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Dcip/dev #650

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merged 218 commits into from Jan 29, 2018
Merged

Dcip/dev #650

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52037fd
Updated read and write UBC_DCobs functions so that they are python3 c…
micmitch Apr 26, 2017
efe0be9
Merge branch 'dev' into dcip/dev
micmitch Apr 26, 2017
58dbd2f
Added writeUBC_DClocs to StaticUtils.
micmitch Jun 23, 2017
9866c7c
Merge branch 'dev' into dcip/dev
thast Jun 23, 2017
8cc0565
Merge remote-tracking branch 'origin/em/dev' into dcip/dev
thast Jun 23, 2017
5b33794
Make sure that we are using the abs(dobs) when computing uncertainties.
micmitch Jun 28, 2017
90a399b
Print statement for computing uncertainties when survey.std is a float.
micmitch Oct 30, 2017
cf984b7
Working on Survey Design tools for DC
Nov 8, 2017
5c6a03e
Add Field object to 2.5D DC problems (for field visualization purposes)
Nov 9, 2017
0b08375
minor changes to pass travis for testing SurveyDesign class
Nov 9, 2017
c92c632
deprecate plotting in tests
Nov 9, 2017
61929cc
Add __init__.py for IP so that one can do
Nov 9, 2017
408c37e
put an option to deprecate plotting function
Nov 9, 2017
c8cf200
Implementing Mixed boundary condition for Pole-Pole geometry
Nov 10, 2017
3c027a8
- ProblemDC.py: choose center location of the mesh as a reference for…
Nov 10, 2017
74cc941
Implementing Mixed B.C for 2.5D DC problem, and tests
Nov 10, 2017
00d354e
add comments about pole-pole setup.
Nov 10, 2017
06d3125
Change default `bc_type` as `Mixed` for both 2D and 3D Problem_CC,
Nov 10, 2017
849c640
Merge branch 'dev' into dcip/dev
sgkang Nov 10, 2017
9774813
Fix issue for #584
Nov 10, 2017
8ba9c32
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Nov 10, 2017
6ede129
minor fix.
Nov 11, 2017
9900d25
Default is back to `Neumann`
Nov 16, 2017
d533424
Merge branch 'master' into dcip/dev
sgkang Nov 16, 2017
f85d49f
Merge branch 'master' into dcip/dev
thast Nov 21, 2017
0687df7
layout of the webpage for DC examples
thast Nov 21, 2017
236a7fb
back to choosing closest point. May be worthwhile to use UBC's strategy.
Nov 22, 2017
b9a0cad
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Nov 22, 2017
d75d010
add generate topography function
Nov 22, 2017
e1c865e
Dom's updates to Regularization.py so that it will work with tree meshs.
Nov 22, 2017
a7eaacd
cherry pick gen_DCIPsurvey from DCIPdev_4Mike
Nov 23, 2017
3e874f8
cherry pick getJ from DCIPdev4Mike
Nov 23, 2017
ad6d68c
Make sure Jmat is updated at every iteration.
sgkang Nov 23, 2017
9269600
Implement getJ for 2.5 DC problem.
Nov 23, 2017
3983b3f
Tested storeJ option for DC for both 2.5D and 3D problems.
Nov 23, 2017
bf3c587
Merge branch 'dcip/dev' into dcip_dev_Testing
Nov 23, 2017
6fde1dc
Added utility to calculate electrode separation distances.
micmitch Nov 24, 2017
724c948
Added utility to calculate apparent resistivity.
micmitch Nov 24, 2017
e911d44
Fixed bugs in calc_rhoApp and calc_ElecSep related to error handling …
micmitch Nov 24, 2017
c20dbb0
handling topography
Nov 25, 2017
b654db0
Finished debugging calc_ElecSep and calc_rhoApp. Tested with a dipole…
micmitch Nov 25, 2017
c96793a
DC implementation for octree.
Nov 27, 2017
07ac0f3
DC implementation for tree mesh
Nov 27, 2017
3a1eacf
comment for mesh.nodalGrad
Nov 27, 2017
ca1908c
Merge branch 'dcip_dev_Testing' of https://github.com/simpeg/simpeg i…
Nov 27, 2017
dd631f7
Recognize TREE mesh has interpolation operator!!
