diff --git a/.gitignore b/.gitignore index ded60678..14e3cc80 100644 --- a/.gitignore +++ b/.gitignore @@ -34,3 +34,7 @@ nosetests.xml .mr.developer.cfg .project .pydevproject + +*.sublime-project +*.sublime-workspace +docs/_build/ diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 00000000..7895062e --- /dev/null +++ b/.travis.yml @@ -0,0 +1,14 @@ +language: python +python: + - "2.7" +virtualenv: + system_site_packages: true +before_install: + - sudo apt-get install -qq python-numpy python-scipy python-matplotlib + - python SimPEG/setup.py + - git clone https://github.com/simpeg/simpeg.git + - ls +# command to install dependencies +install: "pip install -r requirements.txt --use-mirrors" +# command to run tests +script: nosetests -v diff --git a/LICENSE b/LICENSE index 5a4b9aff..f94a23fd 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ The MIT License (MIT) -Copyright (c) 2014 SimPEG +Copyright (c) 2013-2014 SimPEG Developers Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..bee80244 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,153 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/SimPEG.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/SimPEG.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/SimPEG" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/SimPEG" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." diff --git a/docs/api_DC.rst b/docs/api_DC.rst new file mode 100644 index 00000000..5d3410a3 --- /dev/null +++ b/docs/api_DC.rst @@ -0,0 +1,11 @@ +.. _api_DC: + + +DC +** + +.. automodule:: simpegDC.DC + :show-inheritance: + :members: + :undoc-members: + :inherited-members: diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 00000000..86aacce4 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,244 @@ +# -*- coding: utf-8 -*- +# +# SimPEG documentation build configuration file, created by +# sphinx-quickstart on Fri Aug 30 18:42:44 2013. +# +# This file is execfile()d with the current directory set to its containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys, os + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('.')) + +sys.path.append('../') + +# -- General configuration ----------------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = ['sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', 'sphinx.ext.autodoc', 'matplotlib.sphinxext.plot_directive'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'SimPEG' +copyright = u'2013, SimPEG Developers' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '0.0.1' +# The full version, including alpha/beta/rc tags. +release = '0.0.1' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + + +# -- Options for HTML output --------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'SimPEGdoc' + + +# -- Options for LaTeX output -------------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', 'SimPEG.tex', u'SimPEG Documentation', + u'Rowan Cockett', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output -------------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'simpeg', u'SimPEG Documentation', + [u'Rowan Cockett'], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------------ + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', 'SimPEG', u'SimPEG Documentation', + u'Rowan Cockett', 'SimPEG', 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +#texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 00000000..663cf75e --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,45 @@ +.. image:: simpeg-logo.png + :width: 300 px + :alt: SimPEG + :align: center + +SimPEG (Simulation and Parameter Estimation in Geophysics) is a python +package for simulation and gradient based parameter estimation in the +context of geoscience applications. + +SimPEG-DC uses SimPEG as the framework for the forward and inverse +direct current resistivity geophysical problem. + + +DC +== + +.. toctree:: + :maxdepth: 2 + + api_DC + + +Testing SimPEG +============== + +* Master Branch + .. image:: https://travis-ci.org/simpeg/simpeg.png?branch=master + :target: https://travis-ci.org/simpeg/simpeg + :alt: Master Branch + :align: center + +* Develop Branch + .. image:: https://travis-ci.org/simpeg/simpeg.png?branch=develop + :target: https://travis-ci.org/simpeg/simpeg + :alt: Develop Branch + :align: center + + +Project Index & Search +====================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 00000000..2ac3df69 