def autoProcAZtecImage(fwMicrons, wrkDir, barWid=0.1, barHt=9, barFnt=24, barCol="Black", barLoc="Lower Right"): imp = IJ.getImage() fName = imp.getShortTitle() wid = imp.getWidth() argThree = "distance=%g known=%f pixel=1 unit=um" % (wid, fwMicrons) IJ.run(imp, "Set Scale...", argThree) IJ.run(imp, "Enhance Contrast", "saturated=0.35") fs = FileSaver(imp) if path.exists(wrkDir) and path.isdir(wrkDir): print "folder exists:", wrkDir tifName = fName + ".tif" tifPath = path.join(wrkDir, tifName) print(tifPath) if fs.saveAsTiff(tifPath): print "Tif saved successfully at ", tifPath IJ.run(imp, "RGB Color", "") # dummy to get things set foo = imp.duplicate() s2 = "width=%g height=%g font=%g color=%s location=[%s] bold" % (barWid, barHt, barFnt, barCol, barLoc) IJ.run(foo, "Add Scale Bar", s2) # explicitly save preferences Prefs.savePreferences() foo.changes = False foo.close() IJ.run(imp, "Add Scale Bar", s2) fs = FileSaver(imp) pngName = fName + ".png" pngPath = path.join(wrkDir, pngName) if fs.saveAsPng(pngPath): print "png saved successfully at ", pngPath
def showDialogR(R, val):
""" Create dialog for input and save R values in settings
"""
gui = GenericDialog("Heterogeneous Z Correction")
msg = "Heterogeneous Z Correction calculates an optical model\n"\
"based on rational fluorescence intensity attenuation\n"\
"over depth, in the form of (ax+b)/(x+c). Please specify\n"\
"(a,b,c) for each region. You should provide a z-stack with\n"\
"unique pixel values for each region.\n"
gui.addMessage(msg)
for ii in range(len(val)):
gui.addNumericField(
"Region " + str(ii) + " (" + str(val[ii]) + "): a", R[ii][0], 2)
gui.addToSameRow()
gui.addNumericField("b", R[ii][1], 2)
gui.addToSameRow()
gui.addNumericField("c", R[ii][2], 2)
gui.addHelp(
r"https://github.com/alexandrebastien/heterogeneous-z-correction")
gui.showDialog()
if gui.wasOKed():
R = []
for ii in range(len(val)):
R = R + [
(gui.getNextNumber(), gui.getNextNumber(), gui.getNextNumber())
]
Prefs.set("HetZCorr.R", str(R))
return R
else:
return
def addDefaultOptions(self):
'''
Add default GUI items
- checkbox runMeasurement
- add to Manager, nextSlice, runMeasurement
- resource message
- help button
'''
# Checkbox next slice and run Measure
self.addCheckbox("Auto next slice/image file",
bool(Prefs.get("annot.doNext", True)))
if self.browseMode == "stack":
self.addToSameRow()
self.addChoice("- dimension (for hyperstack)", hyperstackDim,
Prefs.get("annot.dimension", hyperstackDim[0]))
elif self.browseMode == "directory":
# Add button previous/next
self.addButton(BrowseButton.LABEL_PREVIOUS, BrowseButton())
self.addToSameRow()
self.addButton(BrowseButton.LABEL_NEXT, BrowseButton())
self.addMessage(
"Documentation and generic analysis workflows available on the GitHub repo (click Help)"
)
# Add Help button pointing to the github
self.addHelp(
r"https://github.com/LauLauThom/Fiji-QualiAnnotations#readme")
self.hideCancelButton()
def actionPerformed(self, event):
"""Delete the last row"""
# Generate a save dialog
dialog = JFileChooser(Prefs.get("roiGroup.importDir", ""))
dialog.setSelectedFile(File("roiGroups.txt"))
dialog.setFileFilter(FileNameExtensionFilter("Text file", ["txt"]))
output = dialog.showOpenDialog(
self.groupTable) # could be None argument too
if output in [JFileChooser.CANCEL_OPTION, JFileChooser.ERROR_OPTION]:
return
selectedFile = dialog.getSelectedFile()
directory = selectedFile.getParent()
Prefs.set("roiGroup.importDir", directory)
if not selectedFile.isFile(): return
filePath = selectedFile.getPath()
# Read comma-separated group from file
with open(filePath, "r") as textFile:
stringGroup = textFile.readline().rstrip()
# Update table with content of file
tableModel = self.groupTable.tableModel
tableModel.setGroupColumn(stringGroup)