Nov 27, 2017
4f4947c
surface2ind_topo for TREE mesh
Nov 28, 2017
92b87cc
gettopoCC for TREE mesh
Nov 29, 2017
0ec8640
drapeTopotoLoc for octree mesh
Nov 29, 2017
c223449
fix bug for DCUtils.readUBC_DC3Dobs + pep8 improvements
thast Nov 30, 2017
362e3e1
fix for DCUtils.readUBC_DC3Dobs to make it work for pole-dipole surve…
thast Nov 30, 2017
fb12926
conitnue fixing bugs in DCUtils.read_DC3Dobs
thast Nov 30, 2017
371171e
add dobs as a variable for `plot_pseudoSection`
Dec 7, 2017
bd56821
minor fix.
Dec 7, 2017
e0ba5c3
Merge branch 'master' into dcip/dev
lheagy Dec 8, 2017
d88fd85
working on DCIO (IO.py)
Dec 8, 2017
9b7be41
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 8, 2017
8f9b6bc
minor fixes
Dec 8, 2017
5927ca6
change factor for depth 1/3
Dec 8, 2017
712a6cc
add 2D inversion example with DCIO
Dec 9, 2017
d67db72
add comments for 2D DC inversion
Dec 9, 2017
ddd761c
Merge branch 'dcip/dev' into dcip_addUtils
thast Dec 9, 2017
5e486b9
minor changes
Dec 12, 2017
5c4d7ba
incorporate lindsey's comments.
Dec 12, 2017
378425b
incorporate linden's comments.
Dec 13, 2017
acf2c69
fix minor bugs
Dec 13, 2017
86ffcd0
inherit SuveyDC for IP survey
Dec 13, 2017
8b34750
improve codify
Dec 13, 2017
ebdb219
delete spurious comment.
micmitch Dec 13, 2017
53551fc
Merge branch 'dcip/dev' into dcip_addUtils
thast Dec 13, 2017
142acd3
pep8 and docs improvements
thast Dec 14, 2017
fd37e6d
add regularizer for computing appRes
thast Dec 14, 2017
df77db6
fix sign of regularizer
thast Dec 14, 2017
0e1f178
fix conflict with plot_pseudosections
thast Dec 14, 2017
860f571
restore import griddata for plot_pseudosections
thast Dec 14, 2017
5011306
Merge remote-tracking branch 'origin/dcip/dev' into dcip_addUtils
thast Dec 14, 2017
328585f
remove redundant getSourceTerm
Dec 14, 2017
63335c0
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 14, 2017
b27c15c
first use of super()
Dec 14, 2017
7cc8d08
start implementing tests for DCUtils
thast Dec 14, 2017
a6c714f
added test for DCutils, moved benchmark files to cloud
thast Dec 14, 2017
fec4230
Merge remote-tracking branch 'origin/dcip/dev' into dcip_addUtils
thast Dec 14, 2017
e4b4b62
Merge pull request #654 from simpeg/dcip_addUtils
thast Dec 14, 2017
096a7dd
fix issue with pole Tx or Rx in calculate electrode separations
thast Dec 14, 2017
17f7cc2
StaticUtils: add fct calc_midpoint + various bug fixes + update to pl…
thast Dec 14, 2017
58c0635
fix typo in write_UBC_DCobs
thast Dec 15, 2017
8e53776
making DCUtils consistent and accepting all types of configurations: …
thast Dec 15, 2017
0a26d45
fix slight shift of the mesh in DC3D example
thast Dec 15, 2017
2e66014
change default of AppRes for Half-Space instead of Full-Space
thast Dec 15, 2017
62289b5
add Geometric Factor Utils + various fix
thast Dec 15, 2017
5d182b4
same def of Geometric Factor as in the GPG
thast Dec 15, 2017
c921db1
small fix for testing to reflect changes
thast Dec 15, 2017
250deba
improvements to readUBC_DC3Dobs to handle pole receivers
thast Dec 15, 2017
0624d82
Testing for generating, outputing, reading Survey and compute AppRes …
thast Dec 15, 2017
1b1ace5
change order
thast Dec 15, 2017
5a98289
fix typo
thast Dec 15, 2017
ad8134b
Running Tests for StaticUtils (need to change URL later)
thast Dec 16, 2017
6d86267
pep8 improvements and removing unused imported packages
thast Dec 16, 2017
d08ce94
removed unused variable
thast Dec 16, 2017
3dbf707
add some exceptions for robustness
thast Dec 16, 2017
b44e2bd
codacy improvements
thast Dec 16, 2017
9e1fb09
change back url for test file to SimPEG repo
thast Dec 18, 2017
15e485f
restore Regularization.py from master
