diff --git a/doc/widgets/polar.md b/doc/widgets/polar.md index be1b7dc07..45ddbf316 100644 --- a/doc/widgets/polar.md +++ b/doc/widgets/polar.md @@ -1,7 +1,7 @@ -4+ Angle Polarisation +4+ Angle Polarization ============ -Calculates vibrational mode orientation from polarised infrared spectroscopy datasets +Calculates vibrational mode orientation from polarized infrared spectroscopy datasets **Inputs** @@ -12,21 +12,21 @@ Calculates vibrational mode orientation from polarised infrared spectroscopy dat - Polar Data: dataset with selected feature(s) orientation information - Curve Fit Model Data: dataset with the optimal parameters of the curve fit model -The **4+ Angle Polarisation** widget allows you to calculate orientation information of selected features using polarised spectroscopy data collected at 4 or more polarisation angles. The implemented algorithm is the same as that outlined by Hikima et al. (2013)1 +The **4+ Angle Polarization** widget allows you to calculate orientation information of selected features using polarized spectroscopy data collected at 4 or more polarization angles. The implemented algorithm is the same as that outlined by Hikima et al. (2013)1 If you use this widget for your data analysis, please cite the articles in which the method (Hikima et al. (2013)1) and widget (Gassner et al. (2025)2) are introduced. ![](images/Polar-stamped.png) -1. Inputs: Define the polarisation angles of the input dataset. Data can be passed to widget with two methods: - - *Multifile Input*: A single input with data from all polarisation angles in a single dataset. (Each polarisation angle must be separated with a categorical variable). - - *Multiple Inputs*: 1 input per polarisation angle. +1. Inputs: Define the polarization angles of the input dataset. Data can be passed to widget with two methods: + - *Multifile Input*: A single input with data from all polarization angles in a single dataset. (Each polarization angle must be separated with a categorical variable). + - *Multiple Inputs*: 1 input per polarization angle. 2. Features: Select the features to calculate the orientation of. Features are selected by clicking on the desired feature(s) and assigning a TDM value (see point 5). A default value is assigned using the current value in the "TDM Tilt (°)" box, changing this value will change the associated value of the selected feature(s). Deselecting features will not remove them from the list to be calculated, only features with ("Not used") will not be calculated (see point 8). 3. Data XY Selection: Define the attributes for the x and y axes for 2D datasets. 4. Spectra Type: The type of spectra on the input. A conversion to *Absorptance* is performed before calculating orientation information when *Absorbance* or *Transmittance* is selected (this does not affect meta and class variables). 5. TDM Tilt (°): The angle of the Transition Dipole Moment with respect to the molecular axis. Used in calculation of the value of Herman's orientation function. 6. Invert Angles: Invert the calculated Azimuth Angles about the 0 degree axis (i.e. so that 90 degrees is output as -90 degrees). -7. Average Spectra: Average all output variables across polarisation angles. +7. Average Spectra: Average all output variables across polarization angles. 8. Don't use selected features: Remove the selected features from the list to be used in calculations Input Examples @@ -47,4 +47,4 @@ References 1. Hikima, Y.; Morikawa, J.; Hashimoto, T., Wavenumber Dependence of FT-IR Image of Molecular Orientation in Banded Spherulites of Poly(3-hydroxybutyrate) and Poly(L-lactic acid). Macromolecules 2013, 46, 1582-1590. -2. Gassner, C.; Vongsvivut, J.; Ryu, M.; Ng, S.H.; Toplak, M.; Takkalkar, P.; Fac, M.L.; Sims, N.A.; Wood, B.R.; Tobin, M.J.; Juodkazis, S.; Morikawa, J., 4+ Angle Polarisation: New Multiple-Angle FTIR Polarisation Widget for Molecular Orientation Analysis in the Open-Source Quasar Platform. +2. Gassner, C.; Vongsvivut, J.; Ryu, M.; Ng, S.H.; Toplak, M.; Takkalkar, P.; Fac, M.L.; Sims, N.A.; Wood, B.R.; Tobin, M.J.; Juodkazis, S.; Morikawa, J., 4+ Angle Polarization: New Multiple-Angle FTIR Polarization Widget for Molecular Orientation Analysis in the Open-Source Quasar Platform. diff --git a/orangecontrib/spectroscopy/widgets/owpolar.py b/orangecontrib/spectroscopy/widgets/owpolar.py index e8af97cdb..08a42580d 100644 --- a/orangecontrib/spectroscopy/widgets/owpolar.py +++ b/orangecontrib/spectroscopy/widgets/owpolar.py @@ -131,7 +131,7 @@ def run(data, feature, alphas, map_x, map_y, invert_angles, polangles, average, ometadom = data[0].domain.metas if average is False: values = tuple(f'{i} Degrees' for i in polangles) - PolAng = DiscreteVariable.make('Polarisation Angle', values=values) + PolAng = DiscreteVariable.make('Polarization Angle', values=values) outmetadom = (ometadom + tuple([PolAng]) + tuple(outaddmetas)) modmetadom = (ometadom + tuple([PolAng]) + tuple(modaddmetas)) output_stack = tuple(output for i in polangles) @@ -451,12 +451,12 @@ def process_polar_abs(images, alphas, feature, map_x, map_y, invert, polangles, class OWPolar(OWWidget, ConcurrentWidgetMixin): # Widget's name as displayed in the canvas - name = "4+ Angle Polarisation" + name = "4+ Angle Polarization" # Short widget description description = ( "Calculate Azimuth Angle, Orientation function, Amplitude and Intensity of " - "vibrational mode(s) using polarised data measured at 4 or more polarisation angles.") + "vibrational mode(s) using polarized data measured at 4 or more polarization angles.") icon = "icons/polar.svg" @@ -492,7 +492,7 @@ class Warning(OWWidget.Warning): # noang = Msg("Must receive 4 angles at specified polarisation") nofeat = Msg("Select one or more Features to calculate orientations with") noxy = Msg("Select X and Y variables") - pol = Msg("Invalid Polarisation angles") + pol = Msg("Invalid Polarization angles") notenough = Msg("Must have >= 4 angles") wrongdata = Msg("Model returns inf. Inappropriate data") # tomany = Msg("Widget must receive data at data input or discrete angles only")