Displaying scalar images
- PyLorentz.visualize.show.show_im(image, title=None, scale=None, simple=False, save=None, cmap='gray', figax=None, roi=None, cbar_title=None, cbar=None, intensity_range='minmax', origin='upper', **kwargs)[source]
Display an image with optional features like colorbar, title, and scale.
- Parameters:
image (np.ndarray) – 2D image to be displayed.
title (str, optional) – Title of the plot.
scale (float, optional) – Scale in nm/pixel for axis markers.
simple (bool) – Simplified display without colorbar and labels.
save (str, optional) – Path to save the figure.
cmap (str) – Colormap for displaying the image.
figax (tuple, optional) – Figure and axis to plot on.
roi (dict, optional) – Region of interest to highlight.
cbar_title (str, optional) – Title for the colorbar.
cbar (bool, optional) – Whether to display the colorbar.
intensity_range (str) – Method to set intensity range. ‘minmax’ or ‘ordered’.
origin (str) – Image origin (‘upper’ or ‘lower’).
**kwargs – Additional keyword arguments.
- Return type:
None
- Returns:
None
- PyLorentz.visualize.show.show_stack(images, titles=None, scale_each=True, **kwargs)[source]
Display a stack of images interactively using a slider.
- Parameters:
images (list) – List of 2D numpy arrays representing the images.
titles (list, optional) – List of titles for each image.
scale_each (bool) – Scale each image individually or use the same scale.
- Return type:
None
- Returns:
None
- PyLorentz.visualize.show.show_sims(phi, im_un, im_in, im_ov, title=None, save=None)[source]
Plot phase, underfocus, infocus, and overfocus images in one plot.
- Parameters:
phi (np.ndarray) – Image of phase shift.
im_un (np.ndarray) – Underfocus image.
im_in (np.ndarray) – Infocus image.
im_ov (np.ndarray) – Overfocus image.
title (str, optional) – Title for the plot.
save (str, optional) – Path to save the figure.
- Return type:
None- Returns:
None
- PyLorentz.visualize.show.show_im_peaks(im=None, peaks=None, peaks2=None, title=None, cbar=False, **kwargs)[source]
Show image with overlaid peaks.
- Parameters:
im (np.ndarray, optional) – Image to display.
peaks (np.ndarray, optional) – Peaks to overlay on the image.
peaks2 (np.ndarray, optional) – Second set of peaks to overlay.
title (str, optional) – Title for the plot.
cbar (bool) – Whether to display a colorbar.
- Return type:
None- Returns:
None
- PyLorentz.visualize.show.tick_label_formatter(ticks, fov, scale, scale_unit=None)[source]
Format tick labels for display.
- Parameters:
ticks (np.ndarray) – Tick positions.
fov (float) – Field of view.
scale (float) – Scale in nm/pixel.
scale_unit (str, optional) – Units for the scale.
- Returns:
Formatted labels and unit.
- Return type:
tuple[List[str], str]
- PyLorentz.visualize.show.show_fft(im, window=True, log=False, alpha=1, gaussian_sigma1=0, gaussian_sigma2=0, **kwargs)[source]
Compute and display the FFT of an image with logarithmic scaling.
- Parameters:
im (np.ndarray) – the image for which the FFT will be computed and displayed.
window (bool) – Whether or not to window the image before taking the fft. Default True.
**kwargs – Additional keyword arguments passed to show_im.
- Return type:
None- Returns:
None
- PyLorentz.visualize.show.lineplot_im(image, center=None, phi=0, linewidth=1, line_len=-1, show=False, **kwargs)[source]
Generate a line plot through an image.
- Parameters:
image (np.ndarray) – Image to analyze.
center (tuple, optional) – Center point for the line plot (cy, cx).
phi (float) – Angle for the line plot in degrees.
linewidth (int) – Line width for the plot.
line_len (int) – Length of the line plot.
show (bool) – Whether to display the plot.
**kwargs – Additional keyword arguments passed to show_im()
- Returns:
Line plot data.
- Return type:
np.ndarray