def writeCSV(filePath, results, header):
""" Write a table as an csv file """
rt = ResultsTable()
for i in range(len(results[1])):
rt.incrementCounter()
for j in range(len(results)):
rt.addValue(str(header[j]), results[j][i])
rt.show("Results")
rt.saveAs(filePath)
def writeCSV(filePath, results, header):
""" Write a table as an csv file """
rt = ResultsTable()
for i in range(len(results[1])):
rt.incrementCounter()
for j in range(len(results)):
rt.addValue(str(header[j]), results[j][i])
rt.show("Results")
rt.saveAs(filePath);
def show_as_table(title, data, order=[]):
"""Helper function to display group and data information as a ResultsTable"""
table = ResultsTable()
for d in data:
table.incrementCounter()
order = [k for k in order]
order.extend([k for k in d.keys() if not d in order])
for k in order:
table.addValue(k, d[k])
table.show(title)
def reportClustersAsTable(clusters,
allPoints,
XColumn='X',
YColumn='Y',
ZColumn='Z',
NRColumn='NR'):
'''
Report the clustered and unclustered points in the tables 'clusters' and 'unclustered'.
'''
rt = ResultsTable()
counter = 1
clusterCounter = 1
clusteredPoints = []
for c in clusters:
for dp in c.getPoints():
rt.incrementCounter()
p = dp.getPoint()
rt.addValue(NRColumn, counter)
rt.addValue(XColumn, p[0])
rt.addValue(YColumn, p[1])
rt.addValue(ZColumn, p[2])
rt.addValue("C", clusterCounter)
counter = counter + 1
clusteredPoints.append([p[0], p[1], p[2]])
clusterCounter = clusterCounter + 1
rt.show("clusters")
win = WindowManager.getWindow("Results")
rt = win.getResultsTable()
X, Y, Z = getColumns(XColumn, YColumn, ZColumn)
if not rt.columnExists(NRColumn):
for i in range(0, len(X)):
rt.setValue(NRColumn, i, i + 1)
rt.updateResults()
NR = getColumn(NRColumn)
unclusteredPoints = [
[point.getPoint()[0],
point.getPoint()[1],
point.getPoint()[2]] for point in allPoints
if [point.getPoint()[0],
point.getPoint()[1],
point.getPoint()[2]] not in clusteredPoints
]
counter = 1
rt = ResultsTable()
for p in unclusteredPoints:
rt.incrementCounter()
rt.addValue(NRColumn, counter)
rt.addValue(XColumn, p[0])
rt.addValue(YColumn, p[1])
rt.addValue(ZColumn, p[2])
counter = counter + 1
rt.show("unclustered")
WindowManager.setWindow(win)
def myResults(results):
myResultsTable = ResultsTable()
for idx, graph in enumerate(results.getGraph()):
for edge in graph.getEdges():
edgeLength = edge.getLength()
v1 = edge.getV1()
v2 = edge.getV2()
dist = euclideanDistance(v1, v2)
#print('v1:', type(v1), v1.getPoints())
#
myResultsTable.incrementCounter() # add a row to results table
myResultsTable.addValue('graphID', idx)
myResultsTable.addValue('length_3d', edgeLength)
myResultsTable.addValue('dist', dist)
if dist > 0:
myResultsTable.addValue('tort', edgeLength / dist)
else:
myResultsTable.addValue('tort', 'inf')
myResultsTable.setPrecision(6)
myResultsTable.show('samiSkel_results')
def process(srcDir, dstDir, currentDir, fileName, keepDirectories, Channel_1, Channel_2, radius_background, sigmaSmaller, sigmaLarger, minPeakValue, min_dist):
IJ.run("Close All", "")
# Opening the image
IJ.log("Open image file:" + fileName)
#imp = IJ.openImage(os.path.join(currentDir, fileName))
#imp = IJ.getImage()
imp = BF.openImagePlus(os.path.join(currentDir, fileName))
imp = imp[0]
# getDimensions(width, height, channels, slices, frames)
IJ.log("Computing Max Intensity Projection")
if imp.getDimensions()[3] > 1:
imp_max = ZProjector.run(imp,"max")
else:
imp_max = imp
ip1, ip2 = extract_channel(imp_max, Channel_1, Channel_2)
IJ.log("Substract background")
imp1, imp2 = back_substraction(ip1, ip2, radius_background)
IJ.log("Finding Peaks")
ip1_1, ip2_1, peaks_1, peaks_2 = find_peaks(imp1, imp2, sigmaSmaller, sigmaLarger, minPeakValue)
# Create a PointRoi from the DoG peaks, for visualization
roi_1 = PointRoi(0, 0)
roi_2 = PointRoi(0, 0)
roi_3 = PointRoi(0, 0)
roi_4 = PointRoi(0, 0)
# A temporary array of integers, one per dimension the image has
p_1 = zeros(ip1_1.numDimensions(), 'i')
p_2 = zeros(ip2_1.numDimensions(), 'i')
# Load every peak as a point in the PointRoi
for peak in peaks_1:
# Read peak coordinates into an array of integers
peak.localize(p_1)
roi_1.addPoint(imp1, p_1[0], p_1[1])
for peak in peaks_2:
# Read peak coordinates into an array of integers
peak.localize(p_2)
roi_2.addPoint(imp2, p_2[0], p_2[1])
# Chose minimum distance in pixel
#min_dist = 20
for peak_1 in peaks_1:
peak_1.localize(p_1)
for peak_2 in peaks_2:
peak_2.localize(p_2)
d1 = distance(p_1, p_2)
if d1 < min_dist:
roi_3.addPoint(imp1, p_2[0], p_2[1])
break
for peak_2 in peaks_2:
peak_2.localize(p_2)
for peak_1 in peaks_1:
peak_1.localize(p_1)
d2 = distance(p_2, p_1)
if d2 < min_dist:
roi_4.addPoint(imp1, p_2[0], p_2[1])
break
cal = imp.getCalibration()
min_distance = str(round((cal.pixelWidth * min_dist),1))
table = ResultsTable()
table.incrementCounter()
table.addValue("Numbers of Neuron Markers", roi_1.getCount(0))
table.addValue("Numbers of Glioma Markers", roi_2.getCount(0))
table.addValue("Numbers of Glioma within %s um of Neurons" %(min_distance), roi_3.getCount(0))
table.addValue("Numbers of Neurons within %s um of Glioma" %(min_distance), roi_4.getCount(0))
#table.show("Results Analysis")
saveDir = currentDir.replace(srcDir, dstDir) if keepDirectories else dstDir
if not os.path.exists(saveDir):
os.makedirs(saveDir)
IJ.log("Saving to" + saveDir)
table.save(os.path.join(saveDir, fileName + ".csv"))
IJ.selectWindow("Log")
IJ.saveAs("Text", os.path.join(saveDir, fileName + ".csv"));
class MandersPlugin(ImageListener, WindowAdapter):
def __init__(self):
self.imp = None
self.preview = None
self.createMainWindow()
self.cells = None
self.files = []
self.results = ResultsTable()
ImagePlus.addImageListener(self)
self.selectInputDir()
self.selectOutputDir()
self.pairs = []
self.methods = []
self.processNextFile()
def selectInputDir(self):
inputDialog = DirectoryChooser("Please select a directory contaning your images")
inputDir = inputDialog.getDirectory()
for imageFile in os.listdir(inputDir):
self.files.append(inputDir + imageFile)
def selectOutputDir(self):
outputDialog = DirectoryChooser("Please select a directory to save your results")
self.outputDir = outputDialog.getDirectory()
def closeImage(self):
if self.imp is not None:
self.imp.close()
self.imp = None
if self.preview is not None:
self.preview.close()
self.preview = None
def openImage(self, imageFile):
try:
images = BF.openImagePlus(imageFile)
self.imp = images[0]
except UnknownFormatException:
return None
if self.imp.getNChannels() < 2:
IJ.error("Bad image format", "Image must contain at lease 2 channels!")
return None
if not self.pairs or \
not self.methods:
self.getOptionsDialog(self.imp)
title = self.imp.title
self.imp.title = title[:title.rfind('.')]
