prysm.detector¶

Detector-related simulations.

class prysm.detector.Detector(pitch_x=None, pitch_y=None, pixel='rectangle', resolution=(1024, 1024), nbits=16, framebuffer=10)¶

Bases: object

Model of a image sensor.

capture(convolvable)¶

Sample a convolvable, mimics capturing a photo of an oversampled representation of an image.

Parameters: convolvable (prysm.Convolvable) – a convolvable object
Returns: a new convolvable object, as it would be sampled by the detector
Return type: prysm.convolvable
Raises: ValueError – if the convolvable would have to become supersampled by the detector; this would lead to an inaccurate result and is not supported

save_image(path, which='last')¶

Save an image captured by the detector.

Parameters

path (string) – path to save the image to
which (string or int) – if string, “first” or “last”, otherwise index into the capture buffer of the camera.

Raises

ValueError – bad target frame to save; should always be the a valid int < buffer_depth

show_image(which='last', fig=None, ax=None)¶

Show an image captured by the detector.

Parameters

which (string or int) – if string, “first” or “last”, otherwise index into the capture buffer of the camera
fig (matplotlib.figure.Figure, optional) – Figure containing the plot
ax (matplotlib.axes.Axis, optional) – Axis containing the plot

Returns

fig (`matplotlib.figure.Figure) – Figure containing the plot
ax (matplotlib.axes.Axis) – Axis containing the plot

pitch¶: 1D pixel pitch - minimum of x/y pitches.

fill_factor_x¶: Fill factor in the X axis.

fill_factor_y¶: Fill factor in the Y axis.

fill_factor¶: 1D fill factor – minimum of x/y fill factors.

fs¶: Sampling frequency in cy/mm.

nyquist¶: Nyquist frequency in cy/mm.

last¶: Last frame captured.

class prysm.detector.OLPF(width_x, width_y=None, sample_spacing=0, samples_x=None, samples_y=None)¶

Bases: prysm.convolution.Convolvable

Optical Low Pass Filter.

analytic_ft(x, y)¶

Analytic fourier transform of a pixel aperture.

Parameters

x (numpy.ndarray) – sample points in x axis
y (numpy.ndarray) – sample points in y axis

Returns

2D numpy array containing the analytic fourier transform

Return type

numpy.ndarray

astype(other_type)¶

Change this instance of one type into another.

Useful to access methods of the other class.

Parameters: other_type (object) – the name of the other type to “cast” to, e.g. Interferogram. Not a string.
Returns: type-converted to the other type.
Return type: self

center_x¶: Center “pixel” in x.

center_y¶: Center “pixel” in y.

change_xy_unit(to, inplace=True)¶

Change the x/y unit to a new one, scaling the data in the process.

Parameters

to (astropy.unit or str) – if not an astropy unit, a string that is a valid attribute of astropy.units.
inplace (bool, optional) – if True, returns self. Otherwise returns the modified data.

Returns

RichData – self, if inplace=True
numpy.ndarray, numpy.ndarray – x, y from self, if inplace=False

change_z_unit(to, inplace=True)¶

Change the z unit to a new one, scaling the data in the process.

Parameters

to (astropy.unit or str) – if not an astropy unit, a string that is a valid attribute of astropy.units.
inplace (bool, optional) – if True, returns self. Otherwise returns the modified data.

Returns

RichData – self, if inplace=True
numpy.ndarray – data from self, if inplace=False

conv(other)¶

Convolves this convolvable with another.

Parameters: other (Convolvable) – A convolvable object
Returns: a convolvable object
Return type: Convolvable

Notes

If self and other both have analytic Fourier transforms, no math will be done and the aFTs are merged directly.

If only one of self or other has an analytic Fourier transform, the output grid will be defined by the object which does not have an analytic Fourier transform.

If neither has an analytic transform, the output grid will: - span max(self.support, other.support) - have sample spacing min(self.sample_spacing, other.sample_spacing)

This ensures the signal remains Nyquist sampled and (probably) doesn’t expand beyond the extent of the output window. The latter condition will be violated when two large convolvables are convolved.

copy()¶: Return a (deep) copy of this instance.

deconv(other, balance=1000, reg=None, is_real=True, clip=False, postnormalize=True)¶

Perform the deconvolution of this convolvable object by another.