def setReaderOptions(imagefile, stitchtiles=False,
setflatres=True,
setconcat=False,
openallseries=False,
showomexml=False,
attach=False,
autoscale=True):
czi_options = DynamicMetadataOptions()
czi_options.setBoolean("zeissczi.autostitch", stitchtiles)
czi_options.setBoolean("zeissczi.attachments", attach)
# set the option for the CZIReader
czireader = ImportTools.setCZIReaderOptions(imagefile, czi_options, setflatres=setflatres)
# Set the preferences in the ImageJ plugin
# Note although these preferences are applied, they are not refreshed in the UI
Prefs.set("bioformats.zeissczi.allow.autostitch", str(stitchtiles).lower())
Prefs.set("bioformats.zeissczi.include.attachments", str(attach).lower())
# set the option for the BioFormats import
reader_options = ImporterOptions()
reader_options.setOpenAllSeries(openallseries)
reader_options.setShowOMEXML(showomexml)
reader_options.setConcatenate(setconcat)
reader_options.setAutoscale(autoscale)
reader_options.setStitchTiles(stitchtiles)
reader_options.setId(imagefile)
return reader_options, czireader
def __init__(self):
self.window = None
self.tags = {}
self.prefkeys = ["{0}.{1}".format(SUBKEY, name) for name in COLORS]
self.userprefs = Prefs()
self.load()
while not self.tags:
self.edit("Please set at least one colortag.\n\n")
def getListCategories(self):
"""
Read the new category names entered by user in the GUI.
Save the values as a comma-separated string in persistence.
"""
listCategories = []
for textField in self.panel.getComponents():
newCategory = textField.getText()
if newCategory: listCategories.append(newCategory)
Prefs.set("annot.listCat", ",".join(listCategories) ) # save the new list of categories
return listCategories
def makeCategoryComponent(self, category):
"""
Generates a checkbox with the new category name, to add to the GUI
Overwrite the original method
"""
stringCat = Prefs.get("annot.listCat", "")
newStringCat = stringCat + "," + category if stringCat else category
Prefs.set("annot.listCat", newStringCat)
# Make a new checkbox with the category name
checkbox = Checkbox(category, False)
checkbox.setFocusable(
False) # important to have the keybard shortcut working
return checkbox
self.defaultActionSequence()
def makeCategoryComponent(self, category):
"""Return a button with the new category name, and mapped to the action"""
listCat.append(category)
# Save the new category in memory
Prefs.set("annot.listCat", ",".join(listCat) )
button = JButton(category)
button.addActionListener(categoryAction)
button.setFocusable(False)
# Add button tooltip if fit in the F1-F12 button range
nCat = len(listCat)
if nCat <= 12: button.setToolTipText("Keyboard shortcut: F" + str(nCat)) # F shortcut labels are 1-based, ie match the len value
def main(*R):
""" Main function
"""
# Show intial progress bar
IJ.showProgress(0, 50)
IJ.showStatus("Heterogeneous Z Correction")
# Retrieve the values R (with default values) from previous attempts
Rstr = "[(-0.05977, 83.3, 78.73),(-0.05976, 41.65, 39.36)]"
R = eval(Prefs.get("HetZCorr.R", Rstr))
# Load current image and get infos
imp = IJ.getImage()
stk = imp.getStack()
(sx, sy, sz) = stackSize(stk)
cal = imp.getCalibration()
# Get unique values
val = getUniqueValues(stk)
# Get R from dialog
R = showDialogR(R, val)
# Generate optical model
correction = generateModel(stk, R, val)
imp.setCalibration(cal)
#Show model image
correction.show()
correction.setSlice(sz)
IJ.run(correction, "Enhance Contrast", "saturated=0.35")
IJ.run(correction, "Fire", "")
def GetLastMeasureCount():
myCount = Prefs.get("JRM.meas.counter", int(-1))
if myCount < 0:
# it was not set, so set it to zero
resetLastMeasureCount()
return 0
else:
myCount = int(myCount)
return myCount
def actionPerformed(self, event):
'''
