4 add visualization functionality for morphology checker

[delongchamp]

Description

Adds visualizer method to morphology class with detailed arguments for returning and tailoring outputs.

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

How Has This Been Tested?

I've run the visualizer on my models and it produces results similar to checkH5.
I have run it on the Euler PGN morphology to verify that the two-tone psi colorwheel operates as intended.
Quiver functionality also tested correct for PGN morphology.

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules

[pbeaucage]

I'm not sure I follow this, but couldn't you simply do

Suggested change

	def visualize_materials(
	self,
	z_slice=0,
	subsample=None,
	translate_x = None,
	translate_y = None,
	screen_euler = True,
	outputmat=None,
	outputplot=None,
	outputaxes=True,
	vfrac_range=None,
	S_range=None,
	vfrac_cmap=None,
	S_cmap=None,
	runquiet=False,
	plotstyle="light",
	dpi=300,
	):
	"""
	Reads in morphology HDF5 file and checks that the format is consistent for CyRSoXS. Optionally plots and returns select quantities.
	Parameters
	----------
	filename : str or path
	Name of HDF5 morphology file to check
	z_slice : int
	Which z-slice of the array to plot.
	subsample : int
	Number of voxels to display in X and Y
	translate_x : int
	Number of voxels to translate image in x; meant for use with subsample
	translate_y : int
	Number of voxels to translate image in y; meant for use with subsample
	screen_euler : bool
	Suppress visualization of euler angles where vfrac < 0.05 or S < 0.05; intended to hilight edges
	outputmat : list of ints
	Number of which materials to return
	outputplot : list of strings
	Number of which plots to return, can include 'vfrac', 'S', 'theta', 'psi'
	vfrac_range: list of tuples as [float, float]
	A custom range for vfrac colorbar
	S_range: list of tuples as [float, float]
	A custom range for S colorbar
	vfrac_cmap: str
	A custom substitution for vfrac colormap
	S_cmap: str
	A custom substitution for vfrac colormap
	outputaxes : bool
	If a plot is returned, include its axes
	runquiet : bool
	Boolean flag for running without plotting or outputting to console
	plotstyle : str
	Use a light or dark background for plots. 'dark' - dark, 'light' - light
	dpi : integer
	The dpi at which the plot is generated. Per-material plot dimensions are 8.5" x 12.75"
	Returns
	-------
	If outputmat and outputplot are correctly entered, will return an index list of images of the selected material and plot. Each list element will be a numpy array in RGB format that be displayed with imshow
	"""
	return morphology_visualizer(
	self,
	z_slice=z_slice,
	subsample=subsample,
	translate_x = translate_x,
	translate_y = translate_y,
	screen_euler = screen_euler,
	outputmat=outputmat,
	outputplot=outputplot,
	outputaxes=outputaxes,
	vfrac_range=vfrac_range,
	S_range=S_range,
	vfrac_cmap=vfrac_cmap,
	S_cmap=S_cmap,
	runquiet=runquiet,
	plotstyle=plotstyle,
	dpi=dpi,
	)
	visualize_materials = morphology_visualizer

? If the method signatures are the same this should be a lot cleaner.

You might need to put this in the constructor, like

self.visualize_materials = morphology_visualizer

[delongchamp]

@pbeaucage, thanks. I suggested it this way in case we someday wanted to deviate the signature of the class method from the function in visualizer.py with additional arguments or something, but I agree that it creates clutter and potential for confusion, so maybe better to write this cleaner, as you suggest, and then cross that bridge if it ever becomes necessary.

[pbeaucage]

Gotcha. One could also do:

def passthru_function(*args,**kwargs):
    return real_function(*args,**kwargs)
passthru_function.__doc__ = real_function.__doc__

to preserve the stub method and be a bit more readable.