Category Archives: General

Scientists Use Enthought’s Virtual Core Software to Study Asteroid Impact

Chicxulub Impact Crater Expedition Recovers Core to Further Discovery on the Impact on Life and the Historical Dinosaur Extinction

From April to May 2016, a team of international scientists drilled into the site of an asteroid impact, known as the Chicxulub Impact Crater, which occurred 66 million years ago. The crater is buried several hundred meters below the surface in the Yucatán region of Mexico. Until that time, dinosaurs and marine reptiles dominated the world, but the series of catastrophic events that followed the impact caused the extinction of all large animals, leading to the rise of mammals and evolution of mankind. This joint expedition, organized by the International Ocean Discovery Program (IODP) and International Continental Scientific Drilling Program (ICDP) recovered a nearly complete set of rock cores from 506 to 1335 meters below the modern day seafloor.  These cores are now being studied in detail by an international team of scientists to understand the effects of the impact on life and as a case study of how impacts affect planets.

CT Scans of Cores Provide Deeper Insight Into Core Description and Analysis

Before being shipped to Germany (where the onshore science party took place from September to October 2016), the cores were sent to Houston, TX for CT scanning and imaging. The scanning was done at Weatherford Labs, who performed a high resolution dual energy scan on the entire core.  Dual energy scanning utilizes x-rays at two different energy levels. This provides the information necessary to calculate the bulk density and effective atomic numbers of the core. Enthought processed the raw CT data, and provided cleaned CT data along with density and effective atomic number images.  The expedition scientists were able to use these images to assist with core description and analysis.

CT Scans of Chicxulub Crater Core Samples

Digital images of the CT scans of the recovered core are displayed side by side with the physical cores for analysis

chicxulub-virtual-core-scan-core-detail

Information not evident in physical observation (bottom, core photograph) can be observed in CT scans (top)

These images are helping scientists understand the processes that occurred during the impact, how the rock was damaged, and how the properties of the rock were affected.  From analysis of images, well log data and laboratory tests it appears that the impact had a permanent effect on rock properties such as density, and the shattered granite in the core is yielding new insights into the mechanics of large impacts.

Virtual Core Provides Co-Visualization of CT Data with Well Log Data, Borehole Images, and Line Scan Photographs for Detailed Interrogation

Enthought’s Virtual Core software was used by the expedition scientists to integrate the CT data along with well log data, borehole images and line scan photographs.  This gave the scientists access to high resolution 2D and 3D images of the core, and allowed them to quickly interrogate regions in more detail when questions arose. Virtual Core also provides machine learning feature detection intelligence and visualization capabilities for detailed insight into the composition and structure of the core, which has proved to be a valuable tool both during the onshore science party and ongoing studies of the Chicxulub core.

chicxulub-virtual-core-digital-co-visualization

Enthought’s Virtual Core software was used by the expedition scientists to visualize the CT data alongside well log data, borehole images and line scan photographs.

Related Articles

Drilling to Doomsday
Discover Magazine, October 27, 2016

Chicxulub ‘dinosaur crater’ investigation begins in earnest
BBC News, October 11, 2016

How CT scans help Chicxulub Crater scientists
Integrated Ocean Drilling Program (IODP) Chicxulub Impact Crater Expedition Blog, October 3, 2016

Chicxulub ‘dinosaur’ crater drill project declared a success
BBC Science, May 25, 2016

Scientists hit pay dirt in drilling of dinosaur-killing impact crater
Science Magazine, May 3, 2016

Scientists gear up to drill into ‘ground zero’ of the impact that killed the dinosaurs
Science Magazine, March 3, 2016

Texas scientists probe crater they think led to dinosaur doomsday
Austin American-Statesman, June 2, 2016

Mayavi (Python 3D Data Visualization and Plotting Library) adds major new features in recent release

Key updates include: Jupyter notebook integration, movie recording capabilities, time series animation, updated VTK compatibility, and Python 3 support

by Prabhu Ramachandran, core developer of Mayavi and director, Enthought India

The Mayavi development team is pleased to announce Mayavi 4.5.0, which is an important release both for new features and core functionality updates.

