slmsuite.holography.algorithms.SpotHologram

class SpotHologram(shape, spot_vectors, basis='knm', spot_amp=None, cameraslm=None, null_vectors=None, null_radius=None, null_region=None, null_region_radius_frac=None, subpixel=False, **kwargs)

Bases: FeedbackHologram

Holography optimized for the generation of optical focal arrays.

Is a subclass of FeedbackHologram, but falls back to non-camera-feedback routines if cameraslm is not passed.

Tip

Quality of life features to generate noise regions for mixed region amplitude freedom (MRAF) algorithms are supported. Specifically, set null_region parameters to help specify where the noise region is not.

spot_knm, spot_kxy, spot_ij

Stored vectors with shape (2, N) in the style of format_2vectors(). These vectors are floats. The subscript refers to the basis of the vectors, the transformations between which are autocomputed. If necessary transformations do not exist, spot_ij is set to None.

Type

array_like of float OR None

spot_knm_rounded

spot_knm rounded to nearest integers (indices). These vectors are integers. This is necessary because GS algorithms operate on a pixel grid, and the target for each spot in a SpotHologram is a single pixel (index).

Type

array_like of int

spot_kxy_rounded, spot_ij_rounded

Once spot_knm_rounded is rounded, the original spot_kxy and spot_ij are no longer accurate. Transformations are again used to backcompute the positions in the "ij" and "kxy" bases corresponding to the true computational location of a given spot. These vectors are floats.

Type

array_like of float

spot_amp

The target amplitude for each spot. Must have length corresponding to the number of spots. For instance, the user can request dimmer or brighter spots.

Type

array_like of float

external_spot_amp

When using "external_spot" feedback or the "external_spot" stat group, the user must supply external data. This data is transferred through this attribute. For iterative feedback, have the callback() function set external_spot_amp dynamically. By default, this variable is set to even distribution of amplitude.

Type

array_like of float

spot_integration_width_knm

For spot-specific feedback methods, better SNR is achieved when integrating over many farfield pixels. This variable stores the width of the integration region in "knm" (farfield) space.

Type

int

spot_integration_width_ij

For spot-specific feedback methods, better SNR is achieved when integrating over many camera pixels. This variable stores the width of the integration region in "ij" (camera) space.

Type

int

null_knm

In addition to points where power is desired, SpotHologram is equipped with quality of life features to select points where power is undesired. These points are stored in null_knm with shape (2, M) in the style of format_2vectors(). A region around these points is set to zero (null) and not allowed to participate in the noise region.

Type

array_like of float OR None

null_radius_knm

The radius in "knm" space around the points null_knm to zero or null (prevent from participating in the nan noise region). This is useful to prevent power being deflected to very high orders, which are unlikely to be properly represented in practice on a physical SLM.

Type

float

null_region_knm

Array of shape shape. Where True, sets the background to zero instead of nan. If None, has no effect.

Type

array_like of bool OR None

subpixel_beamradius_knm

The radius in knm space corresponding to the beamradius of the Gaussian spot which is targeted when subpixel features are enabled. In the future, a non-Gaussian kernel might be used instead. This radius is computed based upon the stored amplitude in the SLM (if passed). This is an experimental feature and should be used with caution.

Type

float

Methods

GS	GPU-accelerated Gerchberg-Saxton (GS) iterative phase retrieval.
calculate_padded_shape	Helper function to calculate the shape of the computational space.
export_stats	Uses write_h5() to export the statistics hierarchy to a given h5 file.
extract_farfield	Collects the current complex farfield from the GPU with cupy.ndarray.get().
extract_phase	Collects the current nearfield phase from the GPU with cupy.ndarray.get().
get_mempool_limit	Helper function to get the cupy memory pool size.
ijcam_to_knmslm	Convert an image in the camera domain to computational SLM k-space using, in part, the affine transformation stored in a cameraslm's Fourier calibration.
import_stats	Uses write_h5() to import the statistics hierarchy from a given h5 file.
make_rectangular_array	Helper function to initialize a rectangular 2D array of spots, with certain size and pitch.
measure	Method to request a measurement to occur.
optimize	Optimizers to solve the "phase problem": approximating the near-field phase that transforms a known near-field source amplitude to a desired far-field target amplitude.
plot_farfield	Plots an overview (left) and zoom (right) view of source.
plot_nearfield	Plots the amplitude (left) and phase (right) of the nearfield (plane of the SLM).
plot_stats	Plots the statistics contained in the given dictionary.
refine_offset	Hones the positions of the produced spots toward the desired targets to compensate for Fourier calibration imperfections.
reset	Resets the hologram to an initial state.
reset_phase	Resets the hologram to a random state or to a provided phase.
reset_weights	Resets the hologram weights to the target defaults.
set_mempool_limit	Helper function to set the cupy memory pool size.
update_stats	Calculate statistics corresponding to the desired stat_groups.
update_target	From the spot locations stored in spot_knm, update the target pattern.

