`dtmm.field_viewer`¶

Matplotlib-based field visualizer (polarizing miscroscope simulator) and pom image calculation functions

High level functions¶

pom_viewer() for polarizing optical microscope simulation.
field_viewer() for raw field_data visualization.
bulk_viewer() for raw bulk_data visualization.
calculate_pom_field() calculates polarizing optical microscope field.

Classes¶

FieldViewer is the actual field viewer object.
BulkViewer is the actual bulk viewer object.
POMViewer is the actual microscope viewer object.

Module Contents¶

dtmm.field_viewer.calculate_pom_field(field, jvec=None, pmat=None, dmat=None, window=None, input_fft=False, output_fft=False, out=None)¶

Calculates polarizing optical microscope field from the input field.

This function refocuses the field, applies polarizer and analayzers

Parameters

field (ndarray) – Input array of shape (…,:,4,:,:) describing multiwavelength polarized field array or an array of shape (…,2,:,4,:,:) describing unpolarized (x nad y polarized) multiwavelength field arrays. Works also with jones multiwavelengths fields of shapes (…,:,2,:,:) and (…,2,:,2,:,:).
jvec (jonesvec, optional) – Normalized jones vector describing which polarization state of the input field to choose. Input field must be of unpolarized type if this parameter is specified.
pmat (ndarray, optional) – A 4x4 or 2x2 matrix describing the analyzer and retarder matrix. This matrix is applied in real space only if both input_fft and output_fft are False, otherwise, the matrix is applied in Fourier space.
dmat (ndarray, optional) – A diffraction matrix.
window (array, optional) – If specified, windowing is applied after field is diffracted.
input_fft (bool) – If specified, it idicates that we are working with fft data. pmat must be computed with mode_jonesmat4x4.
output_fft (bool) – If specified, output data is left in FFT space. No inverse Fourier transform is performed if this parameter is set to True.
out (ndarray, optional) – Output array.

Returns

pom_field – Computed field od

Return type

ndarray

Examples

>>> polarizer_jvec = dtmm.jones4.jonesvec((1,0))
>>> analyzer_jvec = dtmm.jones4.jonesvec((0,1))
>>> fmat = dtmm.tmm.f_iso()
>>> pmat = dtmm.jones4.polarizer4x4(analyzer_jvec,fmat)
>>> field_out = calculate_pom_field(field_in, polarizer_jvec, pmat)

dtmm.field_viewer.bulk_viewer(field_data, **kwargs)¶

Returns a BulkViewer object for bulk field data visualization. See field_viewer() for parameters.

Returns: out – A BulkViewer viewer object
Return type: BulkViewer

dtmm.field_viewer.field_viewer(field_data, cmf=None, bulk_data=False, n=1.0, mode=None, is_polarized=None, window=None, diffraction=True, polarization_mode='normal', betamax=BETAMAX, beta=None, **parameters)¶

Returns a FieldViewer object for field data visualization.

Parameters

field_data (tuple[np.ndarray]) – Input field data
cmf (str, ndarray or None, optional) – Color matching function (table). If provided as an array, it must match input field wavelengths. If provided as a string, it must match one of available CMF names or be a valid path to tabulated data. See load_tcmf.
bulk_data (bool) – Specifies whether data is to be treated as bulk data, e.g as returned by the transfer.transfer_field() function with ret_bulk = True.
n (float, optional) – Refractive index of the output material. Set this to the value used in the calculation of the field.
mode ([ 't' | 'r' | None], optional) – Viewer mode ‘t’ for transmission mode, ‘r’ for reflection mode None for as is data (no projection calculation - default).
is_polarized (bool, optional) – If specified, it defines whether the field is polarize or not. For non-polarized fields, the field must be of shape […,2,:,4,:,:]. If not provided, the polarization state is guessed from the shape of the input data. Setting this to False(and having non-polarized field) will allow setting the polarizer and sample rotation.
window (ndarray, optional) – Window function by which the calculated field is multiplied. This can be used for removing artefact from the boundaries.
diffraction (bool, optional) – Specifies whether field is treated as diffractive field or not (if it was calculated by diffraction > 0 algorithm or not). If set to False refocusing is disabled.
polarization_mode (str, optional) – Defines polarization mode. That is, how the polarization of the light is treated after passing the analyzer. By default, polarizer is applied in real space (normal) which is good for normal (or mostly normal) incidence light. You can use mode instead of normal for more accurate, but slower computation. Here polarizers are applied to mode coefficients in fft space.
betamax (float) – Betamax parameter used in the diffraction calculation function. With this you can simulate finite NA of the microscope (NA = betamax).
parameters (kwargs, optional) – Extra parameters passed directly to the FieldViewer.set_parameters()