Mayavi is a general purpose, cross-platform Python package for interactive 2-D and 3-D scientific data visualization. Mayavi integrates seamlessly with NumPy (fast numeric computation library for Python) and provides a convenient Pythonic wrapper for the powerful VTK (Visualization Toolkit) library. Mayavi provides a standalone UI to help visualize data, and is easy to extend and embed in your own dialogs and UIs. For full information, please see the Mayavi documentation.

Mayavi is part of the Enthought Tool Suite of open source application development packages and is available to install through Enthought Canopy’s Package Manager (you can download Canopy here).

Mayavi 4.5.0 is an important release which adds the following features:

  1. Jupyter notebook support: Adds basic support for displaying Mayavi images or interactive X3D scenes
  2. Support for recording movies and animating time series
  3. Support for the new matplotlib color schemes
  4. Improvements on the experimental Python 3 support from the previous release
  5. Compatibility with VTK-5.x, VTK-6.x, and 7.x. For more details on the full set of changes see here.

Let’s take a look at some of these new features in more detail:

Jupyter Notebook Support

This feature is still basic and experimental, but it is convenient. The feature allows one to embed either a static PNG image of the scene or a richer X3D scene into a Jupyter notebook. To use this feature, one should first initialize the notebook with the following:

from mayavi import mlab
mlab.init_notebook()

Subsequently, one may simply do:

s = mlab.test_plot3d()
s

This will embed a 3-D visualization producing something like this:

Mayavi in a Jupyter Notebook

Embedded 3-D visualization in a Jupyter notebook using Mayavi

When the init_notebook method is called it configures the Mayavi objects so they can be rendered on the Jupyter notebook. By default the init_notebook function selects the X3D backend. This will require a network connection and also reasonable off-screen support. This currently will not work on a remote Linux/OS X server unless VTK has been built with off-screen support via OSMesa as discussed here.

For more documentation on the Jupyter support see here.

Animating Time Series

This feature makes it very easy to animate a time series. Let us say one has a set of files that constitute a time series (files of the form some_name[0-9]*.ext). If one were to load any file that is part of this time series like so:

from mayavi import mlab
src = mlab.pipeline.open('data_01.vti')

Animating these is now very easy if one simply does the following:

src.play = True

This can also be done on the UI. There is also a convenient option to synchronize multiple time series files using the “sync timestep” option on the UI or from Python. The screenshot below highlights the new features in action on the UI:

Time Series Animation in Mayavi

New time series animation feature in the Python Mayavi 3D visualization library.

Recording Movies

One can also create a movie (really a stack of images) while playing a time series or running any animation. On the UI, one can select a Mayavi scene and navigate to the movie tab and select the “record” checkbox. Any animations will then record screenshots of the scene. For example:

from mayavi import mlab
f = mlab.figure()
f.scene.movie_maker.record = True
mlab.test_contour3d_anim()

This will create a set of images, one for each step of the animation. A gif animation of these is shown below:

Recording movies with Mayavi

Recording movies as gif animations using Mayavi

More than 50 pull requests were merged since the last release. We are thankful to Prabhu Ramachandran, Ioannis Tziakos, Kit Choi, Stefano Borini, Gregory R. Lee, Patrick Snape, Ryan Pepper, SiggyF, and daytonb for their contributions towards this release.

Additional Resources on Mayavi:

Geophysical Tutorial: Facies Classification using Machine Learning and Python

Published in the October 2016 edition of The Leading Edge magazine by the Society of Exploration Geophysicists. Read the full article here.