return self.imp
def getOptionsDialog(self, imp):
thr_methods = ["None", "Default", "Huang", "Intermodes", "IsoData", "Li", "MaxEntropy","Mean", "MinError(I)", "Minimum", "Moments", "Otsu", "Percentile", "RenyiEntropy", "Shanbhag" , "Triangle", "Yen"]
gd = GenericDialog("Please select channels to collocalize")
for i in range(1, imp.getNChannels() + 1):
gd.addChoice("Threshold method for channel %i" % i, thr_methods, "None")
gd.showDialog()
if gd.wasCanceled():
self.exit()
channels = []
for i in range(1, imp.getNChannels() + 1):
method = gd.getNextChoice()
self.methods.append(method)
if method != "None":
channels.append(i)
for x in channels:
for y in channels:
if x < y:
self.pairs.append((x, y))
def processNextFile(self):
if self.files:
imageFile = self.files.pop(0)
return self.processFile(imageFile)
else:
return False
def processFile(self, imageFile):
imp = self.openImage(imageFile)
if imp is not None:
cell = Cell(imp.NSlices, 1)
self.cells = DelegateListModel([])
self.cells.append(cell)
self.showMainWindow(self.cells)
if self.checkbox3D.isSelected():
self.displayImage(imp)
else:
self.displayImage(imp, False)
self.preview = self.previewImage(imp)
self.displayImage(self.preview)
return True
else:
return self.processNextFile()
def displayImage(self, imp, show = True):
imp.setDisplayMode(IJ.COMPOSITE)
enhancer = ContrastEnhancer()
enhancer.setUseStackHistogram(True)
splitter = ChannelSplitter()
for c in range(1, imp.getNChannels() + 1):
imp.c = c
enhancer.stretchHistogram(imp, 0.35)
if show:
imp.show()
def previewImage(self, imp):
roi = imp.getRoi()
splitter = ChannelSplitter()
channels = []
for c in range(1, imp.getNChannels() + 1):
channel = ImagePlus("Channel %i" % c, splitter.getChannel(imp, c))
projector = ZProjector(channel)
projector.setMethod(ZProjector.MAX_METHOD)
projector.doProjection()
channels.append(projector.getProjection())
image = RGBStackMerge.mergeChannels(channels, False)
image.title = imp.title + " MAX Intensity"
image.luts = imp.luts
imp.setRoi(roi)
return image
def getCroppedChannels(self, imp, cell):
splitter = ChannelSplitter()
imp.setRoi(None)
if cell.mode3D:
cropRoi = cell.getCropRoi()
else:
cropRoi = cell.roi
if cropRoi is None:
return None
crop = cropRoi.getBounds()
channels = []
for c in range(1, imp.getNChannels() + 1):
slices = ImageStack(crop.width, crop.height)
channel = splitter.getChannel(imp, c)
for z in range(1, channel.getSize() + 1):
zslice = channel.getProcessor(z)
zslice.setRoi(cropRoi)
nslice = zslice.crop()
if cell.mode3D:
oroi = cell.slices[z - 1].roi
else:
oroi = cell.roi
if oroi is not None:
roi = oroi.clone()
bounds = roi.getBounds()
roi.setLocation(bounds.x - crop.x, bounds.y - crop.y)
nslice.setColor(Color.black)
nslice.fillOutside(roi)
slices.addSlice(nslice)
channels.append(ImagePlus("Channel %i" % c, slices))
return channels
def getThreshold(self, imp, method):
thresholder = Auto_Threshold()
duplicator = Duplicator()
tmp = duplicator.run(imp)
return thresholder.exec(tmp, method, False, False, True, False, False, True)
def getContainer(self, impA, impB):
imgA = ImagePlusAdapter.wrap(impA)
imgB = ImagePlusAdapter.wrap(impB)
return DataContainer(imgA, imgB, 1, 1, "imageA", "imageB")
def getManders(self, imp, cell):
### Crop channels according to cell mask
channels = self.getCroppedChannels(imp, cell)
if channels is None:
return None
### Calculate channel thresholds
thrs = []
thrimps = []
for c, method in enumerate(self.methods):
if method != "None":
thr, thrimp = self.getThreshold(channels[c], method)
else:
thr, thrimp = None, None
thrs.append(thr)
thrimps.append(thrimp)
### Calculate manders colocalization
manders = MandersColocalization()
raws = []
thrds = []
for chA, chB in self.pairs:
container = self.getContainer(channels[chA - 1], channels[chB - 1])
img1 = container.getSourceImage1()
img2 = container.getSourceImage2()
mask = container.getMask()
cursor = TwinCursor(img1.randomAccess(), img2.randomAccess(), Views.iterable(mask).localizingCursor())
rtype = img1.randomAccess().get().createVariable()
raw = manders.calculateMandersCorrelation(cursor, rtype)
rthr1 = rtype.copy()
rthr2 = rtype.copy()
rthr1.set(thrs[chA - 1])
rthr2.set(thrs[chB - 1])
cursor.reset()
thrd = manders.calculateMandersCorrelation(cursor, rthr1, rthr2, ThresholdMode.Above)
raws.append(raw)
thrds.append(thrd)
return (channels, thrimps, thrs, raws, thrds)
def saveMultichannelImage(self, title, channels, luts):
tmp = RGBStackMerge.mergeChannels(channels, False)
tmp.luts = luts
saver = FileSaver(tmp)
saver.saveAsTiffStack(self.outputDir + title + ".tif")
tmp.close()
def createMainWindow(self):
self.frame = JFrame('Select cells and ROIs',
defaultCloseOperation = JFrame.DISPOSE_ON_CLOSE
)
self.frame.setLayout(GridBagLayout())
self.frame.addWindowListener(self)
self.frame.add(JLabel("Cells"),
GridBagConstraints(0, 0, 1, 1, 0, 0,
GridBagConstraints.CENTER, GridBagConstraints.NONE,
Insets(5, 2, 2, 0), 0, 0
))
self.cellList = JList(DelegateListModel([]),
selectionMode = ListSelectionModel.SINGLE_SELECTION,
cellRenderer = MyRenderer(),
selectedIndex = 0,
valueChanged = self.selectCell
)
self.frame.add(JScrollPane(self.cellList),
GridBagConstraints(0, 1, 1, 5, .5, 1,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
Insets(0, 2, 2, 0), 0, 0
))
self.frame.add(JButton('Add cell', actionPerformed = self.addCell),
GridBagConstraints(1, 2, 1, 2, 0, .25,
GridBagConstraints.CENTER, GridBagConstraints.NONE,
Insets(0, 0, 0, 0), 0, 0
))
self.frame.add(JButton('Remove cell', actionPerformed = self.removeCell),
GridBagConstraints(1, 4, 1, 2, 0, .25,
GridBagConstraints.CENTER, GridBagConstraints.NONE,
Insets(0, 5, 0, 5), 0, 0
))
self.frame.add(JLabel("Slices"),
GridBagConstraints(0, 6, 1, 1, 0, 0,
GridBagConstraints.CENTER, GridBagConstraints.NONE,
Insets(5, 2, 2, 0), 0, 0
))
self.sliceList = JList(DelegateListModel([]),
selectionMode = ListSelectionModel.SINGLE_SELECTION,
cellRenderer = MyRenderer(),
selectedIndex = 0,
valueChanged = self.selectSlice
)
self.frame.add(JScrollPane(self.sliceList),
GridBagConstraints(0, 7, 1, 5, .5, 1,
GridBagConstraints.CENTER, GridBagConstraints.BOTH,
Insets(0, 2, 2, 0), 0, 0
))
self.frame.add(JButton('Update ROI', actionPerformed = self.updateSlice),
GridBagConstraints(1, 8, 1, 2, 0, .25,
GridBagConstraints.CENTER, GridBagConstraints.NONE,
Insets(0, 0, 0, 0), 0, 0
))
self.frame.add(JButton('Done', actionPerformed = self.doneSelecting),
GridBagConstraints(1, 10, 1, 2, 0, .25,
GridBagConstraints.CENTER, GridBagConstraints.NONE,
Insets(0, 0, 0, 0), 0, 0
))
self.checkbox3D = JCheckBox('3D selection mode', True, actionPerformed=self.toggle3D)
self.frame.add(self.checkbox3D,
GridBagConstraints(0, 13, 2, 1, 0, 1,
GridBagConstraints.WEST, GridBagConstraints.NONE,
Insets(0, 0, 0, 0), 0, 0
))
def showMainWindow(self, cells = None):
if cells is not None:
self.cellList.model = cells
if cells:
self.cellList.selectedIndex = 0
self.frame.pack()
self.frame.visible = True
def hideMainWindow(self):
self.frame.visible = False
def closeMainWindow(self):
self.frame.dispose()
def toggle3D(self, event):
mode3D = self.checkbox3D.isSelected()
if mode3D:
self.sliceList.enabled = True
if self.imp is not None:
self.imp.show()
if self.preview is not None:
self.preview.hide()
else:
self.sliceList.enabled = False
if self.preview is None:
self.preview = self.previewImage(self.imp)
self.displayImage(self.preview)
else:
self.preview.show()
if self.imp is not None:
self.imp.hide()
selectedCell = self.cellList.selectedIndex
if selectedCell >= 0:
cell = self.cells[selectedCell]
self.sliceList.model = cell.slices
self.sliceList.selectedIndex = 0
def addCell(self, event):
size = len(self.cells)
if (size > 0):
last = self.cells[size - 1]
n = last.n + 1
else:
n = 1
self.cells.append(Cell(self.imp.NSlices, n))
self.cellList.selectedIndex = size
def removeCell(self, event):
selected = self.cellList.selectedIndex
if selected >= 0:
self.cells.remove(self.cells[selected])
if (selected >= 1):
self.cellList.selectedIndex = selected - 1
else:
self.cellList.selectedIndex = 0
def selectCell(self, event):
selected = self.cellList.selectedIndex
if selected >= 0:
cell = self.cells[selected]
self.sliceList.model = cell.slices
self.sliceList.selectedIndex = 0
else:
self.sliceList.model = DelegateListModel([])
if self.preview is not None:
self.preview.setRoi(cell.roi)
def selectSlice(self, event):
selectedCell = self.cellList.selectedIndex
selectedSlice = self.sliceList.selectedIndex
if selectedCell >= 0 and selectedSlice >= 0:
cell = self.cells[selectedCell]
image = self.imp
mode3D = self.checkbox3D.isSelected()
if image is not None and cell is not None and mode3D:
roi = cell.slices[selectedSlice].roi
if (image.z - 1 != selectedSlice):
image.z = selectedSlice + 1
image.setRoi(roi, True)
if self.preview is not None and not mode3D:
self.preview.setRoi(cell.roi, True)
def updateSlice(self, event):
if self.checkbox3D.isSelected():
self.updateSlice3D(self.imp)
else:
self.updateSlice2D(self.preview)
def updateSlice3D(self, imp):
selectedCell = self.cellList.selectedIndex
selectedSlice = self.sliceList.selectedIndex
if selectedCell >= 0 and selectedSlice >= 0 and imp is not None:
cell = self.cells[selectedCell]
impRoi = imp.getRoi()
if cell is not None and impRoi is not None:
index = selectedSlice + 1
roi = ShapeRoi(impRoi, position = index)
cell.mode3D = True
cell.name = "Cell %i (3D)" % cell.n
cell.slices[selectedSlice].roi = roi
if (index + 1 <= len(cell.slices)):
imp.z = index + 1
self.cellList.repaint(self.cellList.getCellBounds(selectedCell, selectedCell))
self.sliceList.repaint(self.sliceList.getCellBounds(selectedSlice, selectedSlice))
def updateSlice2D(self, imp):
selectedCell = self.cellList.selectedIndex
if selectedCell >= 0 and imp is not None:
cell = self.cells[selectedCell]
impRoi = imp.getRoi()
if cell is not None and impRoi is not None:
roi = ShapeRoi(impRoi, position = 1)
cell.mode3D = False
cell.name = "Cell %i (2D)" % cell.n
cell.roi = roi
self.cellList.repaint(self.cellList.getCellBounds(selectedCell, selectedCell))
def imageOpened(self, imp):
pass
def imageClosed(self, imp):
pass
def imageUpdated(self, imp):
if self.checkbox3D.isSelected():
if imp is not None:
selectedCell = self.cellList.selectedIndex
selectedSlice = imp.z - 1
if imp == self.imp and selectedSlice != self.sliceList.selectedIndex:
self.sliceList.selectedIndex = selectedSlice
def doneSelecting(self, event):
oluts = self.imp.luts
luts = []
channels = []
for c, method in enumerate(self.methods):
if method != "None":
luts.append(oluts[c])
channels.append(c)
for cell in self.cells:
manders = self.getManders(self.imp, cell)
if manders is not None:
chimps, thrimps, thrs, raws, thrds = manders
index = self.cells.index(cell) + 1
title = "Cell_%i-" % index + self.imp.title
self.saveMultichannelImage(title, chimps, oluts)
title = "Cell_%i_thrd-" % index + self.imp.title
self.saveMultichannelImage(title, thrimps, luts)
self.results.incrementCounter()
row = self.results.getCounter() - 1
for i, thr in enumerate(thrs):
if thr is not None:
self.results.setValue("Threshold %i" % (i + 1), row, int(thr))
for i, pair in enumerate(self.pairs):
self.results.setValue("%i-%i M1 raw" % pair, row, float(raws[i].m1))
self.results.setValue("%i-%i M2 raw" % pair, row, float(raws[i].m2))
self.results.setValue("%i-%i M1 thrd" % pair, row, float(thrds[i].m1))
self.results.setValue("%i-%i M2 thrd" % pair, row, float(thrds[i].m2))
self.closeImage()
if not self.processNextFile():
print "All done - happy analysis!"
self.results.show("Manders collocalization results")
self.exit()
def windowClosing(self, e):
print "Closing plugin - BYE!!!"
self.exit()
def exit(self):
ImagePlus.removeImageListener(self)
self.closeImage()
self.closeMainWindow()
def batch_open_Rois(pathRoi,
file_typeRoi=None,
name_filterRoi=None,
recursive=False):
'''Open all files in the given folder.
