Dcip/dev #650

sgkang · 2017-11-10T21:54:37Z

Survey Design for 2.5D Problem
Implementing Mixed B.C for 2.5D and 3D Problem_CC

@thast contribution:
Major updates to StaticUtils:

IO functions for UBC-GIF codes DCIP2D and DCIP3D
add Utils such electrode_separations or geometric_factor
Utils are now compatible with all types of survey

@fourndo contribution:

Add getJ forming sensitivity matrix explicitly
Add sensitivity weighting directive
Add functionality in Regularization to handle TreeMesh
Update IRLS directive
Change to Directive to convert reg, misfit to ComboObjective
Update SaveEveryIteration Directives for Combo

…ompatible. Changed the ”3D” “General” case so that it flips the sign on the z-component of Tx and Rx locs for the DCoctree code. Flipping sign was overwriting locs in original survey object so added some .copy() statements to safeguard this.

Clean up Rx and Src for DC Test SurveyDesign Class for DC

`from SimPEG import IP`

(This only works for ProblemCC)

… setting mixed BC - SurveyDesign.py: visualize currents, fields, charges, and potentials

and test them.

codecov · 2017-11-10T21:54:42Z

Codecov Report

Merging #650 into master will increase coverage by 2.93%.
The diff coverage is 56.68%.

@@            Coverage Diff             @@
##           master     #650      +/-   ##
==========================================
+ Coverage   71.03%   73.96%   +2.93%     
==========================================
  Files         104       99       -5     
  Lines       14429    14637     +208     
==========================================
+ Hits        10249    10826     +577     
+ Misses       4180     3811     -369

Impacted Files	Coverage Δ
SimPEG/EM/__init__.py	`100% <ø> (ø)`	⬆️
SimPEG/EM/Static/SIP/RxSIP.py	`90.74% <ø> (ø)`	⬆️
SimPEG/EM/Static/DC/FieldsDC.py	`68.6% <0%> (ø)`	⬆️
SimPEG/EM/Static/IP/SurveyIP.py	`100% <100%> (ø)`	⬆️
SimPEG/PF/Gravity.py	`62.55% <100%> (+0.67%)`	⬆️
SimPEG/EM/Static/DC/RxDC.py	`94.65% <100%> (+0.04%)`	⬆️
SimPEG/EM/Static/DC/__init__.py	`100% <100%> (ø)`	⬆️
SimPEG/EM/Static/DC/SrcDC.py	`95.83% <100%> (+0.48%)`	⬆️
SimPEG/PF/Magnetics.py	`62.1% <100%> (+0.25%)`	⬆️
SimPEG/Problem.py	`80.34% <20%> (-2.7%)`	⬇️
... and 22 more

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…/dev

sgkang · 2017-11-11T00:20:46Z

Not sure why there are solver issues ...
any ideas? @lheagy

…/dev

sgkang · 2018-01-23T02:07:12Z

hi @lheagy i went through your comments and modified. Will be great to be merged.

thast · 2018-01-23T05:13:44Z

hey @sgkang , most tests fails because of this missing package. Is it needed?

lheagy · 2018-01-23T16:09:51Z

SimPEG/EM/Static/DC/ProblemDC.py

@@ -11,6 +11,7 @@
 import scipy as sp
 from SimPEG.Utils import Zero
 from .BoundaryUtils import getxBCyBC_CC
+from profilehooks import profile


@sgkang: can we remove this for now? I am not sure we want profilehooks to be something we require for SimPEG

lheagy · 2018-01-23T16:11:34Z

Thanks @sgkang, this is looking good. If you don't mind, could you remove the profilehooks for now - I know it is useful for developing / diagnosing code efficiency issues, but I think we want to use it internally only and not distribute SimPEG code that relies on it

lheagy

Thanks for all of your work on this everyone @sgkang, @thast, @fourndo, @micmitch!! There are lots of improvements here. I will post an issue related to the densifying of the projection matrices - we should be able to stay with sparse, but for now I think that can be addressed elsewhere.

I will give @rowanc1 a chance to take a look if you like and we can get this in 🎉

…/dev

lheagy · 2018-01-26T04:04:50Z

@sgkang: would you mind generating some release notes that highlight the major changes here? You can write them in the comment box on this pr and I will generate the release from there.

@thast, @fourndo: I will also ask you to also take a look and contribute a few bullet points of things that you have done!

sgkang · 2018-01-28T06:30:22Z

Release note for dcip/dev branch

This release is motivated by enhancing DC/IP packages in SimPEG, and several contributors have sweated on this release for the past several months. There are four main categories that developments have been carried out:

Physics
Utilities
Inversion Directives

Highlights of each development is summarized below.

Physics

Handling Pole-Pole data

Mixed boundary condition for Problem2D_CC and Problem3D_CC

Easy import for DC and IP problems

Now DC and IP can be easily imported:

 from SimPEG import DC, IP

Storing Sensitivity

Sensitivity can be stored, and this option can be used in the inversion:

problem = DC.Problem3D_CC(mesh, storeJ=True, ...) 
J = problem.getJ(m)

Working DC octree inversion (thanks to @fourndo and @micmitch)

This is limited in a specific branch of discretize package: discretize/TreeMesh_CellGrad
Regularization and DC problems have been improved to handle octree and working!
Mesh generation utility has not been updated in this branch, but will be included in the next release.
IP problem has not been tested for octree yet.