__init__(shape, spot_vectors, basis='knm', spot_amp=None, cameraslm=None, null_vectors=None, null_radius=None, null_region=None, null_region_radius_frac=None, subpixel=False, **kwargs)

Initializes a SpotHologram targeting given spots at spot_vectors.

Parameters

• shape ((int, int)) – Computational shape of the SLM. See Hologram.__init__().

• spot_vectors (array_like) – Spot position vectors with shape (2, N) in the style of format_2vectors().

• basis (str) –

  The spots can be in any of the following bases:

  • "ij" for camera coordinates (pixels),

  • "kxy" for centered normalized SLM k-space (radians).

  • "knm" for computational SLM k-space (pixels).

  Defaults to "knm" if None.

• spot_amp (array_like OR None) – The amplitude to target for each spot. See SpotHologram.spot_amp. If None, all spots are assumed to have the same amplitude. Normalization is performed automatically; the user is not required to normalize.

• cameraslm (slmsuite.hardware.cameraslms.FourierSLM OR None) – If the "ij" basis is chosen, and/or if the user wants to make use of camera feedback, a cameraslm must be provided.

• null_vectors (array_like OR None) – Null position vectors with shape (2, N) in the style of format_2vectors(). MRAF methods are forced zero around these points.

• null_radius (float OR None) – Radius to null around in the given basis. Note that basis conversions are imperfect for anisotropic basis transformations. The radius will always be set to be circular in "knm" space, and will attempt to match to the closest circle to the (potentially elliptical) projection into "knm" from the given basis.

• null_region (array_like OR None) – Array of shape shape. Where True, sets the background to zero instead of nan. If None, has no effect.

• null_region_radius_frac (float OR None) – Helper function to set the null_region to zero for Fourier space radius fractions above null_region_radius_frac. This is useful to prevent power being deflected to very high orders, which are unlikely to be properly represented in practice on a physical SLM.

• subpixel (bool) –

  If enabled, the target is set to a series of Gaussian spots with radius subpixel_beamradius_knm instead of a series of single pixel spots (the default for SpotHologram). The major benefit here is:

  • Greater resolution with limited padding. With 2-3 orders of padding, the farfield has sufficient resolution to render a Gaussian positioned inbetween farfield pixels, allowing for greater resolutions without having to pad further. This is especially important when operating at the memory limits of a system.

  Defaults to False. This is an experimental feature and should be used with caution. Currently, there are issues with the initial phase causing some spots to be permanently attenuated.

• **kwargs – Passed to FeedbackHologram.__init__().

GS(iterations, callback)

GPU-accelerated Gerchberg-Saxton (GS) iterative phase retrieval.

Solves the “phase problem”: approximates the near-field phase that transforms a known near-field source amplitude to a desired far-field target amplitude.

Caution

This function should be called through optimize() and not called directly. It is left as a public function exposed in documentation to clarify how the internals of optimize() work.

Note

FFTs are not in-place in this algorithm. In both non-cupy and cupy implementations, numpy.fft does not support in-place operations. However, scipy.fft does in both. In the future, we may move to the scipy implementation. However, neither numpy or scipy fftshift support in-place movement (for obvious reasons). For even faster computation, algorithms should consider not shifting the FFT result, and instead shifting measurement data / etc to this unshifted basis. We might also implement get_fft_plan for even faster FFTing.

Parameters

• iterations (iterable) – Number of loop iterations to run. Is an iterable to pass a tqdm iterable.

• callback (callable OR None) – See optimize().

static calculate_padded_shape(slm_shape, padding_order=1, square_padding=True, precision=inf, precision_basis='kxy')

Helper function to calculate the shape of the computational space. For a given base slm_shape, pads to the user’s requirements. If the user chooses multiple requirements, the largest dimensions for the shape are selected. By default, pads to the smallest square power of two that encapsulates the original slm_shape.

