all tags
self.voxelx = 1
self.voxely = 1
self.voxelz = 1
#self.numChannels = 1
#self.bitsPerPixel = 8
self.zoom = 1
self.motorx = None
self.motory = None
self.motorz = None
self.scanImageVersion = ''
self.msPerLine = None
self.dwellTime = None
# read file headers (date, time, voxel size)
if isZeiss:
self.readZeissHeader(self.infoStr)
elif istif:
self.readTiffHeader(self.infoStr)
self.updateInfoStr()
self.channelWindows = []
self.channelImp = []
if self.numChannels == 1:
self.channelWindows.append(self.windowname)
self.channelImp.append(self.imp)
else:
self.deinterleave()
def updateInfoStr(self):
# Fill in infoStr with Map Manager tags
self.infoStr += 'Folder2MapManager=' + versionStr + '\n'
self.infoStr += 'b_date=' + self.dateStr + '\n'
self.infoStr += 'b_time=' + self.timeStr + '\n'
# yevgeniya 20180314
#if (self.numChannels > 3):
# self.numChannels = 3
self.infoStr += 'b_numChannels=' + str(self.numChannels) + '\n'
self.infoStr += 'b_pixelsPerline=' + str(self.width) + '\n'
self.infoStr += 'b_linesPerFrame=' + str(self.height) + '\n'
self.infoStr += 'b_numSlices=' + str(self.numSlices) + '\n'
self.infoStr += 'b_voxelX=' + str(self.voxelx) + '\n'
self.infoStr += 'b_voxelY=' + str(self.voxely) + '\n'
self.infoStr += 'b_voxelZ=' + str(self.voxelz) + '\n'
#self.infoStr += 'b_bitsPerPixel=' + str(self.bitsPerPixel) + '\n'
self.infoStr += 'b_zoom=' + str(self.zoom) + '\n'
self.infoStr += 'b_motorx=' + str(self.motorx) + '\n'
self.infoStr += 'b_motory=' + str(self.motory) + '\n'
self.infoStr += 'b_motorz=' + str(self.motorz) + '\n'
self.infoStr += 'b_msPerLine=' + str(self.msPerLine) + '\n'
self.infoStr += 'b_scanImageVersion=' + self.scanImageVersion + '\n'
def readTiffHeader(self, infoStr):
"""
Read ScanImage 3/4 .tif headers
"""
logLevel = 3
# splitting on '\r' for scanimage 3.x works
# splitting on '\n' for scanimage 4.x works
#we need to search whole infoStr to figure out scanimage 3 or 4.
# we can't split info string because si3 uses \r and si4 uses \n
infoStrDelim = '\n'
if infoStr.find('scanimage.SI4') != -1:
infoStrDelim = '\n'
bPrintLog('Assuming SI4 infoStr to be delimited with backslash n', logLevel)
elif infoStr.find('state.software.version') != -1:
infoStrDelim = '\r'
bPrintLog('Assuming SI3 infoStr to be delimited with backslash r', logLevel)
else:
bPrintLog('Splitting infoStr using backslah n', logLevel)
# if we don't find zoom then voxel is an error (see end of function)
foundZoom = False
#for line in infoStr.split('\n'):
for line in infoStr.split(infoStrDelim):
#
# ScanImage 4.x
#
# scanimage.SI4.versionMajor = 4.2
if line.find('scanimage.SI4.versionMajor') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
self.scanImageVersion = rhs
# scanimage.SI4.motorPosition = [-33936.5 -106316 -55308.5]
if line.find('scanimage.SI4.motorPosition') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
rhs = rhs.replace('[','')
rhs = rhs.replace(']','')
floats = [float(x) for x in rhs.split()]
self.motorx = floats[0]
self.motory = floats[1]
self.motorz = floats[2]
# scanimage.SI4.channelsSave = [1;2]
if line.find('scanimage.SI4.channelsSave') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
rhs = rhs.replace('[','')
rhs = rhs.replace(']','')
channels = [int(x) for x in rhs.split(';')]
bPrintLog('reading scanimage.SI4.channelsSave inferred channels:' + str(channels), logLevel)
self.numChannels = len(channels)
# scanimage.SI4.scanZoomFactor = 5.9
if line.find('scanimage.SI4.scanZoomFactor') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
self.zoom = float(rhs)
foundZoom = True
#self.voxelx = magic_scan_image_scale / self.zoom
#self.voxely = magic_scan_image_scale / self.zoom
# scanimage.SI4.triggerClockTimeFirst = '18-05-2015 11:58:43.788'
if line.find('scanimage.SI4.triggerClockTimeFirst') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
rhs = rhs.replace("'","") # remove enclosing ' and '
if rhs.startswith(' '): # if date string starts with space, remove it
rhs = rhs[1:-1]
datetime = rhs.split(' ')
# 20170811, there is an extra f*****g space before datestr on the rhs
# convert mm/dd/yyyy to yyyymmdd
#print 'rhs:' + "'" + rhs + "'"
#print 'datetime:', datetime
datestr = bFixDate(datetime[0], logLevel)
self.dateStr = datestr
self.timeStr = datetime[1]
#
# ScanImage 3.x
#
# state.software.version = 3.8
if line.find('state.software.version') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
self.scanImageVersion = rhs
# state.acq.numberOfChannelsAcquire = 2
if line.find('state.acq.numberOfChannelsAcquire') != -1:
#print '\rDEBUG 12345'
bPrintLog(line, logLevel)
#print '\rDEBUG 12345'
rhs = line.split('=')[1]
self.numChannels = int(rhs)
# state.acq.zoomFactor = 2.5
if line.find('state.acq.zoomFactor') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
self.zoom = float(rhs)
foundZoom = True
# set (voxelx, voxely)
#self.voxelx = magic_scan_image_scale / self.zoom
#self.voxely = magic_scan_image_scale / self.zoom
# state.acq.msPerLine = 2.32
if line.find('state.acq.msPerLine') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
self.msPerLine = float(rhs)
# state.acq.pixelTime = 3.2e-06
if line.find('state.acq.pixelTime') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
self.dwellTime = float(rhs)
# state.motor.absXPosition = -9894.4
if line.find('state.motor.absXPosition') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
self.motorx = float(rhs)
# state.motor.absYPosition = -18423.4
if line.find('state.motor.absYPosition') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
self.motory = float(rhs)
# state.motor.absZPosition = -23615.04
if line.find('state.motor.absZPosition') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
self.motorz = float(rhs)
# state.acq.zStepSize = 2
if line.find('state.acq.zStepSize') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
self.voxelz = float(rhs)
# state.internal.triggerTimeString = '10/2/2014 12:29:22.796'
if line.find('state.internal.triggerTimeString') != -1:
bPrintLog(line, logLevel)
rhs = line.split('=')[1]
rhs = rhs.replace("'","")
if rhs.startswith(' '): # if date string starts with space, remove it
rhs = rhs[1:-1]
datetime = rhs.split(' ')
# 20170811, there is an extra f*****g space before datestr on the rhs
# convert mm/dd/yyyy to yyyymmdd
#print 'rhs:' + "'" + rhs + "'"
#print 'datetime:', datetime
self.dateStr = bFixDate(datetime[0], logLevel)
self.timeStr = bFixTime(datetime[1], logLevel)