:param path: The path from were to open the Rois. String and java.io.File are allowed.
:param file_type: Only accept files with the given extension (default: None).
:param name_filter: Reject files that contain the given string (default: wild characters).
:param recursive: Process directories recursively (default: False).
'''
# Converting a File object to a string.
if isinstance(pathRoi, File):
pathRoi = pathRoi.getAbsolutePath()
def check_type(string):
'''This function is used to check the file type.
It is possible to use a single string or a list/tuple of strings as filter.
This function can access the variables of the surrounding function.
:param string: The filename to perform the check on.
'''
if file_typeRoi:
# The first branch is used if file_type is a list or a tuple.
if isinstance(file_typeRoi, (list, tuple)):
for file_type_ in file_typeRoi:
if string.endswith(file_type_):
# Exit the function with True.
return True
else:
# Next iteration of the for loop.
continue
# The second branch is used if file_type is a string.
elif isinstance(file_typeRoi, string):
if string.endswith(file_typeRoi):
return True
else:
return False
return False
# Accept all files if file_type is None.
else:
return True
# We collect all files to open in a list.
path_to_Roi = []
# Replacing some abbreviations (e.g. $HOME on Linux).
path = os.path.expanduser(pathRoi)
# If we don't want a recursive search, we can use os.listdir().
if not recursive:
for file_name in os.listdir(pathRoi):
full_path = os.path.join(pathRoi, file_name)
if os.path.isfile(full_path):
if check_type(file_name):
path_to_Roi.append(full_path)
# For a recursive search os.walk() is used.
else:
# os.walk() is iterable.
# Each iteration of the for loop processes a different directory.
# the first return value represents the current directory.
# The second return value is a list of included directories.
# The third return value is a list of included files.
for directory, dir_names, file_names in os.walk(pathRoi):
# We are only interested in files.
for file_name in file_names:
# The list contains only the file names.
# The full path needs to be reconstructed.
full_path = os.path.join(directory, file_name)
# Both checks are performed to filter the files.
if check_type(file_name):
# Add the file to the list of Rois to open.
path_to_Roi.append([
full_path,
os.path.basename(os.path.splitext(full_path)[0])
])
# Create the list that will be returned by this function.
RoisX = []
RoisY = []
print('path', path_to_Roi)
for roi_path in path_to_Roi:
print('path', roi_path)
# An object equals True and None equals False.
rm = RoiManager.getInstance()
if (rm == None):
rm = RoiManager()
Roi = IJ.open(roi_path)
roi_points = rm.getRoisAsArray()
table = ResultsTable()
for Roi in roi_points:
xpoints = Roi.getPolygon().xpoints
ypoints = Roi.getPolygon().ypoints
for i in range(len(xpoints)):
table.incrementCounter()
table.addValue("Index", i)
table.addValue("X", xpoints[i])
table.addValue("Y", ypoints[i])
table.show("XY-Coordinates")
return roi_points
thr1, thrimp1 = calculateThreshold(imp1, roi, methods[0])
thr2, thrimp2 = calculateThreshold(imp2, roi, methods[1])
cursor = TwinCursor(img1.randomAccess(), img2.randomAccess(), Views.iterable(mask).localizingCursor())
rtype = img1.randomAccess().get().createVariable()
raw = manders.calculateMandersCorrelation(cursor, rtype)
rthr1 = rtype.copy()
rthr2 = rtype.copy()
rthr1.set(thr1)
rthr2.set(thr2)
cursor.reset()
thrd = manders.calculateMandersCorrelation(cursor, rthr1, rthr2, ThresholdMode.Above)
print "Results are: %f %f %f %f" % (raw.m1, raw.m2, thrd.m1, thrd.m2)
results.incrementCounter()
rowno = results.getCounter() - 1
results.setValue("Cell", rowno, int(rowno))
results.setValue("Threshold 1", rowno, int(thr1))
results.setValue("Threshold 2", rowno, int(thr2))
results.setValue("M1 raw", rowno, float(raw.m1))
results.setValue("M2 raw", rowno, float(raw.m2))
results.setValue("M1 thrd", rowno, float(thrd.m1))
results.setValue("M2 thrd", rowno, float(thrd.m2))
thrimp = RGBStackMerge.mergeChannels([thrimp1, thrimp2], False)
saver = FileSaver(thrimp)
saver.saveAsTiffStack(outputDir + "Cell_%i-" % results.getCounter() + title + ".tif")
thrimp.close()
results.show("Colocalization results")
# we get XY coordinates of the foci
x = int(rt.getValue("X", count))
y = int(rt.getValue("Y", count))
# if that cell contains these coordinates, add the cell
# number as "cell" value for that foci
if roi.contains(x, y):
rt.setValue("cell", count, cell)
cell = cell + 1
# save this results table
rt.save(directory + "/" + filename + "_GFP.csv")
print("saving at ", directory + "/" + filename + "_GFP.csv")
# create summary resulta table, with "cell" and "foci_count" columns
consol = ResultsTable()
consol.incrementCounter()
consol.addValue("cell", 0)
consol.addValue("foci_count", 0)
rowcount = 1
# loop over all cells, add cell number to the "cell" column
for count in range(cell):
consol.setValue("cell", count, count)
# loop over all foci
for count in range(rt.size()):
# get in which cell that foci is and increase the
# counter on the summary results table
currcell = int(rt.getValue("cell", count))
consol.setValue(
def main():
rt = RT.open2(table_file.getAbsolutePath())
if not rt: return
log(" --- --- --- ")
log("Loaded %s" % table_file.getAbsolutePath())
log("Loading column lists...")
# Get column indices from imported file
headings = getColumnHeadings(rt)
id_col = getColumnIndex(headings, "TID")
t_col = getColumnIndex(headings, "t [")
d2p_col = getColumnIndex(headings, "D2P [")
angle_col = getColumnIndex(headings, u'\u03B1 [deg]')
delta_col = getColumnIndex(headings, u'\u0394\u03B1 [deg]')
if angle_col == RT.COLUMN_NOT_FOUND:
log("Failed to detect index for angle column. Re-trying...")
angle_col = getColumnIndex(headings, u'? [deg]')
if delta_col == RT.COLUMN_NOT_FOUND:
log("Failed to detect index for delta angle column. Re-trying...")
delta_col = getColumnIndex(headings, u'?? [deg]')
log("Last column index is %s" % rt.getLastColumn())
if RT.COLUMN_NOT_FOUND in (id_col, d2p_col, delta_col, angle_col):
uiservice.showDialog("Error: Some key columns were not found!",
"Invalid Table?")
return
log("Settings: BOUT_WINDOW= %s, MIN_D2P= %s, DEF_FRAME_INTERVAL= %s" %
(BOUT_WINDOW, '{0:.4f}'.format(MIN_D2P), DEF_FRAME_INTERVAL))
# Store all data on dedicated lists
track_id_rows = rt.getColumnAsDoubles(id_col)
d2p_rows = rt.getColumnAsDoubles(d2p_col)
angle_rows = rt.getColumnAsDoubles(angle_col)
delta_rows = rt.getColumnAsDoubles(delta_col)
t_rows = rt.getColumnAsDoubles(t_col)
# Assess n of data points and extract unique path ids
n_rows = len(track_id_rows)
row_indices = range(n_rows)
track_ids = set(track_id_rows)
n_tracks = len(track_ids)
log("Table has %g rows" % n_rows)
log("Table has %g tracks" % n_tracks)
log("Parsing tracks...")
for track_id in track_ids:
for row, next_row in zip(row_indices, row_indices[1:]):
if track_id_rows[row] != track_id:
continue
if not isNumber(angle_rows[row]):
rt.setValue("FLAG", row, "NA")
continue
lower_bound = max(0, row - BOUT_WINDOW + 1)
upper_bound = min(n_rows - 1, row + BOUT_WINDOW)
win_d2p = []
for _ in range(lower_bound, upper_bound):
win_d2p.append(d2p_rows[row])
if sum(win_d2p) <= MIN_D2P * len(win_d2p):
rt.setValue("FLAG", row, 0)
else:
current_angle = angle_rows[row]
next_angle = angle_rows[next_row]
current_delta = delta_rows[row]
flag = -1 if current_angle < 0 else 1
delta_change = (abs(current_delta) > 90)
same_sign = ((current_angle < 0) == (next_angle < 0))
if delta_change and not same_sign:
flag *= -1
rt.setValue("FLAG", row, flag)
if next_row == n_rows - 1:
rt.setValue("FLAG", next_row, flag)
if rt.save(table_file.getAbsolutePath()):
log("Processed table successfully saved (file overwritten)")
else:
log("Could not override input file. Displaying it...")
rt.show(table_file.name)
log("Creating onset table...")
onset_rt = RT()
onset_rt.showRowNumbers(False)
frame_int = DEF_FRAME_INTERVAL
if "table" in frame_rate_detection:
frame_int = getFrameIntervalFromTable(row_indices, track_id_rows,
t_rows)
elif "image" in frame_rate_detection:
frame_int = getFrameIntervalFromImage(image_file.getAbsolutePath())
else:
log("Using default frame rate")
for track_id in track_ids:
for prev_row, row in zip(row_indices, row_indices[1:]):
if not track_id in (track_id_rows[prev_row], track_id_rows[row]):
continue
flag = rt.getValue("FLAG", row)
if not isNumber(flag):
continue
flag = int(flag)
if flag == 0:
continue
if flag == 1 or flag == -1:
srow = onset_rt.getCounter()
onset_rt.incrementCounter()
onset_rt.setValue("TID", srow, track_id)
from_frame = int(t_rows[prev_row] / frame_int) + 1
to_frame = int(t_rows[row] / frame_int) + 1
onset_rt.setValue("First disp. [t]", srow,
"%s to %s" % (t_rows[prev_row], t_rows[row]))
onset_rt.setValue("First disp. [frames]", srow,
"%s to %s" % (from_frame, to_frame))
onset_rt.setValue("ManualTag", srow, "")
break
out_path = suffixed_path(table_file.getAbsolutePath(), "ManualTagging")
if onset_rt.save(out_path):
log("Summary table successfully saved: %s" % out_path)
else:
log("File not saved... Displaying onset table")
onset_rt.show("Onsets %s" % table_file.name)
maximaip = findmaximashow.getProcessor()
maximahist = maximaip.getHistogram()
CountMethod2 = maximahist[255]
print "Using the findMaxima method with a threshold of " + str(
THRESH) + ", I found " + str(CountMethod2) + " maxima."