Tip

See also the first tip in the constructor of Hologram for more information about the importance of padding.

Note

Under development: a parameter to pad based on available memory (see _calculate_memory_constrained_shape()).

Parameters

• slm_shape ((int, int) OR slmsuite.hardware.FourierSLM) – The original shape of the SLM in numpy (h, w) form. The user can pass a slmsuite.hardware.FourierSLM instead, and should pass this when using the precision parameter.

• padding_order (int) – Scales to the padding_order th larger power of 2. A padding_order of zero does nothing. For instance, an SLM with shape (720, 1280) would yield (720, 1280) for padding_order=0, (1024, 2048) for padding_order=1, and (2048, 4096) for padding_order=2.

• square_padding (bool) – If True, sets the smaller shape dimension to that of the larger, yielding a square.

• precision (float) – Returns the shape that produces a computational k-space with resolution smaller than precision. The default, infinity, requests a padded shape larger than zero, so padding_order will dominate.

• precision_basis (str) – Basis for the precision. Can be "ij" (camera) or "kxy" (normalized blaze).

Returns

Shape of the computational space which satisfies the above requirements.

Return type

(int, int)

export_stats(file_path, include_state=True)

Uses write_h5() to export the statistics hierarchy to a given h5 file.

Parameters

• file_path (str) – Full path to the file to read the data from.

• include_state (bool) – If True, also includes all other attributes of Hologram except for dtype (cannot pickle) and amp_ff (can regenerate). These attributes are converted to numpy if necessary. Note that the intent is not to produce a runnable Hologram by default (as this would require pickling hardware interfaces), but rather to provide extra information for debugging.

extract_farfield()

Collects the current complex farfield from the GPU with cupy.ndarray.get().

Returns

Current farfield computed by GS.

Return type

numpy.ndarray

extract_phase()

Collects the current nearfield phase from the GPU with cupy.ndarray.get(). Also shifts the \([-\pi, \pi]\) range of numpy.arctan2() to \([0, 2\pi]\) for faster writing to the SLM (see write()).

Returns

Current nearfield phase computed by GS.

Return type

numpy.ndarray

static get_mempool_limit(device=0)

Helper function to get the cupy memory pool size.

Parameters

device (int) – Which GPU to set the limit on. Passed to cupy.cuda.Device().

Returns

Current memory pool limit in bytes

Return type

int

ijcam_to_knmslm(img, out=None, blur_ij=None, order=3)

Convert an image in the camera domain to computational SLM k-space using, in part, the affine transformation stored in a cameraslm’s Fourier calibration.

Note

This includes two transformations:

• The affine transformation "ij" -> "kxy" (camera pixels to normalized k-space).

• The scaling "kxy" -> "knm" (normalized k-space to computational k-space pixels).

Parameters

• img (numpy.ndarray OR cupy.ndarray) – Image to transform. This should be the same shape as images returned by the camera.

• out (numpy.ndarray OR cupy.ndarray OR None) – If out is not None, this array will be used to write the memory in-place.

• blur_ij (int OR None) – Applies a blur_ij pixel-width Gaussian blur to img. If None, defaults to the "blur_ij" flag if present; otherwise zero.

• order (int) – Order of interpolation used for transformation. Defaults to 3 (cubic).

Returns

Image transformed into "knm" space.

Return type

numpy.ndarray OR cupy.ndarray

import_stats(file_path, include_state=True)

Uses write_h5() to import the statistics hierarchy from a given h5 file.

Tip

Enabling the "raw_stats" flag will export feedback data from each iteration instead of only derived statistics. Consider enabling this to save more detailed information upon export.

Parameters

• file_path (str) – Full path to the file to read the data from.

• include_state (bool) – If True, also overwrite all other attributes of Hologram except for dtype and amp_ff.

measure(basis='ij')

Method to request a measurement to occur. If img_ij is None, then a new image will be grabbed from the camera (this is done automatically in algorithms).

Parameters

basis (str) –

The cached image to be sure to fill with new data. Can be "ij" or "knm".

• If "knm", then img_ij and img_knm are filled.

• If "ij", then img_ij is filled, and img_knm is ignored.

This is useful to avoid (expensive) transformation from the "ij" to the "knm" basis if img_knm is not needed.

optimize(method='GS', maxiter=20, verbose=True, callback=None, feedback=None, stat_groups=[], **kwargs)

Optimizers to solve the “phase problem”: approximating the near-field phase that transforms a known near-field source amplitude to a desired far-field target amplitude. Supported optimization methods include:

• Gerchberg-Saxton (GS) phase retrieval.

