đź“š Want to Read More Books in 2021 — Try 2X Speed

As an academic, I rarely have time to read “for fun books” and instead devote my reading time to keeping up with new discoveries and theories divulged in esoteric journal articles. This changed when I stumbled upon a YouTube video by Ali Abdaal espousing the merits of listening at 2X speed and faster. Wow, a typical non-fiction audiobook between 8-10 hours now only requires 4-10 hours to complete, and even 30 hour epic fantasy novels are manageable at 15 hours. After finding this superpower in September 2020, I have now completed 19 books over the last four months.

  1. Educated, Tara Westover
  2. The Stone Sky, N.K. Jemisin
  3. Hidden Figures, Margot Shetterly
  4. The Obelisk Gate, N.K. Jemisin
  5. Andromeda Strain Evolution, Michael Crichton
  6. How to Change Your Mind, Michael Pollan
  7. In Defense of Food, Michael Pollan
  8. The End of Everything, Katie Mack
  9. The Gathering Storm, Brandon Sanderson/Robert Jordan
  10. Towers of Midnight, Brandon Sanderson/Robert Jordan
  11. White Fragility, Robin Diangelo
  12. Why We Sleep, Matthew Walker
  13. A Memory of the Light, Brandon Sanderson/Robert Jordan
  14. Brain on Fire, Susannah Cahalan
  15. The Princess Diarist, Carrie Fisher
  16. Go Set a Watchman, Harper Lee
  17. Hidden Reality, Brian Greene
  18. Armada, Ernest Cline
  19. Storm Front, Jim Butcher

Adjusting to 2X speed took me only a few minutes, and I enjoy listening to books more at double speed. I could finally finish the Robert Jordan’s Wheel of Time series that I started as a teenager in the 1990s. I also read many non-fiction books that I found interesting, but was never going to read without listening to the audiobook version at 2X speed.

I used the Libby app and my local library card to access these great books for free. The Libby app is much improved, very user-friendly to find new audiobooks, and even works in my vehicle via CarPlay. Most of my listening takes place while working out on my bike. I feel like my life has greatly improved as new words enter my ears and my legs grind out the miles each morning.

Create 3D Terrain Models from Real World Locations

3D model of Ngornogo Conservation Area — World Heritage Site
3D model of Ngornogo Conservation Area — World Heritage Site

Software Needed:

QGIS: Geographical Information Software

Adobe Photoshop

Atlas 3D Map Generator (Photoshop plug-in)

I have been creating 3D models of terrain for uploading to SketchFab and also generating 3D models for use in my World Heritage sites class. With GIS, it is possible to add any additional information to the 3D models as needed. I like this approach because it is straightforward to create whatever 3D content you need with just a few clicks. It did take me a while to figure out this workflow, so hopefully this post will save somebody some time and effort.

My General Workflow:

QGIS

  1. Capture with screenshots digital elevation models (DEMs) and aerial imagery within QGIS. The advantage of this approach is that any other GIS layers can be added on top of the DEM models in the final 3D modeling rendering.
    a. Navigate to a real world of interest within QGIS.
    b. I typically use the QGIS SRTM plug-in for automatically downloading the DEMs that cover the current extent. If there are more than one DEM, I merge them together.

Raster ⇨Miscellaneous ⇨ Merge. Then add the recently downloaded SRTM files and click merge.

To use this SRTM plug-in, create a free profile at https//urs.earthdata.nasa.gov.

c. Take screenshots of both the DEM and aerial imagery for the overlaying 3D model’s texture. Make sure the screenshots cover the same area of the screen so that they overlay each other.

Photoshop

  1. Open the DEM raster layer in Photoshop.
  2. Create a new layer in Photoshop and embed the texture layer (aerial imagery or other GIS layers), and label this new layer as texture.
  3. Create New Terrain using the Atlas plug-in
  4. Modify the terrain settings and export the 3D model from Photoshop.

I normally export the 3D model with 600 cm width dimensions which seems to work well with uploading to SketchFab. I also save the texture files as JPEGS which SketchFab can process.

Upload to Sketchfab

  1. Compress the exported .obj and other supporting files. On a Mac highlight all the files, right-click and then select compress. Upload the .zip file to SketchFab.