IJ.setRawThreshold(findmaximashow, 255, 255, "red")
IJ.run(findmaximashow, "Create Selection", "")
rm.addRoi(findmaximashow.getRoi())
rm.rename(1, "Maxima with threshold")
# ---- METHOD 3-4: API getMaxima WITH THE POINTS COUNTED OR ADDED TO THE RESULTS TABLE
maxima = mf.getMaxima(ip, 100.0, False)
CountMethod3 = maxima.npoints
print "Using the getMaxima method with no threshold , I found " + str(
CountMethod3) + " maxima."
rt = ResultsTable()
for i in range(maxima.npoints):
rt.incrementCounter()
rt.addValue("X", maxima.xpoints[i])
rt.addValue("Y", maxima.ypoints[i])
rt.show("Results")
CountMethod4 = rt.getCounter()
print "By counting points generated by getMaxima, I found " + str(
CountMethod4) + " maxima."
# TODO: add these to the ROI mgr
# TODO: as alternative, check out HMaxima transform from landini, basically subtracting the threshold before running the find maxima
def setUp(self):
unittest.TestCase.setUp(self)
rt = ResultsTable()
rt.incrementCounter()
rt.addLabel('LABEL', 'ID00002')
rt.addValue('ID', 2)
rt.addValue('TRACK_ID', 2)
rt.addValue('QUALITY', 1)
rt.addValue('POSITION_X', 738.9)
rt.addValue('POSITION_Y', 670.0)
rt.addValue('POSITION_Z', 0)
rt.addValue('POSITION_T', 0)
rt.incrementCounter()
rt.addLabel('LABEL', 'ID00003')
rt.addValue('ID', 3)
rt.addValue('TRACK_ID', 3)
rt.addValue('QUALITY', 1)
rt.addValue('POSITION_X', 672.1)
rt.addValue('POSITION_Y', 729.3)
rt.addValue('POSITION_Z', 0)
rt.addValue('POSITION_T', 0)
rt.incrementCounter()
rt.addLabel('LABEL', 'ID00001')
rt.addValue('ID', 31)
rt.addValue('TRACK_ID', 1)
rt.addValue('QUALITY', 1)
rt.addValue('POSITION_X', 953.2)
rt.addValue('POSITION_Y', 803.5)
rt.addValue('POSITION_Z', 0)
rt.addValue('POSITION_T', 1)
rt.incrementCounter()
rt.addLabel('LABEL', 'ID000032')
rt.addValue('ID', 32)
rt.addValue('TRACK_ID', 2)
rt.addValue('QUALITY', 1)
rt.addValue('POSITION_X', 739.5)
rt.addValue('POSITION_Y', 665.0)
rt.addValue('POSITION_Z', 0)
rt.addValue('POSITION_T', 1)
rt.incrementCounter()
rt.addLabel('LABEL', 'ID000033')
rt.addValue('ID', 33)
rt.addValue('TRACK_ID', 3)
rt.addValue('QUALITY', 1)
rt.addValue('POSITION_X', 667.0)
rt.addValue('POSITION_Y', 729.8)
rt.addValue('POSITION_Z', 0)
rt.addValue('POSITION_T', 1)
rt.incrementCounter()
rt.addLabel('LABEL', 'ID000061')
rt.addValue('ID', 61)
rt.addValue('TRACK_ID', 1)
rt.addValue('QUALITY', 1)
rt.addValue('POSITION_X', 959.0)
rt.addValue('POSITION_Y', 805.5)
rt.addValue('POSITION_Z', 0)
rt.addValue('POSITION_T', 2)
self.table = rt
def main():
rt = RT.open2(table_file.getAbsolutePath())
if not rt: return
log(" --- --- --- ")
log("Loaded %s" % table_file.getAbsolutePath())
log("Loading column lists...")
# Get column indices from imported file
headings = getColumnHeadings(rt)
id_col = getColumnIndex(headings, "TID")
t_col = getColumnIndex(headings, "t [")
d2p_col = getColumnIndex(headings, "D2P [")
angle_col = getColumnIndex(headings, u'\u03B1 [deg]')
delta_col = getColumnIndex(headings, u'\u0394\u03B1 [deg]')
if angle_col == RT.COLUMN_NOT_FOUND:
log("Failed to detect index for angle column. Re-trying...")
angle_col = getColumnIndex(headings, u'? [deg]')
if delta_col == RT.COLUMN_NOT_FOUND:
log("Failed to detect index for delta angle column. Re-trying...")
delta_col = getColumnIndex(headings, u'?? [deg]')
log("Last column index is %s" % rt.getLastColumn())
if RT.COLUMN_NOT_FOUND in (id_col, d2p_col, delta_col, angle_col):
uiservice.showDialog("Error: Some key columns were not found!", "Invalid Table?")
return
log("Settings: BOUT_WINDOW= %s, MIN_D2P= %s, DEF_FRAME_INTERVAL= %s"
% (BOUT_WINDOW, '{0:.4f}'.format(MIN_D2P), DEF_FRAME_INTERVAL))
# Store all data on dedicated lists
track_id_rows = rt.getColumnAsDoubles(id_col)
d2p_rows = rt.getColumnAsDoubles(d2p_col)
angle_rows = rt.getColumnAsDoubles(angle_col)
delta_rows = rt.getColumnAsDoubles(delta_col)
t_rows = rt.getColumnAsDoubles(t_col)
# Assess n of data points and extract unique path ids
n_rows = len(track_id_rows)
row_indices = range(n_rows)
track_ids = set(track_id_rows)
n_tracks = len(track_ids)
log("Table has %g rows" % n_rows)
log("Table has %g tracks" % n_tracks)
log("Parsing tracks...")
for track_id in track_ids:
for row, next_row in zip(row_indices, row_indices[1:]):
if track_id_rows[row] != track_id:
continue
if not isNumber(angle_rows[row]):
rt.setValue("FLAG", row, "NA")
continue
lower_bound = max(0, row - BOUT_WINDOW + 1)
upper_bound = min(n_rows-1, row + BOUT_WINDOW)
win_d2p = []
for _ in range(lower_bound, upper_bound):
win_d2p.append(d2p_rows[row])
if sum(win_d2p) <= MIN_D2P * len(win_d2p):
rt.setValue("FLAG", row, 0)
else:
current_angle = angle_rows[row]
next_angle = angle_rows[next_row]
current_delta = delta_rows[row]
flag = -1 if current_angle < 0 else 1
delta_change = (abs(current_delta) > 90)
same_sign = ((current_angle<0) == (next_angle<0))
if delta_change and not same_sign:
flag *= -1
rt.setValue("FLAG", row, flag)
if next_row == n_rows - 1:
rt.setValue("FLAG", next_row, flag)
if rt.save(table_file.getAbsolutePath()):
log("Processed table successfully saved (file overwritten)")
else:
log("Could not override input file. Displaying it...")
rt.show(table_file.name)
log("Creating onset table...")
