From ba0461d4cc6874eed3cae2157e733734346369e1 Mon Sep 17 00:00:00 2001 From: Simon Brooke Date: Thu, 2 May 2024 14:14:28 +0100 Subject: [PATCH] First commit. Currently generating random genomes, and reading features from genomes, successfully. Generating parented genomes doesn't seem to be working perfectly. --- CHANGELOG.md | 24 ++ LICENSE.md | 361 ++++++++++++++++++ README.md | 93 +++++ doc/intro.md | 3 + project.clj | 14 + src/cc/journeyman/simulated_genetics/core.clj | 7 + .../journeyman/simulated_genetics/genome.clj | 78 ++++ .../journeyman/simulated_genetics/utils.clj | 35 ++ 8 files changed, 615 insertions(+) create mode 100644 CHANGELOG.md create mode 100644 LICENSE.md create mode 100644 README.md create mode 100644 doc/intro.md create mode 100644 project.clj create mode 100644 src/cc/journeyman/simulated_genetics/core.clj create mode 100644 src/cc/journeyman/simulated_genetics/genome.clj create mode 100644 src/cc/journeyman/simulated_genetics/utils.clj diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..2c74db1 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,24 @@ +# Change Log +All notable changes to this project will be documented in this file. This change log follows the conventions of [keepachangelog.com](http://keepachangelog.com/). + +## [Unreleased] +### Changed +- Add a new arity to `make-widget-async` to provide a different widget shape. + +## [0.1.1] - 2024-04-29 +### Changed +- Documentation on how to make the widgets. + +### Removed +- `make-widget-sync` - we're all async, all the time. + +### Fixed +- Fixed widget maker to keep working when daylight savings switches over. + +## 0.1.0 - 2024-04-29 +### Added +- Files from the new template. +- Widget maker public API - `make-widget-sync`. + +[Unreleased]: https://sourcehost.site/your-name/simulated-genetics/compare/0.1.1...HEAD +[0.1.1]: https://sourcehost.site/your-name/simulated-genetics/compare/0.1.0...0.1.1 diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..8147eb0 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,361 @@ +### GNU GENERAL PUBLIC LICENSE + +Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc. + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + +### Preamble + +The licenses for most software are designed to take away your freedom +to share and change it. 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See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +Also add information on how to contact you by electronic and paper +mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details + type `show w'. This is free software, and you are welcome + to redistribute it under certain conditions; type `show c' + for details. + +The hypothetical commands \`show w' and \`show c' should show the +appropriate parts of the General Public License. Of course, the +commands you use may be called something other than \`show w' and +\`show c'; they could even be mouse-clicks or menu items--whatever +suits your program. + +You should also get your employer (if you work as a programmer) or +your school, if any, to sign a "copyright disclaimer" for the program, +if necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright + interest in the program `Gnomovision' + (which makes passes at compilers) written + by James Hacker. + + signature of Ty Coon, 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, +you may consider it more useful to permit linking proprietary +applications with the library. If this is what you want to do, use the +[GNU Lesser General Public +License](https://www.gnu.org/licenses/lgpl.html) instead of this +License. diff --git a/README.md b/README.md new file mode 100644 index 0000000..7052da2 --- /dev/null +++ b/README.md @@ -0,0 +1,93 @@ +# simulated-genetics + +A clojure library (OK, at this moment it's an app, but that's during development only) to generate character models for games, such that characters who are represented as related to one another will have systematically similar appearance, as creatures of natural species (including humans) do. This is specifically **NOT** simulating genetics on any deep or quasi-scientific level, just experimenting to see how adequate a solution can be achieved with simple code and limited data. + +## Status + +Very pre-alpha. + +## Concept + +If we're going to have a world with a multi-generational population of hundreds of thousands of procedurally generated characters, and we're to persuasively represent each character as being related to others, then we have to have a mechanism