ATOR (Arc-Team Open Research).
The blog spreads tests, problems and results of Arc-Team research in archaeology, following the guidelines of the OpArc (Open Archaeology) project.
Graduated
symbolology for vector layers is largely used in archaeology, e.g. for
classifying with different colors, dimensions or symbols excavation
grids, survey's squares, site points, etc.
The
graduated symbology is built by the “classification” of a numeric
variable: for example, if we have an excavation grid of 60 squares that
register the weight of finds for each of them, vector layer
classification consists of defining the number of weight's classes (e.g.
5), intervals in which data are grouped (0-10 g, 11-20 g, 21-30 g,
etc.) and colors or symbols representing each class.
This
classification may be different depending on the different mathematical
and statistical method applied. Different classification methods yield
different results, as you can see in this picture:
In order to using the proper classification method is necessary to know the shape of frequency distribution that the variable we want to classify assumes: for uniform distributions "Equal Interval" or "Pretty Breaks" methods are good; for normal distributions "Standrd Deviation" or "Quantile" methods are better; for bi- or polimodal distributions "Natural Breaks (Jenks)" method is the best choice.
In Archaeology exponential (positive skewed) distributions are frequent. Here you can see an example of exponential distribution of data:
When we deal with an exponential distribution of our data, the proper classification method is "Geometric Intervals" (Dent B. D. 1999, Cartography. Thematic Map Design. Fifth Edition, London, pp. 146; 406. Conolly J., Lake M. 2006, Geographical Information Systems in Archaeology, Cambridge, pp. 141-145).
As
far as I know, GIS FLOSS (QGIS, GRASS, gvSIG, Openjump, Saga, etc.)
don't include this classification method. I tried to develop it for QGIS
using the opportunities provided by its Console Python.
Here I would like to post an example of usage step by step:
1.
Open geometric_class.py in a text editor and modify your variables
(field of numeric data to classify and number of classes). Save the
modified file.
2. In QGIS load your shapefile, select it and open "CONSOLE PYTHON" from Plugin. In Console type:
Press
ENTER (1) and then UPDATE button in QGIS toolbar (2). Open Vector Style
Manager (double click on your vector layer) for viewing legend and
changing color ramp (3).
3. The resulting map should look like this:
Remember that my script isunder development andin need of improvementand testing: use it without warranties! Test and suggestions are welcome.
Face of a
reconstruction turning into an Australopithecus afarensis.
Model originally created in MakeHuman and Blender later deformed with
ShapeKeys. Animated GIF and effects generated with Imagemagick.
I remember in late 2011 I bought a classic book called Forensic Art Art & Illustration. After studying the process of facial reconstruction I decided to apply it on a skull acquired from a CT scan, and to my happiness, it all went successful.
The year 2012 was prolific in reconstructing faces, and by 2013 I developed a methodology for facial reconstruction based on pre-structured models, in partnership with Dr. Paulo Miamoto. We aimed at a more rapid completion of work and more than that, we also in thought about providing the beginner with the ability to make their own reconstructions without the need to study for years in order to develop the mastery of sculpting a 3D face digitally.
Face adapted from a
photo background view. The goal was to only define the volumetric
shape, without setting beard, hair and accessories. The terracotta
face on the left is the standard model of MakeHuman.
Even with the development of a pre-configured template, the task of revealing faces from skulls was still difficult for those who were starting and it forced us to look for more reasonable alternatives. That's when MakeHuman appeared.
First of all it must be explained how our "assembly line" of faces works. Initially I get a skull, usually without much information. When I say "get a skull" in fact it is either a CT or a laser scan. Then I send the material to Dr. Miamoto, who observes it and estimates the sex, age and the ancestry of the individual, based on knowledge from forensic protocols.
Face adaptation in
MakeHuman, using a background image as a reference.
For many months, Dr. Miamoto and I did hours and hours of virtual meetings, so called "hangouts", in which we exchanged information. He handed me knowledge inherent to Forensic Dentistry and Anthropology and I taught him how to use 3D computer graphics open software. Gradually he learned the processes, and started handing me the skull aligned and with the soft tissue markers placed (those little pegs on the surface of the skull that are estimates of the thickness of the skin, fat and muscle in the region).
Just the fact that he handed me this stage of work already done quickened the wprkflow considerably. Our challenge became another step... the basic modeling of the face. Even with all the knowledge gained in computer graphics, Dr. Miamoto saw himself struggling to handle the template we had developed, because even though it was preset, handling it demanded a some ability of the user, which could only be gained by many months of dedication.