# state.acq.acqDelay = 0.000122
# state.acq.bidirectionalScan = 0
# state.acq.fillFraction = 0.706206896551724
# state.acq.frameRate = 0.841864224137931
# huganir lab keeps this off, image pixel intensities are 2^11 * samplesperpixel (e.g. binFactor?)
# state.acq.binFactor = 16
# state.internal.averageSamples = 1
# the real image bit depth is usually inputBitDepth-1 (1 bit is not used?)
# state.acq.inputBitDepth = 12
if foundZoom:
self.voxelx = magic_scan_image_scale / self.zoom * (1024 / self.width)
self.voxely = magic_scan_image_scale / self.zoom * (1024 / self.height)
else:
bPrintLog('ERROR: Did not find zoom in SI header, voxel x/y will be wrong', logLevel)
def readZeissHeader(self, infoStr):
# This is incredibly difficult to get working as (date, time, voxels) are in different obscure places in lsm and czi
# Furthermore, just trying to read the raw ome xls is futile
#
# parsing ome xml as a string and searching it with regular expression(re) does not work
# it is beyond the scope of my work to figure this out
# the fact that it does not work and there is little documentaiton is a pretty big waste of time
#
# get and parse xml to find date/time
#fi = self.imp.getOriginalFileInfo(); # returns a FileInfo object
#omexml = fi.description #omexml is a string
#omexml = omexml.encode('utf-8')
#omexml = omexml.replaceAll("[^\\x20-\\x7e]", "") # see: https://stackoverflow.com/questions/2599919/java-parsing-xml-document-gives-content-not-allowed-in-prolog-error
# (1) try and search the ome xml like a string, this gives errors
#docsPattern = '<AcquisitionDate>.*</AcquisitionDate>'
#searchresult = re.search(docsPattern, omexml)
#print 'searchresult:', searchresult.group(0)
# 2) treat the ome xml like any other xml (because it's xml, right?)
# well this raises errors too
#omexml has <AcquisitionDate>2016-08-17T15:21:50</AcquisitionDate>
#import xml.etree.ElementTree
#e = xml.etree.ElementTree.fromstring(omexml).getroot() #print omexml
#for atype in e.findall('AcquisitionDate'):
# print 'AcquisitionDate:', atype #.get('foobar')
#
#
if self.islsm:
# lsm have date hidden in omeMeta.getImageAcquisitionDate(0)
# this is copied from code at: https://gist.github.com/ctrueden/6282856
reader = ImageReader()
omeMeta = MetadataTools.createOMEXMLMetadata() #omeMeta.getImageAcquisitionDate(0)
reader.setMetadataStore(omeMeta)
reader.setId(self.filepath)
#seriesCount = reader.getSeriesCount()
dateTimeStr = omeMeta.getImageAcquisitionDate(0) #2016-08-17T16:36:26
reader.close()
if dateTimeStr:
self.dateStr, self.timeStr = dateTimeStr.toString().split('T')
self.dateStr = bFixDate(self.dateStr)
self.timeStr = bFixTime(self.timeStr)
#bPrintLog('LSM date/time is: ' + self.dateStr + ' ' + self.timeStr, 3)
else:
bPrintLog('WARNING: did not get Zeiss date/time string')
# lsm have voxels in infoStr
for line in infoStr.split('\n'):
#print line
if line.find('VoxelSizeX') != -1:
self.voxelx = float(line.split('=')[1])
if line.find('VoxelSizeY') != -1:
self.voxely = float(line.split('=')[1])
if line.find('VoxelSizeZ') != -1:
self.voxelz = float(line.split('=')[1])
if line.find('SizeC') != -1:
self.numChannels = int(line.split('=')[1])
#if line.find('BitsPerPixel') and not line.startswith('Experiment') != -1: # 20170811, startswith is for czi
# self.bitsPerPixel = int(line.split('=')[1])
if line.find('RecordingZoomX#1') != -1:
self.zoom = int(line.split('=')[1])
if self.isczi:
# czi has date/time in infoStr (lsm does not)
for line in infoStr.split('\n'):
if line.find('CreationDate #1') != -1: # w.t.f. is #1 referring to?
lhs, rhs = line.split('=')
rhs = rhs.replace(' ', ' ')
if rhs.startswith(' '):
rhs = rhs[1:-1]
#print "lhs: '" + lhs + "'" + "rhs: '" + rhs + "'"
if rhs.find('T') != -1:
self.dateStr, self.timeStr = rhs.split('T')
else:
self.dateStr, self.timeStr = rhs.split(' ')
self.dateStr = bFixDate(self.dateStr)
self.timeStr = bFixTime(self.timeStr)
#bPrintLog('CZI date/time is: ' + self.dateStr + ' ' + self.timeStr, 3)
# .czi
# <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="0.20756645602494875" PhysicalSizeXUnit="µm" PhysicalSizeY="0.20756645602494875" PhysicalSizeYUnit="µm" PhysicalSizeZ="0.75" PhysicalSizeZUnit="µm" SignificantBits="8" SizeC="1" SizeT="1" SizeX="1024" SizeY="1024" SizeZ="50" Type="uint8">
# czi have voxel in calibration
self.voxelx = self.imp.getCalibration().pixelWidth;
self.voxely = self.imp.getCalibration().pixelHeight;
self.voxelz = self.imp.getCalibration().pixelDepth;
#bPrintLog('readZeissHeader() read czi scale as: ' + str(self.voxelx) + ' ' + str(self.voxely) + ' ' + str(self.voxelz), 3)
# CLEARING self.infoStr for CZI ... it was WAY to big to parse in Map Manager
self.infoStr = ''
def printParams(self, loglevel=3): # careful, thefunction print() is already taken?
