added documentation under class method

NRSS/morphology.py

@@ -490,6 +490,59 @@ def check_materials(self, quiet=True):
  print('All material checks have passed')
 
  def visualize_materials(self, *args,**kwargs):
+ """
+ Reads in morphology HDF5 file and checks that the format is consistent for CyRSoXS. Optionally plots and returns select quantities.
+
+ Parameters
+ ----------
+
+ 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
+ add_quiver : bool
+ Adds lines to every voxel on the psi plot that indicate in-plane direction. Not recommended for resolutions larger than 128x128, best for resolutions 64x64 or lower.
+ quiver_bw : bool
+ Intended to be used when add_quiver == True, when quiver_bw is True, the quiver arrows will be black and white instead of colored.
+ 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'
+ outputaxes : bool
+ If a plot is returned, include its axes
+ 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
+ runquiet : bool
+ Boolean flag for running without plotting or outputting to console
+ batchMode : bool
+ if true, prints console output and generates plots but doesnt show (provide exportDir for export)
+ plotstyle : str
+ Use a light or dark background for plots. 'dark' - dark, 'light' - light
+ dpi : int
+ The dpi at which the plot is generated. Per-material plot dimensions are 8.5" x 12.75"
+ exportDir : str, optional
+ if provided, export directory to save any generated figures into,
+ by default, will respect dpi and save as png, use exportParams to override
+ exportParams : dict, optional
+ additional params to unpack into matplotlib.pyplot.savefig. Overrides existing params.
+ ex: exportParams = {'dpi':600, format='svg'}
+ 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, *args,**kwargs)
  visualize_materials.__doc__ = morphology_visualizer.__doc__