lheagy Dec 18, 2017
78e2397
naming convention + docs
thast Dec 18, 2017
6badfc0
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
thast Dec 18, 2017
61d38ac
Add regmesh operators for Treemesh back
fourndo Dec 18, 2017
6af65d6
pep8 cleanup
fourndo Dec 18, 2017
9d2fe68
Change name for Directive.UpdatePreconditioner
fourndo Dec 18, 2017
6395714
Add Directive Sensitivity weighting
fourndo Dec 18, 2017
bc955fb
straightening the use of matplotlib
thast Dec 18, 2017
ee8fd00
Cleanup directive for sensitivity weighting
fourndo Dec 18, 2017
58cc4c8
documentation
micmitch Dec 18, 2017
4934139
fix plot functions and tests
thast Dec 18, 2017
aa93a06
working on linden's comments
Dec 18, 2017
b2b83df
Major update to directives and reg. Change name space for Jmatrix in …
fourndo Dec 18, 2017
0d5c72c
Merge branch 'master' into dcip/dev
lheagy Dec 18, 2017
37f922d
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
fourndo Dec 18, 2017
a6ac830
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 18, 2017
59f6eb5
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 18, 2017
7fec046
Attempt to restructure electrode_separation function.
micmitch Dec 18, 2017
00ae7dc
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
micmitch Dec 18, 2017
2ee61da
add some comments.
Dec 18, 2017
1c5d029
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 18, 2017
77202cb
fix issue with dict keys in DCUtils
thast Dec 18, 2017
e60a6cd
extending full J implementation for 2D DC problems.
Dec 18, 2017
1512da6
fix to tests
fourndo Dec 18, 2017
6c03a60
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
fourndo Dec 18, 2017
2630dfb
fix some Raise Exception in DCUtils
thast Dec 18, 2017
40bb61b
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
thast Dec 18, 2017
3643949
pep8 and Raise
thast Dec 18, 2017
0b3f548
pep8 and raise exception
thast Dec 19, 2017
aa33cbf
fix tests
thast Dec 19, 2017
56566f7
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 19, 2017
60f2891
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 19, 2017
68757e9
general pep8
thast Dec 19, 2017
7582a44
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
thast Dec 19, 2017
bf92eb1
pep8
thast Dec 19, 2017
fae3318
gen_survey does not take a mesh anymore
thast Dec 19, 2017
2bf357e
Revert to getJ. Fix examples
fourndo Dec 19, 2017
edadcbd
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
fourndo Dec 19, 2017
9fde95c
getting rid of mesh for gen_DCsurvey
thast Dec 19, 2017
b14aa3c
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
thast Dec 19, 2017
9cfbe7b
Tikonov with TREE mesh
Dec 19, 2017
ec4391d
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 19, 2017
e5bb2fb
change default figure for plot_pseudosection
thast Dec 19, 2017
140ec66
pep8 improvements
thast Dec 19, 2017
3fee8b9
change how we check inner faces
Dec 19, 2017
3cb8f1d
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 19, 2017
a4bcdeb
Add sens weights for coverage
fourndo Dec 19, 2017
b2c03ec
Remove reg_type in sparse. PF tests should pass
fourndo Dec 19, 2017
a878de2
improve finding boundary faces for tree mesh
Dec 19, 2017
fc27ba5
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 19, 2017
c881f72
remove problematic delete_files for tests
thast Dec 20, 2017
e2576aa
use own folder for testing
thast Dec 20, 2017
cdd31c8
try: add plotIt
thast Dec 20, 2017
92cb748
clean up DCIO
Dec 20, 2017
83960e0
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 20, 2017
5581980
deprecate survey design stuff
Dec 20, 2017
790bb68
own file folder for each test class of DCUtils
thast Dec 20, 2017
bd4582c
remove SurveyDesign from init