Parameters

other (Convolvable) – another convolvable object, used as the PSF in a Wiener deconvolution
balance (float, optional) – regularization parameter; passed through to skimage
reg (numpy.ndarray, optional) – regularization operator, passed through to skimage
is_real (bool, optional) – True if self and other are both real
clip (bool, optional) – clips self and other into (0,1)
postnormalize (bool, optional) – normalize the result such that it falls in [0,1]

Returns

a new Convolable object

Return type

Convolvable

Notes

See skimage: http://scikit-image.org/docs/dev/api/skimage.restoration.html#skimage.restoration.wiener

exact_polar(rho, phi=None)¶

Retrieve data at the specified radial coordinates pairs.

Parameters

r (iterable) – radial coordinate(s) to sample
phi (iterable) – azimuthal coordinate(s) to sample

Returns

data at the given points

Return type

numpy.ndarray

exact_x(x)¶

Return data at an exact x coordinate along the y=0 axis.

Parameters: x (number or numpy.ndarray) – x coordinate(s) to return
Returns: ndarray of values
Return type: numpy.ndarray

exact_xy(x, y=None)¶

Retrieve data at the specified X-Y frequency pairs.

Parameters

x (iterable) – X coordinate(s) to retrieve
y (iterable) – Y coordinate(s) to retrieve

Returns

data at the given points

Return type

numpy.ndarray

exact_y(y)¶

Return data at an exact y coordinate along the x=0 axis.

Parameters: y (number or numpy.ndarray) – y coordinate(s) to return
Returns: ndarray of values
Return type: numpy.ndarray

static from_file(path, scale)¶

Read a monochrome 8 bit per pixel file into a new Image instance.

Parameters

path (string) – path to a file
scale (float) – pixel scale, in microns

Returns

a new image object

Return type

Convolvable

msaa(factor=2)¶

Multi-Sample anti-aliasing.

Perform anti-aliasing by averaging blocks of (factor, factor) pixels into a simple value.

Parameters: factor (int, optional) – factor by which to decimate the data
Returns: self
Return type: Convolvable

plot2d(xlim=None, ylim=None, clim=None, cmap=None, log=False, power=1, interpolation=None, show_colorbar=True, show_axlabels=True, fig=None, ax=None)¶

Plot the data in 2D.

Parameters

xlim (float or iterable, optional) – x axis limits. If not iterable, symmetric version of the single value
ylim (float or iterable, optional) – y axis limits. If None and xlim is not None, copied from xlim. If not iterable, symmetric version of the single value.
clim (iterable, optional) – clim passed directly to matplotlib. If None, looked up on self._default_clim.
cmap (str, optional) – colormap to use, passed directly to matplotlib if not None. If None, looks up the default cmap for self._data_type on config
log (bool, optional) – if True, plot on a log color scale
power (float, optional) – if not 1, plot on a power stretched color scale
interpolation (str, optional) – interpolation method to use, passed directly to matplotlib
show_colorbar (bool, optional) – if True, draws the colorbar
show_axlabels (bool, optional) – if True, draws the axis labels
fig (matplotlib.figure.Figure) – Figure containing the plot
ax (matplotlib.axes.Axis) – Axis containing the plot

Returns

fig (matplotlib.figure.Figure) – Figure containing the plot
ax (matplotlib.axes.Axis) – Axis containing the plot

renorm()¶: Renormalize so that the peak is at a value of unity and the minimum value is zero.

sample_spacing¶: center-to-center sample spacing.

samples_x¶: Number of samples in the x dimension.

samples_y¶: Number of samples in the y dimension.

save(path, nbits=8)¶

Write the image to a png, jpg, tiff, etc.

Parameters

path (string) – path to write the image to
nbits (int) – number of bits in the output image

shape¶: Proxy to phase or data shape.

size¶: Proxy to phase or data size.

slices(twosided=None)¶

Create a Slices instance from this instance.

Parameters: twosided (bool, optional) – if None, copied from self._default_twosided
Returns: a Slices object
Return type: Slices

support¶: Width of the domain.

support_x¶: Width of the domain in X.

support_y¶: Width of the domain in Y.

class prysm.detector.PixelAperture(width_x, width_y=None, sample_spacing=0, samples_x=None, samples_y=None)¶

Bases: prysm.convolution.Convolvable

The aperture of a rectangular pixel.

analytic_ft(x, y)¶

Analytic fourier transform of a pixel aperture.

