class gui(JFrame):
def __init__(self): # constructor
#origing of coordinates
self.coordx = 10
self.coordy = 10
#inintialize values
self.Canvas = None
#create panel (what is inside the GUI)
self.panel = self.getContentPane()
self.panel.setLayout(GridLayout(9, 2))
self.setTitle('Subdividing ROIs')
#define buttons here:
self.Dapi_files = DefaultListModel()
mylist = JList(self.Dapi_files, valueChanged=self.open_dapi_image)
#mylist.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
mylist.setLayoutOrientation(JList.VERTICAL)
mylist.setVisibleRowCount(-1)
listScroller1 = JScrollPane(mylist)
listScroller1.setPreferredSize(Dimension(300, 80))
self.output_files = DefaultListModel()
mylist2 = JList(self.output_files)
#mylist.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
mylist2.setLayoutOrientation(JList.VERTICAL)
mylist2.setVisibleRowCount(-1)
listScroller2 = JScrollPane(mylist2)
listScroller2.setPreferredSize(Dimension(300, 80))
quitButton = JButton("Quit", actionPerformed=self.quit)
selectInputFolderButton = JButton("Select Input",
actionPerformed=self.select_input)
cubifyROIButton = JButton("Cubify ROI",
actionPerformed=self.cubify_ROI)
saveButton = JButton("Save ROIs", actionPerformed=self.save)
summsaveButton = JButton("Save Summary",
actionPerformed=self.save_summary)
self.textfield1 = JTextField('500')
#add buttons here
self.panel.add(listScroller1)
self.panel.add(listScroller2)
self.panel.add(selectInputFolderButton)
self.panel.add(Label("Adjust the size of the ROIs"))
self.panel.add(self.textfield1)
self.panel.add(cubifyROIButton)
self.panel.add(saveButton)
self.panel.add(summsaveButton)
self.panel.add(quitButton)
#self.panel.add(saveButton)
#self.panel.add(Zslider)
#other stuff to improve the look
self.pack() # packs the frame
self.setVisible(True) # shows the JFrame
self.setLocation(self.coordx, self.coordy)
#define functions for the buttons:
def quit(self, event): #quit the gui
self.dispose()
IJ.run("Close All")
def select_input(self, event):
self.input_path = IJ.getDirectory(
"Select Directory containing your data")
# get the files in that directory
self.input_files = listdir(self.input_path)
self.input_dapi = [s for s in self.input_files if "DAPI.tif" in s]
self.core_names = get_core_names(self.input_dapi)
# create output directory
self.output_path = path.join(
path.dirname(path.dirname(self.input_path)), "Cubified_ROIs")
if path.isdir(self.output_path):
print "Output path already created"
else:
mkdir(self.output_path)
print "Output path created"
# get the processed data
self.processed_files = listdir(self.output_path)
self.out_core_names = get_core_names(
get_core_names(self.processed_files)
) # needs the channel and roi to be removed
# populate the lists
for f in set(self.core_names):
if f not in set(self.out_core_names): # skip if processed
self.Dapi_files.addElement(f)
for f in set(self.out_core_names
): # a set so that only unique ones are shown
self.output_files.addElement(f)
def open_dapi_image(self, e):
sender = e.getSource()
IJ.run("Close All")
if not e.getValueIsAdjusting():
self.name = sender.getSelectedValue()
print self.name
dapi_filename = path.join(self.input_path, self.name + '_DAPI.tif')
#print dapi_filename
if not path.exists(dapi_filename):
print "I don't find the DAPI file, which is weird as I just found it before"
else:
#open stack and make the reslice
self.dapi_image = ImagePlus(dapi_filename) #read the image
# duplicate image to play with that one, and do the real processing in the background
self.imp_main = Duplicator().run(self.dapi_image)
self.imp_main.setTitle(self.name)
self.imp_main.show() #show image on the left
#self.original_image.getWindow().setLocation(self.coordx-self.original_image.getWindow().getWidth()-10,self.coordy-10) #reposition image
def cubify_ROI(self, e):
self.L = int(self.textfield1.text)
# get info
tit = self.imp_main.getTitle()
self.roi = self.imp_main.getRoi()
# get corners
corners = get_corners(self.roi, self.L)
self.corners_cleaned = clean_corners(corners, self.roi, self.L)
print 'found corners'
# get the overlay
self.ov = overlay_corners(self.corners_cleaned, self.L)
self.ov = overlay_roi(self.roi, self.ov)
# write roi name
self.ov = write_roi_numbers(self.ov, self.corners_cleaned, self.L)
# overlay
self.imp_main.setOverlay(self.ov)
self.imp_main.updateAndDraw()
def save(self, e):
# open the other channels
d1_filename = path.join(self.input_path, self.name + '_D1.tif')
d2_filename = path.join(self.input_path, self.name + '_D2.tif')
self.d1_image = ImagePlus(d1_filename) #read the image
print "d1 image opened"
self.d2_image = ImagePlus(d2_filename) #read the image
print "d2 image opened"
for image in [self.dapi_image, self.d1_image, self.d2_image]:
print "saving rois for image " + image.getTitle()
save_rois(image, self.corners_cleaned, self.L, self.output_path)
print "ROIs saved"
def save_summary(self, e):
IJ.selectWindow(self.name)
IJ.run("Flatten")
imp = IJ.getImage()
# downsample
# scale ENLARGING or SHRINKING the canvas dimensions
scale_factor = .2
new_width = str(int(imp.getWidth() * scale_factor))
new_height = str(int(imp.getHeight() * scale_factor))
IJ.selectWindow(self.name + "-1")
str_to_scale = "x=" + str(scale_factor) + " y=" + str(
scale_factor
) + " width=" + new_width + " height=" + new_height + " interpolation=Bilinear average create"
IJ.run("Scale...", str_to_scale)
# save
imp2 = IJ.getImage()
#IJ.saveAs("Tiff", path.join(OUTDIR, self.name + "_summaryOfROIs"))
IJ.saveAsTiff(
imp2, path.join(self.output_path,
self.name + "_summaryOfROIs.tif"))
print "summary image saved"
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)
