a little bit of everything

Category: Uncategorized

Visualization blunders

As a jack of all trades I feel I know a lot and not at all at the same time. But one thing I know is about visualization, I just love it, I love to tell stories and ideas and provide insight on data and see the looks on people’s faces when they discover things they never thought before.

So when I see visualization blunders on the web I can’t help but to notice, laugh, and even take note as to not make such silly mistakes.

Here I will put the ones I collect over time.


This figure makes heights disproportionate. The Y-axis (vertical) doesn’t start at 0. So any comparison with this is completely useless, maybe even disrespecful.

The only thing I like about this, is the answers that people write on twitter.

This is not what Student-T means

People who claim to be scientists actually did this graph. Maybe they saw that scientific articles normally have graphs with some weird little squiggles that resemble capital letter Ts and thought “hmm I will just put Ts here to make it look more professional and no one will be the wiser” well no, the whole interenet noticed. This nice article covered the whole story.

Abnormal map

This might be a bit niche. But when I was teaching computer graphics and I asked them to render meshes with their normals, one student just added a material with a color that was “similar” to a normal map. I can’t believe he thought I wouldn’t notice. To this day I don’t understand why students do this 🙁

Good book on datavis

A friend shared this book with me long ago and I still love it. I like part II: Principles of figure design

17 The principle of proportional ink
18 Handling overlapping points
19 Common pitfalls of color use
20 Redundant coding
21 Multi-panel figures
22 Titles, captions, and tables
23 Balance the data and the context
24 Use larger axis labels
25 Avoid line drawings
26 Don’t go 3D

How I made my Curriculum Vitae

Since this is my website and I can write whatever I want, and few loving people will read it, I wanted to write about my latest CV and what it contains more in detail.

Page 1

Here’s my main info. About my education, bachelor, masters x2, and PhD. I also wanted to show selected publications since this is an important aspect of my career so far. Publications are almost a currency in academy, and whether I continue in academy or not, these works show that I am a researcher and that I like to write, create and solve problems. Additionally I show contact details, skills in many areas and languages, human ones at least.

Long ago in 2007 I started the way to a 5 year bachelor program that is so good that it is equivalent to European program where people do 3+2 years and while they end up as “masters” I was still considered a bachelor. Then I started my master in Colombia and before finished I was offered to start an M2 in France. After I finished that master I came back to finish the one in Colombia. This is why The road is displayed like this, I like to tell stories. Also it resembles the branching and merging of version control.

This is my favorite part of the CV. I took it from my thesis defense. All the aspects of being an image analyst and computer scientist and researcher are colorfully displayed in the bottom. Each of those aspects can be covered in the publications and I wanted to show which aspects could be found in each paper, I love this idea I had to basically summarize the paper in a small image. Additionally on the side there is a square containing the type of microscopy image used. Microscopy is an enormous and beautiful field where many different modalities are used.

This is my tool belt. In order to do what I do, a lot of magic is needed. I speak human and computer languages. I also learned how to use the frameworks for Artificial Intelligence but most specifically PyTorch and Scikit-Learn. I use Pandas to store and process my data and I also know how to use MySQl databases although I prefer NoSQL databases like MongoDB. I use, love and promote Linux but I also work on Windows if necessary. As you may know I love and use Blender for everything. I also use other visualization tools like D3 and Seaborn. It’s safe to say I know how to use a lot more software and tools but I haven’t used them professionally or at work but I am a box of surprises.

Finally, easy, the languages. My native language is Spanish but I think one doesn’t ever discover all the wonderful things about a language which is why I leave a little part uncovered. The same for English, I have used it all my life but I am not a native. My impostor syndrome tells me I know less french than I do but the proof is that I lived in France and I studied a master in the language so I must know enough to have managed that at least. I am learning Swedish and it has been a difficult language because I don’t have time anymore, doing a PhD was tough and I had little time but I tried, on my own and with friends and now I finally have time and money to pay for a small group course.

All other pages

Since I will apply to academic positions I need to have a list of publications which is page 2. I add all my other Academic experience in page 3 and work experience in page 4 and since It was a bit white and cold and lonely I put the art I made for my thesis which is quite nice, if I may say so myself.