bPrintLog('file:' + self.filepath, loglevel)
bPrintLog("date:'" + self.dateStr + "' time:'" + self.timeStr + "'", loglevel)
bPrintLog('channels:' + str(self.numChannels), loglevel)
bPrintLog('zoom:' + str(self.zoom), loglevel)
bPrintLog('pixels:' + str(self.width) + ',' + str(self.height)+ ',' + str(self.numSlices), loglevel)
bPrintLog('voxels:' + str(self.voxelx) + ',' + str(self.voxely)+ ',' + str(self.voxelz), loglevel)
def deinterleave(self):
if self.numChannels == 1:
bPrintLog('Warning: deinterleave() did not deinterleave with num channels 1', 0)
return -1
#IJ.run('Deinterleave', 'how=' + str(self.numChannels) +' keep') #makes ' #1' and ' #2', with ' #2' frontmost
cmdStr = 'how=' + str(self.numChannels) + ' keep'
IJ.run('Deinterleave', cmdStr) #makes ' #1' and ' #2', with ' #2' frontmost
for i in range(self.numChannels):
currenChannel = i + 1
currentWindowName = self.windowname + ' #' + str(currenChannel)
self.channelWindows.append(currentWindowName)
currentImp = WindowManager.getImage(currentWindowName)
if currentImp:
self.channelImp.append(currentImp)
else:
bPrintLog('ERROR: deinterleave() did not find window names:' + currentWindowName, 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 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 closeAll(self):
self.imp.close()
for imp in self.channelImp:
imp.close()
def runOneFile(fullFilePath):
global gNumChannels
global gAlignBatchVersion
if not os.path.isfile(fullFilePath):
bPrintLog(
'\nERROR: runOneFile() did not find file: ' + fullFilePath + '\n',
0)
return 0
bPrintLog(
time.strftime("%H:%M:%S") + ' starting runOneFile(): ' + fullFilePath,
1)
enclosingPath = os.path.dirname(fullFilePath)
head, tail = os.path.split(enclosingPath)
enclosingPath += '/'
#make output folders
destFolder = enclosingPath + tail + '_channels/'
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
destMaxFolder = destFolder + 'max/'
if not os.path.isdir(destMaxFolder):
os.makedirs(destMaxFolder)
if gDoAlign:
destAlignmentFolder = destFolder + 'alignment/'
if not os.path.isdir(destAlignmentFolder):
os.makedirs(destAlignmentFolder)
if gSave8bit:
eightBitFolder = destFolder + 'channels8/'
if not os.path.isdir(eightBitFolder):
os.makedirs(eightBitFolder)
eightBitMaxFolder = eightBitFolder + 'max/'
if not os.path.isdir(eightBitMaxFolder):
os.makedirs(eightBitMaxFolder)
# open image
imp = Opener().openImage(fullFilePath)
# get parameters of image
(width, height, nChannels, nSlices, nFrames) = imp.getDimensions()
bitDepth = imp.getBitDepth()
infoStr = imp.getProperty("Info") #get all .tif tags
if not infoStr:
infoStr = ''
infoStr += 'bAlignBatch_Version=' + str(gAlignBatchVersion) + '\n'
infoStr += 'bAlignBatch_Time=' + time.strftime(
"%Y%m%d") + '_' + time.strftime("%H%M%S") + '\n'
msgStr = 'w:' + str(width) + ' h:' + str(height) + ' slices:' + str(nSlices) \
+ ' channels:' + str(nChannels) + ' frames:' + str(nFrames) + ' bitDepth:' + str(bitDepth)
bPrintLog(msgStr, 1)
path, filename = os.path.split(fullFilePath)
shortName, fileExtension = os.path.splitext(filename)
#
# look for num channels in ScanImage infoStr
if gGetNumChanFromScanImage:
for line in infoStr.split('\n'):
#scanimage.SI4.channelsSave = [1;2]
scanimage4 = find(line, 'scanimage.SI4.channelsSave =') == 0
#state.acq.numberOfChannelsSave=2
scanimage3 = find(line, 'state.acq.numberOfChannelsSave=') == 0
if scanimage3:
#print 'line:', line
equalIdx = find(line, '=')
line2 = line[equalIdx + 1:]
if gGetNumChanFromScanImage:
gNumChannels = int(line2)
bPrintLog(
'over-riding gNumChannels with: ' + str(gNumChannels),
2)
if scanimage4:
#print ' we have a scanimage 4 file ... now i need to exptract the number of channel'
#print 'line:', line
equalIdx = find(line, '=')
line2 = line[equalIdx + 1:]
for delim in ';[]':
line2 = line2.replace(delim, ' ')
if gGetNumChanFromScanImage:
gNumChannels = len(line2.split())
bPrintLog(
'over-riding gNumChannels with: ' + str(gNumChannels),
2)
# show
imp.show()
# split channels if necc. and grab the original window names
if gNumChannels == 1:
origImpWinStr = imp.getTitle() #use this when only one channel
origImpWin = WindowManager.getWindow(
origImpWinStr) #returns java.awt.Window
if gNumChannels == 2:
winTitle = imp.getTitle()
bPrintLog('Deinterleaving 2 channels...', 1)
IJ.run('Deinterleave',
'how=2 keep') #makes ' #1' and ' #2', with ' #2' frontmost
origCh1WinStr = winTitle + ' #1'
origCh2WinStr = winTitle + ' #2'
origCh1Imp = WindowManager.getImage(origCh1WinStr)
origCh2Imp = WindowManager.getImage(origCh2WinStr)
origCh1File = destFolder + shortName + '_ch1.tif'
origCh2File = destFolder + shortName + '_ch2.tif'
# work on a copy, mostly for alignment with cropping
copy = Duplicator().run(imp)
#copy.copyAttributes(imp) #don't copy attributes, it copies the name (which we do not want)
copy.show()
#
# crop (on copy)
if gDoCrop:
bPrintLog('making cropping rectangle (left,top,width,height) ', 1)
bPrintLog(
str(gCropLeft) + ' ' + str(gCropTop) + ' ' + str(gCropWidth) +
' ' + str(gCropHeight), 2)
roi = Roi(gCropLeft, gCropTop, gCropWidth,
gCropHeight) #left,top,width,height
copy.setRoi(roi)
time.sleep(
0.5
) # otherwise, crop SOMETIMES failes. WHAT THE F**K FIJI DEVELOPERS, REALLY, WHAT THE F**K
#bPrintLog('cropping', 1)
IJ.run('Crop')
infoStr += 'bCropping=' + str(gCropLeft) + ',' + str(
gCropTop) + ',' + str(gCropWidth) + ',' + str(gCropHeight) + '\n'
#
# remove calibration ( on original)
if gRemoveCalibration:
cal = imp.getCalibration()
calCoeff = cal.getCoefficients()
if calCoeff:
msgStr = 'Calibration is y=a+bx' + ' a=' + str(
calCoeff[0]) + ' b=' + str(calCoeff[1])
bPrintLog(msgStr, 1)
#remove calibration
bPrintLog('\tRemoving Calibration', 2)
imp.setCalibration(None)
#without these, 8-bit conversion goes to all 0 !!! what the f**k !!!
#bPrintLog('calling imp.resetStack() and imp.resetDisplayRange()', 2)
imp.resetStack()
imp.resetDisplayRange()
#get and print out min/max
origMin = StackStatistics(imp).min
origMax = StackStatistics(imp).max
msgStr = '\torig min=' + str(origMin) + ' max=' + str(origMax)
bPrintLog(msgStr, 2)
# 20150723, 'shift everybody over by linear calibration intercept calCoeff[0] - (magic number)
if 1:
# [1] was this
#msgStr = 'Subtracting original min '+str(origMin) + ' from stack.'
#bPrintLog(msgStr, 2)
#subArgVal = 'value=%s stack' % (origMin,)
#IJ.run('Subtract...', subArgVal)
# [2] now this
#msgStr = 'Adding calCoeff[0] '+str(calCoeff[0]) + ' from stack.'
#bPrintLog(msgStr, 2)
#addArgVal = 'value=%s stack' % (int(calCoeff[0]),)
#IJ.run('Add...', addArgVal)
# [3] subtract a magic number 2^15-2^7 = 32768 - 128
magicNumber = gLinearShift #2^15 - 128
msgStr = 'Subtracting a magic number (linear shift) ' + str(
magicNumber) + ' from stack.'
bPrintLog(msgStr, 2)
infoStr += 'bLinearShift=' + str(gLinearShift) + '\n'
subArgVal = 'value=%s stack' % (gLinearShift, )
IJ.run(imp, 'Subtract...', subArgVal)
# 20150701, set any pixel <0 to 0
if 0:
ip = imp.getProcessor() # returns a reference
pixels = ip.getPixels() # returns a reference
msgStr = '\tSet all pixels <0 to 0. This was added 20150701 ...'
