def setproperties(imp,
scaleX=1.0,
scaleY=1.0,
scaleZ=1.0,
unit="micron",
sizeC=1,
sizeZ=1,
sizeT=1):
"""Set properties of image in Fiji
:param imp: Image
:type imp: ImgPlus
:param scaleX: scaleX, defaults to 1.0
:type scaleX: float, optional
:param scaleY: scaleY, defaults to 1.0
:type scaleY: float, optional
:param scaleZ: scaleZ, defaults to 1.0
:type scaleZ: float, optional
:param unit: scale unit, defaults to "micron"
:type unit: str, optional
:param sizeC: sizeC, defaults to 1
:type sizeC: int, optional
:param sizeZ: sizeZ, defaults to 1
:type sizeZ: int, optional
:param sizeT: sizeT, defaults to 1
:type sizeT: int, optional
:return: Image
:rtype: ImgPlus
"""
# check if scaleZ has a valid value to call modify the properties
if scaleZ is None:
scaleZ = 1
# run the image properties tool
IJ.run(imp, "Properties...", "channels=" + str(sizeC) +
" slices=" + str(sizeZ)
+ " frames=" + str(sizeT)
+ " unit=" + unit
+ " pixel_width=" + str(scaleX)
+ " pixel_height=" + str(scaleY)
+ " voxel_depth=" + str(scaleZ))
# create new Calibration object
newCal = Calibration()
# set the new paramters
newCal.pixelWidth = scaleX
newCal.pixelHeight = scaleY
newCal.pixelDepth = scaleZ
# set the correct unit fro the scaling
newCal.setXUnit(unit)
newCal.setYUnit(unit)
newCal.setZUnit(unit)
# apply the new calibration
imp.setCalibration(newCal)
return imp
def setscale(imp,
scaleX=1.0,
scaleY=1.0,
scaleZ=1.0,
unit="micron"):
# check if scaleZ has a valid value to call modify the scaling
if scaleZ is None:
scaleZ = 1.0
# create new Calibration object
newCal = Calibration()
# set the new paramters
newCal.pixelWidth = scaleX
newCal.pixelHeight = scaleY
newCal.pixelDepth = scaleZ
# set the correct unit fro the scaling
newCal.setXUnit(unit)
newCal.setYUnit(unit)
newCal.setZUnit(unit)
# apply the new calibration
imp.setCalibration(newCal)
return imp
def prepare_image_stacks(image_dir):
""" For each stack directory in image_dir, load the image sequence as
a stack and spatially calibrate the stack.
Returns:
images (list): The list containing the calibrated image stacks.
Args:
image_dir (str): The directory containing the image stack directories.
"""
images = []
for stack_dir in os.listdir(image_dir):
stack_dir_full_path = str(image_dir) + '/' + stack_dir
imp = FolderOpener.open(stack_dir_full_path)
cal = Calibration()
cal.setUnit('um')
cal.pixelWidth = 0.3296485
cal.pixelHeight = 0.3296485
cal.pixelDepth = 0.998834955
imp.setCalibration(cal)
imp.setTitle(
stack_dir) # name the image after its directory, e.g. OP_1
images.append(imp)
return images
def set_xyz_calibration(imp, dx, dy, dz, unit): cal = Calibration(imp) cal.setUnit(unit) cal.pixelWidth = dx cal.pixelHeight = dy cal.pixelDepth = dz imp.setCalibration(cal) return imp
def setscale(imp,
scaleX=1.0,
scaleY=1.0,
scaleZ=1.0,
unit="micron"):
"""Set new scaling for image.
:param imp: image
:type imp: ImgPlus
:param scaleX: scaleX, defaults to 1.0
:type scaleX: float, optional
:param scaleY: scaleY, defaults to 1.0
:type scaleY: float, optional
:param scaleZ: scaleZ, defaults to 1.0
:type scaleZ: float, optional
:param unit: scaling unit, defaults to "micron"
:type unit: str, optional
:return: image
:rtype: ImgPlus
"""
# check if scaleZ has a valid value to call modify the scaling
if scaleZ is None:
scaleZ = 1.0
# create new Calibration object
newCal = Calibration()
# set the new paramters
newCal.pixelWidth = scaleX
newCal.pixelHeight = scaleY
newCal.pixelDepth = scaleZ
# set the correct unit fro the scaling
newCal.setXUnit(unit)
newCal.setYUnit(unit)
newCal.setZUnit(unit)
# apply the new calibratiion
imp.setCalibration(newCal)
return imp
def setproperties(imp,
scaleX=1.0,
scaleY=1.0,
scaleZ=1.0,
unit="micron",
sizeC=1,
sizeZ=1,
sizeT=1):
# check if scaleZ has a valid value to call modify the properties
if scaleZ is None:
scaleZ = 1
# run the image properties tool
IJ.run(imp, "Properties...", "channels=" + str(sizeC)
+ " slices=" + str(sizeZ)
+ " frames=" + str(sizeT)
+ " unit=" + unit
+ " pixel_width=" + str(scaleX)
+ " pixel_height=" + str(scaleY)
+ " voxel_depth=" + str(scaleZ))
# create new Calibration object
newCal = Calibration()
# set the new paramters
newCal.pixelWidth = scaleX
newCal.pixelHeight = scaleY
newCal.pixelDepth = scaleZ
# set the correct unit fro the scaling
newCal.setXUnit(unit)
newCal.setYUnit(unit)
newCal.setZUnit(unit)
# apply the new calibration
imp.setCalibration(newCal)
return imp
n_channels = 1
n_slices = 1 # Z slices
n_frames = 1 # time frames
# Get current image
image = IJ.getImage()
# Check that we have correct dimensions
stack_size = image.getImageStackSize() # raw number of images in the stack
if n_channels * n_slices * n_frames == stack_size:
image.setDimensions(n_channels, n_slices, n_frames)
else:
IJ.log('The product of channels (' + str(n_channels) + '), slices (' +
str(n_slices) + ')')
IJ.log('and frames (' + str(n_frames) + ') must equal the stack size (' +
str(stack_size) + ').')