onset_rt = RT()
onset_rt.showRowNumbers(False)
frame_int = DEF_FRAME_INTERVAL
if "table" in frame_rate_detection:
frame_int = getFrameIntervalFromTable(row_indices, track_id_rows, t_rows)
elif "image" in frame_rate_detection:
frame_int = getFrameIntervalFromImage(image_file.getAbsolutePath())
else:
log("Using default frame rate")
for track_id in track_ids:
for prev_row, row in zip(row_indices, row_indices[1:]):
if not track_id in (track_id_rows[prev_row], track_id_rows[row]):
continue
flag = rt.getValue("FLAG", row)
if not isNumber(flag):
continue
flag = int(flag)
if flag == 0:
continue
if flag == 1 or flag == -1:
srow = onset_rt.getCounter()
onset_rt.incrementCounter()
onset_rt.setValue("TID", srow, track_id)
from_frame = int(t_rows[prev_row]/frame_int) + 1
to_frame = int(t_rows[row]/frame_int) + 1
onset_rt.setValue("First disp. [t]", srow,
"%s to %s" % (t_rows[prev_row], t_rows[row]))
onset_rt.setValue("First disp. [frames]", srow,
"%s to %s" % (from_frame, to_frame))
onset_rt.setValue("ManualTag", srow, "")
break
out_path = suffixed_path(table_file.getAbsolutePath(), "ManualTagging")
if onset_rt.save(out_path):
log("Summary table successfully saved: %s" % out_path)
else:
log("File not saved... Displaying onset table")
onset_rt.show("Onsets %s" % table_file.name)
CELL_LABEL_COLUMN = "cell"
FEATURES = ["POSITION_X", "POSITION_Y", "FRAME"]
trackIDs = model.getTrackModel().trackIDs(True)
results = ResultsTable()
# Parse spots to insert values as objects
for trackID in trackIDs:
track = model.getTrackModel().trackSpots(trackID)
# Sort by frame
sortedTrack = list(track)
sortedTrack.sort(key=lambda s: s.getFeature("FRAME"))
for spot in sortedTrack:
results.incrementCounter()
results.addValue(ID_COLUMN, "" + str(spot.ID()))
# results.addValue(CELL_LABEL_COLUMN,str(int(spot.getFeature("MAX_INTENSITY"))))
results.addValue(CELL_LABEL_COLUMN, spot.getName())
results.addValue(TRACK_ID_COLUMN, "" + str(trackID))
for feature in FEATURES:
val = spot.getFeature(feature)
if math.isnan(val):
results.addValue(feature.lower(), "None")
else:
results.addValue(feature.lower(), "" + str(int(val)))
parents = []
children = []
for edge in model.getTrackModel().edgesOf(spot):
source, target = model.getTrackModel().getEdgeSource(
def main(imp,options):
from ij.plugin import ChannelSplitter
from ij.gui import Roi,PointRoi, PolygonRoi, Overlay, Line
from java.awt import Color
from ij import WindowManager
from ij.measure import ResultsTable
from ij.text import TextWindow
active_z=imp.getZ()
imps = ChannelSplitter.split(imp)
imp.setZ(active_z)
roi_int = imp.getRoi()
comp_imp=Zproj(imps[options["comp_ch"]],
"SUM",
active_z,
options["z_range"])
comp_imp=mode_subtract(comp_imp,roi_int)
loci_imp=Zproj(imps[options["loci_ch"]],
"SUM",
imp.getZ(),
options["z_range"])
loci_imp=mode_subtract(loci_imp,roi_int)
#Finding the boundaries of compartment and loci
comp_roi=thresh(sum_prj=comp_imp,thresh=options["comp_T"],roi=roi_int,method="boundary")
print "ok"
if (options["loci_method"]== "locus center"):
loci_roi=thresh(sum_prj=loci_imp,
thresh=options["loci_T"],
roi=roi_int,
method="point")
elif options["loci_method"]== "locus boundary":
loci_roi=thresh(sum_prj=loci_imp,
thresh=options["loci_T"],
roi=roi_int,
method="boundary")
if options["loci_method"]== "locus center":
dist,xc,yc,xl,yl=get_center_edge_dist(imp,comp_roi, loci_roi)
elif options["loci_method"]== "locus boundary":
dist,xc,yc,xl,yl=get_closest_points(imp,comp_roi,loci_roi)
rt_exist = WindowManager.getWindow("Loci distance to compartment")
if rt_exist==None or not isinstance(rt_exist, TextWindow):
table= ResultsTable()
else:
table = rt_exist.getTextPanel().getOrCreateResultsTable()
table.incrementCounter()
table.addValue("Label", imp.title)
table.addValue("Distance(micron)", dist)
if options['measure_feret']:
feret_roi,loci_feret,loci_area= feret(sum_prj=loci_imp,thresh=options["loci_T"],
roi=roi_int,pixel_size=imp.getCalibration().pixelWidth)
table.addValue("Loci feret", loci_feret)
table.addValue("Loci area", loci_area)
table.show("Loci distance to compartment")
## Adding loci overlay
ov=imp.getOverlay()
if ov==None:
ov=Overlay()
line = Line(xc,yc, xl,yl)
line.setStrokeWidth(0.2)
line.setStrokeColor(Color.PINK)
ov.add(line)
if options["loci_method"]== "locus center":
ov.add(PointRoi(loci_roi["x"],loci_roi["y"]))
elif options["loci_method"]== "locus boundary":
ov.add(loci_roi)
if options['measure_feret']:
ov.add(feret_roi)
ov.add(comp_roi)
imp.setOverlay(ov)
def runScript():
# find table with trajectories
rt = findResultsTable(inputTableName)
if rt == None:
print("Results table window titled [" + inputTableName +
"] not found!")
return
# get input image and its properties
img = WindowManager.getCurrentImage()
if img == None:
print("Could not access input image!")
return
print("Processing image:", img)
xLen = img.getWidth()
yLen = img.getHeight()
zLen = img.getNSlices()
noOfFrames = img.getNFrames()
noOfChannels = img.getNChannels()
stack = img.getStack()
if (noOfChannels > 1):
print(
"Cannot process images with channels. Convert image to single channel first!"
)
return
# Start processin data row by row...
numOfRows = rt.getCounter()
if numOfRows > 1:
#create output tableName
if showOutputTable: outputTable = ResultsTable()
# if output in csv format requested print header
if printOutputData:
print("trajectory;frame;m0;sizeInPixels;avgIntensity")
for idx in range(0, numOfRows):
trajectoryId = rt.getValue("Trajectory", idx)
x = rt.getValue("x", idx)
y = rt.getValue("y", idx)
z = rt.getValue("z", idx)
frame = rt.getValue("Frame", idx)
m0, size, avgInt = getIntensityData(stack, radius, frame, x, y, z,
xLen, yLen, zLen)
# if output in csv format requested print it
if printOutputData:
print(
str(int(trajectoryId)) + ";" + str(frame) + ";" + str(m0) +
";" + str(size) + ";" + str(avgInt))
# if output table requested update it with data
if showOutputTable:
outputTable.incrementCounter()
outputTable.addValue("", idx + 1)
outputTable.addValue("trajectory", int(trajectoryId))
outputTable.addValue("frame", frame)
outputTable.addValue("m0", m0)
outputTable.addValue("sizeInPixels", size)
outputTable.addValue("avgIntensity", avgInt)
if showOutputTable: outputTable.show(outputTableName)
resultsTable = ResultsTable()
resultsTable.showRowNumbers(False)
for i in range(0, len(results)):
if options['oneShot']:
localBackground = options['localBackground']
seedRadius = options['seedRadius']
gaussXY = options['gaussXY']
gaussZ = options['gaussZ']
else:
localBackground = parameters[i]['localBackground']
seedRadius = parameters[i]['seedRadius']
gaussXY = parameters[i]['gaussXY']
gaussZ = parameters[i]['gaussZ']
resultsTable.incrementCounter()
resultsTable.addValue("Threshold", localBackground)
resultsTable.addValue("Seed radius", seedRadius)
resultsTable.addValue("GXY", gaussXY)
resultsTable.addValue("GZ", gaussZ)
resultsTable.addValue("TOTAL", results[i]['all'])
resultsTable.addValue("0-250", results[i]['0'])
resultsTable.addValue("251-500", results[i]['250'])
resultsTable.addValue("501-750", results[i]['500'])
resultsTable.addValue("751-1000", results[i]['750'])
resultsTable.addValue("1001-1500", results[i]['1000'])
resultsTable.addValue(">1501", results[i]['1500'])
resultsTable.addValue("Skipped", results[i]['edge'])
resultsTable.save(options['outputDir'] + options['outputFile'])
def open_Octopus_file():
# set up a file info structure
fi = FileInfo()
fi.fileFormat = fi.RAW
fi.fileType=FileInfo.GRAY16_UNSIGNED
fi.intelByteOrder = True
fi.nImages = 1
op = OpenDialog("Choose Octopus .dth file...", "")
if not op.getDirectory(): return False
# get the file extension
file_extension = re.search('(\.[a-z][a-z][a-z])', op.getFileName()).group(1)
if file_extension != ".dth":
dlg = GenericDialog("Warning")
dlg.addMessage("Please select an octopus .dth file")
dlg.showDialog()
return False
# now strip the filename into a stem and index
file_parse = re.match('([a-zA-z0-9_]*_)([0-9]+)\.dth', op.getFileName())
file_stem = file_parse.group(1)
file_index = int( file_parse.group(2) )
# ok now we need to parse the header info
header = get_Octopus_header(op.getDirectory(), file_stem, file_index)
fi.nImages = len(header['N'])
# check to see whether we have a bit depth, if not, assume 16-bit
if 'Bit_Depth' in header:
print header['Bit_Depth']
bit_depth = int(header['Bit_Depth'][0])
if bit_depth == 8: fi.fileType = FileInfo.GRAY8
else:
bit_depth = 16
# will assume that all files have the same size
fi.width = int( header['W'][0] )
fi.height = int( header['H'][0] )
file_timestamp = strftime("%a, %d %b %Y %H:%M:%S", gmtime(float(header['Time'][0])) )
# make a new imagestack to store the data
stack = ImageStack(fi.width, fi.height)
# finally, we need to make a list of files to import as sometimes we have
# non contiguous file numbers
try:
files = os.listdir(op.getDirectory())
except IOError:
raise IOError( "No files exist in directory: " + op.getDirectory())
filenums = []
for f in files:
# strip off the stem, and get the number
targetfile = re.match(file_stem+'([0-9]+)\.dth', f)
# only take thosefiles which match the formatting requirements
if targetfile:
filenums.append( int(targetfile.group(1)) )
# sort the file numbers
sorted_filenums = sorted(filenums)
# make a file stats string
file_stats_str = file_stem + '\n' + str(fi.width) +'x' + str(fi.height) + 'x' + \
str(len(sorted_filenums)) +' ('+str(bit_depth)+'-bit)\n' + file_timestamp
# now open a dialog to let the user set options
dlg = GenericDialog("Load Octopus Stream (v"+__version__+")")
dlg.addMessage(file_stats_str)
dlg.addStringField("Title: ", file_stem)
dlg.addNumericField("Start: ", 1, 0);
dlg.addNumericField("End: ", len(sorted_filenums), 0)
dlg.addCheckbox("Open headers", True)
dlg.addCheckbox("Contiguous stream?", False)
dlg.addCheckbox("8-bit unsigned", bit_depth==8)
dlg.showDialog()
# if we cancel the dialog, exit here
if dlg.wasCanceled():
return
# set some params
file_title = dlg.getNextString()
file_start = dlg.getNextNumber()
file_end = dlg.getNextNumber()
DISPLAY_HEADER = bool( dlg.getNextBoolean() )
# check the ranges
if file_start > file_end:
file_start, file_end = file_end, file_start
if file_start < 1:
file_start = 1
if file_end > len(sorted_filenums):
file_end = len(sorted_filenums)
# now set these to the actual file numbers in the stream
file_start = sorted_filenums[int(file_start)-1]
file_end = sorted_filenums[int(file_end)-1]
files_to_open = [n for n in sorted_filenums if n>=file_start and n<=file_end]
# if we've got too many, truncate the list
if (len(files_to_open) * fi.nImages * fi.width * fi.height) > (MAX_FRAMES_TO_IMPORT*512*512):
dlg = GenericDialog("Warning")
dlg.addMessage("This may use a lot of memory. Continue?")