bPrintLog(msgStr, 2)
pixels = map(lambda x: 0 if x < 0 else x, pixels)
bPrintLog('\t\t... done', 2)
#get and print out min/max
newMin = StackStatistics(imp).min
newMax = StackStatistics(imp).max
msgStr = '\tnew min=' + str(newMin) + ' max=' + str(newMax)
bPrintLog(msgStr, 2)
#append calibration to info string
infoStr += 'bCalibCoeff_a = ' + str(calCoeff[0]) + '\n'
infoStr += 'bCalibCoeff_b = ' + str(calCoeff[1]) + '\n'
infoStr += 'bNewMin = ' + str(newMin) + '\n'
infoStr += 'bNewMax = ' + str(newMax) + '\n'
#
# set up
if gNumChannels == 1:
impWinStr = copy.getTitle() #use this when only one channel
impWin = WindowManager.getWindow(impWinStr) #returns java.awt.Window
if gNumChannels == 2:
winTitle = copy.getTitle()
bPrintLog('Deinterleaving 2 channels...', 1)
IJ.run('Deinterleave',
'how=2 keep') #makes ' #1' and ' #2', with ' #2' frontmost
ch1WinStr = winTitle + ' #1'
ch2WinStr = winTitle + ' #2'
ch1Imp = WindowManager.getImage(ch1WinStr)
ch2Imp = WindowManager.getImage(ch2WinStr)
ch1File = destFolder + shortName + '_ch1.tif'
ch2File = destFolder + shortName + '_ch2.tif'
#
# alignment
if gDoAlign and gNumChannels == 1 and copy.getNSlices() > 1:
infoStr += 'AlignOnChannel=1' + '\n'
#snap to middle slice
if gAlignOnMiddleSlice:
middleSlice = int(
math.floor(copy.getNSlices() /
2)) #int() is necc., python is f*****g picky
else:
middleSlice = gAlignOnThisSlice
copy.setSlice(middleSlice)
transformationFile = destAlignmentFolder + shortName + '.txt'
bPrintLog('MultiStackReg aligning:' + impWinStr, 1)
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)
infoStr += 'AlignOnSlice=' + str(middleSlice) + '\n'
#20150723, we just aligned on a cropped copy, apply alignment to original imp
origImpTitle = imp.getTitle()
stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' % (
origImpTitle, transformationFile)
IJ.run('MultiStackReg', stackRegParams)
if gDoAlign and gNumChannels == 2 and ch1Imp.getNSlices(
) > 1 and ch2Imp.getNSlices() > 1:
#apply to gAlignThisChannel
alignThisWindow = ''
applyAlignmentToThisWindow = ''
if gAlignThisChannel == 1:
infoStr += 'AlignOnChannel=1' + '\n'
transformationFile = destAlignmentFolder + shortName + '_ch1.txt'
alignThisWindow = ch1WinStr
applyAlignmentToThisWindow = ch2WinStr
else:
infoStr += 'AlignOnChannel=2' + '\n'
transformationFile = destAlignmentFolder + shortName + '_ch2.txt'
alignThisWindow = ch2WinStr
applyAlignmentToThisWindow = ch1WinStr
alignThisImp = WindowManager.getImage(alignThisWindow)
#snap to middle slice
if gAlignOnMiddleSlice:
middleSlice = int(
math.floor(alignThisImp.getNSlices() /
2)) #int() is necc., python is f*****g picky
else:
middleSlice = gAlignOnThisSlice
alignThisImp.setSlice(middleSlice)
infoStr += 'bAlignOnSlice=' + str(middleSlice) + '\n'
bPrintLog('MultiStackReg aligning:' + alignThisWindow, 1)
stackRegParams = 'stack_1=[%s] action_1=Align file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body] save' % (
alignThisWindow, transformationFile)
IJ.run('MultiStackReg', stackRegParams)
# 20150723, we just aligned on a copy, apply alignment to both channels of original
# ch1
bPrintLog('MultiStackReg applying alignment to:' + origCh1WinStr, 1)
stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' % (
origCh1WinStr, transformationFile)
IJ.run('MultiStackReg', stackRegParams)
# ch2
bPrintLog('MultiStackReg applying alignment to:' + origCh2WinStr, 1)
stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' % (
origCh2WinStr, transformationFile)
IJ.run('MultiStackReg', stackRegParams)
#apply alignment to other window
#bPrintLog('MultiStackReg applying alignment to:' + applyAlignmentToThisWindow, 1)
#applyAlignThisImp = WindowManager.getImage(applyAlignmentToThisWindow)
#stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' %(applyAlignmentToThisWindow,transformationFile)
#IJ.run('MultiStackReg', stackRegParams)
elif gDoAlign:
bPrintLog('Skipping alignment, there may be only one slice?', 3)
#
# save
if gNumChannels == 1:
imp.setProperty("Info", infoStr)
impFile = destFolder + shortName + '.tif'
#bPrintLog('Saving:' + impFile, 1)
bSaveStack(imp, impFile)
#max project
bSaveZProject(imp, destMaxFolder, shortName)
if gNumChannels == 2:
#ch1
origCh1Imp.setProperty("Info", infoStr)
#bPrintLog('Saving:' + ch1File, 1)
bSaveStack(origCh1Imp, ch1File)
#max project
bSaveZProject(origCh1Imp, destMaxFolder, shortName + '_ch1')
#ch2
origCh2Imp.setProperty("Info", infoStr)
#bPrintLog('Saving:' + ch2File, 1)
bSaveStack(origCh2Imp, ch2File)
#max project
bSaveZProject(origCh2Imp, destMaxFolder, shortName + '_ch2')
#
# post convert to 8-bit and save
if gSave8bit:
if bitDepth == 16:
if gNumChannels == 1:
bPrintLog('Converting to 8-bit:' + impWinStr, 1)
IJ.selectWindow(impWinStr)
#IJ.run('resetMinAndMax()')
IJ.run("8-bit")
impFile = eightBitFolder + shortName + '.tif'
bPrintLog('Saving 8-bit:' + impFile, 2)
bSaveStack(imp, impFile)
#max project
bSaveZProject(imp, eightBitMaxFolder, shortName)
if gNumChannels == 2:
#
bPrintLog('Converting to 8-bit:' + origCh1WinStr, 1)
IJ.selectWindow(origCh1WinStr)
IJ.run("8-bit")
impFile = eightBitFolder + shortName + '_ch1.tif'
bPrintLog('Saving 8-bit:' + impFile, 2)
bSaveStack(origCh1Imp, impFile)
#max project
bSaveZProject(origCh1Imp, eightBitMaxFolder,
shortName + '_ch1')
#
bPrintLog('Converting to 8-bit:' + origCh2WinStr, 1)
IJ.selectWindow(origCh2WinStr)
#IJ.run('resetMinAndMax()')
IJ.run("8-bit")
impFile = eightBitFolder + shortName + '_ch2.tif'
bPrintLog('Saving 8-bit:' + impFile, 2)
bSaveStack(origCh2Imp, impFile)
#max project
bSaveZProject(origCh2Imp, eightBitMaxFolder,
shortName + '_ch2')
#
# close original window
imp.changes = 0
imp.close()
#copy
copy.changes = 0
copy.close()