The luck turned to our side at the moment I received the news of the new version of the free software MakeHuman. Not that I had not used it before, in fact I knew it fairly well, but I didn't find it very suitable in previous versions, due to some incompatibilities on importation of human models in Blender. However, as I tested the scripts provided by the developers I had a pleasant surprise as I realized that everything worked perfectly.
For those unfamiliar, we can sey long story short that MakeHuman is a "human factory" tool. When we open the software we are presented to a standard model which may be adapted to any gender, age or ancestry just by manipulating a series of attributes intuitively organized into its interface. Everything visually and in real time.
In theory we can create any type of human being, and the most interesting is that given its ease of use, anyone can operate it in a few minutes.
The idea that came to mind was that, as Dr. Miamoto had dominated the first part of the process he could also set up the model based on the anthropological profile assessed from the skull, and send me the file so that I would use it to adapt the shape defined by skull itself, the markers in the nasal tissue and other projections.
The first test I did was with a skull that I had reconstructed two years ago. I sent the skull, he observed it and assessed sex, age and ancestry. Then he set up a model in MakeHuman based on the data collected and clues provided by the skull. Once finished he sent it to me via email.
Back in 2012 when modeled it from scratch, that face took about 8 hours to be done. By adapting the face according to the data received from Dr. Miamoto it did not take me more than 20 minutes to finish the volumetric face! I was amazed after I imported the mesh that I had done in 2012 and verified that the two were very compatible with each other.
The test was successful, and the more interesting... it was not only the head, but an already articulated whole body, ready to be animated in case it was necessary!
Skull aligned and
profile sketched by Dr. Miamoto
Above, an example of soft tissue pegs being positioned over a skull and then the outline of the profile, made by Dr. Miamoto.
Adaptation process
of the 3D face set in MakeHuman and then imported into Blender, done
by Dr. Miamoto.
After setting up the face of the individual based on the anthropological assessments, he imported the model of MakeHuman into Blender and gradually adapted the facial tissue according to the projections of the profile.
Final stage of the
adaptation of the face profile using as reference the layout of the
profile.
Note that Blender
and other programs are running under Linux. According to him, it made
the job much easier and practical.
Below are some words of Dr. Miamoto himself about MakeHuman and the proposed new methodology for digital facial reconstruction addressed in this post:
Fourth
class of the graduate course in Forensic Dentistry at the Faculty of
Dentistry of Ribeirão Preto (FORP-USP). Classes on forensic facial
reconstruction with open software.
Dr. Miamoto explaining how photography-based 3D scanning works.
Below are some words of Dr. Miamoto himself about MakeHuman and the
proposed new methodology for digital facial reconstruction addressed in
this post:
"In Brazil, increasingly, the postgraduate courses in Forensic Dentistry include in their curriculi contents on forensic facial reconstruction. Generally, students are initiated in the manual technique and soon feel motivated to deepen their knowledge. It's an almost instinctive curiosity about the digital techniques, often with romaticized views (influenced by TV series), in which it is believed that there is an unique software that does all the work and everything is automatic. There are also intimidated views, as if the digital world is an extremely hostile terrain for "outsiders" such as dentists. The partnership that Cicero and I are working, always with the broad support of many partners in Brazil and abroad, helps make teaching beginners the digital techniques reality. The protocol we developed is constantly improving, and undoubtedly MakeHuman constitutes a keystone, which takes the weight of digitally modeling a very coherent face from a few polygons off the back of beginners (and also the experienced). In other words, although artistic skills are and always will be desirable, it is possible to start to work in 3D environment even if one is not an extremely skilled forensic artist. In addition, MakeHuman's intuitive interface combined with its excellent software development also allows for a real demonstration of the key features of each ancestry, differences between sizes and shapes of faces and cranial vaults, development aging of the human body, as well as other nuances of the human variation that are very useful to the teaching of Forensic Dentistry and Forensic Anthropology. By mastering some functions and basic concepts of Blender, the avatar that is imported from MakeHuman can be adapted to the skull with relative ease, while maintaining the characteristics of sex, age and ancestry, providing the student with the crystallization of a technique regarded as very complex or difficult, namely, computerized forensic facial reconstruction. The satisfaction and pride that a student feels when actually modeling a face on the computer is a spark that we believe to be a possible trigger for changes in the panorama of Brazilian forensic science, which certainly has in the motivation and training of its own human resources one of the cornerstones for its growth and consolidation. Thanks to the work of the open source software comunity, new solutions to old problems can be glimpsed, with the advantage of the wide accessibility to tools as well as their low or even nonexistent cost. Long live the open software applied to Forensic Sciences!”