Handle buttons clicks, delegates to custom methods
OK: save parameters in memory
Add new category: delegate to addCategoryComponent() (should be overwritten in daughter)
Add: delegate to addAction()
NB: NEVER use getNext methods here, since we call them several time
'''
source = event.getSource() # test here if it is a button
if isinstance(
source, Button
): # if type is a button get label, and check command, otherwise pass to GenericDialogPlus.actionPeformed
sourceLabel = source.getLabel()
if sourceLabel == CustomDialog.LABEL_OK:
# Check options and save them in persistence
checkboxes = self.getCheckboxes()
doNext = checkboxes[-1].getState()
Prefs.set("annot.doNext", doNext)
# Save selected dimension if mode stack
if self.browseMode == "stack":
Prefs.set("annot.dimension", self.getSelectedDimension())
elif sourceLabel == "Add new category":
self.addCategoryComponent()
elif sourceLabel == self.LABEL_ADD:
self.addAction()
else:
pass
# Anyway do the mother class usual action handling
GenericDialogPlus.actionPerformed(self, event)
def actionPerformed(self, event):
"""Delete the last row"""
# Generate a save dialog
dialog = JFileChooser(Prefs.get("roiGroup.exportDir", ""))
dialog.setSelectedFile(File("roiGroups.txt"))
dialog.setFileFilter(FileNameExtensionFilter("Text file", ["txt"]))
output = dialog.showSaveDialog(
self.groupTable) # could be argument None too
if output in [JFileChooser.CANCEL_OPTION, JFileChooser.ERROR_OPTION]:
return
selectedFile = dialog.getSelectedFile()
directory = selectedFile.getParent()
Prefs.set("roiGroup.exportDir", directory)
filePath = selectedFile.getPath()
if not ("." in filePath):
filePath += ".txt" # Add extension if missing
# Write the groupString to the file
groupString = self.groupTable.tableModel.getGroupString()
with open(filePath, "w") as textFile:
textFile.write(groupString)
def debug_mode():
"""Wrapper to check if 'imcf.debugging' is enabled.
This is a workaround for a Jython issue in ImageJ with values that are
stored in the "IJ_Prefs.txt" file being cast to the wrong types and / or
values in Python. Callling Prefs.get() using a (Python) boolean as the
second parameter always leads to the return value '0.0' (Python type float),
no matter what is actually stored in the preferences. Doing the same in e.g.
Groovy behaves correctly.
Calling Prefs.get() as below with the second parameter being a string and
subsequently checking the string value leads to the expected result.
"""
debug = Prefs.get("imcf.debugging", "false")
return debug == "true"
def readCZI(imagefile,
metainfo,
stitchtiles=False,
setflatres=False,
readpylevel=0,
setconcat=False,
openallseries=True,
showomexml=False,
attach=False,
autoscale=True):
options = DynamicMetadataOptions()
options.setBoolean("zeissczi.autostitch", stitchtiles)
options.setBoolean("zeissczi.attachments", attach)
czireader = ZeissCZIReader()
czireader.setFlattenedResolutions(setflatres)
czireader.setMetadataOptions(options)
czireader.setId(imagefile)
# Set the preferences in the ImageJ plugin
# Note although these preferences are applied, they are not refreshed in the UI
Prefs.set("bioformats.zeissczi.allow.autostitch", str(stitchtiles).lower())
Prefs.set("bioformats.zeissczi.include.attachments", str(attach).lower())
# metainfo = {}
metainfo['rescount'] = czireader.getResolutionCount()
metainfo['SeriesCount_CZI'] = czireader.getSeriesCount()
metainfo['flatres'] = czireader.hasFlattenedResolutions()
# metainfo['getreslevel'] = czireader.getResolution()
# Dimensions
metainfo['SizeT'] = czireader.getSizeT()
metainfo['SizeZ'] = czireader.getSizeZ()
metainfo['SizeC'] = czireader.getSizeC()
metainfo['SizeX'] = czireader.getSizeX()
metainfo['SizeY'] = czireader.getSizeY()
# check for autostitching and possibility to read attachment
metainfo['AllowAutoStitching'] = czireader.allowAutostitching()