Returns

out – A FieldViewer or BulkViewer viewer object

Return type

FieldViewer

class dtmm.field_viewer.FieldViewer(shape, wavelengths, pixelsize, **kwargs)¶

Bases: object

Field viewer. See field_viewer()

property ffield(self)¶: Fourier transform of the field

property focus(self)¶: Focus position, relative to the calculated field position.

property masked_ffield(self)¶: Fourier transform of the field

property sample(self)¶: Sample rotation angle

property sample_angle(self)¶: Sample rotation angle in degrees in float

property aperture(self)¶: Illumination field aperture

property polarizer(self)¶: Polarizer angle. Can be ‘h’,’v’, ‘lcp’, ‘rcp’, ‘none’, angle float or a jones vector

property analyzer(self)¶: Analyzer angle. Can be ‘h’,’v’, ‘lcp’, ‘rcp’, ‘none’, angle float or a jones vector

property intensity(self)¶: Input light intensity

property input_jones(self)¶: Input field jones vector

property diffraction_matrix(self)¶: Diffraction matrix for diffraction calculation

property output_matrix(self)¶: 4x4 jones output matrix

set_parameters(self, **kwargs)¶: Sets viewer parameters. Any of the VIEWER_PARAMETERS

get_parameters(self)¶: Returns viewer parameters as dict

plot(self, fig=None, ax=None, sliders=None, show_sliders=None, show_scalebar=None, show_ticks=None, **kwargs)¶

Plots field intensity profile. You can set any of the below listed arguments. Additionaly, you can set any argument that imshow of matplotlib uses (e.g. ‘interpolation = “sinc”’).

Parameters

show_slider (bool, optional) – Specifies whether to show sliders or not.
show_scalebar (bool, optional) – Specifies whether to show scalebar or not.
show_ticks (bool, optional) – Specifies whether to show ticks in imshow or not.
fmin (float, optional) – Minimimum value for the focus setting.
fmax (float, optional) – Maximum value for the focus setting.
imin (float, optional) – Minimimum value for then intensity setting.
imax (float, optional) – Maximum value for then intensity setting.
pmin (float, optional) – Minimimum value for the polarizer angle.
pmax (float, optional) – Maximum value for the polarizer angle.
smin (float, optional) – Minimimum value for the sample rotation angle.
smax (float, optional) – Maximum value for the sample rotation angle.
amin (float, optional) – Minimimum value for the analyzer angle.
amax (float, optional) – Maximum value for the analyzer angle.
namin (float, optional) – Minimimum value for the numerical aperture.
namax (float, optional) – Maximum value for the numerical aperture.

calculate_specter(self, **params)¶

Calculates field specter.

Parameters: params (kwargs, optional) – Any additional keyword arguments that are passed dirrectly to set_parameters method.

calculate_image(self, **params)¶

Calculates RGB image.

Parameters: params (keyword arguments) – Any additional keyword arguments that are passed dirrectly to set_parameters method.

save_image(self, fname, origin='lower', **kwargs)¶

Calculates and saves image to file using matplotlib.image.imsave.

Parameters

fname (str) – Output filename or file object.
origin ([ 'upper' | 'lower' ]) – Indicates whether the (0, 0) index of the array is in the upper left or lower left corner of the axes. Defaults to ‘lower’
kwargs (optional) – Any extra keyword argument that is supported by matplotlib.image.imsave

update_plot(self)¶: Triggers plot redraw

show(self)¶: Shows plot

class dtmm.field_viewer.BulkViewer(shape, wavelengths, pixelsize, **kwargs)¶

Bases: dtmm.field_viewer.FieldViewer

Field viewer. See field_viewer()

property focus(self)¶: Focus position

property masked_ffield(self)¶: Fourier transform of the field

dtmm.field_viewer¶

High level functions¶

Classes¶

Module Contents¶

`dtmm.field_viewer`¶