  'GS'

  An iterative algorithm for phase retrieval, accomplished by moving back and forth between the imaging and Fourier domains, with amplitude corrections applied to each. This is implemented using fast Fourier transforms, potentially GPU-accelerated.

• Weighted Gerchberg-Saxton (WGS) phase retrieval algorithms of various flavors. Improves the uniformity of GS-computed focus arrays using weighting methods and techniques from literature. The method keywords are:

  'WGS-Leonardo'

  The original WGS algorithm. Weights the target amplitudes by the ratio of mean amplitude to computed amplitude, which amplifies weak spots while attenuating strong spots. Uses the following weighting function:

  \[\mathcal{W} = \mathcal{W}\left(\frac{\mathcal{T}}{\mathcal{F}}\right)^p\]

  where \(\mathcal{W}\), \(\mathcal{T}\), and \(\mathcal{F}\) are the weight amplitudes, target (goal) amplitudes, and feedback (measured) amplitudes, and \(p\) is the power passed as "feedback_exponent" in flags (see kwargs). The power \(p\) defaults to .9 if not passed. In general, smaller \(p\) will lead to slower yet more stable optimization.

  'WGS-Kim'

  Improves the convergence of WGS-Leonardo by fixing the far-field phase strictly after a desired number of net iterations specified by "fix_phase_iteration" or after exceeding a desired efficiency (fraction of far-field energy at the desired points) specified by "fix_phase_efficiency"

  'WGS-Nogrette'

  Weights target intensities by a tunable gain factor.

  \[\mathcal{W} = \mathcal{W}/\left(1 - f\left(1 - \mathcal{F}/\mathcal{T}\right)\right)\]

  where \(f\) is the gain factor passed as "feedback_factor" in flags (see kwargs). The factor \(f\) defaults to .1 if not passed.

  Note that while Nogrette et al compares powers, this implementation compares amplitudes for speed. These are identical to first order.

• The option for Mixed Region Amplitude Freedom (MRAF) feedback. In standard iterative algorithms, the entire Fourier-domain unpatterned field is replaced with zeros. This is disadvantageous because a desired farfield pattern might not be especially compatible with a given nearfield amplitude, or otherwise. MRAF enables “noise regions” where some fraction of the given farfield is not replaced with zeros and instead is allowed to vary. In practice, MRAF is enabled by setting parts of the target to nan; these regions act as the noise regions. The "mraf_factor" flag in flags allows the user to partially attenuate the noise regions. A factor of 0 fully attenuates the noise region (normal WGS behavior). A factor of 1 does not attenuate the noise region at all (the default). Middle ground is recommended, but is application-dependent as a tradeoff between improving pattern fidelity and maintaining pattern efficiency.

  As examples, consider two cases where MRAF can be useful:

  • Sloping a top hat. Suppose we want very flat amplitude on a beam. Requesting a sharp edge to this beam can lead to fringing effects at the boundary which mitigate flatness both inside and outside the beam. If instead a noise region is defined in a band surrounding the beam, the noise region will be filled with whatever slope best enables the desired flat beam.

  • Mitigating diffractive orders. Without MRAF, spot patterns with high crystallinity often have “ghost” diffractive orders which continue the pattern past the edges of requested spots. Even though these orders are attenuated during each phase retrieval iteration, they remain part of the best solution for the recovered phase. With MRAF, a noise region can help solve for retrieved phase which does not generate these undesired orders.

Caution

Requesting stat_groups will slow the speed of optimization due to the overhead of processing and saving statistics, especially in the case of GPU-accelerated optimization where significant time cost is incurred by moving these statistics to the CPU. This is especially apparent in the case of fully-computational holography, where this effect can slow what is otherwise a fully-GPU-contained loop by an order magnitude.

Tip

This function uses a parameter naming convention borrowed from scipy.optimize.minimize() and other functions in scipy.optimize. The parameters method, maxiter, and callback have the same functionality as the equivalently-named parameters in scipy.optimize.minimize().

Parameters

• method (str) – Optimization method to use. See the list of optimization methods above.

• maxiter (int) – Number of iterations to optimize before terminating.