Keeping Track of New Academic Journal Articles

Generate new ideas and stay ahead in your research

Reading the latest articles from journals in your field of study is vital for staying ahead of information that impacts your work, and for generating new research ideas. Today, this is a difficult task with the proliferation of new journals, and an increase in the number of articles released each day. The publication industry over the last two decades has largely switched from paper-based to digital (Chen, 2019), and as a result researchers now have more options than ever to find a journal to publish their work. The National Science Foundation documented that the number of journal articles published in scientific and engineering journals grew by 4% over the last decade.

Although keeping up with and reading new publications often feels like drinking water from a fire hose, using the best tools that works for you can save time, prevent burnout, and keep you focused on what matters most — your research and having a life.

RSS (Really Simple Syndication) Readers

Most journals in your field will offer an RSS subscription link. Navigate to the journal’s website and copy and paste the RSS feed link into your RSS reader of choice. RSS readers are apps that conglomerate the RSS feeds that you follow and present them in a magazine style for easy navigation. Interesting blogs or websites that share their research with an RSS feed can also be added to your RSS reader.

Many RSS apps are free to use, however, some like Feedly or Unread offer more features that are worth a subscription or download cost.

The Researcher App is a new academically focused RSS reader and free to use. For scholars that only want to keep up with academic journals than the Researcher App is the best choice. The key benefit of Researcher is that journal RSS feeds are added within the app, and a user simply follows their journals. If a journal is missing, email the Researcher App developers and have the journal added. Another unique feature is that you can integrate a Zotero or Mendeley account. Zotero and Mendeley are reference management apps that keep track of citations, associated PDFs, and offer Cite While You Write capabilities. When connected, flagged articles within the Researcher App are automatically populated within your Zotero or Mendeley database.

Email Notifications

Journals and academic databases, such as Google Scholar and Web of Science, offer users email notifications as new papers are published. To receive updates navigate to the journal’s website and sign up to receive a table of contents when issues are published.

Another method is to create a free account associated with an academic database. With an account, you can receive notifications from specific journals, or notifications related to a custom keyword. The advantage of the keyword approach is that all journals within the academic database are searched, not just the ones you subscribe too.

My Keyword Alerts Used in Web of Science.
My Keyword Alerts Used in Web of Science.

Reference Management Apps

Many reference management apps, now owned by the major academic publishers (e.g., Elsevier — Mendeley, Wiley — Papers Readcube), suggest new papers to read based on your PDF library. This integration will further improve as the recommendation algorithms advance within these apps.

For Mac or iPad users another potential solution is Devonthink. Devonthink is more of an information management database and unlike reference management apps it does not organize or create reference citations. Researchers use Devonthink, however, to maintain and organize their PDF library and to take advantage of its superior search capabilities. A bonus of Devonthink is its integrated RSS feeds. You can use Devonthink as an RSS reader, and conduct literature searches that span both your PDFs and new publications from your RSS feed results.

Keeping up with the latest discoveries and theories in your field can have profound results in your research. Choose which method works best for you. Are you an email master and like receiving emails in your inbox? Then sign up for email notifications. If your inbox is a source of anxiety, then try an RSS reader or a reference management app. Although staying on top of the academic literature may feel overwhelming, if you develop a system, you can live a more productive and less stressful life.

Grammarly Keyboard Update — Works Well with Ulysses App on iPad

The Grammarly App for iOS was recently updated, and it now includes access to the Grammarly editor on iPad rather than having to upload text to their website. This is a nice new feature, however, I am impressed by the updated Grammarly keyboard and how it integrates with Ulysses. I think this integration now solves the issue of having an advanced grammar checker available to check your text on Ulysses.

Using the Grammarly keyboard with the Ulysses App on my iPad.

I have tried the Grammarly keyboard with Apple’s Pages and Microsoft Word, and it does not work very well with these word processors. Maybe, the Grammarly keyboard works better with plain text and markdown rather than rich text?

Cite While You Write on the iPad

For academics, inserting citations from a popular citation manager, such as Endnote, Mendeley, Readcube, etc., is an integral part of their writing workflow. Researchers use citation managers to save time and the hassle of properly formatting citations that different journals require. The sandbox security of iPadOS, however, has limited the ability of these citation managers to integrate with word processors.

