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)
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 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)