metainfo['CanReadAttachments'] = czireader.canReadAttachments()
# read in and display ImagePlus(es) with arguments
options = ImporterOptions()
options.setOpenAllSeries(openallseries)
options.setShowOMEXML(showomexml)
options.setConcatenate(setconcat)
options.setAutoscale(autoscale)
options.setId(imagefile)
# open the ImgPlus
imps = BF.openImagePlus(options)
metainfo['Pyramid Level Output'] = readpylevel
# read image data using the specified pyramid level
imp, slices, width, height, pylevel = ImageTools.getImageSeries(imps, series=readpylevel)
metainfo['Pyramid Level Output'] = pylevel
metainfo['Output Slices'] = slices
metainfo['Output SizeX'] = width
metainfo['Output SizeY'] = height
# calc scaling in case of pyramid
# scale = float(metainfo['Output SizeX']) / float(metainfo['SizeX'])
scale = float(metainfo['SizeX']) / float(metainfo['Output SizeX'])
metainfo['Pyramid Scale Factor'] = scale
metainfo['ScaleX Output'] = metainfo['ScaleX'] * scale
metainfo['ScaleY Output'] = metainfo['ScaleY'] * scale
"""
imp = MiscTools.setproperties(imp, scaleX=metainfo['ScaleX Output'],
scaleY=metainfo['ScaleX Output'],
scaleZ=metainfo['ScaleZ'],
unit="micron",
sizeC=metainfo['SizeC'],
sizeZ=metainfo['SizeZ'],
sizeT=metainfo['SizeT'])
"""
imp = MiscTools.setscale(imp, scaleX=metainfo['ScaleX Output'],
scaleY=metainfo['ScaleX Output'],
scaleZ=metainfo['ScaleZ'],
unit="micron")
# close czireader
czireader.close()
return imp, metainfo
def setLastMeasureCount(count):
count = int(count)
Prefs.set("JRM.meas.counter", count)
IJ.open(imgPath);
IJ.run("Properties...", "channels=1 slices=1 frames=1 unit=um pixel_width=0.03143555 pixel_height=0.03144531 voxel_depth=1.0000000");
orig = IJ.getImage();
ti = orig.getShortTitle();
pngPath = homDir + relDir + "/" + ti + ".png"
strBar = "width=%g height=%g font=%g color=%s location=[%s] bold" % (barW, barH, barF, barC, barL)
# a hack to get the scale bars to work reliably
IJ.run(orig, "RGB Color", "")
# dummy to get things set
foo = orig.duplicate()
IJ.run(foo, "Add Scale Bar", strBar)
# explicitly save preferences
Prefs.savePreferences()
foo.changes = False
foo.close()
IJ.run(orig, "Add Scale Bar", strBar)
print(pngPath)
fs = FileSaver(orig)
if fs.saveAsPng(pngPath):
print "png saved successfully at ", pngPath
time.sleep(sleepTime)
orig.close()
def main():
Interpreter.batchMode = True
if (lambda_flat == 0) ^ (lambda_dark == 0):
print ("ERROR: Both of lambda_flat and lambda_dark must be zero,"
" or both non-zero.")
return
lambda_estimate = "Automatic" if lambda_flat == 0 else "Manual"
print "Loading images..."
# For multi-scene .CZI files, we need raw tiles instead of the
# auto-stitched mosaic and we don't want labels or overview images. This
# only affects BF.openImagePlus, not direct use of the BioFormats reader
# classes which we also do (see below)
Prefs.set("bioformats.zeissczi.allow.autostitch", "false")
Prefs.set("bioformats.zeissczi.include.attachments", "false")
# Use BioFormats reader directly to determine dataset dimensions without
# reading every single image. The series count (num_images) is the one value
# we can't easily get any other way, but we might as well grab the others
# while we have the reader available.
dyn_options = DynamicMetadataOptions()
# Directly calling a BioFormats reader will not use the IJ Prefs settings
# so we need to pass these options explicitly.
dyn_options.setBoolean("zeissczi.autostitch", False)
dyn_options.setBoolean("zeissczi.attachments", False)
bfreader = ImageReader()
bfreader.setMetadataOptions(dyn_options)
bfreader.id = str(filename)
num_images = bfreader.seriesCount
num_channels = bfreader.sizeC
width = bfreader.sizeX
height = bfreader.sizeY
bfreader.close()
