pwspy.dataTypes.ExtraReflectanceCube¶
- class pwspy.dataTypes.ExtraReflectanceCube(data, wavelengths, metadata)[source]¶
Bases:
pwspy.dataTypes._data.ICBase
This class represents a 3D data cube of the extra reflectance in a PWS system.
- Parameters
data (
ndarray
) – A 3D array of the extra reflectance in the system. It’s values are in units of reflectance (between 0 and 1).wavelengths (
Tuple
[float
,...
]) – The wavelengths associated with each 2D slice along the 3rd axis of the data array.metadata (
ERMetaData
) – Metadata
- metadata¶
metadata
- Type
- data¶
data
- Type
ndarray
- 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 pixelSizepixelSize (
float
) – The pixel size in microns. Settings this to 1 will effectively causes sigma to be in units of pixels rather than microns.
- classmethod fromHdfDataset(d, filePath=None)[source]¶
Load the ExtraReflectanceCube from d, an HDF5 dataset.
- Parameters
d (
Dataset
) – The h5py.Dataset to load the cube from.filePath (
Optional
[str
]) – The path to the HDF file that the dataset came from.
- Return type
- Returns
A new instance of ExtraReflectanceCube loaded from HDF.
- classmethod fromHdfFile(directory, name)[source]¶
Load an ExtraReflectanceCube from an HDF5 file. name should be the file name, excluding the ‘_ExtraReflectance.h5’ suffix.
- Parameters
directory (
str
) – The path to the folder containing the HDF file.name (
str
) – The name that the cube was saved as.
- Return type
- Returns
A new instance of ExtraReflectanceCube loaded from HDF.
- classmethod fromMetadata(md)[source]¶
Load an ExtraReflectanceCube from an ERMetaData object corresponding to an HDF5 file.
- Parameters
md (
ERMetaData
) – The metadata to be used for loading the data file.
- 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
- 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)[source]¶
Save the ExtraReflectanceCube to an HDF5 dataset. g should be an h5py Group or File.
- Parameters
g (
Group
) – The h5py.Group to save to.- Return type
Group
- toHdfFile(directory, name)[source]¶
Save an ExtraReflectanceCube to an HDF5 file. The filename will be name with the ‘_ExtraReflectance.h5’ suffix.
- Parameters
directory (
str
) – The path to the folder to save the HDF file to.name (
str
) – The name that the cube should be saved as.
- property index: Tuple[float, ...]¶
Returns: The values of the datacube’s index
- Return type
Tuple
[float
,...
]
- property wavelengths: Tuple[float, ...]¶
Returns: The wavelengths corresponding to each element along the 3rd axis of self.data.
- Return type
Tuple
[float
,...
]