fix failures to byteswap images (in imageManager and imagepreview)

[openc2e.git] / Creature.cpp

/*
 *  Creature.cpp
 *  openc2e
 *
 *  Created by Alyssa Milburn on Tue May 25 2004.
 *  Copyright (c) 2004-2006 Alyssa Milburn. All rights reserved.
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public
 *  License as published by the Free Software Foundation; either
 *  version 2 of the License, or (at your option) any later version.
 *
 *  This library 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
 *  Lesser General Public License for more details.
 *
 */

#include "Creature.h"
#include "CreatureAgent.h"
#include "World.h"
#include "Catalogue.h"
#include <cmath> // powf
#include "c2eBrain.h"
#include "oldBrain.h"

Creature::Creature(shared_ptr<genomeFile> g, bool is_female, unsigned char _variant, CreatureAgent *a) {
        assert(g);
        genome = g;

        female = is_female;
        genus = 0; // TODO: really, we shouldn't do this, and should instead later assert that a genus was set
        variant = _variant;
        stage = baby;

        assert(a);
        parent = a;
        
        alive = true; // ?
        asleep = false; // ?
        dreaming = false; // ?
        tickage = false;
        zombie = false;

        age = ticks = 0;

        attn = decn = -1;

        for (unsigned int i = 0; i < 5; i++)
                tintinfo[i] = 128;
}

Creature::~Creature() {
}

void Creature::finishInit() {
        processGenes();
}

bool Creature::shouldProcessGene(gene *g) {
        geneFlags &flags = g->header.flags;

        // non-expressed genes are to be ignored
        if (flags.notexpressed) return false;

        // gender-specific genes are only to be processed if they are of this 
        if (flags.femaleonly && !female) return false;
        if (flags.maleonly && female) return false;

        // obviously we only switch on at the stage in question
        if (g->header.switchontime != stage) return false;

        // TODO: header.variant?
        
        return true;
}

void Creature::processGenes() {
        for (vector<gene *>::iterator i = genome->genes.begin(); i != genome->genes.end(); i++) {
                if (shouldProcessGene(*i)) addGene(*i);
        }
}

void oldCreature::processGenes() {
        brain->processGenes();
        Creature::processGenes();
}

void c2eCreature::processGenes() {
        // brain must be processed first (to create loci etc)
        // organs should be processed last, because new ones will be created by normal processGenes()

        brain->processGenes();
        Creature::processGenes();
        for (std::vector<shared_ptr<c2eOrgan> >::iterator x = organs.begin(); x != organs.end(); x++) {
                (*x)->processGenes();
        }
}

void Creature::addGene(gene *g) {
        if (typeid(*g) == typeid(creatureInstinctGene)) {
                unprocessedinstincts.push_back((creatureInstinctGene *)g);
        } else if (typeid(*g) == typeid(creatureGenusGene)) {
                // TODO: mmh, genus changes after setup shouldn't be valid
                genus = ((creatureGenusGene *)g)->genus;
                parent->genus = genus + 1;
        } else if (typeid(*g) == typeid(creaturePigmentGene)) {
                creaturePigmentGene &p = *((creaturePigmentGene *)g);
                // TODO: we don't sanity-check
                tintinfo[p.color] = p.amount;
        } else if (typeid(*g) == typeid(creaturePigmentGene)) {
                creaturePigmentBleedGene &p = *((creaturePigmentBleedGene *)g);
                tintinfo[3] = p.rotation;
                tintinfo[4] = p.swap;
        }
}

void Creature::ageCreature() {
        if (stage >= senile) return; // TODO
        
        stage = (lifestage)((int)stage + 1);
        processGenes();

        assert(parent);
        parent->creatureAged();
#ifndef _CREATURE_STANDALONE    
        world.history.getMoniker(world.history.findMoniker(genome)).addEvent(4, "", ""); // aged event
#endif
}

void Creature::setAsleep(bool a) {
        // TODO: skeletalcreature might need to close eyes? or should that just be done during the skeletal update?
        if (!a && dreaming)
                setDreaming(false);
        asleep = a;
}

void Creature::setDreaming(bool d) {
        if (d && !asleep)
                setAsleep(true);
        dreaming = d;
}

void Creature::born() {
        parent->creatureBorn();

