pwspy.dataTypes.ExtraReflectionCube

class pwspy.dataTypes.ExtraReflectionCube(data, wavelengths, metadata)[source]

Bases: pwspy.dataTypes._data.ICBase

This class is meant to be constructed from an ExtraReflectanceCube along with additional reference measurement information. Rather than being in units of reflectance (between 0 and 1) it is in the same units as the reference measurement that is provided with, usually counts/ms or just counts.

Parameters

  • data (ndarray) – The 3D array of the extra reflection in the system. In units of counts/ms or just counts

  • wavelengths (Tuple[float, ...]) – The wavelengths associated with each 2D slice along the 3rd axis of the data array.

  • metadata (ERMetaData) – Metadata

classmethod create(reflectance, theoryR, reference)[source]

Construct and ExtraReflectionCube from an ExtraReflectanceCube and a reference measurement. The resulting ExtraReflectionCube will be in the same units as reference. theoryR should be a spectrum describing the theoretically expected reflectance of the reference data cube. Both theoryR and reflectance should be in units of reflectance (between 0 and 1).

Parameters

  • reflectance (ExtraReflectanceCube) – The ExtraReflectanceCube to construct an ExtraReflectionCube from.

  • theoryR (Series) – The theoretically predicted reflectance of material imaged in reference.

  • reference (PwsCube) – A PWS image of a blank glass-{material} interface, usually water.

Return type

ExtraReflectionCube

Returns

A new instance of ExtraReflectionCube.

classmethod decodeHdf(d)

Load a new instance of ICBase from an h5py.Dataset

Parameters

d (Dataset) – The dataset that the ICBase has been saved to

Returns

(data: The 3D array of data, index: A tuple containing the index)

Return type

A tuple containing

filterDust(sigma, pixelSize)

Blurs the data cube in the X and Y dimensions. Often used to remove the effects of dust on a normalization.

Parameters

  • sigma (float) – This specifies the radius of the gaussian filter used for blurring. The units of the value are determined by pixelSize

  • pixelSize (float) – The pixel size in microns. Settings this to 1 will effectively causes sigma to be in units of pixels rather than microns.

getMeanSpectra(mask=None)

Calculate the average spectra within a region of the data.

Parameters

mask (Union[Roi, ndarray, None]) – An optional other.Roi or boolean numpy array used to select pixels from the X and Y dimensions of the data array. If left as None then the full data array will be used as the region.

Return type

Tuple[ndarray, ndarray]

Returns

The average spectra within the region, the standard deviation of the spectra within the region

plotMean()
Return type

Tuple[Figure, Axes]

Returns

A figure and attached axes plotting the mean of the data along the index axis.

corresponds to the mean reflectance in most cases.

selIndex(start, stop)
Parameters

  • start (Optional[float]) – The beginning value of the index in the new object. Pass None to include everything.

  • stop (Optional[float]) – The ending value of the index in the new object. Pass None to include everything.

Return type

Tuple[ndarray, Sequence]

Returns

A new instance of ICBase with only data from start to stop in the index.

selectLassoROI(displayIndex=None, clim=None)

Allow the user to draw a freehand ROI on an image of the acquisition.

Parameters

displayIndex (Optional[int]) – Display a particular z-slice of the array for mask drawing. If None then the mean along Z is displayed.

Return type

Roi

Returns

An array of vertices of the polygon drawn.

selectRectangleROI(displayIndex=None)

Allow the user to draw a rectangular ROI on an image of the acquisition.

Parameters

displayIndex (int) – is used to display a particular z-slice for mask drawing. If None then the mean along Z is displayed. Returns an array of vertices of the rectangle.

Returns

An array of the 4 XY vertices of the rectangle.

Return type

np.ndarray

toHdfDataset(g, name, fixedPointCompression=True, compression=None)

Save the data of this class to a new HDF dataset.

Parameters

  • g (h5py.Group) – the parent HDF Group of the new dataset.

  • name (str) – the name of the new HDF dataset in group g.

  • fixedPointCompression (bool) – if True then save the data in a special 16bit fixed-point format. Testing has shown that this has a maximum conversion error of 1.4e-3 percent. Saving is ~10% faster but requires only 50% the hard drive space.

  • compression (Optional[str]) – The value of this argument will be passed to h5py.create_dataset for numpy arrays. See h5py documentation for available options.

Returns

This is the the same h5py.Group that was passed in a g. It should now have a new dataset by the name of ‘name’

Return type

h5py.Group

property index: Tuple[float, ...]

Returns: The values of the datacube’s index

Return type

Tuple[float, ...]