#
# close ch1/ch2
if gNumChannels == 2:
#original
origCh1Imp.changes = 0
origCh1Imp.close()
origCh2Imp.changes = 0
origCh2Imp.close()
#copy
ch1Imp.changes = 0
ch1Imp.close()
ch2Imp.changes = 0
ch2Imp.close()
bPrintLog(
time.strftime("%H:%M:%S") + ' finished runOneFile(): ' + fullFilePath,
1)
def runOneFile(fullFilePath):
global gFileType
global gNumChannels
global gAlignBatchVersion
if not os.path.isfile(fullFilePath):
bPrintLog('\nERROR: runOneFile() did not find file: ' + fullFilePath + '\n',0)
return 0
bPrintLog(time.strftime("%H:%M:%S") + ' starting runOneFile(): ' + fullFilePath, 1)
enclosingPath = os.path.dirname(fullFilePath)
head, tail = os.path.split(enclosingPath)
enclosingPath += '/'
#make output folders
destFolder = enclosingPath + tail + '_channels/'
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
destMaxFolder = destFolder + 'max/'
if not os.path.isdir(destMaxFolder):
os.makedirs(destMaxFolder)
if gDoAlign:
destAlignmentFolder = destFolder + 'alignment/'
if not os.path.isdir(destAlignmentFolder):
os.makedirs(destAlignmentFolder)
if gSave8bit:
eightBitFolder = destFolder + 'channels8/'
if not os.path.isdir(eightBitFolder):
os.makedirs(eightBitFolder)
eightBitMaxFolder = eightBitFolder + 'max/'
if not os.path.isdir(eightBitMaxFolder):
os.makedirs(eightBitMaxFolder)
if gFileType=='tif':
# open .tif image
imp = Opener().openImage(fullFilePath)
else:
# open .lsm
cmdStr = 'open=%s autoscale color_mode=Default view=Hyperstack stack_order=XYCZT' % (fullFilePath,)
IJ.run('Bio-Formats Importer', cmdStr)
lsmpath, lsmfilename = os.path.split(fullFilePath)
lsWindow = lsmfilename
imp = WindowManager.getImage(lsWindow)
# get parameters of image
(width, height, nChannels, nSlices, nFrames) = imp.getDimensions()
bitDepth = imp.getBitDepth()
infoStr = imp.getProperty("Info") #get all .tif tags
if not infoStr:
infoStr = ''
infoStr += 'bAlignBatch_Version=' + str(gAlignBatchVersion) + '\n'
infoStr += 'bAlignBatch_Time=' + time.strftime("%Y%m%d") + '_' + time.strftime("%H%M%S") + '\n'
msgStr = 'w:' + str(width) + ' h:' + str(height) + ' slices:' + str(nSlices) \
+ ' channels:' + str(nChannels) + ' frames:' + str(nFrames) + ' bitDepth:' + str(bitDepth)
bPrintLog(msgStr, 1)
path, filename = os.path.split(fullFilePath)
shortName, fileExtension = os.path.splitext(filename)
#
# look for num channels in ScanImage infoStr
if gGetNumChanFromScanImage:
for line in infoStr.split('\n'):
#scanimage.SI4.channelsSave = [1;2]
scanimage4 = find(line, 'scanimage.SI4.channelsSave =') == 0
#state.acq.numberOfChannelsSave=2
scanimage3 = find(line, 'state.acq.numberOfChannelsSave=') == 0
if scanimage3:
#print 'line:', line
equalIdx = find(line, '=')
line2 = line[equalIdx+1:]
if gGetNumChanFromScanImage:
gNumChannels = int(line2)
bPrintLog('over-riding gNumChannels with: ' + str(gNumChannels), 2)
if scanimage4:
#print ' we have a scanimage 4 file ... now i need to exptract the number of channel'
#print 'line:', line
equalIdx = find(line, '=')
line2 = line[equalIdx+1:]
for delim in ';[]':
line2 = line2.replace(delim, ' ')
if gGetNumChanFromScanImage:
gNumChannels = len(line2.split())
bPrintLog('over-riding gNumChannels with: ' + str(gNumChannels), 2)
# show
imp.show()
# split channels if necc. and grab the original window names
if gNumChannels == 1:
origImpWinStr = imp.getTitle() #use this when only one channel
origImpWin = WindowManager.getWindow(origImpWinStr) #returns java.awt.Window
if gNumChannels == 2:
winTitle = imp.getTitle()
bPrintLog('Deinterleaving 2 channels...', 1)
IJ.run('Deinterleave', 'how=2 keep') #makes ' #1' and ' #2', with ' #2' frontmost
origCh1WinStr = winTitle + ' #1'
origCh2WinStr = winTitle + ' #2'
origCh1Imp = WindowManager.getImage(origCh1WinStr)
origCh2Imp = WindowManager.getImage(origCh2WinStr)
origCh1File = destFolder + shortName + '_ch1.tif'
origCh2File = destFolder + shortName + '_ch2.tif'
# work on a copy, mostly for alignment with cropping
copy = Duplicator().run(imp)
#copy.copyAttributes(imp) #don't copy attributes, it copies the name (which we do not want)
copy.show()
#
# crop (on copy)
if gDoCrop:
bPrintLog('making cropping rectangle (left,top,width,height) ',1)
bPrintLog(str(gCropLeft) + ' ' + str(gCropTop) + ' ' +str(gCropWidth) + ' ' +str(gCropHeight), 2)
roi = Roi(gCropLeft, gCropTop, gCropWidth, gCropHeight) #left,top,width,height
copy.setRoi(roi)
time.sleep(0.5) # otherwise, crop SOMETIMES failes. WHAT THE F**K FIJI DEVELOPERS, REALLY, WHAT THE F**K
#bPrintLog('cropping', 1)
IJ.run('Crop')
infoStr += 'bCropping=' + str(gCropLeft) + ',' + str(gCropTop) + ',' + str(gCropWidth) + ',' + str(gCropHeight) + '\n'
#
# remove calibration ( on original)
if gRemoveCalibration:
cal = imp.getCalibration()
calCoeff = cal.getCoefficients()
if calCoeff:
msgStr = 'Calibration is y=a+bx' + ' a=' + str(calCoeff[0]) + ' b=' + str(calCoeff[1])
bPrintLog(msgStr, 1)
#remove calibration
bPrintLog('\tRemoving Calibration', 2)
imp.setCalibration(None)
#without these, 8-bit conversion goes to all 0 !!! what the f**k !!!
#bPrintLog('calling imp.resetStack() and imp.resetDisplayRange()', 2)
imp.resetStack()
imp.resetDisplayRange()
#get and print out min/max
origMin = StackStatistics(imp).min
origMax = StackStatistics(imp).max
msgStr = '\torig min=' + str(origMin) + ' max=' + str(origMax)
bPrintLog(msgStr, 2)
# 20150723, 'shift everybody over by linear calibration intercept calCoeff[0] - (magic number)
if 1:
# [1] was this
#msgStr = 'Subtracting original min '+str(origMin) + ' from stack.'
#bPrintLog(msgStr, 2)
#subArgVal = 'value=%s stack' % (origMin,)
#IJ.run('Subtract...', subArgVal)
# [2] now this
#msgStr = 'Adding calCoeff[0] '+str(calCoeff[0]) + ' from stack.'