# Set calibration
pixel_width = 1
pixel_height = 1
pixel_depth = 1
space_unit = 'µm'
frame_interval = 1
time_unit = 's'
calibration = Calibration() # new empty calibration
calibration.pixelWidth = pixel_width
calibration.pixelHeight = pixel_height
calibration.pixelDepth = pixel_depth
calibration.frameInterval = frame_interval
calibration.setUnit(space_unit)
calibration.setTimeUnit(time_unit)
image.setCalibration(calibration)
image.repaintWindow()
# Set dimensions
n_channels = 1
n_slices = 1 # Z slices
n_frames = 1 # time frames
# Get current image
image = IJ.getImage()
# Check that we have correct dimensions
stack_size = image.getImageStackSize() # raw number of images in the stack
if n_channels * n_slices * n_frames == stack_size:
image.setDimensions(n_channels, n_slices, n_frames)
else:
IJ.log('The product of channels ('+str(n_channels)+'), slices ('+str(n_slices)+')')
IJ.log('and frames ('+str(n_frames)+') must equal the stack size ('+str(stack_size)+').')
# Set calibration
pixel_width = 1
pixel_height = 1
pixel_depth = 1
space_unit = 'µm'
frame_interval = 1
time_unit = 's'
calibration = Calibration() # new empty calibration
calibration.pixelWidth = pixel_width
calibration.pixelHeight = pixel_height
calibration.pixelDepth = pixel_depth
calibration.frameInterval = frame_interval
calibration.setUnit(space_unit)
calibration.setTimeUnit(time_unit)
image.setCalibration(calibration)
image.repaintWindow()
imps = BF.openImagePlus(input_file)
imp = imps[0]
imp.setDisplayMode(IJ.COLOR)
imp.setC(color)
# imp.setDisplayRange(0.0, 3.0)
# imp.show()
log_info += 'frames: ' + str(imp.getNFrames()) + '\n'
log_info += 'width: ' + str(imp.getWidth()) + '\n'
log_info += 'height: ' + str(imp.getHeight()) + '\n'
cal = Calibration()
cal.setUnit('micron')
cal.pixelHeight = resolution
cal.pixelWidth = resolution
cal.pixelDepth = 0.
cal.fps = 1
cal.frameInterval = 1
imp.setCalibration(cal)
#-------------------------
# Instantiate model object
#-------------------------
model = Model()
model.setPhysicalUnits('micron', 'frames')
# Set logger
model.setLogger(Logger.IJ_LOGGER)
#------------------------
########## END EDITING
# Iterate over input files.
for input_file in input_files:
# Get image and calibrate
imps = BF.openImagePlus(input_file)
imp = imps[0]
imp.setDisplayMode(IJ.COLOR)
imp.show()
cal = Calibration()
cal.setUnit('micron')
cal.pixelHeight = resolution
cal.pixelWidth = resolution
cal.pixelDepth = 2**16
cal.fps = 10
cal.frameInterval = 1
imp.setCalibration(cal)
#-------------------------
# Instantiate model object
#-------------------------
model = Model()
model.setPhysicalUnits('micron', 'frames')
# Set logger
model.setLogger(Logger.IJ_LOGGER)
#------------------------
filters.setup("median", frame)
filters.rank(processor, filter_window, filters.MEDIAN)
# Perform gamma correction
processor.gamma(gamma)
frame = ImagePlus("Frame " + str(frame_i), processor)
# Rolling ball background subtraction
processor = frame.getProcessor()
bg_subtractor = BackgroundSubtracter()
bg_subtractor.setup("", frame)
bg_subtractor.rollingBallBackground(processor, rolling_ball_size/pixel_size, False, False, False, False, True)
frame = ImagePlus("Frame " + str(frame_i), processor)
# Calibrate pixels
calibration = Calibration()
calibration.setUnit("pixel")
calibration.pixelWidth = pixel_size
calibration.pixelHeight = pixel_size
calibration.pixelDepth = 1.0
frame.setCalibration(calibration)
# Save to output dir
file_name = output_dir + "/" + str(frame_i).zfill(4) + ".tif"
FileSaver(frame).saveAsTiff(file_name)
frame_i = frame_i + 1