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,190 @@ +@ECHO OFF + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set BUILDDIR=_build +set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . +set I18NSPHINXOPTS=%SPHINXOPTS% . +if NOT "%PAPER%" == "" ( + set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% + set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% +) + +if "%1" == "" goto help + +if "%1" == "help" ( + :help + echo.Please use `make ^` where ^ is one of + echo. html to make standalone HTML files + echo. dirhtml to make HTML files named index.html in directories + echo. singlehtml to make a single large HTML file + echo. pickle to make pickle files + echo. json to make JSON files + echo. htmlhelp to make HTML files and a HTML help project + echo. qthelp to make HTML files and a qthelp project + echo. devhelp to make HTML files and a Devhelp project + echo. epub to make an epub + echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter + echo. text to make text files + echo. man to make manual pages + echo. texinfo to make Texinfo files + echo. gettext to make PO message catalogs + echo. changes to make an overview over all changed/added/deprecated items + echo. linkcheck to check all external links for integrity + echo. doctest to run all doctests embedded in the documentation if enabled + goto end +) + +if "%1" == "clean" ( + for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i + del /q /s %BUILDDIR%\* + goto end +) + +if "%1" == "html" ( + %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/html. + goto end +) + +if "%1" == "dirhtml" ( + %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. + goto end +) + +if "%1" == "singlehtml" ( + %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. + goto end +) + +if "%1" == "pickle" ( + %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the pickle files. + goto end +) + +if "%1" == "json" ( + %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the JSON files. + goto end +) + +if "%1" == "htmlhelp" ( + %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run HTML Help Workshop with the ^ +.hhp project file in %BUILDDIR%/htmlhelp. + goto end +) + +if "%1" == "qthelp" ( + %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run "qcollectiongenerator" with the ^ +.qhcp project file in %BUILDDIR%/qthelp, like this: + echo.^> qcollectiongenerator %BUILDDIR%\qthelp\SimPEG.qhcp + echo.To view the help file: + echo.^> assistant -collectionFile %BUILDDIR%\qthelp\SimPEG.ghc + goto end +) + +if "%1" == "devhelp" ( + %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. + goto end +) + +if "%1" == "epub" ( + %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The epub file is in %BUILDDIR%/epub. + goto end +) + +if "%1" == "latex" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "text" ( + %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The text files are in %BUILDDIR%/text. + goto end +) + +if "%1" == "man" ( + %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The manual pages are in %BUILDDIR%/man. + goto end +) + +if "%1" == "texinfo" ( + %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. + goto end +) + +if "%1" == "gettext" ( + %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The message catalogs are in %BUILDDIR%/locale. + goto end +) + +if "%1" == "changes" ( + %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes + if errorlevel 1 exit /b 1 + echo. + echo.The overview file is in %BUILDDIR%/changes. + goto end +) + +if "%1" == "linkcheck" ( + %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck + if errorlevel 1 exit /b 1 + echo. + echo.Link check complete; look for any errors in the above output ^ +or in %BUILDDIR%/linkcheck/output.txt. + goto end +) + +if "%1" == "doctest" ( + %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest + if errorlevel 1 exit /b 1 + echo. + echo.Testing of doctests in the sources finished, look at the ^ +results in %BUILDDIR%/doctest/output.txt. + goto end +) + +:end diff --git a/docs/simpeg-logo.png b/docs/simpeg-logo.png new file mode 100644 index 00000000..a0ec740f Binary files /dev/null and b/docs/simpeg-logo.png differ diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..6b7df820 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,4 @@ +numpy +scipy +ipython +matplotlib diff --git a/simpegDC/DC.py b/simpegDC/DC.py new file mode 100644 index 00000000..b0a022b0 --- /dev/null +++ b/simpegDC/DC.py @@ -0,0 +1,248 @@ +from SimPEG import * + + +class DCData(Data.BaseData): + """ + **DCData** + + Geophysical DC resistivity data. + + """ + + P = None #: projection + + def __init__(self, **kwargs): + Data.BaseData.