for making children look reasonably like their parents, to have family resemblances among cousins, and so on. We need to do this at reasonably low data storage and algorithmic cost, firstly because we have to store all these characters, and secondly because (especially when the player approaches an urban centre), we may need to instantiate models for a lot of them in limited time. + +This note discusses how this might be done. + +### The pseudo-genome + +Suppose we have a binary vector of memory, such that when a 'child' was born to two parents, bits were taken at random from the parents' chromosomes to populate the child's genome -- which is sort of, very roughly, what happens in actual biology -- how big would that genome have to be? After all, the full data size of the human genetic code is enormous. But actually, we don't need to simulate anything like so large. After all, all our genome needs to encode is morphology, and only sufficiently to enable the player to recognise and distinguish characters. + +My hunch is that a 64 bit genome is more than sufficient, if we code it carefully. So here's how such a genome might be structured: + +| Field | Bits | Interpretation | +| -------------------- | ---- | ------------------------------------------------------------ | +| Ethnic type | 4 | Ethnic type. Most significant bits both indicate dark skin, with [??11] indicating dark skin/curly hair and [??01] indicating dark skin/straight hair | +| Skin tone | 3 | Plus most significant bit from ethnic type (i.e. [???1]) as most significant bit. This means sixteen distinct tones, with the darkest tone of 'pale skinned' ethnicities just very slightly lighter than the palest tone of 'dark skinned' ethnicities. | +| Freckles? | 2 | [11] means freckles, any other value means no freckles. Freckles won't be visible on very dark skin. | +| Hair colour | 3 | Plus most significant bit from ethnic type (i.e. [???1]) as most significant bit. Least significant bit does not contribute to tone but indicates red tint. Thus eight distinct degrees of darkness from pale blond to black, plus red tint which can affect any degree of darkness. | +| Eye colour | 2 | Plus most significant bit from ethnic type (i.e. [???1]) as most significant bit. Thus eight values: [000] blue; [001] hazel; [010]...[111] shades of brown lighter->darker. | +| Height | 3 | Height when adult; children will have a scaled proportion of their adult height, and the same height value in the genome will result in female body models 95% the height of an equivalent male body model. So [000] codes for 150mm, [111] codes for 200mm, with eight distinct values | +| Gracility/Robustness | 3 | Slenderness to stockiness of skeleton/armature build, with [000] being very slender and [111] being very broad/heavy. | +| Age-related change | 3 | People get white haired at different ages; some men go bald and some do not. The sons of the daughter of a bald man should have a chance of inheriting age-related baldness, although their mother won't express that gene. So I'm allowing here for eight different profiles for age related change, although I'm not yet clear what the exact values would mean. | + +That's twenty-nine of our sixty-four bits, leaving plenty for face models, gender + +### What's not included in the genome + +Things which are cultural are not included in the genome; things which are lifestyle related are not included in the genome. So, for example, gracility/robustness, is not the same as skinniness/fatness, which are mostly lifestyle/diet related rather than genetic. There are some occupations (e.g., blacksmith) where you'd be unlikely to be fat (but might be very robust). Also, the same character might grow fatter (or thinner) over time. + +Similarly, hairstyle and beard-wearing are cultural (and occupational) rather than genetic, and closely related to choice of clothing. So while we do need to represent these things, they're not things which should be represented in the genome. + +Injury-related change -- which would especially affect soldiers and outlaws especially but could affect any character -- also needs to be encoded somehow (and may cause real problems), but this is also not a problem for the genome. + +### What additionally might be included in the pseudo-genome + +There is a variable I'm proposing for non-player characters that I'm calling `disposition`, which has a range of values between -5 (surly) and +5 (sunny), which stands in for the general friendliness of the character towards