dlg.showDialog()
if dlg.wasCanceled(): return False
IJ.log( "Opening file: " + op.getDirectory() + op.getFileName() )
IJ.log( file_stats_str + "\nFile range: " + str(files_to_open[0]) + \
"-" + str(files_to_open[-1]) +"\n" )
# make a results table for the metadata
# NOTE: horrible looping at the moment, but works
if DISPLAY_HEADER:
rt = ResultsTable()
# ok now we can put the files together into the stack
for i in files_to_open:
# open the original .dat file and get the stack
fi.fileName = get_Octopus_filename( op.getDirectory(), file_stem, i)
if os.path.isfile( fi.fileName ):
fo = FileOpener(fi)
imp = fo.open(False).getStack()
# put the slices into the stack
for im_slice in xrange( imp.getSize() ):
ip = imp.getProcessor( im_slice+1 )
if bit_depth == 8:
bi = ip.getBufferedImage()
else:
bi = ip.get16BitBufferedImage()
stack.addSlice( file_title, ip )
if DISPLAY_HEADER:
header = get_Octopus_header(op.getDirectory(), file_stem, i)
for n in xrange(len(header['N'])):
rt.incrementCounter()
for k in header.keys():
rt.addValue(k, parse_header( header[k][n] ) )
else:
break
# done!
output = ImagePlus('Octopus ('+file_stem+')', stack)
output.show()
if DISPLAY_HEADER:
rt.show("Octopus header metadata")
return True
Prefs.blackBackground = False
IJ.run(mask, "Make Binary", "")
IJ.run(mask, "Invert", "")
#Colocalization Test
IJ.run(
red, "Colocalization Test",
"channel_1=[" + red.getTitle() + "] channel_2=[" + green.getTitle() +
"] roi=mask randomization=[Fay (x,y,z translation)]")
red.close()
green.close()
mask.changes = False
mask.close()
#get ResultsTable object and save it
textpanel = WindowManager.getFrame("Results").getTextPanel()
resultline = textpanel.getLine(textpanel.getLineCount() - 1)
value = float(resultline.split('\t')[1])
print value
allResultsTitle = "Summary"
frame = WindowManager.getFrame(allResultsTitle)
summaryrt = None
if frame is not None:
summaryrt = frame.getTextPanel().getResultsTable()
else:
summaryrt = ResultsTable()
summaryrt.incrementCounter()
summaryrt.addValue("Image", imp.getTitle())
summaryrt.addValue("R(obs)", value)
summaryrt.show(allResultsTitle)
#imagetitle = image.getTitle().split(".")[0]
#rtfile = path.join(outputdir, str(size)+"Summary_" + imagetitle + ".csv")
def run(imp, preprocessor_path, postprocessor_path, threshold_method,
user_comment):
output_parameters = {
"image title": "",
"preprocessor path": float,
"post processor path": float,
"thresholding op": float,
"use ridge detection": bool,
"high contrast": int,
"low contrast": int,
"line width": int,
"minimum line length": int,
"mitochondrial footprint": float,
"branch length mean": float,
"branch length median": float,
"branch length stdevp": float,
"summed branch lengths mean": float,
"summed branch lengths median": float,
"summed branch lengths stdevp": float,
"network branches mean": float,
"network branches median": float,
"network branches stdevp": float
}
output_order = [
"image title", "preprocessor path", "post processor path",
"thresholding op", "use ridge detection", "high contrast",
"low contrast", "line width", "minimum line length",
"mitochondrial footprint", "branch length mean",
"branch length median", "branch length stdevp",
"summed branch lengths mean", "summed branch lengths median",
"summed branch lengths stdevp", "network branches mean",
"network branches median", "network branches stdevp"
]
# Perform any preprocessing steps...
status.showStatus("Preprocessing image...")
if preprocessor_path != None:
if preprocessor_path.exists():
preprocessor_thread = scripts.run(preprocessor_path, True)
preprocessor_thread.get()
imp = WindowManager.getCurrentImage()
else:
pass
# Store all of the analysis parameters in the table
if preprocessor_path == None:
preprocessor_str = ""
else:
preprocessor_str = preprocessor_path.getCanonicalPath()
if postprocessor_path == None:
postprocessor_str = ""
else:
postprocessor_str = preprocessor_path.getCanonicalPath()
output_parameters["preprocessor path"] = preprocessor_str
output_parameters["post processor path"] = postprocessor_str
output_parameters["thresholding op"] = threshold_method
output_parameters["use ridge detection"] = str(use_ridge_detection)
output_parameters["high contrast"] = rd_max
output_parameters["low contrast"] = rd_min
output_parameters["line width"] = rd_width
output_parameters["minimum line length"] = rd_length
# Create and ImgPlus copy of the ImagePlus for thresholding with ops...
status.showStatus("Determining threshold level...")
imp_title = imp.getTitle()
slices = imp.getNSlices()
frames = imp.getNFrames()
output_parameters["image title"] = imp_title
imp_calibration = imp.getCalibration()
imp_channel = Duplicator().run(imp, imp.getChannel(), imp.getChannel(), 1,
slices, 1, frames)
img = ImageJFunctions.wrap(imp_channel)
# Determine the threshold value if not manual...
binary_img = ops.run("threshold.%s" % threshold_method, img)
binary = ImageJFunctions.wrap(binary_img, 'binary')
binary.setCalibration(imp_calibration)
binary.setDimensions(1, slices, 1)
# Get the total_area
if binary.getNSlices() == 1:
area = binary.getStatistics(Measurements.AREA).area
area_fraction = binary.getStatistics(
Measurements.AREA_FRACTION).areaFraction
output_parameters[
"mitochondrial footprint"] = area * area_fraction / 100.0
else:
mito_footprint = 0.0
for slice in range(binary.getNSlices()):
binary.setSliceWithoutUpdate(slice)
area = binary.getStatistics(Measurements.AREA).area
area_fraction = binary.getStatistics(
Measurements.AREA_FRACTION).areaFraction
mito_footprint += area * area_fraction / 100.0
output_parameters[
"mitochondrial footprint"] = mito_footprint * imp_calibration.pixelDepth
# Generate skeleton from masked binary ...
# Generate ridges first if using Ridge Detection
if use_ridge_detection and (imp.getNSlices() == 1):
skeleton = ridge_detect(imp, rd_max, rd_min, rd_width, rd_length)
else:
skeleton = Duplicator().run(binary)
IJ.run(skeleton, "Skeletonize (2D/3D)", "")
# Analyze the skeleton...
status.showStatus("Setting up skeleton analysis...")
skel = AnalyzeSkeleton_()
skel.setup("", skeleton)
status.showStatus("Analyzing skeleton...")
skel_result = skel.run()
status.showStatus("Computing graph based parameters...")
branch_lengths = []
summed_lengths = []
graphs = skel_result.getGraph()
for graph in graphs:
summed_length = 0.0
edges = graph.getEdges()
for edge in edges:
length = edge.getLength()
branch_lengths.append(length)
summed_length += length
summed_lengths.append(summed_length)
output_parameters["branch length mean"] = eztables.statistical.average(
branch_lengths)
output_parameters["branch length median"] = eztables.statistical.median(
branch_lengths)
output_parameters["branch length stdevp"] = eztables.statistical.stdevp(
branch_lengths)
output_parameters[
"summed branch lengths mean"] = eztables.statistical.average(
summed_lengths)
output_parameters[
"summed branch lengths median"] = eztables.statistical.median(
summed_lengths)
output_parameters[
"summed branch lengths stdevp"] = eztables.statistical.stdevp(
summed_lengths)
branches = list(skel_result.getBranches())
output_parameters["network branches mean"] = eztables.statistical.average(
branches)
output_parameters["network branches median"] = eztables.statistical.median(
branches)
output_parameters["network branches stdevp"] = eztables.statistical.stdevp(
branches)
# Create/append results to a ResultsTable...
status.showStatus("Display results...")
if "Mito Morphology" in list(WindowManager.getNonImageTitles()):
rt = WindowManager.getWindow(
"Mito Morphology").getTextPanel().getOrCreateResultsTable()
else:
rt = ResultsTable()
rt.incrementCounter()
for key in output_order:
rt.addValue(key, str(output_parameters[key]))
# Add user comments intelligently
if user_comment != None and user_comment != "":
if "=" in user_comment:
comments = user_comment.split(",")
for comment in comments:
rt.addValue(comment.split("=")[0], comment.split("=")[1])
else:
rt.addValue("Comment", user_comment)
rt.show("Mito Morphology")
# Create overlays on the original ImagePlus and display them if 2D...
if imp.getNSlices() == 1:
status.showStatus("Generate overlays...")
IJ.run(skeleton, "Green", "")
IJ.run(binary, "Magenta", "")
skeleton_ROI = ImageRoi(0, 0, skeleton.getProcessor())
skeleton_ROI.setZeroTransparent(True)
skeleton_ROI.setOpacity(1.0)
binary_ROI = ImageRoi(0, 0, binary.getProcessor())
binary_ROI.setZeroTransparent(True)
binary_ROI.setOpacity(0.25)
overlay = Overlay()
overlay.add(binary_ROI)
overlay.add(skeleton_ROI)
imp.setOverlay(overlay)
imp.updateAndDraw()
# Generate a 3D model if a stack
if imp.getNSlices() > 1:
univ = Image3DUniverse()
univ.show()
pixelWidth = imp_calibration.pixelWidth
pixelHeight = imp_calibration.pixelHeight
pixelDepth = imp_calibration.pixelDepth
# Add end points in yellow
end_points = skel_result.getListOfEndPoints()
end_point_list = []
for p in end_points:
end_point_list.append(
Point3f(p.x * pixelWidth, p.y * pixelHeight, p.z * pixelDepth))
univ.addIcospheres(end_point_list, Color3f(255.0, 255.0, 0.0), 2,
1 * pixelDepth, "endpoints")
# Add junctions in magenta
junctions = skel_result.getListOfJunctionVoxels()
junction_list = []
for p in junctions:
junction_list.append(
Point3f(p.x * pixelWidth, p.y * pixelHeight, p.z * pixelDepth))
univ.addIcospheres(junction_list, Color3f(255.0, 0.0, 255.0), 2,
1 * pixelDepth, "junctions")
# Add the lines in green
graphs = skel_result.getGraph()
for graph in range(len(graphs)):
edges = graphs[graph].getEdges()
for edge in range(len(edges)):
branch_points = []
for p in edges[edge].getSlabs():
branch_points.append(
Point3f(p.x * pixelWidth, p.y * pixelHeight,
p.z * pixelDepth))
univ.addLineMesh(branch_points, Color3f(0.0, 255.0, 0.0),
"branch-%s-%s" % (graph, edge), True)
# Add the surface
univ.addMesh(binary)
univ.getContent("binary").setTransparency(0.5)
# Perform any postprocessing steps...
status.showStatus("Running postprocessing...")
if postprocessor_path != None:
if postprocessor_path.exists():
postprocessor_thread = scripts.run(postprocessor_path, True)
postprocessor_thread.get()
else:
pass
status.showStatus("Done analysis!")
def runScript():
# find table with trajectories
rt = findResultsTable(inputTableName)
if rt == None:
print("Results table window titled [" + inputTableName +
"] not found!")