# The internal initialization of the BaSiC code fails when we invoke it via
# scripting, unless we explicitly set a the private 'noOfSlices' field.
# Since it's private, we need to use Java reflection to access it.
Basic_noOfSlices = Basic.getDeclaredField('noOfSlices')
Basic_noOfSlices.setAccessible(True)
basic = Basic()
Basic_noOfSlices.setInt(basic, num_images)
# Pre-allocate the output profile images, since we have all the dimensions.
ff_image = IJ.createImage("Flat-field", width, height, num_channels, 32);
df_image = IJ.createImage("Dark-field", width, height, num_channels, 32);
print("\n\n")
# BaSiC works on one channel at a time, so we only read the images from one
# channel at a time to limit memory usage.
for channel in range(num_channels):
print "Processing channel %d/%d..." % (channel + 1, num_channels)
print "==========================="
options = ImporterOptions()
options.id = str(filename)
options.setOpenAllSeries(True)
# concatenate=True gives us a single stack rather than a list of
# separate images.
options.setConcatenate(True)
# Limit the reader to the channel we're currently working on. This loop
# is mainly why we need to know num_images before opening anything.
for i in range(num_images):
options.setCBegin(i, channel)
options.setCEnd(i, channel)
# openImagePlus returns a list of images, but we expect just one (a
# stack).
input_image = BF.openImagePlus(options)[0]
# BaSiC seems to require the input image is actually the ImageJ
# "current" image, otherwise it prints an error and aborts.
WindowManager.setTempCurrentImage(input_image)
basic.exec(
input_image, None, None,
"Estimate shading profiles", "Estimate both flat-field and dark-field",
lambda_estimate, lambda_flat, lambda_dark,
"Ignore", "Compute shading only"
)
input_image.close()
# Copy the pixels from the BaSiC-generated profile images to the
# corresponding channel of our output images.
ff_channel = WindowManager.getImage("Flat-field:%s" % input_image.title)
ff_image.slice = channel + 1
ff_image.getProcessor().insert(ff_channel.getProcessor(), 0, 0)
ff_channel.close()
df_channel = WindowManager.getImage("Dark-field:%s" % input_image.title)
df_image.slice = channel + 1
df_image.getProcessor().insert(df_channel.getProcessor(), 0, 0)
df_channel.close()
print("\n\n")
template = '%s/%s-%%s.tif' % (output_dir, experiment_name)
ff_filename = template % 'ffp'
IJ.saveAsTiff(ff_image, ff_filename)
ff_image.close()
df_filename = template % 'dfp'
IJ.saveAsTiff(df_image, df_filename)
df_image.close()
print "Done!"
def getCategoriesFromPersistence():
"""Return categories saved in memory as a list."""
stringCat = Prefs.get(
"annot.listCat", "Category1"
) # Retrieve the list of categories as a comma separated list, if not defined default to Category1
return stringCat.split(",") if stringCat else []
""" getPrefsDirImageJ.py ImageJ Jython - J. R. Minter - 2018-07-09 Modifications Date Who Ver What ---------- --- ------ --------------------------------------------- 2018-07-09 JRM 0.1.00 First implementation """ from ij import IJ, Prefs st = Prefs.getPrefsDir() print(st)
def measureFeatureLength(imp, lw = 2, csvPath=None, bAppend=True,
offset = -30, digits = 3,
font = 18, linCol = Color.YELLOW,
labCol = Color.WHITE,
bDebug = False):
"""
measureFeatureLength(imp, lw = 2, csvPath=None, bAppend=True,
offset = -30, digits = 3,
font = 18, linCol = Color.YELLOW,
labCol = Color.WHITE,
bDebug = False)
Manually measure the length of a feature in a calibrated ImagePlus
and write the results to the overlay.
Version of 2016-08-04
Parameters
----------
imp: ImagePlus
The image to process
lw: int (2)
The linewidth for the line
csvPath: string (None)
The path to a csv file to write measurements
bAppend: Boolean (True)
A flag. If True new results are appended to the file
offset: int (-30)
The Y offset for the label. If negative, the label will
be written above the measurement, if positive below.
digits: int (3)
Round the output (in calibrated units) to this number of decimal
points.
font: int (18)
The font size for the measurement.
linCol: A color constant (Color.YELLOW)
The color for the line in the overlay.
labCol: A color constant (Color.WHITE)
The color for the label
bDebug: A Boolean (False)
A flag to print diagnostic incormation
Returns
-------
None - it does draw in the overlay of the image and write an
optional .csv file.