random strangers, their generosity, their optimism, their degree of compassion, and so on. I don't personally believe these things are genetic -- I believe they're nurture, not nature -- but I believe that they are nevertheless inherited through families to some extent. + +If we made a character's setting for `disposition` a function of their parents' dispositions, then that would need to be an entirely unrelated value from the physical appearance values, because otherwise you would end up having some racial appearances being friendlier and more optimistic than others, which would lead to accusations of racism and other bad things. This is simulated genetics, not simulated phrenology! + +I mean, you may be planning the sort of game in which there are races like orcs or kobolds or whatever which are systematically less friendly and generous than characters of other races, in which case you might want to fork this library and change this decision, but if so: + +a. that's on you; and +b. I politely suggest that you might want to examine your own attitudes. + +### Making this all work + +**NOTE:** At this stage none of this works. + +[MakeHuman](http://www.makehumancommunity.org/) exposes an [API](https://github.com/makehumancommunity/community-plugins-mhapi/blob/master/docs/MHAPI.md) which allows at least many of the morphological changes required by the pseudo-genome to be applied to a human model. + +There's a well regarded library, [libpython-clj](https://www.futurile.net/2020/02/20/python-from-clojure-with-libpython-clj/), which allows calling of Python code from Clojure code. So in theory it should be possible to make this work. + +If not, there are other human-model-morphing libraries out there, e.g. [ManuelBastioniLab](https://mb-lab-community.github.io/MB-Lab.github.io/), but they're mainly also in Python. In the worst case, the heavy lifting is in the data, and it might be possible to rewrite the code thatmorphs the data into Clojure. However, development of ManuelBastioniLAB [ceased in 2018](https://www.cgchannel.com/2018/11/manuel-bastioni-to-discontinue-manuel-bastioni-lab/), and although there are forks available on GitHub and elsewhere, none of them seem to be active. + +## Installation + +You can't, it doesn't (yet) work. + +## Usage + +FIXME: explanation + + $ java -jar simulated-genetics-0.1.0-standalone.jar [args] + +## Options + +FIXME: listing of options this app accepts. + +## Examples + +... + +### Bugs + +... + +### Any Other Sections +### That You Think +### Might be Useful + +## License + +Copyright © 2024 Simon Brooke + +This Source Code is made available under the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version, with the GNU Classpath Exception which is available at https://www.gnu.org/software/classpath/license.html. diff --git a/doc/intro.md b/doc/intro.md new file mode 100644 index 0000000..7d6f796 --- /dev/null +++ b/doc/intro.md @@ -0,0 +1,3 @@ +# Introduction to simulated-genetics + +TODO: write [great documentation](http://jacobian.org/writing/what-to-write/) diff --git a/project.clj b/project.clj new file mode 100644 index 0000000..db417cc --- /dev/null +++ b/project.clj @@ -0,0 +1,14 @@ +(defproject simulated-genetics "0.1.0-SNAPSHOT" + :description "A lightweight simulation of genetics, for use in games only." + :url "http://example.com/FIXME" + :license {:name "GNU General Public License,version 2.0 or (at your option) any later version" + :url "https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html"} + :dependencies [[cnuernber/libpython-clj "1.33"] + [com.taoensso/telemere "1.0.0-beta3"] ;; Peter Taoussanis' new replacement for Timbre + [org.clojure/clojure "1.11.1"] + [org.jmonkeyengine/jme3-core "3.6.1-stable"] + [cnuernber/libpython-clj "1.36"]] + :main ^:skip-aot cc.journeyman.simulated-genetics.core + :target-path "target/%s" + :profiles {:uberjar {:aot :all + :jvm-opts ["-Dclojure.compiler.direct-linking=true"]}}) diff --git a/src/cc/journeyman/simulated_genetics/core.clj b/src/cc/journeyman/simulated_genetics/core.clj new file mode 100644 index 0000000..67f314e --- /dev/null +++ b/src/cc/journeyman/simulated_genetics/core.clj @@ -0,0 +1,7 @@ +(ns cc.journeyman.simulated-genetics.core + (:gen-class)) + +(defn -main + "I don't do a whole lot ... yet." + [& args] + (println "Hello, World!")) diff --git a/src/cc/journeyman/simulated_genetics/genome.clj b/src/cc/journeyman/simulated_genetics/genome.clj new file mode 100644 index 0000000..fe63f87 --- /dev/null +++ b/src/cc/journeyman/simulated_genetics/genome.clj @@ -0,0 +1,78 @@ +(ns cc.journeyman.simulated-genetics.genome + "lightweight simulation of a genome." + (:require [cc.journeyman.simulated-genetics.utils :refer [bits-in-genome create-mask long-from-binary-string]] + [clojure.math :refer [pow]] + [taoensso.telemere :refer [error! trace!]])) + +;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; +;;;; +;;;; Genome: create, combine, and extract features from a pseudo-genome. +;;;; +;;;; This program is free software; you can redistribute it and/or +;;;; modify it under the terms of the GNU General Public License +;;;; as published by the Free Software Foundation; either version 2 +;;;; of the License, or (at your option) any later version. +;;;; +;;;; This program is distributed in the hope that it will be useful, +;;;; but WITHOUT ANY WARRANTY; without even the implied warranty of +;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;;; GNU General Public License for more details. +;;;; +;;;; You should have received a copy of the GNU General Public License +;;;; along with this program; if not, write to the Free Software +;;;; Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, +;;;; USA. +;;;; +;;;; Copyright (C) 2024 Simon Brooke +;;;; +;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; + + +(defmacro rand-genome + "Create a random genome." + [] + `(long (rand (dec (pow 2 bits-in-genome))))) ;;Long/MAX_VALUE))) ;; + +(defn create-genome + "Create a new genome; if `father` and `mother` are passed, the result will + comprise bits taken randomly from those genomes." + ([] + (create-genome (rand-genome) (rand-genome))) + ([^Long father ^Long mother] + (let [mask (rand-genome)] + (trace! (format "Parents are %s, %s; mask is %s" + (Long/toBinaryString father) + (Long/toBinaryString mother) + (Long/toBinaryString mask))) + (bit-or (bit-and father mask) (bit-and (bit-not mother) mask))))) + +(defn extract-bits + "Extract, as an integer left-shifted by `start`, those bits from `g` indexed + from `start` (inclusive) to `end` (exclusive)." + [^Long g ^Long start ^Long end] + (let [mask (trace! (create-mask start end))] + (bit-shift-right (bit-and g mask) (- bits-in-genome end)))) + +(defmacro ethnically-biased-feature-index + [genome start end] + `(+ (extract-bits ~genome ~start ~end) + (if (bit-test ~genome 3) + (int (pow (- ~end ~start) 2)) + 0))) + + +(defn expand-genome + [^Long genome] + {:ethnic-type (extract-bits genome 0 4) + :skin-tone (+ (extract-bits genome 4 7) (if (bit-test genome 3) 4 0) 2) + :freckles? (= (extract-bits genome 8 10) 3) + :hair-colour (nth [:blonde :red :russet :cognac :chestnut :coffee :dark-brown :black] + (ethnically-biased-feature-index genome 11 13)) + :eye-colour (nth [:blue :hazel :russet :cognac :chestnut :coffee :dark-brown :black] + (ethnically-biased-feature-index genome 14 16)) + :height (+ 150 (* (extract-bits genome 17 20) 6)) + :robustness (extract-bits genome 21 23) + :aging (extract-bits genome 24 27) + :gender (if (bit-test genome 27) :male :female) + ;; face stuff + }) \ No newline at end of file diff --git a/src/cc/journeyman/simulated_genetics/utils.clj b/src/cc/journeyman/simulated_genetics/utils.clj new file mode 100644 index 0000000..e25e197 --- /dev/null +++ b/src/cc/journeyman/simulated_genetics/utils.clj @@ -0,0 +1,35 @@ +(ns cc.journeyman.simulated-genetics.utils + (:require [taoensso.telemere :refer [error! trace!]])) + +(def ^:const bits-in-genome + "Number of bits we're actually using. **NOTE THAT** as this implementation + is based on Java longs, this number must not be more than 63 or else we've + *a lot* of rewriting to do." + 32) + + +(defn long-from-binary-string + "Mainly for testing, create a long from this binary string. The string is + expected to comprise zeros and ones, only." + [s] + (if (every? #{\0 \1} s) + (Long/parseLong s 2) + (throw (ex-info "Not a binary string" {:s s})))) + +(defn create-binary-string-mask + "Mainly for testing, create a binary string mask with those bits indexed + from `start` (inclusive) to `end` (exclusive) set, and all others cleared." + [start end] + (apply str (concat + (repeat start "0") + (repeat (- end start) "1") + (repeat (- bits-in-genome end) "0") + ))) + +(defn create-mask + "Create a with those bits indexed from `start` (inclusive) to `end` (exclusive) + set, and all others cleared." + ;; TODO TODO: This **really** needs not to go via string representation! + [start end] + (let [s (trace! (create-binary-string-mask start end))] + (long-from-binary-string s)))