pwspy.analysis.pws.PWSAnalysisSettings¶
- class pwspy.analysis.pws.PWSAnalysisSettings(filterOrder, filterCutoff, polynomialOrder, extraReflectanceId, referenceMaterial, wavelengthStart, wavelengthStop, skipAdvanced, autoCorrStopIndex, autoCorrMinSub, numericalAperture, relativeUnits, cameraCorrection, waveNumberCutoff)[source]¶
Bases:
pwspy.analysis._abstract.AbstractAnalysisSettingsThese settings determine the behavior of the PWSAnalysis class.
- filterOrder¶
The order of the buttersworth filter used for lowpass filtering.
- Type
int
- filterCutoff¶
The cutoff frequency of the buttersworth filter used for lowpass filtering. Frequency unit is 1/wavelength . Set to None to skip lowpass filtering.
- Type
float
- polynomialOrder¶
The order of the polynomial which will be fit to the reflectance and then subtracted before calculating the analysis results.
- Type
int
- extraReflectanceId¶
The idtag of the extra reflection used for correction. Set to None if extra reflectance calibration is being skipped.
- Type
str
- wavelengthStart¶
The acquisition spectra will be truncated at this wavelength before analysis. Set to None to bypass this step
- Type
int
- wavelengthStop¶
The acquisition spectra will be truncated after this wavelength before analysis. Set to None to bypass this step
- Type
int
- skipAdvanced¶
If True then skip analysis of the OPD and autocorrelation.
- Type
bool
- autoCorrStopIndex¶
The autocorrelation slope will be calculated up to this number of elements. More elements is theoretically better but it severely limited by SNR.
- Type
int
- autoCorrMinSub¶
If True then subtract the minimum of the ACF from ACF. This prevents numerical issues but doesn’t actually make any sense.
- Type
bool
- numericalAperture¶
The numerical aperture that the acquisition was imaged at.
- Type
float
- relativeUnits¶
relativeUnits: If True then all calculation are performed such that the reflectance is 1 if it matches the reference. If False then we use the theoretical reflectance of the reference (based on NA and reference material) to normalize our results to the actual physical reflectance of the sample (about 0.4% for water)
- Type
bool
- cameraCorrection¶
An object describing the dark counts and non-linearity of the camera used. If the data supplied to the PWSAnalysis class has already been corrected then this setting will not be used. Setting this to None will result in the camera correcting being automatically determined based on the image files’ metadata.
- Type
Optional[pwspy.dataTypes._other.CameraCorrection]
- waveNumberCutoff¶
A cutoff frequency for filtering the signal after converting from wavelength to wavenumber. In units of microns (opd). Note: To convert from depth to opd divide by 2 (because the light makes a round trip) and divide by the RI of the media (nucleus)
- Type
float
- asDict()[source]¶
- Return type
dict- Returns
A dictionary with setting names as the keys and the values of the settings as the values.
- classmethod fromJson(filePath, name)¶
Create a new instance of this class from a json text file.
- Parameters
filePath (
str) – The path to the folder containing the JSON file to be loaded.name (
str) – The name that the analysis was saved as.
- Return type
AbstractAnalysisSettings- Returns
A new instance of an analysis settings class.
- classmethod fromJsonString(string)¶
Use _fromDict to load a new instance of the cls from a json string.
- Parameters
string (
str) – A JSON formatted string to load the object from.- Return type
AbstractAnalysisSettings- Returns
A new instance of analysis settings class.
- toJson(filePath, name)¶
Save this object to a json text file.
- Parameters
filePath (
str) – The path to the folder to contain the new JSON file.name (
str) – The name to save the analysis as.
- toJsonString()¶
Use _asDict to convert an instance of this class to a json string.
- Return type
str- Returns
A JSON formatted string.