Known Issues
------------
With large line widths the length of the drawn line appears lw
pixels too long.
"""
# First define some convenience functions
def resetLastMeasureCount():
Prefs.set("JRM.meas.counter", 0)
def GetLastMeasureCount():
myCount = Prefs.get("JRM.meas.counter", int(-1))
if myCount < 0:
# it was not set, so set it to zero
resetLastMeasureCount()
return 0
else:
myCount = int(myCount)
return myCount
def setLastMeasureCount(count):
count = int(count)
Prefs.set("JRM.meas.counter", count)
imp = IJ.getImage()
if imp == None:
print("You need an image...")
return
else:
roi = imp.getRoi()
if roi != None:
if roi.getType() == Roi.LINE:
# print(roi)
cal = imp.getCalibration()
# print(cal)
unit = cal.getUnits()
width = cal.pixelWidth
height = cal.pixelHeight
x1 = roi.x1 * width
y1 = roi.y1 * height
x2 = roi.x2 * width
y2 = roi.y2 * height
length = sqrt((x2-x1)*(x2-x1)+(y2-y1)*(y2-y1));
if bDebug:
sOut = "X1: %d Y1 %d X2 %d Y2 %d" % (roi.x1, roi.y1,
roi.x2, roi.y2)
print(sOut)
print(length, unit)
ip = imp.getProcessor()
ip.setColor(linCol)
oldLW = ip.getLineWidth()
ip.setLineWidth(lw)
ip.drawLine(roi.x1, roi.y1, roi.x2, roi.y2)
ip.setLineWidth(oldLW)
imp.updateAndDraw()
ol = imp.getOverlay()
if ol == None:
ol = Overlay()
res = imp.duplicate()
# first a dummy text ROI to set the font
tr = TextRoi(10, 10, "Foo")
tr.setColor(labCol)
tr.setFont("SanSerif", font, 1)
tr.setJustification(TextRoi.CENTER)
tr.setAntialiased(True)
# explicitly save preferences
Prefs.savePreferences()
xL = roi.x1 + roi.x2
xL /= 2
if offset < 0:
yL = min(roi.y1, roi.y2)
yL += offset
else:
yL = max(roi.y1, roi.y2)
yL += offset
length = round(length, 3)
label = "%g %s" % (length, unit)
tr = TextRoi(xL, yL, label)
tr.setColor(labCol)
tr.setFont("SanSerif", font, 1)
tr.setJustification(TextRoi.CENTER)
tr.setAntialiased(True)
ol.add(tr)
imp.setOverlay(ol)
imp.show()
if csvPath != None:
if bAppend:
if os.path.isfile(csvPath):
theCount = GetLastMeasureCount() + 1
f=open(csvPath, 'a')
else:
f=open(csvPath, 'w')
resetLastMeasureCount()
theCount = 1
strLine = 'img, num, length (%s)\n' % unit
f.write(strLine)
else:
f=open(csvPath, 'w')
resetLastMeasureCount()
theCount = 1
strLine = 'img, num, length (%s)\n' % unit
f.write(strLine)
strLine = "%s, %d, %.6f\n" % (imp.getShortTitle(), theCount, length)
f.write(strLine)
f.close()
setLastMeasureCount(theCount)
strMsg = "measured %s count = %d" % (imp.getShortTitle(), theCount)
print(strMsg)
else:
print("You need a line ROI")
# finally deselect
IJ.run("Select None")
class Colortags:
'''
This class handles persistence of the name of different color channels.
It instantiates a GUI window to capture and show the color names in use.
Other classes such as ColorMerger needs this to determine the color of the channel being processed.
'''
def __init__(self):
self.window = None
self.tags = {}
self.prefkeys = ["{0}.{1}".format(SUBKEY, name) for name in COLORS]
self.userprefs = Prefs()
self.load()
while not self.tags:
self.edit("Please set at least one colortag.\n\n")
def load(self):
'''
Tries to load IBPlib colortags from IJ prefs.
