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