Recently, I have come across two solutions that work on iPadOS.

1. In Microsoft Word, use the Mendeley add-on within Word on the iPad.

Using the Mendeley Add-On within Microsoft Word on iPad.
  1. For Google docs, Paperpile now works as an add-on if writing within the Safari browser. Paperpile works via Safari since Safari is now a full-fledged desktop-class web browser on mobile. Chrome will not work.
Using Paperpile with Google Docs on iPad via Safari.

I hope to see other citation managers such as Zotero, Endnote, Bookends, and Readcube offer an iPadOS solution. I particularly hope that they can also integrate with Ulysses or Apple’s Pages.

How to create amazing GIFs that tell a story

the amazing tools in Apple’s iWork Keynote

Adding animations to presentations and your writing can make what you have to say more clear and stand out. The update to Apple’s Keynote presentation software (Keynote 5.0) now makes creating GIF animiations easier than ever.

I recently created a GIF to illustrate the difference between the aggregation and social boundary defense models I use in my archaeological research on territoriality. A dry topic for some, but the difference between the two models comes alive with an animated GIF.

Animated GIF Created in Keynote 5.0

Five Steps:

  1. Find or create elements (e.g., pictures, vector art) and add them to a new Keynote slide.
  2. Animate element actions in the slide.
  3. Order element actions to sequence the GIF story.
  4. Alter the timing duration for each element’s action.
  5. Export the slide as a GIF.

Create GIF in iWork Keynote 5.0 Workflow Example

  1. Find or create elements (e.g., pictures, vector art) and add them to a new Keynote slide.
Add or create elements in Keynote

In this example, all of my slide’s elements were created within Keynote. The human figures were people shapes added from the Keynote shape menu. I made the “spear” that the woman is holding by modifying an arrow shape.

2. Animate element actions in the slide.

Selecting a slide element brings up the option menu in iOS (iPad or iPhone). On MacOS the same options are available on the slide’s right side. Animation options are Build In, Action, and Build Out.

Animation options Build In, Action and Build Out within the Animation menu in iOS Keynote

Build In and Build Out make slide elements appear or disappear in different ways (appear, dissolve, move in, etc.). In this example, I used the Build In and Build Out animations to make the words Aggregation and Social Boundary Defense to appear and disappear using the appear option.

Action is used to move a slide’s element on the slide in different ways (along a path, rotate, scale, etc.). In this example, I moved the human figures along a path. Note, on MacOS it is referred to as Move rather than Create a Path on iOS.

3. Order element actions to sequence the GIF story.

I created an action to move the human figures along a path from within the Animation menu in Keynote.

This step is necessary to double check the order in which the animations will occur. In most animations, the timing of Build In, Build Out, and Actions are important to sequence the story. In this example, I had to change the order of the animations several times until they were in the right sequence.

Adjust the animation sequence and animation timing within the Build Order menu in Keynote

The Build Order menu is accessed through Animation. Place the animations in order of occurrence (top first – bottom last) by dragging and dropping.

4. Alter the timing duration for each element’s action.

The time duration needed for each element to complete its animation is also adjustable within the Build Order menu. In this example, my words Aggregation and Social Boundary Defense were appearing and disappearing too quickly. I adjusted the timing duration for each of these elements to more slowly appear and disappear.

At the bottom of the Build Order menu are the options: On Tap, With Build, After Build. This menu is used to determine how the animations will be initiated during a presentation. A click or touch is required to initiate an animation with On Tap. With Build is used when more than one animation needs to occur simultaneously. It is grouping animations together. Select After Build if an animation needs to happen after a previous animation. In creating GIFs the On Tap and After Build are the same option. When Keynote exports the GIF it automates the presenter’s tap or click.

5. Export the slide as a GIF.

The export menu is reached by tapping the three dots on the upper right corner in iOS or through the Files menu on a Mac. Animated GIF is one of the export options. Within the Animated GIF menu are several choices to further customize the GIF including resolution, frame rate, and auto-advance. The Auto-Advance feature is how Keynote automates the presenter’s tap or click. Adjusting these settings will change the size of the final image and the speed of the animated GIF. In this example, I changed the size of the animated GIF from medium to large.