__init__(self, **kwargs) + Utils.setKwargs(self, **kwargs) + + def reshapeFields(self, u): + if len(u.shape) == 1: + u = u.reshape([-1, self.RHS.shape[1]], order='F') + return u + + def projectField(self, u): + """ + Predicted data. + + .. math:: + d_\\text{pred} = Pu(m) + """ + u = self.reshapeFields(u) + return Utils.mkvc(self.P*u) + + + +class DCProblem(Problem.BaseProblem): + """ + **DCProblem** + + Geophysical DC resistivity problem. + + """ + + dataPair = DCData + + def __init__(self, mesh, model, **kwargs): + Problem.BaseProblem.__init__(self, mesh, model) + self.mesh.setCellGradBC('neumann') + Utils.setKwargs(self, **kwargs) + + + def createMatrix(self, m): + """ + Makes the matrix A(m) for the DC resistivity problem. + + :param numpy.array m: model + :rtype: scipy.csc_matrix + :return: A(m) + + .. math:: + c(m,u) = A(m)u - q = G\\text{sdiag}(M(mT(m)))Du - q = 0 + + Where M() is the mass matrix and mT is the model transform. + """ + D = self.mesh.faceDiv + G = self.mesh.cellGrad + sigma = self.model.transform(m) + Msig = self.mesh.getFaceMass(sigma) + A = D*Msig*G + return A.tocsc() + + def field(self, m): + A = self.createMatrix(m) + solve = Solver(A) + phi = solve.solve(self.data.RHS) + return Utils.mkvc(phi) + + def J(self, m, v, u=None): + """ + :param numpy.array m: model + :param numpy.array v: vector to multiply + :param numpy.array u: fields + :rtype: numpy.array + :return: Jv + + .. math:: + c(m,u) = A(m)u - q = G\\text{sdiag}(M(mT(m)))Du - q = 0 + + \\nabla_u (A(m)u - q) = A(m) + + \\nabla_m (A(m)u - q) = G\\text{sdiag}(Du)\\nabla_m(M(mT(m))) + + Where M() is the mass matrix and mT is the model transform. + + .. math:: + J = - P \left( \\nabla_u c(m, u) \\right)^{-1} \\nabla_m c(m, u) + + J(v) = - P ( A(m)^{-1} ( G\\text{sdiag}(Du)\\nabla_m(M(mT(m))) v ) ) + """ + if u is None: + u = self.field(m) + + u = self.data.reshapeFields(u) + + P = self.data.P + D = self.mesh.faceDiv + G = self.mesh.cellGrad + A = self.createMatrix(m) + Av_dm = self.mesh.getFaceMassDeriv() + mT_dm = self.model.transformDeriv(m) + + dCdu = A + + dCdm = np.empty_like(u) + for i, ui in enumerate(u.T): # loop over each column + dCdm[:, i] = D * ( Utils.sdiag( G * ui ) * ( Av_dm * ( mT_dm * v ) ) ) + + solve = Solver(dCdu) + Jv = - P * solve.solve(dCdm) + return Utils.mkvc(Jv) + + def Jt(self, m, v, u=None): + """Takes data, turns it into a model..ish""" + + if u is None: + u = self.field(m) + + u = self.data.reshapeFields(u) + v = self.data.reshapeFields(v) + + P = self.data.P + D = self.mesh.faceDiv + G = self.mesh.cellGrad + A = self.createMatrix(m) + Av_dm = self.mesh.getFaceMassDeriv() + mT_dm = self.model.transformDeriv(m) + + dCdu = A.T + solve = Solver(dCdu) + + w = solve.solve(P.T*v) + + Jtv = 0 + for i, ui in enumerate(u.T): # loop over each column + Jtv += Utils.sdiag( G * ui ) * ( D.T * w[:,i] ) + + Jtv = - mT_dm.T * ( Av_dm.T * Jtv ) + return Jtv + + + +def genTxRxmat(nelec, spacelec, surfloc, elecini, mesh): + """ Generate projection matrix (Q) and """ + elecend = 0.5+spacelec*(nelec-1) + elecLocR = np.linspace(elecini, elecend, nelec) + elecLocT = elecLocR+1 + nrx = nelec-1 + ntx = nelec-1 + q = np.zeros((mesh.nC, ntx)) + Q = np.zeros((mesh.nC, nrx)) + + for i in range(nrx): + + rxind1 = np.argwhere((mesh.gridCC[:,0]==surfloc) & (mesh.gridCC[:,1]==elecLocR[i])) + rxind2 = np.argwhere((mesh.gridCC[:,0]==surfloc) & (mesh.gridCC[:,1]==elecLocR[i+1])) + + txind1 = np.argwhere((mesh.gridCC[:,0]==surfloc) & (mesh.gridCC[:,1]==elecLocT[i])) + txind2 = np.argwhere((mesh.gridCC[:,0]==surfloc) & (mesh.gridCC[:,1]==elecLocT[i+1])) + + q[txind1,i] = 1 + q[txind2,i] = -1 + Q[rxind1,i] = 1 + Q[rxind2,i] = -1 + + Q = sp.csr_matrix(Q) + rxmidLoc = (elecLocR[0:nelec-1]+elecLocR[1:nelec])*0.5 + return q, Q, rxmidLoc + + +if __name__ == '__main__': + import matplotlib.pyplot as plt + + # Create the mesh + h1 = np.ones(20) + h2 = np.ones(100) + M = Mesh.TensorMesh([h1,h2]) + + # Create some parameters for the model + sig1 = np.log(1) + sig2 = np.log(0.01) + + # Create a synthetic model from a block in a half-space + p0 = [5, 10] + p1 = [15, 50] + condVals = [sig1, sig2] + mSynth = Utils.ModelBuilder.defineBlockConductivity(M.gridCC,p0,p1,condVals) + plt.colorbar(M.plotImage(mSynth)) + # plt.show() + + # Set