'''
for i in range(7):
storedtags = self.userprefs.getString(".{0}".format(self.prefkeys[i]), "")
if not storedtags:
continue
trimmedtagslist = [t.strip() for t in storedtags.split(",")]
self.tags.update({i:trimmedtagslist})
def edit(self, msg=""):
'''
Opens the color tags dialog to update color tags
'''
self.window = GenericDialog("ColorMerger - Edit color tags")
self.window.addMessage("{0}Separate tags with a comma.\nBlank values will be ignored.".format(msg))
for i in range(7):
try:
self.window.addStringField(COLORS[i], ", ".join(self.tags[i]), 30)
except KeyError:
self.window.addStringField(COLORS[i], "", 30)
self.window.setOKLabel("Save")
self.window.showDialog()
if self.window.wasOKed():
self.__savetags()
self.load()
def __validate(self):
fields = self.window.getStringFields()
newvalues = {}
for i in range(len(fields)):
txt = fields[i].getText()
newvalues.update({i: txt.strip()})
return newvalues
def __savetags(self):
newvalues = self.__validate()
for i, tags in newvalues.items():
key = self.prefkeys[i]
self.userprefs.set(key, tags)
self.userprefs.savePreferences()
def readczi(imagefile,
stitchtiles=True,
setflatres=False,
readpylevel=0,
setconcat=True,
openallseries=True,
showomexml=False,
attach=False,
autoscale=True):
log.info('Filename : ' + imagefile)
metainfo = {}
# checking for thr file Extension
metainfo['Extension'] = MiscTools.getextension(MiscTools.splitext_recurse(imagefile))
log.info('Detected File Extension : ' + metainfo['Extension'])
# initialize the reader and get the OME metadata
reader = ImageReader()
omeMeta = MetadataTools.createOMEXMLMetadata()
#metainfo['ImageCount_OME'] = omeMeta.getImageCount()
reader.setMetadataStore(omeMeta)
reader.setId(imagefile)
metainfo['SeriesCount_BF'] = reader.getSeriesCount()
reader.close()
# get the scaling for XYZ
physSizeX = omeMeta.getPixelsPhysicalSizeX(0)
physSizeY = omeMeta.getPixelsPhysicalSizeY(0)
physSizeZ = omeMeta.getPixelsPhysicalSizeZ(0)
if physSizeX is not None:
metainfo['ScaleX'] = round(physSizeX.value(), 3)
metainfo['ScaleY'] = round(physSizeX.value(), 3)
if physSizeX is None:
metainfo['ScaleX'] = None
metainfo['ScaleY'] = None
if physSizeZ is not None:
metainfo['ScaleZ'] = round(physSizeZ.value(), 3)
if physSizeZ is None:
metainfo['ScaleZ'] = None
options = DynamicMetadataOptions()
options.setBoolean("zeissczi.autostitch", stitchtiles)
options.setBoolean("zeissczi.attachments", attach)
czireader = ZeissCZIReader()
czireader.setFlattenedResolutions(setflatres)
czireader.setMetadataOptions(options)
czireader.setId(imagefile)
# Set the preferences in the ImageJ plugin
# Note although these preferences are applied, they are not refreshed in the UI
Prefs.set("bioformats.zeissczi.allow.autostitch", str(stitchtiles).lower())
Prefs.set("bioformats.zeissczi.include.attachments", str(attach).lower())
# metainfo = {}
metainfo['rescount'] = czireader.getResolutionCount()
metainfo['SeriesCount_CZI'] = czireader.getSeriesCount()
#metainfo['flatres'] = czireader.hasFlattenedResolutions()
#metainfo['getreslevel'] = czireader.getResolution()
# Dimensions
metainfo['SizeT'] = czireader.getSizeT()
metainfo['SizeZ'] = czireader.getSizeZ()
metainfo['SizeC'] = czireader.getSizeC()
metainfo['SizeX'] = czireader.getSizeX()
metainfo['SizeY'] = czireader.getSizeY()
# check for autostitching and possibility to read attachment
metainfo['AllowAutoStitching'] = czireader.allowAutostitching()
metainfo['CanReadAttachments'] = czireader.canReadAttachments()
# read in and display ImagePlus(es) with arguments
options = ImporterOptions()
options.setOpenAllSeries(openallseries)
options.setShowOMEXML(showomexml)
options.setConcatenate(setconcat)
options.setAutoscale(autoscale)
options.setId(imagefile)
# open the ImgPlus
imps = BF.openImagePlus(options)
metainfo['Pyramid Level Output'] = readpylevel + 1
try:
imp = imps[readpylevel]
pylevelout = metainfo['SeriesCount_CZI']
except:
# fallback option
log.info('PyLevel=' + str(readpylevel) + ' does not exist.')
