Spatial Data Science in ArcGIS: Making the Most of the Ecosytem · Python for Data Analysis: Data...

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Spatial Data Science in ArcGIS: The Ecosystem Shaun Walbridge Kevin Butler

Transcript of Spatial Data Science in ArcGIS: Making the Most of the Ecosytem · Python for Data Analysis: Data...

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SpatialDataScienceinArcGIS:TheEcosystem

ShaunWalbridge

KevinButler

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https://github.com/scw/ds-scipy-devsummit-2020-talk

HighQualityPDF(5MB)

ResourcesSection

https://github.com/scw/ds-scipy-devsummit-2020-talk
https://4326.us/esri/ds-scipy-2020/devsummit-2020-ds-ecosystem-arcgis-presentation-full.pdf
https://4326.us/esri/ds-scipy-2020/#resources
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DataScience

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Theapplicationofcomputationalmethodstoallaspectsoftheprocessofscientificinvestigation–dataacquisition,datamanagement,analysis,visualization,andsharingofmethodsandresults.

DataScience

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ArcGISforspatialdatascience

ArcGISisasystemofrecord.Combinedataandanalysisfrommanyfieldsandintoacommonenvironment.Whyextend?Can’tdoitall,wesupportover1600GPtools—enablingintegrationwithotherenvironmentstoextendtheplatform.ArcGISisanecosystemthatlendsitselfverynicelytothewaythatspatialdatascientistsalreadywork.

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What’sintheEcosystem

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PythoninArcGISPythonAPIfordrivingArcGISDesktopandServerAfullyintegratedmodule:importarcpyInteractiveWindow,PythonAddins,PythonTooboxesArcGISAPIforPythonHostedNotebooksNotebooksinArcGISPro

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Demo:NotebooksinPro

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CorePythonLibraries

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WhySciPy?Mostlanguagesdon’tsupportthingsusefulforscience,e.g.:

VectorprimitivesComplexnumbersStatistics

Objectorientedprogrammingisn’talwaystherightparadigmforanalysisapplications,butistheonlywaytogoinmanymodernlanguagesSciPybringsthepiecesthatmatterforscientificproblemstoPython.

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IncludedSciPyPackage KLOC Contributors Stars

52 229 4293

36 587 13408

85 214 7396

236 738 9868

183 1433 18431

387 699 5522

243 730 5617

Andover100additionalpackages.Checkthemout!

dask

IPython

JupyterLab

NumPy

Pandas

SciPy

SymPy

https://dask.org/
https://ipython.readthedocs.io/en/stable/
https://jupyterlab.readthedocs.io/
https://www.numpy.org/
https://pandas.pydata.org/
https://scipy.org/scipylib/
https://sympy.org/
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PlottinglibraryandAPIforNumPydata

Proalsoincludesarcpy.chartforplottingviaProcharts

UC2020:EmbeddedProchartsinnotebooks

MatplotlibGallery

http://matplotlib.org/gallery.html
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ArcGISwithNumPy

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1. Anarrayobjectofarbitraryhomogeneousitems2. Fastmathematicaloperationsoverarrays

,CC-BYSciPyLectures

https://scipy-lectures.github.io/intro/numpy/array_object.html#indexing-and-slicing
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ArcGISandNumPycaninteroperateonraster,table,andfeaturedata.SeeIn-memorydatamodel.Examplescriptto

ifworkingwithlargerdata.Usearcgis’SeDFifyouneedahigh-levelinterface

forfeaturedata

WorkingwithNumPyinArcGISprocessby

blocks

http://desktop.arcgis.com/en/desktop/latest/analyze/python/working-with-numpy-in-arcgis.htm
https://4326.us/esri/examples/process-by-blocks.py
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ArcGISwithNumPy

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Computationalmethodsfor:

