Field of view plot
Functions to visualize 2D and 3D images:
Plot images
Plot 2D images or slices of 3D images:
- bigfish.plot.plot_yx(image, r=0, c=0, z=0, rescale=False, contrast=False, title=None, framesize=(10, 10), remove_frame=True, path_output=None, ext='png', show=True)
Plot the selected yx plan of the selected dimensions of an image.
- Parameters:
- imagenp.ndarray
A 2-d, 3-d, 4-d or 5-d image with shape (y, x), (z, y, x), (c, z, y, x) or (r, c, z, y, x) respectively.
- rint, default=0
Index of the round to keep.
- cint, default=0
Index of the channel to keep.
- zint, default=0
Index of the z slice to keep.
- rescalebool, default=False
Rescale pixel values of the image (made by default in matplotlib).
- contrastbool, default=False
Contrast image.
- titlestr, optional
Title of the image.
- framesizetuple=(10, 10)
Size of the frame used to plot with
plt.figure(figsize=framesize).- remove_framebool, default=True
Remove axes and frame.
- path_outputstr, optional
Path to save the image (without extension).
- extstr or list, default=’png’
Extension used to save the plot. If it is a list of strings, the plot will be saved several times.
- showbool, default=True
Show the figure or not.
- bigfish.plot.plot_images(images, rescale=False, contrast=False, titles=None, framesize=(15, 10), remove_frame=True, path_output=None, ext='png', show=True)
Plot or subplot of 2-d images.
- Parameters:
- imagesnp.ndarray or list
Image or list of images with shape (y, x).
- rescalebool, default=False
Rescale pixel values of the image (made by default in matplotlib).
- contrastbool, default=False
Contrast image.
- titlesstr or list, optional
Titles of the subplots.
- framesizetuple, default=(15, 10)
Size of the frame used to plot with
plt.figure(figsize=framesize).- remove_framebool, default=True
Remove axes and frame.
- path_outputstr, optional
Path to save the image (without extension).
- extstr or list, default=’png’
Extension used to save the plot. If it is a list of strings, the plot will be saved several times.
- showbool, default=True
Show the figure or not.
Plot quality measure of an image
Plot focus measures for a 3D image:
- bigfish.plot.plot_sharpness(focus_measures, labels=None, title=None, framesize=(5, 5), size_title=20, size_axes=15, size_legend=15, path_output=None, ext='png', show=True)
Plot focus measures of a 3-d image, at the z-slice level.
A measure of focus for each z-slice can be computed by averaging the pixel-wise focus measure returned from
bigfish.stack.compute_focus().- Parameters:
- focus_measuresnp.ndarray or list
A list of 1-d arrays with the sharpness measure for each z-slices.
- labelsstr or list, optional
List of labels for the different measures to compare.
- titlestr, optional
Title of the plot.
- framesizetuple, default=(5, 5)
Size of the frame used to plot with
plt.figure(figsize=framesize).- size_titleint, default=20
Size of the title.
- size_axesint, default=15
Size of the axes label.
- size_legendint, default=15
Size of the legend.
- path_outputstr, optional
Path to save the image (without extension).
- extstr or list, default=’png’
Extension used to save the plot. If it is a list of strings, the plot will be saved several times.
- showbool, default=True
Show the figure or not.