log.info('Using Pyramid Level = 0 as fallback.')
imp = imps[0]
pylevelout = 0
metainfo['Pyramid Level Output'] = pylevelout
# get the stack and some info
imgstack = imp.getImageStack()
metainfo['Output Slices'] = imgstack.getSize()
metainfo['Output SizeX'] = imgstack.getWidth()
metainfo['Output SizeY'] = imgstack.getHeight()
# calc scaling in case of pyramid
scale = float(metainfo['SizeX']) / float(metainfo['Output SizeX'])
metainfo['Pyramid Scale Factor'] = scale
metainfo['ScaleX Output'] = metainfo['ScaleX'] * scale
metainfo['ScaleY Output'] = metainfo['ScaleY'] * scale
# set the correct scaling
imp = MiscTools.setscale(imp, scaleX=metainfo['ScaleX Output'],
scaleY=metainfo['ScaleX Output'],
scaleZ=metainfo['ScaleZ'],
unit="micron")
# close czireader
czireader.close()
return imp, metainfo
# for Ambro 2016-05-16
# gLo = 500
# gHi = 3800
# for Kang LM 2016-05-24
gLo = 730
gHi = 2850
bDoTiltCorrect = False
mu = IJ.micronSymbol
scaUm = mu + "m"
lastPath = Prefs.get("Last.Image.Dir", "None")
if os.path.exists(lastPath):
os.chdir(lastPath)
dc = DirectoryChooser("Choose directory")
basePath = dc.getDirectory()
print(basePath)
Prefs.set("Last.Image.Dir", basePath)
names = []
for file in os.listdir(basePath):
if file.endswith(".tif"):
name = os.path.splitext(file)[0]
names.append(name)
def resetLastMeasureCount():
Prefs.set("JRM.meas.counter", 0)
def getCZIinfo(imagefile, showimage=False, setreslevel=0, setflat2=False, openallseries=True, showomexml=False,setconcat=False,filepath1="./"):
options = DynamicMetadataOptions()
options.setBoolean("zeissczi.attachments", False)
czireader = ZeissCZIReader()
czireader.setFlattenedResolutions(setflat2)
czireader.setMetadataOptions(options)
czireader.setId(imagefile)
lc = czireader.getSeriesCount()
#get the first occurence of each pyramid stack
location=list()
for i in range(0, int(seriesCount)-2):
location.append(czireader.coreIndexToSeries(i))
c=0
#log.info(location)
loc2=list()
for i,v in enumerate(location):
if i==0:
loc2.append(i)
elif i>0 and v!=c:
loc2.append(i)
c=v
log.info(str(loc2))
# get OME data
omeMeta = MetadataTools.createOMEXMLMetadata()
# Set the preferences in the ImageJ plugin
Prefs.set("bioformats.zeissczi.include.attachments", str(True).lower())
if showimage:
# read in and display ImagePlus(es) with arguments
options = ImporterOptions()
options.setOpenAllSeries(openallseries)
options.setShowOMEXML(showomexml)
options.setConcatenate(setconcat)
options.setId(imagefile)
# open the ImgPlus
imps = BF.openImagePlus(options)
name_list=imagefile.split('/')
name=name_list[len(name_list)-1]
out_path=filepath1 + "/"+name+"_Preview.tif"
log.info(name)
imp=getImageSeries(imps, seriesCount-1)
imp.show()
IJ.run("RGB Color")
imp.close()
IJ.saveAs("tiff", out_path)
IJ.run("Close")
out_path=filepath1 + "/"+name+"_Label.tif"
imp=getImageSeries(imps, (seriesCount-2))
imp.show()
IJ.run("RGB Color")
imp.close()
IJ.saveAs("tiff", out_path)
IJ.run("Close")
c=1
for series in loc2:
out_path=filepath1 + "/"+name+"Scene_" + str(c) + ".tif"
imp=getImageSeries(imps, series)
imp.show()
IJ.run("RGB Color")
imp.close()
IJ.saveAs("tiff", out_path)
IJ.run("Close")
c+=1
czireader.close()