• verbose (bool OR int) – Whether to display tqdm progress bars. These bars are also not displayed for maxiter <= 1. If verbose is greater than 1, then flags are printed as a preamble.

• callback (callable OR None) – Same functionality as the equivalently-named parameter in scipy.optimize.minimize(). callback must accept a Hologram or Hologram subclass as the single argument. If callback returns True, then the optimization exits. Ignored if None.

• feedback (str OR None) –

  Type of feedback to use during optimization, for instance when weighting in "WGS". For direct instances of Hologram, this can only be "computational" feedback. Subclasses support more types of feedback. Supported feedback options include the following:

  • "computational" Uses the the projected farfield pattern (transform of the complex nearfield) as feedback.

  • "experimental" Uses a camera contained in a passed cameraslm as feedback. Specific to subclasses of FeedbackHologram.

  • "computational_spot" Takes the computational result (the projected farfield pattern) and integrates regions around the expected positions of spots in an optical focus array. More stable than "computational" for spots. Specific to subclasses of SpotHologram.

  • "experimental_spot" Takes the experimental result (the image from a camera) and integrates regions around the expected positions of spots in an optical focus array. More stable than "experimental" for spots. Specific to subclasses of SpotHologram.

  • "external_spot" Uses some external user-provided metric for spot feedback. See external_spot_amp. Specific to subclasses of SpotHologram.

• stat_groups (list of str OR None) – Strings representing types of feedback (data gathering) upon which statistics should be derived. These strings correspond to valid types of feedback (see above). For instance, if "experimental" is passed as a stat group, statistics on the pixels in the experimental feedback image will automatically be computed and stored for each iteration of optimization. However, this comes with overhead (see above warning).

• **kwargs (dict, optional) – Various weight keywords and values to pass depending on the weight method. These are passed into flags. See options documented in the constructor.

plot_farfield(source=None, title='', limits=None, units='knm', limit_padding=0.1, figsize=(8, 4), cbar=False)

Plots an overview (left) and zoom (right) view of source.

Parameters

• source (array_like OR None) – Should have shape equal to shape. If None, defaults to amp_ff.

• title (str) – Title of the plots. If "phase" is a substring of title, then the source is treated as a phase.

• limits (((float, float), (float, float)) OR None) – \(x\) and \(y\) limits for the zoom plot in "knm" space. If None, limits are autocomputed as the smallest bounds that show all non-zero values (plus limit_padding). Note that autocomputing on target will perform well, as zero values are set to actually be zero. However, doing so on computational or experimental outputs (e.g. amp_ff) will likely perform poorly, as values in the field deviate slightly from zero and artificially expand the limits.

• units (str) – Far-field units for plots (see convert_blaze_vector() for options). If units requiring a SLM are desired, the attribute cameraslm must be filled.

• limit_padding (float) – Fraction of the width and height to expand the limits of the zoom plot by, only if the passed limits is None (autocompute).

• figsize (tuple) – Size of the plot.

• cbar (bool) – Whether to add colorbars to the plots. Defaults to False.

Returns

Used limits, which may be autocomputed. Autocomputed limits are returned as integers.

Return type

((float, float), (float, float))

plot_nearfield(title='', padded=False, figsize=(8, 4), cbar=False)

Plots the amplitude (left) and phase (right) of the nearfield (plane of the SLM). The amplitude is assumed (whether uniform, or experimentally computed) while the phase is the result of optimization.

Parameters

• title (str) – Title of the plots.

• padded (bool) – If True, shows the full computational nearfield of shape shape. Otherwise, shows the region at the center of the computational space of size slm_shape corresponding to the unpadded SLM.

• figsize (tuple) – Size of the plot.

• cbar (bool) – Whether to add colorbars to the plots. Defaults to False.

plot_stats(stats_dict=None, stat_groups=[], ylim=None)

Plots the statistics contained in the given dictionary.

Parameters

• stats_dict (dict OR None) – Stats to plot in dictionary form. If None, defaults to stats.

• stat_groups (list of str OR None) – Which

• ylim ((int, int) OR None) – Allows the user to pass in desired y limits. If None, the default y limits are used.

reset(reset_phase=True, reset_flags=False)

Resets the hologram to an initial state. Does not restore the preconditioned phase that may have been passed to the constructor (as this information is lost upon optimization). Also uses the current target rather than the target that may have been passed to the constructor (e.g. includes current refine_offset() changes, etc).

Parameters

• reset_phase (bool) – Whether to additionally call reset_phase().