#bPrintLog(msgStr, 2)
#addArgVal = 'value=%s stack' % (int(calCoeff[0]),)
#IJ.run('Add...', addArgVal)
# [3] subtract a magic number 2^15-2^7 = 32768 - 128
magicNumber = gLinearShift #2^15 - 128
msgStr = 'Subtracting a magic number (linear shift) '+str(magicNumber) + ' from stack.'
bPrintLog(msgStr, 2)
infoStr += 'bLinearShift=' + str(gLinearShift) + '\n'
subArgVal = 'value=%s stack' % (gLinearShift,)
IJ.run(imp, 'Subtract...', subArgVal)
# 20150701, set any pixel <0 to 0
if 0:
ip = imp.getProcessor() # returns a reference
pixels = ip.getPixels() # returns a reference
msgStr = '\tSet all pixels <0 to 0. This was added 20150701 ...'
bPrintLog(msgStr, 2)
pixels = map(lambda x: 0 if x<0 else x, pixels)
bPrintLog('\t\t... done', 2)
#get and print out min/max
newMin = StackStatistics(imp).min
newMax = StackStatistics(imp).max
msgStr = '\tnew min=' + str(newMin) + ' max=' + str(newMax)
bPrintLog(msgStr, 2)
#append calibration to info string
infoStr += 'bCalibCoeff_a = ' + str(calCoeff[0]) + '\n'
infoStr += 'bCalibCoeff_b = ' + str(calCoeff[1]) + '\n'
infoStr += 'bNewMin = ' + str(newMin) + '\n'
infoStr += 'bNewMax = ' + str(newMax) + '\n'
#
# set up
if gNumChannels == 1:
impWinStr = copy.getTitle() #use this when only one channel
impWin = WindowManager.getWindow(impWinStr) #returns java.awt.Window
if gNumChannels == 2:
winTitle = copy.getTitle()
bPrintLog('Deinterleaving 2 channels...', 1)
IJ.run('Deinterleave', 'how=2 keep') #makes ' #1' and ' #2', with ' #2' frontmost
ch1WinStr = winTitle + ' #1'
ch2WinStr = winTitle + ' #2'
ch1Imp = WindowManager.getImage(ch1WinStr)
ch2Imp = WindowManager.getImage(ch2WinStr)
ch1File = destFolder + shortName + '_ch1.tif'
ch2File = destFolder + shortName + '_ch2.tif'
#
# alignment
if gDoAlign and gNumChannels == 1 and copy.getNSlices()>1:
infoStr += 'AlignOnChannel=1' + '\n'
#snap to middle slice
if gAlignOnMiddleSlice:
middleSlice = int(math.floor(copy.getNSlices() / 2)) #int() is necc., python is f*****g picky
else:
middleSlice = gAlignOnThisSlice
copy.setSlice(middleSlice)
transformationFile = destAlignmentFolder + shortName + '.txt'
bPrintLog('MultiStackReg aligning:' + impWinStr, 1)
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)
infoStr += 'AlignOnSlice=' + str(middleSlice) + '\n'
#20150723, we just aligned on a cropped copy, apply alignment to original imp
origImpTitle = imp.getTitle()
stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' %(origImpTitle,transformationFile)
IJ.run('MultiStackReg', stackRegParams)
if gDoAlign and gNumChannels == 2 and ch1Imp.getNSlices()>1 and ch2Imp.getNSlices()>1:
#apply to gAlignThisChannel
alignThisWindow = ''
applyAlignmentToThisWindow = ''
if gAlignThisChannel == 1:
infoStr += 'AlignOnChannel=1' + '\n'
transformationFile = destAlignmentFolder + shortName + '_ch1.txt'
alignThisWindow = ch1WinStr
applyAlignmentToThisWindow = ch2WinStr
else:
infoStr += 'AlignOnChannel=2' + '\n'
transformationFile = destAlignmentFolder + shortName + '_ch2.txt'
alignThisWindow = ch2WinStr
applyAlignmentToThisWindow = ch1WinStr
alignThisImp = WindowManager.getImage(alignThisWindow)
#snap to middle slice
if gAlignOnMiddleSlice:
middleSlice = int(math.floor(alignThisImp.getNSlices() / 2)) #int() is necc., python is f*****g picky
else:
middleSlice = gAlignOnThisSlice
alignThisImp.setSlice(middleSlice)
infoStr += 'bAlignOnSlice=' + str(middleSlice) + '\n'
bPrintLog('MultiStackReg aligning:' + alignThisWindow, 1)
stackRegParams = 'stack_1=[%s] action_1=Align file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body] save' %(alignThisWindow,transformationFile)
IJ.run('MultiStackReg', stackRegParams)
# 20150723, we just aligned on a copy, apply alignment to both channels of original
# ch1
bPrintLog('MultiStackReg applying alignment to:' + origCh1WinStr, 1)
stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' %(origCh1WinStr,transformationFile)
IJ.run('MultiStackReg', stackRegParams)
# ch2
bPrintLog('MultiStackReg applying alignment to:' + origCh2WinStr, 1)
stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' %(origCh2WinStr,transformationFile)
IJ.run('MultiStackReg', stackRegParams)
#apply alignment to other window
#bPrintLog('MultiStackReg applying alignment to:' + applyAlignmentToThisWindow, 1)
#applyAlignThisImp = WindowManager.getImage(applyAlignmentToThisWindow)
#stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' %(applyAlignmentToThisWindow,transformationFile)
#IJ.run('MultiStackReg', stackRegParams)
elif gDoAlign:
bPrintLog('Skipping alignment, there may be only one slice?',3)
#
# save
if gNumChannels == 1:
imp.setProperty("Info", infoStr);
impFile = destFolder + shortName + '.tif'
#bPrintLog('Saving:' + impFile, 1)
bSaveStack(imp, impFile)
#max project
bSaveZProject(imp, destMaxFolder, shortName)
if gNumChannels == 2:
#ch1
origCh1Imp.setProperty("Info", infoStr);
#bPrintLog('Saving:' + ch1File, 1)
bSaveStack(origCh1Imp, ch1File)
#max project
bSaveZProject(origCh1Imp, destMaxFolder, shortName+'_ch1')
#ch2
origCh2Imp.setProperty("Info", infoStr);
#bPrintLog('Saving:' + ch2File, 1)
bSaveStack(origCh2Imp, ch2File)
#max project
bSaveZProject(origCh2Imp, destMaxFolder, shortName+'_ch2')
#
# post convert to 8-bit and save
if gSave8bit:
if bitDepth == 16:
if gNumChannels == 1:
bPrintLog('Converting to 8-bit:' + impWinStr, 1)
IJ.selectWindow(impWinStr)
#IJ.run('resetMinAndMax()')
IJ.run("8-bit")
impFile = eightBitFolder + shortName + '.tif'
bPrintLog('Saving 8-bit:' + impFile, 2)
bSaveStack(imp, impFile)
#max project
bSaveZProject(imp, eightBitMaxFolder, shortName)
if gNumChannels == 2:
#
bPrintLog('Converting to 8-bit:' + origCh1WinStr, 1)
IJ.selectWindow(origCh1WinStr)
IJ.run("8-bit")
impFile = eightBitFolder + shortName + '_ch1.tif'
bPrintLog('Saving 8-bit:' + impFile, 2)
bSaveStack(origCh1Imp, impFile)
#max project
bSaveZProject(origCh1Imp, eightBitMaxFolder, shortName+'_ch1')
#
bPrintLog('Converting to 8-bit:' + origCh2WinStr, 1)
IJ.selectWindow(origCh2WinStr)
#IJ.run('resetMinAndMax()')