How to

I have been asked to explain how I do my illustrations and how the whole process goes. So here are some tips. For insights about visualization in general read the last chapter of my thesis, it’s quite short and nicely summarizes everything I think about visualization. I might write a post about it.

I use Inkscape, I only use free and open source tools. Inkscape is a fantastic software for vector graphics and I do all my posters and figures in it, along with GIMP and Blender. I use a lot of shortcuts and I’m quite efficient.

The tools I use the most are:

Fill and stroke

and of course Selection and edit paths by nodes. I really recommend learning key shortcuts. If you want to learn how to use Inkscape let me know. We can talk about it.

Recreate your city in 3D with Blender

In one of my personal projects I wanted to see Uppsala, the city I live in, in 3D. Those who know me know I am a Blenderhead, a Blender die hard fan for reasons I will discuss at some time. But now, how can yo do it by yourself with your own city?

Warning, I actually had to remodel the Cathedral

This was really hard to find, specially open, but I love open stuff and there is OpenStreetmap where you can export an OSM (openstreetmap) file which is some sort of XML file with a lot of information, including where trees and buildings are.

To export a place go to OpenStreetMap and explore, then click export and you will get the longitude and latitude borders of your area. If the area is to big you will have a very big file! obviously! so be careful.

After you get your OSM file you need to convert it to something to open on Blender.

Some german hero created a software called osm2world that can convert OSM to OBJ which is a format that Blender can open. I found it a tad difficult to use but it’s amazing that it has java executables for any operative system, mine is Linux (obviously).

I run it in a console using

java -Xmx2G -jar OSM2World.jar -i input.osm -o output.obj

And it’s as easy as that now you have an OBJ that you can open in Blender like this:

But of course it is not all puppies and rainbows, buildings might not be perfectly modeled and color can be lost, and there is a clutter of things that I didn’t want to see, I don’t care about little benches or traffic lights and many more things that were not correctly placed, not correctly modeled and don’t really add much since I won’t be visiting with that level of detail. I just wanted a panoramic view.

So how do you get rid of all these things? depending on how big of an area you exported, you might get different amount of things, maybe you don’t need to clean. But I did and I will show you how and if you want to do it too, I will give you my code.

What is OBJ

Wavefront .OBJ is a way to save meshes (vertices, edges, faces and color) in plain text, you can open it in a text editor and see what is inside. You can group vertices and edges and name these groups as something recognizable, that you could delete. But given the organization of the file you can’t just delete the text you have to rearrange all the vertices and edges and faces which was an absolute nightmare for me.

Wonderful people who believe in open source create software every now and then that can do things like this, but sometimes they are overkill for a small task, sometimes they don’t work as you intended and I am all up for programming my own things, be them complex or simple. So I made a script that finds all objects, removes all the undesired objects by name and then rearranges all the vertices again and produces a clean OBJ to import in Blender. Mind you, it’s not perfect and could be better but it worked for my purposes so that’s the end of it. You can find the code here.

So now can I see my city please? Yes sure, here it is, ugly buildings and all.

This is NOT what the Uppsala Cathedral looks like

Playing with Blender and architecture

I will not be teaching you Blender here but if you invite me a coffee I might tell you about it. How ever if you are not seeing all your city it might be that you need to expand your view in Blender if the city is too big you can do this in a menu that appears pressing N or by dragging a little cross in the upper right side of the viewport, here you can select to clip the view at a larger distance.

So to model the cathedral (which was a hard task) I wanted to find real blueprints of the building and it was tough because I had to do ti in swedish (which I do not yet master) but a friend helped me by giving me some tips. She works in digital humanities so she knows her stuff.

She told me to search in ALVIN which is a platform for digital collections and digitized cultural heritage. I searched in Alvin and in google for the words

Uppsala domkyrka, domkyrkoarkitekt, ritning, planritning

And eventually found some good examples:

References for modelling the Domkyrka

So my recommendation becomes to know where to search for blueprints and historical archives and speak the language of where you are searching history from.

Anyways, I played with the depth of field with the f-stop the focal length and placing the camera around and with a simple white material on everything I made these two things.

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