return
numOfRows = rt.getCounter()
if numOfRows > 1:
#create output tableName
if showOutputTable: velocityRT = ResultsTable()
# if output in csv format requested print header
if printOutputData:
print("trajectory;pathLen;noOfFrames;velocity;velocity stddev")
# read first data point
trajectoryId = rt.getValue("Trajectory", 0)
posX = rt.getValue("x", 0)
posY = rt.getValue("y", 0)
posZ = rt.getValue("z", 0)
startFrame = rt.getValue("Frame", 0)
frame = startFrame
trajDistances = [] # distances per frame measured in pixels
for idx in range(1, numOfRows):
currTrajectoryId = rt.getValue("Trajectory", idx)
currPosX = rt.getValue("x", idx)
currPosY = rt.getValue("y", idx)
currPosZ = rt.getValue("z", idx)
currFrame = rt.getValue("Frame", idx)
# if true we are still reading data from 'current' trajectory
if trajectoryId == currTrajectoryId:
distance = ((currPosX - posX)**2 + (currPosY - posY)**2 +
(currPosZ - posZ)**2)**(0.5)
# since trajectory data point can "jump" over some frames (depending on link range setting) calculated distance
# is divided to get average per one frame and added multiple time if needed (necessary for calculating correct stddev)
noOfFrames = currFrame - frame
distancePerFrame = distance / (currFrame - frame)
for i in range(int(noOfFrames)):
trajDistances.append(distancePerFrame)
# if true we have read data point from next trajectory or this is very last point of data
# calculate trajectory info
if trajectoryId != currTrajectoryId or idx == numOfRows - 1:
# calculate trajectory lenght
trajDistancesTrueLen = [
pixelResolution * d for d in trajDistances
]
pathLen = sum(trajDistancesTrueLen)
# calculate length of trajectory in frames
if idx == numOfRows - 1:
stopFrame = currFrame
else:
stopFrame = frame
numOfFrames = stopFrame - startFrame
# calculate velocity and std dev
velocity = pathLen / (numOfFrames * frameInterval)
standardDev = stddev(
[d / frameInterval for d in trajDistancesTrueLen])
# if output in csv format requested print it
if printOutputData:
print(
str(int(trajectoryId)) + ";" + str(pathLen) + ";" +
str(numOfFrames) + ";" + str(velocity) + ";" +
str(standardDev))
# if output table requested update it with data
if showOutputTable:
velocityRT.incrementCounter()
velocityRT.addValue("trajectory", int(trajectoryId))
velocityRT.addValue("pathLen", pathLen)
velocityRT.addValue("noOfFrames", numOfFrames)
velocityRT.addValue("velocity", velocity)
velocityRT.addValue("velocity stddev", standardDev)
# beginning of new trajectory
trajDistances = []
startFrame = rt.getValue("Frame", idx)
trajectoryId = currTrajectoryId
posX = currPosX
posY = currPosY
posZ = currPosZ
frame = currFrame
velocityRT.show(outputTableName)
Channel4 = Generate_segmented_manual(imp1, 4, "Moments", 2)
# # # # Generate ROIs by "Analyse Particles"
IJ.run(Channel4, "Analyze Particles...",
"size=5-Infinity pixel add exclude stack")
IJ.run("Clear Results", "")
Channel4_count = RoiManager.getInstance().getCount()
print Channel4_count
time.sleep(0.5)
rm.runCommand("reset")
time.sleep(0.5)
ort = ResultsTable()
ort.setPrecision(2)
ort.incrementCounter()
ort.addValue("Channel1", Channel1_count)
ort.addValue("Channel2", Channel2_count)
ort.addValue("Channel3", Channel3_count)
ort.addValue("Channel4", Channel4_count)
ort.show("Results")
if automatic_save_results:
dataname = imp1.getTitle()
filename = dataname + ".csv"
#files = glob.glob(savepath+"/"+dataname+"*.csv")
savename = savepath + "/" + filename
ort.saveAs(savename)
Channel1.changes = False
Channel1.close()
br_uncorr = math.sqrt((x_col[1] - x_col[0])**2 + (y_col[1] - y_col[0])**2)
br_thick = (z_col[1] - z_col[0]) * z_thick
br_corr = math.sqrt(br_uncorr**2 + br_thick**2)
po_uncorr = math.sqrt((x_col[2] - x_col[1])**2 + (y_col[2] - y_col[1])**2)
po_thick = (z_col[2] - z_col[1]) * z_thick
po_corr = math.sqrt(po_uncorr**2 + po_thick**2)
mbl = math.sqrt((x_col[4] - x_col[3])**2 + (y_col[4] - y_col[3])**2)
sl = math.sqrt((x_col[6] - x_col[5])**2 + (y_col[6] - y_col[5])**2)
sw = math.sqrt((x_col[8] - x_col[7])**2 + (y_col[8] - y_col[7])**2)
IJ.run("Clear Results")
# Append to custom Measurement table or create it if non existing
MeasureTable = WindowManager.getWindow("Measurements")
if MeasureTable == None:
MeasureTable = ResultsTable()
else:
MeasureTable = WindowManager.getWindow("Measurements")
MeasureTable = MeasureTable.getTextPanel().getOrCreateResultsTable()
MeasureTable.incrementCounter()
MeasureTable.addValue("BR", br_corr)
MeasureTable.addValue("PO", po_corr)
MeasureTable.addValue("MBL", mbl)
MeasureTable.addValue("SL", sl)
MeasureTable.addValue("SW", sw)
MeasureTable.show("Measurements")
ipch3 = impch3.getImageStack().getProcessor(int(zA[i]) + 1)
dotRoi = OvalRoi(int(yA[i] - xyoffset), int(xA[i] - xyoffset), thdist, thdist)
ipch2.setRoi(dotRoi)
#stats = IS.getStatistics(ip, options, imp.getCalibration())
stats = IS.getStatistics(ipch2, options, cal)
ipch3.setRoi(dotRoi)
statsch3 = IS.getStatistics(ipch3, options, cal)
print "dot", i
print "...ch2 TotalInt ", stats.area * stats.mean
print "...ch2 Area ", stats.area
print "...ch2 mean ", stats.mean
print ".."
print "...ch3 TotalInt ", statsch3.area * statsch3.mean
print "...ch3 Area ", statsch3.area
print "...ch3 mean ", statsch3.mean
rt.incrementCounter()
rt.setValue("DotID", ct, i)
rt.setValue("DotX", ct, yA[i])
rt.setValue("DotY", ct, xA[i])
rt.setValue("DotZ", ct, zA[i])
rt.setValue("Ch2_TotalIntensity", ct, stats.area * stats.mean)
rt.setValue("Ch2_MeanIntensity", ct, stats.mean)
rt.setValue("Ch3_TotalIntensity", ct, statsch3.area * statsch3.mean)
rt.setValue("Ch3_meanIntensity", ct, statsch3.mean)
ct += 1
rt.show("Dot Intensity")
#AREA, AREA_FRACTION, CENTER_OF_MASS, CENTROID, CIRCULARITY, ELLIPSE, FERET,
#INTEGRATED_DENSITY, INVERT_Y, KURTOSIS, LABELS, LIMIT, MAX_STANDARDS, MEAN,
#MEDIAN, MIN_MAX, MODE, PERIMETER, RECT, SCIENTIFIC_NOTATION, SHAPE_DESCRIPTORS,
def run(imp, preprocessor_path, postprocessor_path, threshold_method, user_comment):
output_parameters = {"image title" : "",
"preprocessor path" : float,
"post processor path" : float,
"thresholding op" : float,
"use ridge detection" : bool,
"high contrast" : int,
"low contrast" : int,
"line width" : int,
"minimum line length" : int,
"mitochondrial footprint" : float,
"branch length mean" : float,
"branch length median" : float,
"branch length stdevp" : float,
"summed branch lengths mean" : float,
"summed branch lengths median" : float,
"summed branch lengths stdevp" : float,
"network branches mean" : float,
"network branches median" : float,
"network branches stdevp" : float}
output_order = ["image title",
"preprocessor path",
"post processor path",
"thresholding op",
"use ridge detection",
"high contrast",
"low contrast",
"line width",
"minimum line length",
"mitochondrial footprint",
"branch length mean",
"branch length median",
"branch length stdevp",
"summed branch lengths mean",
"summed branch lengths median",
"summed branch lengths stdevp",
"network branches mean",
"network branches median",
"network branches stdevp"]
# Perform any preprocessing steps...
status.showStatus("Preprocessing image...")
if preprocessor_path != None:
if preprocessor_path.exists():
preprocessor_thread = scripts.run(preprocessor_path, True)
preprocessor_thread.get()
imp = WindowManager.getCurrentImage()
else:
pass
# Store all of the analysis parameters in the table
if preprocessor_path == None:
preprocessor_str = ""
else:
preprocessor_str = preprocessor_path.getCanonicalPath()
if postprocessor_path == None:
postprocessor_str = ""
else:
postprocessor_str = preprocessor_path.getCanonicalPath()
output_parameters["preprocessor path"] = preprocessor_str
output_parameters["post processor path"] = postprocessor_str
output_parameters["thresholding op"] = threshold_method
output_parameters["use ridge detection"] = str(use_ridge_detection)
output_parameters["high contrast"] = rd_max
output_parameters["low contrast"] = rd_min
output_parameters["line width"] = rd_width
output_parameters["minimum line length"] = rd_length
# Create and ImgPlus copy of the ImagePlus for thresholding with ops...
status.showStatus("Determining threshold level...")
imp_title = imp.getTitle()
slices = imp.getNSlices()
frames = imp.getNFrames()
output_parameters["image title"] = imp_title
imp_calibration = imp.getCalibration()
imp_channel = Duplicator().run(imp, imp.getChannel(), imp.getChannel(), 1, slices, 1, frames)
img = ImageJFunctions.wrap(imp_channel)
# Determine the threshold value if not manual...
binary_img = ops.run("threshold.%s"%threshold_method, img)
binary = ImageJFunctions.wrap(binary_img, 'binary')
binary.setCalibration(imp_calibration)
binary.setDimensions(1, slices, 1)
# Get the total_area
if binary.getNSlices() == 1:
area = binary.getStatistics(Measurements.AREA).area
area_fraction = binary.getStatistics(Measurements.AREA_FRACTION).areaFraction
output_parameters["mitochondrial footprint"] = area * area_fraction / 100.0
else:
mito_footprint = 0.0
for slice in range(binary.getNSlices()):
binary.setSliceWithoutUpdate(slice)
area = binary.getStatistics(Measurements.AREA).area
area_fraction = binary.getStatistics(Measurements.AREA_FRACTION).areaFraction
mito_footprint += area * area_fraction / 100.0
output_parameters["mitochondrial footprint"] = mito_footprint * imp_calibration.pixelDepth
# Generate skeleton from masked binary ...
# Generate ridges first if using Ridge Detection
if use_ridge_detection and (imp.getNSlices() == 1):
skeleton = ridge_detect(imp, rd_max, rd_min, rd_width, rd_length)
else:
skeleton = Duplicator().run(binary)
IJ.run(skeleton, "Skeletonize (2D/3D)", "")
# Analyze the skeleton...
status.showStatus("Setting up skeleton analysis...")