Utilities for DC and IP problems (thanks to @thast )

Updated StaticUtils

IO functions for UBC-GIF codes DCIP2D and DCIP3D
add Utils such electrode_separations or geometric_factor
Utils are now compatible with all types of survey

Survey and I/O

IO class for DC problem is initiated, but still requires further developments.
Synthetic DC survey can be easily generated using StaticUtils + DC.IO + DC.Survey

# Initiate I/O class for DC
IO = DC.IO()
endl = np.array([[xmin, ymin, zmin], [xmax, ymax, zmax]])
# Generate DC survey object
survey = DC.Utils.gen_DCIPsurvey(endl, survey_type=survey_type, dim=2,
                                 a=10, b=10, n=10)
# Obtain ABMN locations
survey.getABMN_locations()
# Obtain 2D TensorMesh
mesh, actind = IO.set_mesh()
# Generate Topography    
topo, mesh1D = DC.Utils.genTopography(mesh, -10, 0, its=100)
# Generate active cells
actind = Utils.surface2ind_topo(mesh, np.c_[mesh1D.vectorCCx, topo])
# Drape electrode locations to topography
survey.drapeTopo(mesh, actind, option="top")

Inversion Directives (thanks to @fourndo!)

Add sensitivity weighting directive
Update IRLS directive
Change to Directive to convert regularization, misfit to ComboObjective

rowanc1

Looks awesome.

micmitch · 2018-01-28T20:05:56Z

@fourndo Dom, I think that I remember you saying you had a fix for the problem we were having with Directives.SaveOutputEveryIteration(). I would be great if we could get that in as well!

…/dev

fourndo · 2018-01-29T16:23:05Z

@micmitch thanks for the reminder, Looks good on my side.

micmitch and others added 18 commits April 25, 2017 17:14

Merge branch 'dev' into dcip/dev

efe0be9

Added writeUBC_DClocs to StaticUtils.

58dbd2f

Merge branch 'dev' into dcip/dev

9866c7c

Merge remote-tracking branch 'origin/em/dev' into dcip/dev

8cc0565

Make sure that we are using the abs(dobs) when computing uncertainties.

5b33794

Print statement for computing uncertainties when survey.std is a float.

90a399b

Working on Survey Design tools for DC

cf984b7

Add Field object to 2.5D DC problems (for field visualization purposes)

5c6a03e

Clean up Rx and Src for DC Test SurveyDesign Class for DC

minor changes to pass travis for testing SurveyDesign class

0b08375

deprecate plotting in tests

c92c632

Add __init__.py for IP so that one can do

61929cc

`from SimPEG import IP`

put an option to deprecate plotting function

408c37e

Implementing Mixed boundary condition for Pole-Pole geometry

c8cf200

(This only works for ProblemCC)

- ProblemDC.py: choose center location of the mesh as a reference for…

3c027a8

… setting mixed BC - SurveyDesign.py: visualize currents, fields, charges, and potentials

Implementing Mixed B.C for 2.5D DC problem, and tests

74cc941

add comments about pole-pole setup.

00d354e

Change default bc_type as Mixed for both 2D and 3D Problem_CC,

06d3125

and test them.

Merge branch 'dev' into dcip/dev

849c640

This was referenced Nov 10, 2017

DC does not handle Pole-Pole data #649

Closed

Pardiso on Windows: difficulty to deal with the null space #429

Closed

DC cleanup #260

Closed

seogi_macbook added 2 commits November 10, 2017 14:13

Fix issue for #584

9774813

Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…

8ba9c32

…/dev

This was referenced Nov 10, 2017

e from DC.Problem3D_CC #584

Closed

Em/emip #613

Closed

minor fix.

6ede129

lheagy changed the base branch from dev to master November 16, 2017 14:25

thast and others added 7 commits January 19, 2018 18:36

some pep8 improvements

f5615d2

some more pep8 improvements

3bfb74f

more pep8 (powered by anacondaST3)

ddd9c24

pep8 by anacondaST3

9ef3d12

profile

8880add

profile

2b06a4a

Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…

b99114c

…/dev

incorporate lheagy's comments

82a4ffb

lheagy reviewed Jan 23, 2018

View reviewed changes

remove profile tags

337f1ec

lheagy approved these changes Jan 23, 2018

View reviewed changes

fourndo and others added 3 commits January 24, 2018 11:35

Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…

fe33412

…/dev

add exception for outputing surveys

8b61356

typo

523ac81

rowanc1 approved these changes Jan 28, 2018

View reviewed changes

fourndo added 3 commits January 28, 2018 23:23

Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…

e69422d

…/dev

Fix for Directive.SaveOutputEveryIter

d797db7

Fix for Directives.SaveOutputDictEveryIteration. Sum all regs for now

8cd807f

Bump version: 0.6.5 → 0.7.0

f8e20ee

lheagy merged commit 0afd266 into master Jan 29, 2018

DC project automation moved this from To do to Done Jan 29, 2018

lheagy removed the ready for review label Jun 10, 2018

lheagy mentioned this pull request Jun 27, 2018

Storing sensitivity option for DC problem #653

Closed

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Dcip/dev #650

Dcip/dev #650

sgkang commented Nov 10, 2017 •

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fourndo commented Jan 29, 2018

Dcip/dev #650

Dcip/dev #650

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sgkang commented Nov 10, 2017 • edited by fourndo

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sgkang commented Jan 28, 2018 • edited

Release note for dcip/dev branch

Physics

Utilities for DC and IP problems (thanks to @thast )

Inversion Directives (thanks to @fourndo!)

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sgkang commented Nov 10, 2017 •

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