By Brendon Hall, Enthought Geosciences Applications Engineer 
Coordinated by Matt Hall, Agile Geoscience

ABSTRACT

There has been much excitement recently about big data and the dire need for data scientists who possess the ability to extract meaning from it. Geoscientists, meanwhile, have been doing science with voluminous data for years, without needing to brag about how big it is. But now that large, complex data sets are widely available, there has been a proliferation of tools and techniques for analyzing them. Many free and open-source packages now exist that provide powerful additions to the geoscientist’s toolbox, much of which used to be only available in proprietary (and expensive) software platforms.

One of the best examples is scikit-learn, a collection of tools for machine learning in Python. What is machine learning? You can think of it as a set of data-analysis methods that includes classification, clustering, and regression. These algorithms can be used to discover features and trends within the data without being explicitly programmed, in essence learning from the data itself.

Well logs and facies classification results from a single well.

Well logs and facies classification results from a single well.

In this tutorial, we will demonstrate how to use a classification algorithm known as a support vector machine to identify lithofacies based on well-log measurements. A support vector machine (or SVM) is a type of supervised-learning algorithm, which needs to be supplied with training data to learn the relationships between the measurements (or features) and the classes to be assigned. In our case, the features will be well-log data from nine gas wells. These wells have already had lithofacies classes assigned based on core descriptions. Once we have trained a classifier, we will use it to assign facies to wells that have not been described.

See the tutorial in The Leading Edge here.

ADDITIONAL RESOURCES:

Webinar: Introducing the NEW Python Integration Toolkit for LabVIEW

See a recording of the webinar:

LabVIEW is a software platform made by National Instruments, used widely in industries such as semiconductors, telecommunications, aerospace, manufacturing, electronics, and automotive for test and measurement applications. In August 2016, Enthought released the Python Integration Toolkit for LabVIEW, which is a “bridge” between the LabVIEW and Python environments.

In this webinar, we’ll demonstrate:

  1. How the new Python Integration Toolkit for LabVIEW from Enthought seamlessly brings the power of the Python ecosystem of scientific and engineering tools to LabVIEW
  2. Examples of how you can extend LabVIEW with Python, including using Python for signal and image processing, cloud computing, web dashboards, machine learning, and more

Continue reading

The Latest Features in Virtual Core: CT Scan, Photo, and Well Log Co-visualization

Enthought is pleased to announce Virtual Core 1.8.  Virtual Core automates aspects of core description for geologists, drastically reducing the time and effort required for core description, and its unified visualization interface displays cleansed whole-core CT data alongside core photographs and well logs.  It provides tools for geoscientists to analyze core data and extract features from sub-millimeter scale to the entire core.

NEW VIRTUAL CORE 1.8 FEATURE: Rotational Alignment on Core CT Sections

Virtual Core 1.8 introduces the ability to perform rotational alignment on core CT sections.  Core sections can become misaligned during extraction and data acquisition.   The alignment tool allows manual realignment of the individual core sections.  Wellbore image logs (like FMI) can be imported and used as a reference when aligning core sections.  The Digital Log Interchange Standard (DLIS) is now fully supported, and can be used to import and export data.

Whole-core CT scans are routinely performed on extracted well cores.  The data produced from these scans is typically presented as static 2D images of cross sections and video scans.  Images are limited to those provided by the vendor, and the raw data, if supplied, is difficult to analyze. However, the CT volume is a rich 3D dataset of compositional and textural information that can be incorporated into core description and analysis workflows.

Enthought’s proprietary Clear Core technology is used to process the raw CT data, which is notoriously difficult to analyze.  Raw CT data is stored in 3 foot sections, with each section consisting of many thousands of individual slice images which are approximately .2 mm thick. Continue reading

The Latest and Greatest Pandas Features (since v 0.11)

On May 28, 2014 Phillip Cloud, core contributor for the Pandas data analytics Python library, spoke at a joint meetup of the New York Quantitative Python User’s Group (NY QPUG) and the NY Finance PUG. Enthought hosted and about 60 people joined us to listen to Phillip present some of the less-well-known, but really useful features that have come out since Pandas version 0.11 and some that are coming soon. We all learned more about how to take full advantage of the Pandas Python library, and got a better sense of how excited Phillip was to discover Pandas during his graduate work.