IJ.run("8-bit")
impFile = eightBitFolder + shortName + '_ch2.tif'
bPrintLog('Saving 8-bit:' + impFile, 2)
bSaveStack(origCh2Imp, impFile)
#max project
bSaveZProject(origCh2Imp, eightBitMaxFolder, shortName+'_ch2')
#
# close original window
imp.changes = 0
imp.close()
#copy
copy.changes = 0
copy.close()
#
# close ch1/ch2
if gNumChannels == 2:
#original
origCh1Imp.changes = 0
origCh1Imp.close()
origCh2Imp.changes = 0
origCh2Imp.close()
#copy
ch1Imp.changes = 0
ch1Imp.close()
ch2Imp.changes = 0
ch2Imp.close()
bPrintLog(time.strftime("%H:%M:%S") + ' finished runOneFile(): ' + fullFilePath, 1)
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
import os
from java.io import File
from ij import ImageJ, ImagePlus
from ij.io import Opener
from net.imglib2.img import Img, ImgFactory
from net.imglib2.img.cell import CellImgFactory
from net.imglib2.img.display.imagej import ImageJFunctions
from net.imglib2.type.numeric.real import FloatType
gitDir = os.environ['GIT_HOME']
relImg = "/OSImageAnalysis/images"
# strImg = gitDir + relImg + "/bridge.gif"
strImg = gitDir + relImg + "/latex.tif"
fi = File(strImg)
imp = Opener().openImage( fi.getAbsolutePath() )
imp.show()
imgFactory = CellImgFactory(5 )
img1 = imgFactory.create( (20, 30, 40), FloatType() )
ImageJFunctions.show( img1 )
img2 = imgFactory.create( img1, img1.firstElement() )
ImageJFunctions.show( img2 )
def runOneFile(fullFilePath):
global gNumChannels
if not os.path.isfile(fullFilePath):
bPrintLog('\nERROR: runOneFile() did not find file: ' + fullFilePath + '\n',0)
return 0
bPrintLog(time.strftime("%H:%M:%S") + ' starting runOneFile(): ' + fullFilePath, 1)
enclosingPath = os.path.dirname(fullFilePath)
head, tail = os.path.split(enclosingPath)
enclosingPath += '/'
#make output folders
destFolder = enclosingPath + tail + '_channels/'
if not os.path.isdir(destFolder):
os.makedirs(destFolder)
destMaxFolder = destFolder + 'max/'
if not os.path.isdir(destMaxFolder):
os.makedirs(destMaxFolder)
if gDoAlign:
destAlignmentFolder = destFolder + 'alignment/'
if not os.path.isdir(destAlignmentFolder):
os.makedirs(destAlignmentFolder)
if gSave8bit:
eightBitFolder = destFolder + 'channels8/'
if not os.path.isdir(eightBitFolder):
os.makedirs(eightBitFolder)
eightBitMaxFolder = eightBitFolder + 'max/'
if not os.path.isdir(eightBitMaxFolder):
os.makedirs(eightBitMaxFolder)
# open image
imp = Opener().openImage(fullFilePath)
# get parameters of image
(width, height, nChannels, nSlices, nFrames) = imp.getDimensions()
bitDepth = imp.getBitDepth()
infoStr = imp.getProperty("Info") #get all .tif tags
if not infoStr:
infoStr = ''
msgStr = 'w:' + str(width) + ' h:' + str(height) + ' slices:' + str(nSlices) \
+ ' channels:' + str(nChannels) + ' frames:' + str(nFrames) + ' bitDepth:' + str(bitDepth)
bPrintLog(msgStr, 1)
path, filename = os.path.split(fullFilePath)
shortName, fileExtension = os.path.splitext(filename)
#this is too much work for ScanImage4
#try and guess channels if it is a scanimage file
#scanImage3 = string.find(infoStr, 'scanimage') != -1
#scanimage4 = find(infoStr, 'scanimage.SI4.channelSave = ')
#print 'scanimage4:', scanimage4
#
# look for num channels in ScanImage infoStr
if gGetNumChanFromScanImage:
for line in infoStr.split('\n'):
#scanimage.SI4.channelsSave = [1;2]
scanimage4 = find(line, 'scanimage.SI4.channelsSave =') == 0
#state.acq.numberOfChannelsSave=2
scanimage3 = find(line, 'state.acq.numberOfChannelsSave=') == 0
if scanimage3:
#print 'line:', line
equalIdx = find(line, '=')
line2 = line[equalIdx+1:]
if gGetNumChanFromScanImage:
gNumChannels = int(line2)
bPrintLog('over-riding gNumChannels with: ' + str(gNumChannels), 2)
if scanimage4:
#print ' we have a scanimage 4 file ... now i need to exptract the number of channel'
#print 'line:', line
equalIdx = find(line, '=')
line2 = line[equalIdx+1:]
for delim in ';[]':
line2 = line2.replace(delim, ' ')
if gGetNumChanFromScanImage:
gNumChannels = len(line2.split())
bPrintLog('over-riding gNumChannels with: ' + str(gNumChannels), 2)
# show
imp.show()
infoStr += 'bAlignBatch6=' + time.strftime("%Y%m%d") + '\n'
#
# crop
if gDoCrop:
bPrintLog('making cropping rectangle (left,top,width,height) ',1)
bPrintLog(str(gCropLeft) + ' ' + str(gCropTop) + ' ' +str(gCropWidth) + ' ' +str(gCropHeight), 2)
roi = Roi(gCropLeft, gCropTop, gCropWidth, gCropHeight) #left,top,width,height
imp.setRoi(roi)
#time.sleep(1)
#bPrintLog('cropping', 1)
IJ.run('Crop')
infoStr += 'cropping=' + str(gCropLeft) + ',' + str(gCropTop) + ',' + str(gCropWidth) + ',' + str(gCropHeight) + '\n'
#
# remove negative (<0) pixel values
#ip = imp.getProcessor()
#pixels = ip.getPixels() # this returns a reference (not a copy)
#for i in xrange(len(pixels)):
# if pixels[i] < 0:
# pixels[i] = 0
# or this, for each pixel 'x', if x<0 then 0 else x
#pixels = map(lambda x: 0 if x<0 else x, pixels)
#set our new values (without pixels <0) back into original (I hope this handles stacks and channels???)
#ip.setPixels(pixels)
#
# remove calibration
if gRemoveCalibration:
cal = imp.getCalibration()
calCoeff = cal.getCoefficients()
if calCoeff:
msgStr = 'Calibration is y=a+bx' + ' a=' + str(calCoeff[0]) + ' b=' + str(calCoeff[1])
bPrintLog(msgStr, 1)
#remove calibration
bPrintLog('\tRemoving Calibration', 2)
imp.setCalibration(None)
#get and print out min/max
origMin = StackStatistics(imp).min
origMax = StackStatistics(imp).max
msgStr = '\torig min=' + str(origMin) + ' max=' + str(origMax)
bPrintLog(msgStr, 2)
#msgStr = 'adding calCoeff[0]='+str(calCoeff[0]) + ' to stack.'
#bPrintLog(msgStr, 2)
#subArgVal = 'value=%s stack' % (calCoeff[0],)
#IJ.run('Add...', subArgVal)
# 20150701, 'shift everybody over by linear calibration intercept calCoeff[0]'
if 1:
# [1] was this
#msgStr = 'Subtracting original min '+str(origMin) + ' from stack.'
#bPrintLog(msgStr, 2)
#subArgVal = 'value=%s stack' % (origMin,)
#IJ.run('Subtract...', subArgVal)
# [2] now this
#msgStr = 'Adding calCoeff[0] '+str(calCoeff[0]) + ' from stack.'
