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 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"):
"""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