Export Animation GIF options in Keynote

Another important feature of animating a GIF within Keynote is that a GIF can be created across one slide or more. In this example, the GIF was created within only one slide. It is possible, however, to use transitions between slides as part of the GIF creation process. The options to create a compelling animated GIF are endless within Keynote.

A Look at Deep Fusion — “Computational Photography Mad Science” Coming to IPhone 11 Pro this Fall

Apple unveiled their latest and greatest new 2019 iPhones in a Keynote event viewed by approximately 2 million people live last Tuesday.

What these viewers may have missed is how Deep Fusion will transform some types of photography.

The two main key features of the new IPhone 11 and IPhone 11 Pro models that sets them apart from last year’s iPhone Xs and Xr models are new camera lenses and A13 bionic processors. The iPhone 11, an upgrade of last year’s Xr model, now has a dual rear lens camera system — a 12 megapixel wide angle and a 12 megapixel ultra wide. I think most iPhone buyers will get more use out of the new ultra wide angle lens, however, I really love the telephoto lens on the iPhone Xs to zoom two times closer to subjects. The lack of the telephoto lens on the iPhone 11 camera will stop me from purchasing this more affordable iPhone.

Phil Schiller Introducing Deep Fusion at the Apple September 10th, 2019 Keynote Event
Phil Schiller Introducing Deep Fusion at the Apple September 10th, 2019 Keynote Event

The iPhone 11 Pro, an upgrade from last year’s iPhone Xs dual camera lens system, now also adds the ultra wide lens to give the Pro three 12 megapixel lenses: a wide angle, ultra wide angle, and telephoto. What really peaked my interest during the keynote is when Phil Schiller introduced Deep Fusion coming to the iPhone Pro later this fall. Schiller playfully referred to this new feature as “computational photography mad science”.

In Deep Fusion, the iPhone 11 Pro cameras takes 4 short and 4 long exposure images simultaneously and combines them into one image that is sharp throughout with very little noise.

Example of Focus Stacking. I Used a Series of 3 Images to create 1 Complete Focus Stacked Image in Photoshop — the Entire Image is Now in Focus.
Example of Focus Stacking. I Used a Series of 3 Images to create 1 Complete Focus Stacked Image in Photoshop — the Entire Image is Now in Focus.

The concept of Deep Fusion, however, is not a new feature to photographers. Deep Fusion is focus stacking — a computational algorithmic used in software like Adobe’s Photoshop that can combine several images together into a new improved image. Photographers focus stack images to bring both the background and foreground in focus in one image.

What is amazing about Deep Fusion is that I do not need a computer and Photoshop for focus stacking. Instead the IPhone Pro 11 can do these intensive CPU tasks within seconds. This speaks to the great progress and innovation the ARM chip designers are making at Apple. I am looking forward to trying out Deep Fusion images to see how they work with macrophotogrammetry — creating 3D models from images this fall.

My Research Using the Highlights App

A simple and productive workflow system

Photo by Josh Sorenson from Pexels

Over the last five years, I have transitioned to using my iPad as my main computer for note-taking, writing, and research. A big snag in my academic workflow, however, was managing my PDF research documents, notes, and citation information. I believe I have tested every combination of citation manager (e.g., Endnote, Mendeley, Papers, Bookends, Zotero), word processor or text editor, and note-taking app imaginable to create a seamless workflow.

I really dislike citation managers. I want to use them to help manage my research information, but they fall short on the iPad for in-text citations, extraction of highlighted notes, PDF reading, etc. Most of the citation managers also require a subscription fee to house your PDFs and notes on their servers for syncing between devices. In addition, many of the citation managers (e.g., Mendeley, Papers) have been purchased by large academic publishing houses that often restrict access to the academic literature.

When the Highlights app was made available for beta testing on the iPad, I immediately signed up. I had used Highlights on my Mac and really enjoyed its ability to extract highlighted texts and annotations to create markdown style notes for research. Highlights’ also has the unique ability, amongst PDF apps, to extract citation information from the journal article if it contains a digital object identifier (DOI) number. Your research notes, therefore, can also automatically contain the associated journal article’s citation information.

https://highlightsapp.net

After a few years of development, Highlights is now available for purchase on the App Store, and I would like to share how I have been using Highlights in my research system.

