diff --git a/NRSS/morphology.py b/NRSS/morphology.py index 6e035d9..c9b6bb2 100644 --- a/NRSS/morphology.py +++ b/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__