skel = AnalyzeSkeleton_()
skel.setup("", skeleton)
status.showStatus("Analyzing skeleton...")
skel_result = skel.run()
status.showStatus("Computing graph based parameters...")
branch_lengths = []
summed_lengths = []
graphs = skel_result.getGraph()
for graph in graphs:
summed_length = 0.0
edges = graph.getEdges()
for edge in edges:
length = edge.getLength()
branch_lengths.append(length)
summed_length += length
summed_lengths.append(summed_length)
output_parameters["branch length mean"] = eztables.statistical.average(branch_lengths)
output_parameters["branch length median"] = eztables.statistical.median(branch_lengths)
output_parameters["branch length stdevp"] = eztables.statistical.stdevp(branch_lengths)
output_parameters["summed branch lengths mean"] = eztables.statistical.average(summed_lengths)
output_parameters["summed branch lengths median"] = eztables.statistical.median(summed_lengths)
output_parameters["summed branch lengths stdevp"] = eztables.statistical.stdevp(summed_lengths)
branches = list(skel_result.getBranches())
output_parameters["network branches mean"] = eztables.statistical.average(branches)
output_parameters["network branches median"] = eztables.statistical.median(branches)
output_parameters["network branches stdevp"] = eztables.statistical.stdevp(branches)
# Create/append results to a ResultsTable...
status.showStatus("Display results...")
if "Mito Morphology" in list(WindowManager.getNonImageTitles()):
rt = WindowManager.getWindow("Mito Morphology").getTextPanel().getOrCreateResultsTable()
else:
rt = ResultsTable()
rt.incrementCounter()
for key in output_order:
rt.addValue(key, str(output_parameters[key]))
# Add user comments intelligently
if user_comment != None and user_comment != "":
if "=" in user_comment:
comments = user_comment.split(",")
for comment in comments:
rt.addValue(comment.split("=")[0], comment.split("=")[1])
else:
rt.addValue("Comment", user_comment)
rt.show("Mito Morphology")
# Create overlays on the original ImagePlus and display them if 2D...
if imp.getNSlices() == 1:
status.showStatus("Generate overlays...")
IJ.run(skeleton, "Green", "")
IJ.run(binary, "Magenta", "")
skeleton_ROI = ImageRoi(0,0,skeleton.getProcessor())
skeleton_ROI.setZeroTransparent(True)
skeleton_ROI.setOpacity(1.0)
binary_ROI = ImageRoi(0,0,binary.getProcessor())
binary_ROI.setZeroTransparent(True)
binary_ROI.setOpacity(0.25)
overlay = Overlay()
overlay.add(binary_ROI)
overlay.add(skeleton_ROI)
imp.setOverlay(overlay)
imp.updateAndDraw()
# Generate a 3D model if a stack
if imp.getNSlices() > 1:
univ = Image3DUniverse()
univ.show()
pixelWidth = imp_calibration.pixelWidth
pixelHeight = imp_calibration.pixelHeight
pixelDepth = imp_calibration.pixelDepth
# Add end points in yellow
end_points = skel_result.getListOfEndPoints()
end_point_list = []
for p in end_points:
end_point_list.append(Point3f(p.x * pixelWidth, p.y * pixelHeight, p.z * pixelDepth))
univ.addIcospheres(end_point_list, Color3f(255.0, 255.0, 0.0), 2, 1*pixelDepth, "endpoints")
# Add junctions in magenta
junctions = skel_result.getListOfJunctionVoxels()
junction_list = []
for p in junctions:
junction_list.append(Point3f(p.x * pixelWidth, p.y * pixelHeight, p.z * pixelDepth))
univ.addIcospheres(junction_list, Color3f(255.0, 0.0, 255.0), 2, 1*pixelDepth, "junctions")
# Add the lines in green
graphs = skel_result.getGraph()
for graph in range(len(graphs)):
edges = graphs[graph].getEdges()
for edge in range(len(edges)):
branch_points = []
for p in edges[edge].getSlabs():
branch_points.append(Point3f(p.x * pixelWidth, p.y * pixelHeight, p.z * pixelDepth))
univ.addLineMesh(branch_points, Color3f(0.0, 255.0, 0.0), "branch-%s-%s"%(graph, edge), True)
# Add the surface
univ.addMesh(binary)
univ.getContent("binary").setTransparency(0.5)
# Perform any postprocessing steps...
status.showStatus("Running postprocessing...")
if postprocessor_path != None:
if postprocessor_path.exists():
postprocessor_thread = scripts.run(postprocessor_path, True)
postprocessor_thread.get()
else:
pass
status.showStatus("Done analysis!")
for peak in peaks:
# Read peak coordinates into an array of integers
peak.localize(p)
roi.addPoint(imp, p[0], p[1])
imp.setRoi(roi)
# Now, iterate each peak, defining a small interval centered at each peak,
# and measure the sum of total pixel intensity,
# and display the results in an ImageJ ResultTable.
table = ResultsTable()
for peak in peaks:
# Read peak coordinates into an array of integers
peak.localize(p)
# Define limits of the interval around the peak:
# (sigmaSmaller is half the radius of the embryo)
minC = [p[i] - sigmaSmaller for i in range(img.numDimensions())]
maxC = [p[i] + sigmaSmaller for i in range(img.numDimensions())]
# View the interval around the peak, as a flat iterable (like an array)
fov = Views.interval(img, minC, maxC)
# Compute sum of pixel intensity values of the interval
# (The t is the Type that mediates access to the pixels, via its get* methods)
s = sum(t.getInteger() for t in fov)
# Add to results table
table.incrementCounter()
table.addValue("x", p[0])
table.addValue("y", p[1])
table.addValue("sum", s)
table.show("Embryo intensities at peaks")
def run():
IJ.run("Close All", "")
IJ.log("\\Clear")
IJ.log("Find_close_peaks")
imp = IJ.run("Bio-Formats Importer")
imp = IJ.getImage()
Channel_1, Channel_2, radius_background, sigmaSmaller, sigmaLarger, minPeakValue, min_dist = getOptions()
IJ.log("option used:" \
+ "\n" + "channel 1:" + str(Channel_1) \
+ "\n" + "channel 2:"+ str(Channel_2) \
+ "\n" + "Radius Background:"+ str(radius_background) \
+ "\n" + "Smaller Sigma:"+ str(sigmaSmaller) \
+ "\n" + "Larger Sigma:"+str(sigmaLarger) \
+ "\n" + "Min Peak Value:"+str(minPeakValue) \
+ "\n" + "Min dist between peaks:"+str(min_dist))
IJ.log("Computing Max Intensity Projection")
if imp.getDimensions()[3] > 1:
imp_max = ZProjector.run(imp,"max")
#imp_max = IJ.run("Z Project...", "projection=[Max Intensity]")
#imp_max = IJ.getImage()
else:
imp_max = imp
ip1, ip2 = extract_channel(imp_max, Channel_1, Channel_2)
imp1, imp2 = back_substraction(ip1, ip2, radius_background)
imp1.show()
imp2.show()
IJ.log("Finding Peaks")
ip1_1, ip2_1, peaks_1, peaks_2 = find_peaks(imp1, imp2, sigmaSmaller, sigmaLarger, minPeakValue)
# Create a PointRoi from the DoG peaks, for visualization
roi_1 = PointRoi(0, 0)
roi_2 = PointRoi(0, 0)
roi_3 = PointRoi(0, 0)
roi_4 = PointRoi(0, 0)
# A temporary array of integers, one per dimension the image has
p_1 = zeros(ip1_1.numDimensions(), 'i')
p_2 = zeros(ip2_1.numDimensions(), 'i')
# Load every peak as a point in the PointRoi
for peak in peaks_1:
# Read peak coordinates into an array of integers
peak.localize(p_1)
roi_1.addPoint(imp1, p_1[0], p_1[1])
for peak in peaks_2:
# Read peak coordinates into an array of integers
peak.localize(p_2)
roi_2.addPoint(imp2, p_2[0], p_2[1])
# Chose minimum distance in pixel
#min_dist = 20
for peak_1 in peaks_1:
peak_1.localize(p_1)
for peak_2 in peaks_2:
peak_2.localize(p_2)
d1 = distance(p_1, p_2)
if d1 < min_dist:
roi_3.addPoint(imp1, p_2[0], p_2[1])
break
for peak_2 in peaks_2:
peak_2.localize(p_2)
for peak_1 in peaks_1:
peak_1.localize(p_1)
d2 = distance(p_2, p_1)
if d2 < min_dist:
roi_4.addPoint(imp1, p_2[0], p_2[1])
break
rm = RoiManager.getInstance()
if not rm:
rm = RoiManager()
rm.reset()
rm.addRoi(roi_1)
rm.addRoi(roi_2)
rm.addRoi(roi_3)
rm.addRoi(roi_4)
rm.select(0)
rm.rename(0, "ROI neuron")
rm.runCommand("Set Color", "yellow")
rm.select(1)
rm.rename(1, "ROI glioma")
rm.runCommand("Set Color", "blue")
rm.select(2)
rm.rename(2, "ROI glioma touching neurons")
rm.runCommand("Set Color", "red")
rm.select(3)
rm.rename(3, "ROI neurons touching glioma")
rm.runCommand("Set Color", "green")
rm.runCommand(imp1, "Show All")
#Change distance to be in um
cal = imp.getCalibration()
min_distance = str(round((cal.pixelWidth * min_dist),1))
table = ResultsTable()
table.incrementCounter()
table.addValue("Numbers of Neuron Markers", roi_1.getCount(0))
table.addValue("Numbers of Glioma Markers", roi_2.getCount(0))
table.addValue("Numbers of Glioma within %s um of Neurons" %(min_distance), roi_3.getCount(0))
table.addValue("Numbers of Neurons within %s um of Glioma" %(min_distance), roi_4.getCount(0))
table.show("Results Analysis")