• reset_flags (bool:) – Whether to erase the information (including passed kwargs) stored in flags.

reset_phase(phase=None)

Resets the hologram to a random state or to a provided phase.

Parameters

phase (array_like OR None) – The near-field initial phase. See phase. phase should only be passed if the user wants to precondition the optimization. Of shape slm_shape.

reset_weights()

Resets the hologram weights to the target defaults.

static set_mempool_limit(device=0, size=None, fraction=None)

Helper function to set the cupy memory pool size.

Parameters

• device (int) – Which GPU to set the limit on. Passed to cupy.cuda.Device().

• size (int) – Desired number of bytes in the pool. Passed to cupy.cuda.MemoryPool.set_limit().

• fraction (float) – Fraction of available memory to use. Passed to cupy.cuda.MemoryPool.set_limit().

static make_rectangular_array(shape, array_shape, array_pitch, array_center=None, basis='knm', orientation_check=False, **kwargs)

Helper function to initialize a rectangular 2D array of spots, with certain size and pitch.

Note

The array can be in SLM k-space coordinates or in camera pixel coordinates, depending upon the choice of basis. For the "ij" basis, cameraslm must be included as one of the kwargs. See __init__() for more basis information.

Important

Spot positions will be rounded to the grid of computational k-space "knm", to create the target image (of finite size) that algorithms optimize towards. Choose array_pitch and array_center carefully to avoid undesired pitch non-uniformity caused by this rounding.

Parameters

• shape ((int, int)) – Computational shape of the SLM in numpy (h, w) form. See SpotHologram.__init__().

• array_shape ((int, int) OR int) – The size of the rectangular array in number of spots (NX, NY). If a scalar N is given, assume (N, N).

• array_pitch ((float, float) OR float) – The spacing between spots in the x and y directions (pitchx, pitchy). If a single pitch is given, assume (pitch, pitch).

• array_center ((float, float) OR None) –

  The shift of the center of the spot array from the zeroth order. Uses (x, y) form in the chosen basis. If None, defaults to the position of the zeroth order, converted into the relevant basis:

  • If "knm", this is (shape[1], shape[0])/2.

  • If "kxy", this is (0,0).

  • If "ij", this is the pixel position of the zeroth order on the camera (calculated via Fourier calibration).

• basis (str) – See __init__().

• orientation_check (bool) – Whether to delete the last two points to check for parity.

• **kwargs – Any other arguments are passed to __init__().

update_target(reset_weights=False, plot=False)

From the spot locations stored in spot_knm, update the target pattern.

Note

If there’s a cameraslm, updates the spot_ij_rounded attribute corresponding to where pixels in the k-space where actually placed (due to rounding to integers, stored in spot_knm_rounded), rather the idealized floats spot_knm.

Note

The target and weights matrices are modified in-place for speed, unlike Hologram or FeedbackHologram which make new matrices. This is because spot positions are expected to be corrected using correct_spots().

Parameters

• reset_weights (bool) – Whether to rest the weights to this new target.

• plot (bool) – Whether to enable debug plotting to see the positions of the spots relative to the shape of the camera and slm.

refine_offset(img=None, basis='kxy', force_affine=True, plot=False)

Hones the positions of the produced spots toward the desired targets to compensate for Fourier calibration imperfections. Works either by moving camera integration regions to the positions where the spots ended up (basis="ij") or by moving the \(k\)-space targets to target the desired camera pixels (basis="knm"/basis="kxy"). This should be run at the user’s request inbetween optimize() iterations.

Parameters

• img (numpy.ndarray OR None) – Image measured by the camera. If None, defaults to img_ij via measure().

• basis (str) –

  The correction can be in any of the following bases:

  • "ij" changes the pixel that the spot is expected at,

  • "kxy", "knm" changes the k-vector which the SLM targets.

  Defaults to "kxy". If basis is set to None, no correction is applied to the data in the SpotHologram.

• force_affine (bool) – Whether to force the offset refinement to behave as an affine transformation between the original and refined coordinate system. This helps to tame outliers. Defaults to True.

• plot (bool) – Enables debug plots.

Returns

Spot shift in the "ij" basis for each spot.

Return type

numpy.ndarray

update_stats(stat_groups=[])

Calculate statistics corresponding to the desired stat_groups.

Parameters

stat_groups (list of str) – Which groups or types of statistics to analyze.