Stream thickness

[micmitch]

Added stream_thickness keyword argument to plotSlice and _plotImage2D functions so that it is possible to scale the thickness of streamlines to reflect the amplitude of the vector field. This functionality was added in a manner similar to the stream_threshold keyword.

stream_thickness keyword currently takes a float which acts as a scaling factor for the streamline thickness. Bounds are hardwired to fix the thickness of the 10% largest and smallest vector amplitudes. Provides good results with the DC current density plots I've made but could probably be generalized in the future for more flexibility.

[codecov]

Codecov Report

Merging #95 into master will decrease coverage by 0.24%.
The diff coverage is 0%.

@@            Coverage Diff             @@
##           master      #95      +/-   ##
==========================================
- Coverage   72.99%   72.75%   -0.25%     
==========================================
  Files          20       20              
  Lines        4503     4518      +15     
==========================================
  Hits         3287     3287              
- Misses       1216     1231      +15

Impacted Files	Coverage Δ
discretize/View.py	18% <0%> (-0.37%)	⬇️

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[lheagy]

Thanks @micmitch: do you have a small example you could include in the discretize examples?

[lheagy]

Hey @micmitch: this looks solid. There are two minor updates I have requested. See what you think and feel free to ping when you are happy with them.

[lheagy]

would you mind cleaning out the commented-out line (523) if it is not needed? Thanks!

[micmitch]

Done!

[lheagy]

Thanks for adding this @micmitch! Do you think we can shorten the title? (The whole title is included on the side-bar). What about

Plotting: Streamline thickness
==============================

A simple example to vary streamline thickness based on the vector amplitudes 

Author: `@micmitch <https://github.com/micmitch>`

[micmitch]

Done!

[lheagy]

@micmitch: would you mind adding a code snippet showing example usage (and perhaps an image from your new example) to the description of this pull request? I will use your notes as the release notes when the version is bumped (e.g. https://github.com/simpeg/discretize/releases/tag/0.3.5)

[micmitch]

`

Plot secondary current densities for a pole transmitter in the ceiling of a tunnel with a conductive block 5 m above.

Set source Index

srcInd = 5
src = srcList_Combined[srcInd]

Set colorbar limits

clim = [5e-11, 4.0e-3]

Set surrent density plotting parameters

label = 'Current Density ($A/m^2$)'
pcolorOpts = {"cmap":"viridis"}
scale='linear'
cb=True

Get secondary current density values from fields object

uTotal = fields_total[src,'j']
uPrim = fields_primary[src,'j']
u = uTotal - uPrim

Set font sizes

labelsize = 30.
ticksize = 30.

Setup figure

fig = plt.figure()
ax = plt.subplot(111)
fig.set_figheight(30)
fig.set_figwidth(15)

Plot slice

dat = mesh.plotSlice(u, ax=ax, normal='X', ind=49, vType='F', view='vec', streamOpts={'color':'w', 'density':2.0}, gridOpts={"color":"k", "alpha":0.1}, grid=True, range_x=[-30, 30], range_y=[-20, 20], clim=[5e-11, 4.0e-3], stream_threshold=1e-8, stream_thickness=3)

Plot outline of conductive block above the tunnel

getBlkOutline(sigmaTrue_Block,mesh,sliceInd,normal=sliceNormal, ax=ax, lineWidth=3.0)

Plot electrode locations

ax.scatter(elecLocs[:,1],elecLocs[:,2], c='w', edgecolors='k', s=150)

Label Tx electrode

A = src.loc
ax.plot(A[1],A[2], marker = 'o',color='red', markersize=15)
yztextA1 = (A[1]-0.6,A[2] + 0.5)
ax.annotate('A', xy=yztextA1, xytext=yztextA1,fontsize = labelsize, color='w', weight='bold')

Add title and set layout

ax.set_title("N-S section at "+ "{0:.2f}".format(mesh.vectorCCx[sliceInd])+"m")
ax.set_xlim(ylim)
ax.set_ylim(zlim)

plt.gca().set_aspect('equal', adjustable='box')
plt.tight_layout()

Add colorbar

if scale == "log":
cbformat = "$10^{%1.1f}$"
elif scale == "linear":
cbformat = "%.1e"

if cb:
if clim is None:
cmin, cmax = dat[0].get_clim()
else:
cmin, cmax = clim[0],clim[1]

cb = add_colorbar(dat[0], format=cbformat, ax=ax, orientation="vertical",ticks = np.linspace(cmin, cmax, 5))

cb.ax.tick_params(labelsize=labelsize-4.0)
cb.set_label(label, fontsize=labelsize)
cb.set_clim([cmin, cmax])`

[micmitch]

Js_SingleLinearArray_Top_Blk5m_8mElecBlkCenter_3x3Tunnel_X=25.pdf

[micmitch]

Is this what you had in mind?

[lheagy]

The image looks great! I didn't mean for you to copy the whole example in, just a minimal part, but I can extract a subset

e.g.

mesh.plotSlice(
    u, ax=ax, normal='X', vType='F', view='vec', stream_threshold=1e-8, stream_thickness=3
)