Integration( )Optimization( )Interpolation( )FourierTransforms( )SignalProcessing( )LinearAlgebra( )Spatial( )Statistics( )Multidimensionalimageprocessing( )

scipy.integratescipy.optimizescipy.interpolate

scipy.fftscipy.signal

scipy.linalgscipy.spatial

scipy.statsscipy.ndimage

http://docs.scipy.org/doc/scipy/reference/tutorial/integrate.html
http://docs.scipy.org/doc/scipy/reference/tutorial/optimize.html
http://docs.scipy.org/doc/scipy/reference/tutorial/interpolate.html
https://docs.scipy.org/doc/scipy/reference/tutorial/fft.html
http://docs.scipy.org/doc/scipy/reference/tutorial/signal.html
http://docs.scipy.org/doc/scipy/reference/tutorial/linalg.html
http://docs.scipy.org/doc/scipy/reference/tutorial/spatial.html
http://docs.scipy.org/doc/scipy/reference/tutorial/integrate.html
http://docs.scipy.org/doc/scipy/reference/tutorial/ndimage.html
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UseCase:BenthicTerrainModeler

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LightweightSciPyIntegration

Usingscipy.ndimagetoperformbasicmultiscale

analysisUsingscipy.statstocomputecircularstatistics

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LightweightSciPyIntegration

Examplesource

importarcpyimportscipy.ndimageasndfrommatplotlibimportpyplotasplt

ras="data/input_raster.tif"r=arcpy.RasterToNumPyArray(ras,"",200,200,0)

fig=plt.figure(figsize=(10,10))

https://4326.us/esri/examples/calculate-bpi-with-scipy.py
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LightweightSciPyIntegration

foriinxrange(25):size=(i+1)*3print"running{}".format(size)med=nd.median_filter(r,size)

a=fig.add_subplot(5,5,i+1)plt.imshow(med,interpolation='nearest')a.set_title('{}x{}'.format(size,size))plt.axis('off')plt.subplots_adjust(hspace=0.1)

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Pandas

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PanelData—likeR“dataframes”BringarobustdataanalysisworkflowtoPythonDataframesarefundamental—treattabular(andmulti-dimensional)dataasalabeled,indexedseriesofobservations.

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SpatialDataFramesSamedataframemodel+geometriesArcPy+ArcGISAPIforPythonContinuestoexpandandimproveperformance

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ArcPyImprovements

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ArcPyImprovementsarcpy.metadatafortransformingyourmetadata

arcpy.naxforrichnetworkanalysis

Rastercelliteratorsforcustomper-cellrasteranalysiswithoutneedingtocopydatausingNumPy#DOCELLRISESarcpy.SetParameterSymbologyforrichanalyticalresultslikeChartsandpopups

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ArcPyImprovementsRichrepresentationsfordatalikearcpygeometries,

rastersMorecomingUC2020

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Integration

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IntegrationOK,sowe’vecoveredcorelibrariesthatexistwithintheProPythondistribution.Whataboutgoingbeyondthis?

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IntegrationWhatkindofcodeisbeingrun?

ThePrincipleofstackminimization

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Demo:MetPy

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MassivedataparallelismthroughPythonComputesgraphsofthecomputationalstructure

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Demo:Dask&TyingItTogether

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Page 38: Spatial Data Science in ArcGIS: Making the Most of the Ecosytem · Python for Data Analysis: Data Wrangling with Pandas, NumPy, and IPython. Packages Only require SciPy Stack: Scikit-learn:

RRStatisticalProgrammingLanguagePowerfulcoredatastructuresforanalysisUnparalleledbreathofstatisticalroutines

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R-ArcGISBridgeAccesstolocalandremotedata

TransformtonativeRspatialtypes(sf,sp,raster)

CallArcPythroughreticulate

UseinRStudio

MakeGPtoolswhichcallR

JupyterNotebookswithR:condainstallr-arcgis-essentials

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Demo:R

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fromfutureimport*

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RoadAheadContinuedimprovementsinDeepLearninginPro—makethisexperienceasseamlessandassimpleaspossibleRichrepresentations(__repr__)formanyobjectsin

ArcPyandProArcPyinExternalCondaenvironments(detectsPro)

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ProExternalEnvironments

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Resources

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NewtoPythonCourses:

Books:

ProgrammingforEverybodyCodecademy:PythonTrack

LearnPythontheHardWayHowtoThinkLikeaComputerScientist

https://www.coursera.org/course/pythonlearn
https://www.codecademy.com/catalog/language/python
http://learnpythonthehardway.org/
https://runestone.academy/runestone/books/published/thinkcspy/index.html
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GISFocusedPythonScriptingforArcGISArcPyandArcGIS-GeospatialAnalysiswithPythonPythonDevelopersGeoNetCommunityGISStackexchange

http://esripress.esri.com/display/index.cfm?fuseaction=display&websiteID=276&moduleID=0
https://www.packtpub.com/application-development/arcpy-and-arcgis-geospatial-analysis-python
https://geonet.esri.com/community/developers/gis-developers/python
https://gis.stackexchange.com/
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ScientificCourses:

PythonScientificLectureNotesHighPerformanceScientificComputingCodingtheMatrix:LinearAlgebrathroughComputerScienceApplicationsTheDataScientist’sToolbox

https://scipy-lectures.github.io/
https://www.coursera.org/course/scicomp
https://www.coursera.org/course/matrix
https://www.coursera.org/course/datascitoolbox
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ScientificBooks:

Free:

verycompellingbookonBayesianmethodsinPython,usesSciPy+PyMC.

ProbabilisticProgramming&BayesianMethodsforHackers

KalmanandBayesianFiltersinPython

https://camdavidsonpilon.github.io/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers/
https://github.com/rlabbe/Kalman-and-Bayesian-Filters-in-Python
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ScientificPaid:

HowtouselinearalgebraandPythontosolveamazingproblems.

ThecannonicalbookonPandasandanalysis.

CodingtheMatrix

PythonforDataAnalysis:DataWranglingwithPandas,NumPy,andIPython

http://www.codingthematrix.com/
http://shop.oreilly.com/product/0636920023784.do
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PackagesOnlyrequireSciPyStack:

Scikit-learn:

IncludesSVMs,canusethoseforimageprocessingamongotherthings…

FilterPy,Kalmanfilteringandoptimalestimation:

Lecturematerial

FilterPyonGitHubAnextensivelistofmachinelearningpackages

http://scipy-lectures.org/packages/scikit-learn/index.html
https://github.com/rlabbe/filterpy
https://github.com/svaksha/pythonidae/blob/master/AI.md
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Code

AnopensourcecollectionoffunctionchainstoshowhowtodocomplexthingsusingNumPy+scipyontheflyforvisualizationpurposes

withahandfulofdescriptivestatisticsincludedinPython3.4+.TIP:WantacodebasethatrunsinPython2and3?

,whichhelpsmaintainasinglecodebasethatsupportsboth.Includesthefuturizescripttoinitiallyaprojectwrittenforoneversion.

ArcPy+SciPyonGithubraster-functions

statisticslibrary

Checkoutfuture

https://github.com/search?p=5&q=scipy+arcpy&type=Code&utf8=%E2%9C%93
https://github.com/Esri/raster-functions
https://docs.python.org/3/library/statistics.html
http://python-future.org/
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ScientificArcGISExtensions

CombinesPython,R,andMATLABtosolveawidevarietyofproblems

speciesdistribution&maximumentropymodels

PySALArcGISToolboxMovementEcologyToolsforArcGIS(ArcMET)MarineGeospatialEcologyTools(MGET)

SDMToolbox

BenthicTerrainModelerGeospatialModelingEnvironmentCircuitScape

https://github.com/Esri/PySAL-ArcGIS-Toolbox
http://www.movementecology.net/
http://mgel.env.duke.edu/mget/
http://sdmtoolbox.org/
http://www.arcgis.com/home/item.html?id=b0d0be66fd33440d97e8c83d220e7926
http://www.spatialecology.com/gme/
http://www.circuitscape.org/
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Conferences

ThelargestgatheringofPythonistasintheworld

AmeetingofScientificPythonusersfromallwalks

ThePythoneventforPythonandGeoenthusiasts

TalksfromPythonconferencesaroundtheworldavailablefreelyonline.

PyCon

SciPy

GeoPython

PyVideo

PyVideoGIStalks

http://pycon.org/
https://scipy.org/
http://www.geopython.net/
http://pyvideo.org/
http://pyvideo.org/search?models=videos.video&q=gis
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Closing

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ThanksGeoprocessingTeamArcGISAPIforPythonTeamThemanyamazingcontributorstotheprojectsdemonstratedhere.