Parameters

x (numpy.ndarray) – sample points in x axis
y (numpy.ndarray) – sample points in y axis

Returns

2D numpy array containing the analytic fourier transform

Return type

numpy.ndarray

astype(other_type)¶

Change this instance of one type into another.

Useful to access methods of the other class.

Parameters: other_type (object) – the name of the other type to “cast” to, e.g. Interferogram. Not a string.
Returns: type-converted to the other type.
Return type: self

center_x¶: Center “pixel” in x.

center_y¶: Center “pixel” in y.

change_xy_unit(to, inplace=True)¶

Change the x/y unit to a new one, scaling the data in the process.

Parameters

to (astropy.unit or str) – if not an astropy unit, a string that is a valid attribute of astropy.units.
inplace (bool, optional) – if True, returns self. Otherwise returns the modified data.

Returns

RichData – self, if inplace=True
numpy.ndarray, numpy.ndarray – x, y from self, if inplace=False

change_z_unit(to, inplace=True)¶

Change the z unit to a new one, scaling the data in the process.

Parameters

to (astropy.unit or str) – if not an astropy unit, a string that is a valid attribute of astropy.units.
inplace (bool, optional) – if True, returns self. Otherwise returns the modified data.

Returns

RichData – self, if inplace=True
numpy.ndarray – data from self, if inplace=False

conv(other)¶

Convolves this convolvable with another.

Parameters: other (Convolvable) – A convolvable object
Returns: a convolvable object
Return type: Convolvable

Notes

If self and other both have analytic Fourier transforms, no math will be done and the aFTs are merged directly.

If only one of self or other has an analytic Fourier transform, the output grid will be defined by the object which does not have an analytic Fourier transform.

If neither has an analytic transform, the output grid will: - span max(self.support, other.support) - have sample spacing min(self.sample_spacing, other.sample_spacing)

This ensures the signal remains Nyquist sampled and (probably) doesn’t expand beyond the extent of the output window. The latter condition will be violated when two large convolvables are convolved.

copy()¶: Return a (deep) copy of this instance.

deconv(other, balance=1000, reg=None, is_real=True, clip=False, postnormalize=True)¶

Perform the deconvolution of this convolvable object by another.

Parameters

other (Convolvable) – another convolvable object, used as the PSF in a Wiener deconvolution
balance (float, optional) – regularization parameter; passed through to skimage
reg (numpy.ndarray, optional) – regularization operator, passed through to skimage
is_real (bool, optional) – True if self and other are both real
clip (bool, optional) – clips self and other into (0,1)
postnormalize (bool, optional) – normalize the result such that it falls in [0,1]

Returns

a new Convolable object

Return type

Convolvable

Notes

See skimage: http://scikit-image.org/docs/dev/api/skimage.restoration.html#skimage.restoration.wiener

exact_polar(rho, phi=None)¶

Retrieve data at the specified radial coordinates pairs.

Parameters

r (iterable) – radial coordinate(s) to sample
phi (iterable) – azimuthal coordinate(s) to sample

Returns

data at the given points

Return type

numpy.ndarray

exact_x(x)¶

Return data at an exact x coordinate along the y=0 axis.

Parameters: x (number or numpy.ndarray) – x coordinate(s) to return
Returns: ndarray of values
Return type: numpy.ndarray

exact_xy(x, y=None)¶

Retrieve data at the specified X-Y frequency pairs.

Parameters

x (iterable) – X coordinate(s) to retrieve
y (iterable) – Y coordinate(s) to retrieve

Returns

data at the given points

Return type

numpy.ndarray

exact_y(y)¶

Return data at an exact y coordinate along the x=0 axis.

Parameters: y (number or numpy.ndarray) – y coordinate(s) to return
Returns: ndarray of values
Return type: numpy.ndarray

static from_file(path, scale)¶

Read a monochrome 8 bit per pixel file into a new Image instance.

Parameters

path (string) – path to a file
scale (float) – pixel scale, in microns

Returns

a new image object

Return type

Convolvable

msaa(factor=2)¶

Multi-Sample anti-aliasing.