#bPrintLog(msgStr, 2)
#addArgVal = 'value=%s stack' % (int(calCoeff[0]),)
#IJ.run('Add...', addArgVal)
# [3] subtract a magic number 2^15-2^7 = 32768 - 128
magicNumber = 32768 - 128
msgStr = 'Subtracting a magic number '+str(magicNumber) + ' from stack.'
bPrintLog(msgStr, 2)
subArgVal = 'value=%s stack' % (origMin,)
IJ.run('Subtract...', subArgVal)
# 20150701, set any pixel <0 to 0
if 0:
ip = imp.getProcessor() # returns a reference
pixels = ip.getPixels() # returns a reference
msgStr = '\tSet all pixels <0 to 0. This was added 20150701 ...'
bPrintLog(msgStr, 2)
pixels = map(lambda x: 0 if x<0 else x, pixels)
bPrintLog('\t\t... done', 2)
#get and print out min/max
newMin = StackStatistics(imp).min
newMax = StackStatistics(imp).max
msgStr = '\tnew min=' + str(newMin) + ' max=' + str(newMax)
bPrintLog(msgStr, 2)
#without these, 8-bit conversion goes to all 0 !!! what the f**k !!!
#bPrintLog('calling imp.resetStack() and imp.resetDisplayRange()', 2)
imp.resetStack()
imp.resetDisplayRange()
#append calibration to info string
infoStr += 'calibCoeff_a = ' + str(calCoeff[0]) + '\n'
infoStr += 'calibCoeff_b = ' + str(calCoeff[1]) + '\n'
infoStr += 'origMin = ' + str(origMin) + '\n'
infoStr += 'origMax = ' + str(origMax) + '\n'
#
# set up
if gNumChannels == 1:
impWinStr = imp.getTitle() #use this when only one channel
impWin = WindowManager.getWindow(impWinStr) #returns java.awt.Window
if gNumChannels == 2:
winTitle = imp.getTitle()
bPrintLog('Deinterleaving 2 channels...', 1)
IJ.run('Deinterleave', 'how=2 keep') #makes ' #1' and ' #2', with ' #2' frontmost
ch1WinStr = winTitle + ' #1'
ch2WinStr = winTitle + ' #2'
ch1Imp = WindowManager.getImage(ch1WinStr)
ch2Imp = WindowManager.getImage(ch2WinStr)
ch1File = destFolder + shortName + '_ch1.tif'
ch2File = destFolder + shortName + '_ch2.tif'
#
# alignment
if gDoAlign and gNumChannels == 1 and imp.getNSlices()>1:
infoStr += 'AlignOnChannel=1' + '\n'
#snap to middle slice
if gAlignOnMiddleSlice:
middleSlice = int(math.floor(imp.getNSlices() / 2)) #int() is necc., python is f*****g picky
else:
middleSlice = gAlignOnThisSlice
imp.setSlice(middleSlice)
transformationFile = destAlignmentFolder + shortName + '.txt'
bPrintLog('MultiStackReg aligning:' + impWinStr, 1)
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)
infoStr += 'AlignOnSlice=' + str(middleSlice) + '\n'
if gDoAlign and gNumChannels == 2 and ch1Imp.getNSlices()>1 and ch2Imp.getNSlices()>1:
#apply to gAlignThisChannel
alignThisWindow = ''
applyAlignmentToThisWindow = ''
if gAlignThisChannel == 1:
infoStr += 'AlignOnChannel=1' + '\n'
transformationFile = destAlignmentFolder + shortName + '_ch1.txt'
alignThisWindow = ch1WinStr
applyAlignmentToThisWindow = ch2WinStr
else:
infoStr += 'AlignOnChannel=2' + '\n'
transformationFile = destAlignmentFolder + shortName + '_ch2.txt'
alignThisWindow = ch2WinStr
applyAlignmentToThisWindow = ch1WinStr
alignThisImp = WindowManager.getImage(alignThisWindow)
#snap to middle slice
if gAlignOnMiddleSlice:
middleSlice = int(math.floor(alignThisImp.getNSlices() / 2)) #int() is necc., python is f*****g picky
else:
middleSlice = gAlignOnThisSlice
alignThisImp.setSlice(middleSlice)
infoStr += 'AlignOnSlice=' + str(middleSlice) + '\n'
bPrintLog('MultiStackReg aligning:' + alignThisWindow, 1)
stackRegParams = 'stack_1=[%s] action_1=Align file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body] save' %(alignThisWindow,transformationFile)
IJ.run('MultiStackReg', stackRegParams)
#apply alignment to other window
bPrintLog('MultiStackReg applying alignment to:' + applyAlignmentToThisWindow, 1)
applyAlignThisImp = WindowManager.getImage(applyAlignmentToThisWindow)
stackRegParams = 'stack_1=[%s] action_1=[Load Transformation File] file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Rigid Body]' %(applyAlignmentToThisWindow,transformationFile)
IJ.run('MultiStackReg', stackRegParams)
elif gDoAlign:
bPrintLog('Skipping alignment, there may be only one slice?',3)
#
# save
if gNumChannels == 1:
imp.setProperty("Info", infoStr);
impFile = destFolder + shortName + '.tif'
#bPrintLog('Saving:' + impFile, 1)
bSaveStack(imp, impFile)
#max project
bSaveZProject(imp, destMaxFolder, shortName)
if gNumChannels == 2:
#ch1
ch1Imp.setProperty("Info", infoStr);
#bPrintLog('Saving:' + ch1File, 1)
bSaveStack(ch1Imp, ch1File)
#max project
bSaveZProject(ch1Imp, destMaxFolder, shortName+'_ch1')
#ch2
ch2Imp.setProperty("Info", infoStr);
#bPrintLog('Saving:' + ch2File, 1)
bSaveStack(ch2Imp, ch2File)
#max project
bSaveZProject(ch2Imp, destMaxFolder, shortName+'_ch2')
#
# post convert to 8-bit and save
if gSave8bit:
if bitDepth == 16:
if gNumChannels == 1:
bPrintLog('Converting to 8-bit:' + impWinStr, 1)
IJ.selectWindow(impWinStr)
#IJ.run('resetMinAndMax()')
IJ.run("8-bit")
impFile = eightBitFolder + shortName + '.tif'
bPrintLog('Saving 8-bit:' + impFile, 2)
bSaveStack(imp, impFile)
#max project
bSaveZProject(imp, eightBitMaxFolder, shortName)
if gNumChannels == 2:
#
bPrintLog('Converting to 8-bit:' + ch1WinStr, 1)
IJ.selectWindow(ch1WinStr)
#IJ.run('resetMinAndMax()')
#ch1Imp.resetStack()
#ch1Imp.resetDisplayRange()
IJ.run("8-bit")
impFile = eightBitFolder + shortName + '_ch1.tif'
bPrintLog('Saving 8-bit:' + impFile, 2)
bSaveStack(ch1Imp, impFile)
#max project
bSaveZProject(ch1Imp, eightBitMaxFolder, shortName+'_ch1')
#
bPrintLog('Converting to 8-bit:' + ch2WinStr, 1)
IJ.selectWindow(ch2WinStr)
#IJ.run('resetMinAndMax()')
IJ.run("8-bit")
impFile = eightBitFolder + shortName + '_ch2.tif'
bPrintLog('Saving 8-bit:' + impFile, 2)
bSaveStack(ch2Imp, impFile)
#max project
bSaveZProject(ch2Imp, eightBitMaxFolder, shortName+'_ch2')
#
# close original window
imp.changes = 0
imp.close()
#
# close ch1/ch2
if 1 and gNumChannels == 2:
ch1Imp.changes = 0
ch1Imp.close()
ch2Imp.changes = 0
ch2Imp.close()
bPrintLog(time.strftime("%H:%M:%S") + ' finished runOneFile(): ' + fullFilePath, 1)