thast Dec 20, 2017
9dbce51
add tests for IO
Dec 20, 2017
cb5363d
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 20, 2017
05b68d8
fix typo
thast Dec 20, 2017
732aaaf
remove SurveyDesign from DC init
thast Dec 20, 2017
eb0ffb4
minor fixes
Dec 20, 2017
84e1fa8
merge
Dec 20, 2017
ffa2bcb
add plotIt option for plot-tests
thast Dec 20, 2017
9c4ee6c
plotIt = False
thast Dec 20, 2017
9097c31
some codacy issues fixed
thast Dec 20, 2017
08a270e
fix bug in BetaEstimate_ByEig (it was not taking care of field object…
Dec 20, 2017
cf9ea5e
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 20, 2017
1b1d19e
codacy improvements for 2.5D example
thast Dec 20, 2017
fcadd3a
add plotIt to test
thast Dec 20, 2017
d77b872
consider lists of f in BetaEstimate_ByEig for combo objective functions
Dec 20, 2017
3cf5315
fix for numpy with py27 (see https://github.com/nipy/nipype/issues/2038)
thast Dec 20, 2017
0e2d9b5
add doc string for 2.5D inversion example
Dec 21, 2017
9dc2d38
update plot_pseudosection example
thast Dec 21, 2017
55b6977
pep8
thast Dec 21, 2017
4693fd5
handling combo objective functions in BetaEstimate_ByEig
Dec 21, 2017
6b7f733
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Dec 21, 2017
34b8b7a
incorporate lindsey's comments
Dec 23, 2017
a0e848a
minor fixes
Dec 23, 2017
7481bdf
fix for generating and writing out 2.5D DCIP surveys
thast Jan 3, 2018
bc301a1
moved DCUtils.readUBC_DC2DModel to discretize
thast Jan 4, 2018
f6c8c92
fix for write_DClocs
thast Jan 5, 2018
8dd7a5c
modify dc io and fix tests
Jan 10, 2018
d995f8c
fix dc example
Jan 10, 2018
b976fe1
add ip in examples
Jan 10, 2018
7222b27
add ip example
Jan 10, 2018
3eaffb3
back to normal for examples.
Jan 10, 2018
0400133
Start reformating saveDirectives
fourndo Jan 16, 2018
be7cad8
try plotting in Test with Travis + remove NSEM example plot
thast Jan 16, 2018
6b5abfb
codacy PR improvements
thast Jan 16, 2018
69c56a5
remove plt backend and plt testing
thast Jan 17, 2018
3d49484
add IODC warning
thast Jan 17, 2018
ea3201f
codacy improvements
thast Jan 17, 2018
5c44bce
update version of sphinx gallery
lheagy Jan 18, 2018
8fc6b8a
temporarily deprecate plotting for flow example.
Jan 18, 2018
2e350e0
update path to Celia flow image
lheagy Jan 18, 2018
2cf5b09
resolve merge conflict
lheagy Jan 18, 2018
c9fc766
revert namechange on examples, remove letsencrypt file
lheagy Jan 19, 2018
29e2457
fix bug
Jan 20, 2018
f5615d2
some pep8 improvements
thast Jan 20, 2018
3bfb74f
some more pep8 improvements
thast Jan 20, 2018
ddd9c24
more pep8 (powered by anacondaST3)
thast Jan 20, 2018
9ef3d12
pep8 by anacondaST3
thast Jan 20, 2018
8880add
profile
Jan 21, 2018
2b06a4a
profile
Jan 22, 2018
b99114c
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
Jan 23, 2018
82a4ffb
incorporate lheagy's comments
Jan 23, 2018
337f1ec
remove profile tags
Jan 23, 2018
fe33412
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
fourndo Jan 24, 2018
8b61356
add exception for outputing surveys
thast Jan 26, 2018
523ac81
typo
thast Jan 26, 2018
e69422d
Merge branch 'dcip/dev' of https://github.com/simpeg/simpeg into dcip…
fourndo Jan 29, 2018
d797db7
Fix for Directive.SaveOutputEveryIter
fourndo Jan 29, 2018
8cd807f
Fix for Directives.SaveOutputDictEveryIteration. Sum all regs for now
fourndo Jan 29, 2018
f8e20ee
Bump version: 0.6.5 → 0.7.0
lheagy Jan 29, 2018
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2 changes: 2 additions & 0 deletions SimPEG/DC/__init__.py
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@@ -0,0 +1,2 @@
from SimPEG.EM.Static.DC import *
from SimPEG.EM.Static.Utils import StaticUtils as Utils