Pandas to MATLAB

After a fairly comprehensive overview of Pandas, Phillip got into the new features. In version 0.11 he covered: Continue reading

Implied Volatility with Python’s Pandas Library AND Python in Excel

Authors: Brett Murphy and Aaron Waters

The March 6 New York Quantitative Python User’s Group (NY QPUG) Meetup included presentations by NAG (Numerical Algorithms Group), known for its high quality numerical computing software and high performance computing (HPC) services, and Enthought, a provider of scientific computing solutions powered by Python.

Brian Spector, a technical consultant at NAG, presented “Implied Volatility using Python’s Pandas Library.” He covered a technique and script for calculating implied volatility for option prices in the Black–Scholes formula using Pandas and nag4py. With this technique, you can determine for what volatility the Black–Scholes equation price equals the market price. This volatility is then denoted as the implied volatility observed in the market. Brian fitted varying degrees of polynomials to the volatility curves, then examined the volatility surface and its sensitivity with respect to the interest rate. See the full presentation in the video below:

Continue reading

Python at Inflection Point in HPC

Authors: Kurt Smith, Robert Grant, and Lauren Johnson

We attended SuperComputing 2013, held November 17-22 in Denver, and saw huge interest around Python. There were several Python related events, including the “Python in HPC” tutorial (Monday), the Python BoF (Tuesday), and a “Python for HPC” workshop held in parallel with the tutorial on Monday. But we had some of our best conversations on the trade show floor.

Python Buzz on the Floor

The Enthought booth had a prominent “Python for HPC: High Productivity Computing” headline, and we looped videos of our parallelized 2D Julia set rendering GUI (video below).  The parallelization used Cython’s OpenMP functionality, came in at around 200 lines of code, and generated lots of discussions.  We also used a laptop to display an animated 3D Julia set rendered in Mayavi and to demo Canopy.

Many people came up to us after seeing our banner and video and asked “I use Python a little bit, but never in HPC – what can you tell me?”  We spoke with hundreds of people and had lots of good conversations.

It really seems like Python has reached an inflection point in HPC.

Python in HPC Tutorial, Monday

Kurt Smith presented a 1/4 day section on Cython, which was a shortened version of what he presented at SciPy 2013.  In addition, Andy Terrel presented “Introduction to Python”; Aron Ahmadia presented “Scaling Python with MPI”; and Travis Oliphant presented “Python and Big Data”. You can find all the material on the PyHPC.org website.

The tutorial was generally well attended: about 100–130 people.  A strong majority of attendees were already programming in Python, with about half using Python in a performance-critical area and perhaps 10% running Python on supercomputers or clusters directly.

In the Cython section of the tutorial, Kurt went into more detail on how to use OpenMP with Cython, which was of interest to many based on questions during the presentation. For the exercises, students were given temporary accounts on  Stampede (TACC’s latest state-of-the-art supercomputer) to help ensure everyone was able to get their exercise environment working.

Andy’s section of the day went well, covering the basics of using Python.  Aron’s section was good for establishing that Python+MPI4Py can scale to ~65,000 nodes on massive supercomputers, and also for adressing people’s concerns regarding the import challenge.

Python in HPC workshop, Monday

There was a day-long workshop of presentations on “Python in HPC” which ran in parallel with the “Python for HPC” tutorial. Of particular interest were the talks on “Doubling the performance of NumPy” and “Bohrium: Unmodified NumPy code on CPU, GPU, and Cluster“.

Python for High Performance and Scientific Computing BoF, Tuesday

Andy Terrel, William Scullin, and Andreas Schreiber organized a Birds-of-a-Feather session on Python, which had about 150 attendees (many thanks to all three for organizing a great session!).  Kurt gave a lightning talk on Enthought’s SBIR work.  The other talks focused on applications of Python in HPC settings, as well as IPython notebooks on the basics of the Navier-Stokes equations.

It was great to see so much interest in Python for HPC!