Paulo Eduardo Miamoto Dias, DDS, MDS, PhD CROSP 91.834
To make it an even more interesting task and prove once and for all that the job gets easier, I decided to test the deformation of the model we reconstructed from MakeHuman in a hominid.
I used an Australopithecus afarensis reconstruction, performed a few months ago for shows in Brazil and Italy, as a reference.
Using Blender's shapekey, which allows one to deform an object preserving the information from the original object, it is possible to track the "morph" of the face.
Technically we can convert the model into many other mammals, like a saber-tooth tiger, a mouse etc., not only other hominids.
If we can make such a different adaptation like this, why would the mild conversion of a human face into another be a problem?
The most interesting is that as we deal with open software with shareable content, there is a great possibility of establishing a partnership with MakeHuman's development team to collaborate on this very interesting project, which makes it accessible to the general public this art that is seen as extremely complex, which is the facial modeling.
Breathing the atmosphere of the World Cup, I would say that the kickoff was given, that contacts were made and that now everything depends on a little time and effort to get things to start happening.
See you next post!
Obs.: Thanks to Dr. Miamoto for the translation to English, from the original post in Portuguese.
See the bust of Saint Anthony in realtime 3D. Use the mouse wheel (+- zoom) and the left mouse button to orbit. Link: https://skfb.ly/AssG
Initially Itranscribethepresentation I madein Italyabout the process ofreconstructionand Printbust"del Santo" (The Saint), thenI will sharesome linksand videosstories presentedon websites andTVsfromBrazil, Italy and othercountries(some examplesabove).
Centro Culturale Altinate | San Gaetano (auditorium) - Photo: Il Mattino di Padova
The presentation was madein Italian, in Padua, June 1020:45 hattheCentro CulturaleAltinate|SanGaetano (auditorium). The images representthe slidesand text, obviouslymy words.
The Presentation
Thanks to Dr. Paulo Miamoto for the translation to English and Luca Bezzi and Emma Varotto for the translation to Italian.
Ladies and gentlemen,
First of all, thank you for the attendance of this event. I'm very excited because it is the first time I participate in a presentation outside my country. I apologize for my Italian, which is not very good, not as good as that of my great-grandparents left here, more precisely Cremona, and went to southern Brazil in the late nineteenth century. I hope to honor them today.
I will briefly explain the process of the facial reconstruction, also referred to as approximation, of St. Anthony of Padua, this such notorious person, not only to the Catholic Church, but to History.
My job in this project was to digitally reconstruct the face of the Saint. Without knowing the identity of the individual, I received the skull to be rebuilt scanned in 3D, with the information that it was a male of European ancestry, aged 30-40 years. With these data initially started work cleaning and aligning the point clouds skull in Italian program MeshLab.
Then I converted this cloud of points in a three-dimensional mesh putting it on a scale compatible with 3D printing.
Then I imported the skull in Blender software, in which I positioned it at the Frankfurt plane, an approximate position of a living person's head when standing.
Then, using research data for soft tissue depth, collected in living European men aged 29-39 years and average BMI, digital pegs were positioned on the surface of the 3D skull model, according De Greef and collaborator's study. (2006.)
Using the reference of depth markers and projections from the skull I drew an outline of the individual's face in profile.
For a more consistent anatomical basis, the larger muscles were adapted from a template created in partnership with the OFLAB at USP, the Laboratory of Forensic Anthropology and Odontology, University of São Paulo.
This template is a file of a facial reconstruction that was made from from scratch, which later started to be used it as a base for this type of job. Through its deformation, it is possible to adapt it to any individual's 3D skull, regardless of sex or age.
So, using this template, the skin was deformed until it fit the references of depth markers and projections extracted directly from the skull.
During this process I counted with the aid of Dr. Paulo Eduardo Miamoto Dias, PhD in Forensic Dentistry.
As soon as the skin was adapted, Blender's sculpt mode was used to furrow its surface and evidentiate expression lines. I changed the settings of the template for the hair and beard and adjusted them to individual's anthropological profile. Then I sent images of it to the staff of Arc-Team and the Museum of Anthropology, University of Padua images reconstruction in two versions: with and without hair and beard.
Once the material was received and analyzed, the Italians disclosed the information about the identity of the individual. It was St. Anthony of Padua. I confess that it took me a while to realize who they were talking about. Obviously I was quite perplexed and greatly honored to know I was working on the reconstruction of such an important and notorious face. St. Anthony is the patron of the city that I live in Brazil (Sinop-MT). The hospital I was born in another city (Chapecó-SC) in southern Brazil is named after him. The name of my grandfather is Antonio Pagliari because of the saint and, even the name of the creator of the software used to reconstruct it, Blender 3D, is Antonius Roosendaal, in honor of the saint. Just to mention some examples.