First, I have abandoned citation managers, and have moved all of my research PDF documents into the Highlights folder within iCloud Drive. I really like this setup since all of my PDFs are now on my iCloud Drive, and not managed by another service that I have to pay an additional subscription fee.

My research related reading now takes place within the Highlights app. I highlight the text I want to come back too as well as add my own note annotations as I am reading. Before closing the research article, I typically export the notes into Ulysses, my writing app of choice, for storage and reference. If I need to quickly refer back to the PDF document directly, I simply follow a page URL link embedded within the reference note and it pulls up the original PDF within the Highlights folder.

https://ulysses.app

I currently have over 1500 PDF documents in my Highlights folder. To find a key piece of information from a journal article or book that I can not remember while researching, I use PDF Search. I have set up the PDF Search app to index my Highlights folder. PDF Search uses AI to search through your PDFs for related terms and then ranks the results. PDF Search is an excellent replacement for cataloging your research documents rather than using a clunky citation manager database.

http://www.pdfsearchapp.com

The only thing I am missing from my research system, that citation managers provide, is the ability to insert formatted citations into my document. I have been doing this manually through copy and paste and formatting the citations to fit the journal’s formatting requirements. This is a worthy trade-off for me at this point to have a more flexible and fast research system rather than trying to fit my workflow with a citation manager.

Integrating Endnote with Ulysses III

As an academic researcher it saves a lot of time to use a bibliography database to automatically output citations in the correct format. Although Pages and Word have direct plug-in capability and is easy to use, often I find myself working in a text editor such as Ulysses III.

Currently I am using Endnote X6, however, it is likely other bibliography databases that have a scan paper function will work as well. To insert citations into Ulysses III so that Endnote will recognize them follow the format guides below.

Steps for generating bibliography with Endnote

  1. Save finished paper as Word .rtf
  2. Open up Endnote, and select Tools > Format Paper. Navigate to the saved file and Endnote will scan the paper and generate a new .rtf file with a bibliography in your chosen Endnote style.

Formatting guide for inserting citations into Ulysses III:

Copy each desired reference within Endnote and then \ Paste reference within Ulysses III.  To avoid using the backslash you can also modify {} as a markup symbol

Ulysses III tips

For author and date:
\{Hurst, 2002 #1796}

Results example:
(Hurst 2002)

For multiple citations:
\{Hurst, 2002 #1796}\{Hurst, 2010 #1636}
\{Hurst, 2010 #1636}\{Johnson, 2011 #739}

Results example:
(Hurst 2002, 2010)
(Hurst 2010; Johnson et al., 2011)

Add prefix to citation:
\{e.g.,\Hurst, 2010 #1636}

Results example:

(e.g., Hurst 2010)

Note:  To get the prefix citation to work you must add the backslash within the RTF document prior to Endnote scanning.  Ulysses removes \ on export to RTF.

Add page numbers:

\{Hurst, 2010 #1636:23-30}

Results example:

(e.g., Hurst, 2010:23-30)

Year only:

Hurst states \{, 2010 #1636} the following

Results example:

Hurst states (2010) the following

Submitting high resolution graphs and figures for publication from iWork’s Pages and Numbers

Recently I submitted a new manuscript for publication.  Within the manuscript I have several figures and line drawings that I created within Numbers and Pages.  Publishers typically require line drawings to be saved in Tiff format and have a resolution of 1200 dpi.

In the past, I copy and pasted my figures and line drawings into Keynote using a really big custom slide.  After scaling up the figure to match the large slide size,  I would then export the Keynote slide as a Tiff and then modify the image size setting and resolution within Photoshop.

This method requires many unnecessary steps.

The easy way is to print the Pages or Numbers document at 1200 dpi resolution and save it as a PDF file.  Then open up the PDF in Photoshop, select the page with the figure or line drawing that you are working on, crop the image, and then save as a Tiff.  That is it.  Repeat for each figure or line drawing.

With this method it is now really easy to use Pages to manage figures, tables, and line drawings for publication.  I typically have one Pages document that contains all of my text, and another Pages document that contains all of my figures, line drawings, and tables.