Perform anti-aliasing by averaging blocks of (factor, factor) pixels into a simple value.

Parameters: factor (int, optional) – factor by which to decimate the data
Returns: self
Return type: Convolvable

plot2d(xlim=None, ylim=None, clim=None, cmap=None, log=False, power=1, interpolation=None, show_colorbar=True, show_axlabels=True, fig=None, ax=None)¶

Plot the data in 2D.

Parameters

xlim (float or iterable, optional) – x axis limits. If not iterable, symmetric version of the single value
ylim (float or iterable, optional) – y axis limits. If None and xlim is not None, copied from xlim. If not iterable, symmetric version of the single value.
clim (iterable, optional) – clim passed directly to matplotlib. If None, looked up on self._default_clim.
cmap (str, optional) – colormap to use, passed directly to matplotlib if not None. If None, looks up the default cmap for self._data_type on config
log (bool, optional) – if True, plot on a log color scale
power (float, optional) – if not 1, plot on a power stretched color scale
interpolation (str, optional) – interpolation method to use, passed directly to matplotlib
show_colorbar (bool, optional) – if True, draws the colorbar
show_axlabels (bool, optional) – if True, draws the axis labels
fig (matplotlib.figure.Figure) – Figure containing the plot
ax (matplotlib.axes.Axis) – Axis containing the plot

Returns

fig (matplotlib.figure.Figure) – Figure containing the plot
ax (matplotlib.axes.Axis) – Axis containing the plot

renorm()¶: Renormalize so that the peak is at a value of unity and the minimum value is zero.

sample_spacing¶: center-to-center sample spacing.

samples_x¶: Number of samples in the x dimension.

samples_y¶: Number of samples in the y dimension.

save(path, nbits=8)¶

Write the image to a png, jpg, tiff, etc.

Parameters

path (string) – path to write the image to
nbits (int) – number of bits in the output image

shape¶: Proxy to phase or data shape.

size¶: Proxy to phase or data size.

slices(twosided=None)¶

Create a Slices instance from this instance.

Parameters: twosided (bool, optional) – if None, copied from self._default_twosided
Returns: a Slices object
Return type: Slices

support¶: Width of the domain.

support_x¶: Width of the domain in X.

support_y¶: Width of the domain in Y.

prysm.detector.pixelaperture_analytic_otf(width_x, width_y, freq_x, freq_y)¶

Analytic MTF of a rectangular pixel aperture.

Parameters

width_x (float) – x diameter of the pixel, in microns
width_y (float) – y diameter of the pixel, in microns
freq_x (numpy.ndarray) – x spatial frequency, in cycles per micron
freq_y (numpy.ndarray) – y spatial frequency, in cycles per micron

Returns

MTF of the pixel aperture

Return type

numpy.ndarray

prysm.detector.bindown(array, nsamples_x, nsamples_y=None, mode='avg')¶

Bin (resample) an array.

Parameters

array (numpy.ndarray) – array of values
nsamples_x (int) – number of samples in x axis to bin by
nsamples_y (int) – number of samples in y axis to bin by. If None, duplicates value from nsamples_x
mode (str, {‘avg’, ‘sum’}) – sum or avg, how to adjust the output signal

Returns

ndarray binned by given number of samples

Return type

numpy.ndarray

Notes

Array should be 2D. TODO: patch to allow 3D data.

If the size of array is not evenly divisible by the number of samples, the algorithm will trim around the border of the array. If the trim length is odd, one extra sample will be lost on the left side as opposed to the right side.

Raises: ValueError – invalid mode

prysm.detector.bindown_with_units(px_x, px_y, source_spacing, source_data)¶

Perform bindown, returning unit axes and data.

Parameters

px_x (float) – pixel pitch in the x direction, microns
px_y (float) – pixel pitch in the y direction, microns
source_spacing (float) – pixel pitch in the source data, microns
source_data (numpy.ndarray) – ndarray of regularly spaced data

Returns

ux (numpy.ndarray) – 1D array of sample coordinates in the x direction
uy (numpy.ndarray) – 1D array of sample coordinates in the y direction
data (numpy.ndarray) – binned-down data

prysm.detector¶

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