Together with the identity of the famous individual, additional information was also disclosed, regarding his clothes and other relevant health data, as gathered by the Center for Studies Antonianos.
It was told that the saint would have had a stout appearance, due to a hydropsy condition near his death. As I did not have a survey depth of tissue taken in individuals with the same condition, I used data from the De Greef table, but for people with high BMI, in order to simulate this corpulence.
After these adjustments the facial structure, the clothing was modeled, the texture of the skin was set using as reference photographs taken from a 28 year-old man of European ancestry, and finally the hair, eyebrows and beard were set.
Here we can see the final image, approved by the Centro Studi Antoniani.
The 3D model was sent to the Information Technology Center Renato Archer (CTI Campinas), an institution linked to the Ministry of Science, Technology and Innovation in Brazil.
A few adjustments so that the mesh could be printed in 3D were necessary. These adjustments consisted in putting thickness to the bust, adjusting the hair texture and then applying a slightly rugged surface to simulate the volume of the facial hair.
3D model consisted of printing more than 1500 layers one over the other, until the bust was completed. Each layer has the thickness of a paper sheet.
Then it was removed from the powder repository with the aid of a vacuum cleaner. The piece went into an oven where it was heated to 65 ° for a few minutes. Then it was taken for the application of resin to another container. After a few hours drying the piece was finished and ready for transport.
Avail here to thank Dr. Jorge Vicente Lopes da Silva and developers Paulo Amorim and Thiago Franco de Moraes, all them from CTI's Division for 3D Technologies, which enabled us to do this 3D impression through a research partnership that we have for over a year.
The first testsof colorprintingthat were madehadsomecolor problems, gettinga darkerpart ofthe left side oftheface.
To resolvethis problemof color, we decidedto get in touchwith aphotographerin my city, the painterMariBueno.
Mariaccepted the challenge toretouchthe piece, with complete freedomof style.The result was amore homogeneoussurface withcolors and anice shinein the eyesof The Saint. Withthis step, we completedwork onthe presentationof the face.
Thanks everyone for coming to the museum and also for the invitation to come here and explain about the processes involving the facial reconstruction of this important man for the church and for the millions of people who worship him. This reconstruction of the face of a holy man, performed with scientific methods, harmonically placed Science itself and religion side by side. Everything we did was based on appreciation for History, observation of technical protocols and respect for the church. Fortunately we were successful and here we have the result of months of work materialized in a bust, bearing not only technology, but also of faith passed down from generation to generation, over almost eight hundred years, since the life of St. Anthony left his body and entered history.
Thank you very much!
On the Media
See below somelinks tovideos andtexts on thefacial reconstructionof St. Anthonypublishedon websitesofvariouslanguages.
L. Bezzi (Arc-Team), C. Moraes (Arc-Team), N. Carrara (Museo Antropologico dell'Università di Padova), Il volto del Santo. La ricostruzione Facciale Forense di Sant'Antonio di Padova (document in Academia; document in ResearchGate)
we are organizing an open lesson in Padua on 5 June. The title is "Digital bones. Nuove tecnologie al servizio delle discipline archeologiche" ("Digital bones. New technologies for anthropological disciplines") and the topic will be the application of Free/Libre and Open Source Software (FLOSS) to Tanatology in archeology and forensic sciences.
The lesson will be held at 10.00 in the Aula Emiciclo of the Orto Botanico, which is the world's oldest academic botanical garden that is still in its original location, as it was founded in 1545 by the Venetian Republic (so it can be also an occasion to visit to this monument).
The Aula Emiciclo (image in Public Domain form PHAIDRA system)
The speakers will be:
Nicola Carrara (Museum of Anthropology of Padua University), with a general introduction to tanatology
Luca Bezzi (Arc-Team), with a lesson/demonstration of 2D documentation through GIS of funerary contexts
Alessandro Bezzi (Arc-Team), with a lesson/demonstration of 3D documentation through SfM/IBM of funerary contexts
Cicero Moraes (Arc-Team), with a lesson/demonstration of digital forensic facial reconstruction
The attendance is free and during the lesson will be also given a preview of ArcheOS 5 (Theodoric), especially regarding its use for archeoanthropological aspects.
ArcheOS for anthopologists!
For more details and informations, here below is the poster of the lesson.
The poster regarding the lesson
You can also visit the FB event page (connected with the exhibition "FACCE. Imolti volti della storia umana"), where, if interested, you can register for the lesson.