up the projection + nelec = 50 + spacelec = 2 + surfloc = 0.5 + elecini = 0.5 + elecend = 0.5+spacelec*(nelec-1) + elecLocR = np.linspace(elecini, elecend, nelec) + rxmidLoc = (elecLocR[0:nelec-1]+elecLocR[1:nelec])*0.5 + q, Q, rxmidloc = genTxRxmat(nelec, spacelec, surfloc, elecini, M) + P = Q.T + + model = Model.LogModel(M) + prob = DCProblem(M, model) + + # Create some data + data = prob.createSyntheticData(mSynth, std=0.05, P=P, RHS=q) + + u = prob.field(mSynth) + u = data.reshapeFields(u) + M.plotImage(u[:,10]) + plt.show() + + # Now set up the prob to do some minimization + # prob.dobs = dobs + # prob.std = dobs*0 + 0.05 + m0 = M.gridCC[:,0]*0+sig2 + + reg = Regularization.Tikhonov(model) + objFunc = ObjFunction.BaseObjFunction(data, reg) + opt = Optimization.InexactGaussNewton(maxIterLS=20, maxIter=3, tolF=1e-6, tolX=1e-6, tolG=1e-6, maxIterCG=6) + inv = Inversion.BaseInversion(objFunc, opt) + + # Check Derivative + derChk = lambda m: [objFunc.dataObj(m), objFunc.dataObjDeriv(m)] + # Tests.checkDerivative(derChk, mSynth) + + print objFunc.dataObj(m0) + print objFunc.dataObj(mSynth) + + m = inv.run(m0) + + plt.colorbar(M.plotImage(m)) + print m + plt.show() + + + + + + diff --git a/simpegDC/Tests/__init__.py b/simpegDC/Tests/__init__.py new file mode 100644 index 00000000..32112042 --- /dev/null +++ b/simpegDC/Tests/__init__.py @@ -0,0 +1,14 @@ +from TestUtils import checkDerivative, Rosenbrock, OrderTest, getQuadratic + + +if __name__ == '__main__': + import os + import glob + import unittest + test_file_strings = glob.glob('test_*.py') + module_strings = [str[0:len(str)-3] for str in test_file_strings] + suites = [unittest.defaultTestLoader.loadTestsFromName(str) for str + in module_strings] + testSuite = unittest.TestSuite(suites) + + unittest.TextTestRunner(verbosity=2).run(testSuite) diff --git a/simpegDC/Tests/test_forward_DCproblem.py b/simpegDC/Tests/test_forward_DCproblem.py new file mode 100644 index 00000000..bbcdc9e7 --- /dev/null +++ b/simpegDC/Tests/test_forward_DCproblem.py @@ -0,0 +1,79 @@ +from SimPEG import * +import unittest +import simpegDC + + +class DCProblemTests(unittest.TestCase): + + def setUp(self): + # Create the mesh + h1 = np.ones(20) + h2 = np.ones(20) + mesh = Mesh.TensorMesh([h1,h2]) + + # Create some parameters for the model + sig1 = 1 + sig2 = 0.01 + + # Create a synthetic model from a block in a half-space + p0 = [2, 2] + p1 = [5, 5] + condVals = [sig1, sig2] + mSynth = Utils.ModelBuilder.defineBlockConductivity(p0,p1,mesh.gridCC,condVals) + + # Set up the projection + nelec = 10 + spacelec = 2 + surfloc = 0.5 + elecini = 0.5 + elecend = 0.5+spacelec*(nelec-1) + elecLocR = np.linspace(elecini, elecend, nelec) + rxmidLoc = (elecLocR[0:nelec-1]+elecLocR[1:nelec])*0.5 + q, Q, rxmidloc = genTxRxmat(nelec, spacelec, surfloc, elecini, mesh) + P = Q.T + + # Create some data + + problem = DCProblem(mesh) + problem.P = P + problem.RHS = q + data = problem.createSyntheticData(mSynth, std=0.05) + + # Now set up the problem to do some minimization + opt = inverse.InexactGaussNewton(maxIterLS=20, maxIter=10, tolF=1e-6, tolX=1e-6, tolG=1e-6, maxIterCG=6) + reg = inverse.Regularization(mesh) + inv = inverse.Inversion(problem, reg, opt, data, beta0=1e4) + + self.inv = inv + self.reg = reg + self.p = problem + self.mesh = mesh + self.m0 = mSynth + self.data = data + + def test_misfit(self): + derChk = lambda m: [self.p.dpred(m), lambda mx: self.p.J(self.m0, mx)] + passed = checkDerivative(derChk, self.m0, plotIt=False) + self.assertTrue(passed) + + def test_adjoint(self): + # Adjoint Test + u = np.random.rand(self.mesh.nC*self.p.RHS.shape[1]) + v = np.random.rand(self.mesh.nC) + w = np.random.rand(self.data.dobs.shape[0]) + wtJv = w.dot(self.p.J(self.m0, v, u=u)) + vtJtw = v.dot(self.p.Jt(self.m0, w, u=u)) + passed = (wtJv - vtJtw) < 1e-10 + self.assertTrue(passed) + + def test_dataObj(self): + derChk = lambda m: [self.inv.dataObj(m), self.inv.dataObjDeriv(m)] + checkDerivative(derChk, self.m0, plotIt=False) + + def test_modelObj(self): + derChk = lambda m: [self.reg.modelObj(m), self.reg.modelObjDeriv(m)] + checkDerivative(derChk, self.m0, plotIt=False) + + +if __name__ == '__main__': + unittest.main() diff --git a/simpegDC/__init__.py b/simpegDC/__init__.py new file mode 100644 index 00000000..5019959f --- /dev/null +++ b/simpegDC/__init__.py @@ -0,0 +1 @@ +from DC import *