Getinvolved!AllareonGitHubandhappilyacceptcontributions.

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Data science-summit MTL 2015 - The end of IT departments and data-science empowered by ipython notebook

Data science-summit MTL 2015 - The end of IT departments and data-science empowered by ipython notebook

Ecosytem goods and services of extensive fishponds Éva Kerepeczki.

Ecosytem goods and services of extensive fishponds Éva Kerepeczki.

Mining Social Web APIs with IPython Notebook - Data Day Texas 2014

Mining Social Web APIs with IPython Notebook - Data Day Texas 2014

What is an Ecosytem? Abiotic factors Biotic factors.

What is an Ecosytem? Abiotic factors Biotic factors.

IPython: averyquickoverviewfperez.org/talks/1010_ipython_overview.pdf · 2010. 11. 4. · IPython: averyquickoverview FernandoPérez,BrianGranger,MinRagan-Kelley and80+contributiors...

IPython: averyquickoverviewfperez.org/talks/1010_ipython_overview.pdf · 2010. 11. 4. · IPython: averyquickoverview FernandoPérez,BrianGranger,MinRagan-Kelley and80+contributiors...

Using IPython to Find Correlation

Using IPython to Find Correlation

Datenanalyse mit IPython und Pandas - Dirk Lossdirk-loss.de/ipython-pandas-2013-05/datenanalyse-ipython-pandas.pdf · python-sympy python-nose. Title: Datenanalyse mit IPython und

Datenanalyse mit IPython und Pandas - Dirk Lossdirk-loss.de/ipython-pandas-2013-05/datenanalyse-ipython-pandas.pdf · python-sympy python-nose. Title: Datenanalyse mit IPython und

Coffin landsat8 data in social values for ecosytem services

Coffin landsat8 data in social values for ecosytem services

Topic Model Visualization with IPython - fruct.org · Topic Model Visualization with IPython Sergey Karpovich1, Alexander Smirnov2,3, Nikolay Teslya2,3, Andrei Grigorev3 1Mos.ru,

Topic Model Visualization with IPython - fruct.org · Topic Model Visualization with IPython Sergey Karpovich1, Alexander Smirnov2,3, Nikolay Teslya2,3, Andrei Grigorev3 1Mos.ru,

Algorithms+and+DataStructures+IPython+– ipython.org+ M Kociński & A Materka, Algorithms & Data Structures, TUL IFE, Łódź 2012 2

Algorithms+and+DataStructures+IPython+– ipython.org+ M Kociński & A Materka, Algorithms & Data Structures, TUL IFE, Łódź 2012 2

Parallel Nsight 1.5 + CUDA Toolkit 3.2 + Ecosytem Update ...

Parallel Nsight 1.5 + CUDA Toolkit 3.2 + Ecosytem Update ...

The OPTIRAD Platform: Cloud-hosted IPython Notebooks for collaborative EO Data Analysis and Processing

The OPTIRAD Platform: Cloud-hosted IPython Notebooks for collaborative EO Data Analysis and Processing

The trade show ecosytem with kappes additions ch

The trade show ecosytem with kappes additions ch

Coffee Farmers and Ecosytem - Water

Coffee Farmers and Ecosytem - Water

1203 ipython pycon

1203 ipython pycon

NumPy and SciPy for Data Mining and Data Analysis Including iPython, SciKits, and matplotlib

NumPy and SciPy for Data Mining and Data Analysis Including iPython, SciKits, and matplotlib

Wait, IPython can do that?!...History of IPython • IPython is the father of the Jupyter Project • Started in 2001 as 259 lines of code executed at Python’s startup, written by

Wait, IPython can do that?!...History of IPython • IPython is the father of the Jupyter Project • Started in 2001 as 259 lines of code executed at Python’s startup, written by

Ecosytem Interactions

Ecosytem Interactions

SDCSB Advanced Tutorial: Reproducible Data Visualization Workflow with Cytoscape and IPython Notebook

SDCSB Advanced Tutorial: Reproducible Data Visualization Workflow with Cytoscape and IPython Notebook

Granger Parallel IPython

Granger Parallel IPython