        // TODO: life event?
#ifndef _CREATURE_STANDALONE
        world.history.getMoniker(world.history.findMoniker(genome)).wasBorn();
        world.history.getMoniker(world.history.findMoniker(genome)).addEvent(3, "", ""); // born event, parents..
#endif

        tickage = true;
}

void Creature::die() {
        parent->creatureDied();

        // TODO: life event?
#ifndef _CREATURE_STANDALONE
        world.history.getMoniker(world.history.findMoniker(genome)).hasDied();
        world.history.getMoniker(world.history.findMoniker(genome)).addEvent(7, "", ""); // died event
#endif
        // TODO: disable brain/biochemistry updates
        // force die script
        // TODO: TODO: TODO: this is c2e-specific
        parent->stopScript();
        parent->queueScript(72);
        // skeletalcreature eyes, also? see setAsleep comment
        alive = false;
}

void Creature::tick() {
        ticks++;

        if (!alive) return;

        if (tickage) age++;
}

/*
 * oldCreature contains the shared elements of C1 of C2 (creatures are mostly identical in both games)
 */
oldCreature::oldCreature(shared_ptr<genomeFile> g, bool is_female, unsigned char _variant, CreatureAgent *a) : Creature(g, is_female, _variant, a) {
        biochemticks = 0;
        halflives = 0;
        
        for (unsigned int i = 0; i < 8; i++) floatingloci[i] = 0;
        for (unsigned int i = 0; i < 7; i++) lifestageloci[i] = 0;
        for (unsigned int i = 0; i < 8; i++) involaction[i] = 0;
        for (unsigned int i = 0; i < 256; i++) chemicals[i] = 0;
        
        muscleenergy = 0;
        fertile = pregnant = receptive = 0;
        dead = 0;

        brain = 0; // just in case
}

c1Creature::c1Creature(shared_ptr<genomeFile> g, bool is_female, unsigned char _variant, CreatureAgent *a) : oldCreature(g, is_female, _variant, a) {
        assert(g->getVersion() == 1);

        for (unsigned int i = 0; i < 6; i++) senses[i] = 0;
        for (unsigned int i = 0; i < 8; i++) gaitloci[i] = 0;
        for (unsigned int i = 0; i < 16; i++) drives[i] = 0;
        
        // TODO: chosenagents size

        brain = new oldBrain(this);
        finishInit();
        brain->init();
}

c2Creature::c2Creature(shared_ptr<genomeFile> g, bool is_female, unsigned char _variant, CreatureAgent *a) : oldCreature(g, is_female, _variant, a) {
        assert(g->getVersion() == 2);

        throw creaturesException("You can't create Creatures 2 creatures yet. Bug fuzzie."); // TODO
        
        for (unsigned int i = 0; i < 14; i++) senses[i] = 0;
        for (unsigned int i = 0; i < 16; i++) gaitloci[i] = 0;
        for (unsigned int i = 0; i < 17; i++) drives[i] = 0;

        mutationchance = 0; mutationdegree = 0;

        // TODO: chosenagents size

        brain = new oldBrain(this);
        finishInit();
        brain->init();  
}

c2eCreature::c2eCreature(shared_ptr<genomeFile> g, bool is_female, unsigned char _variant, CreatureAgent *a) : Creature(g, is_female, _variant, a) {
        assert(g->getVersion() == 3);

        for (unsigned int i = 0; i < 256; i++) chemicals[i] = 0.0f;

        // initialise loci
        for (unsigned int i = 0; i < 7; i++) lifestageloci[i] = 0.0f;
        muscleenergy = 0.0f;
        for (unsigned int i = 0; i < 32; i++) floatingloci[i] = 0.0f;
        fertile = pregnant = ovulate = receptive = chanceofmutation = degreeofmutation = 0.0f;
        dead = 0.0f;
        for (unsigned int i = 0; i < 8; i++) involaction[i] = 0.0f;
        for (unsigned int i = 0; i < 16; i++) gaitloci[i] = 0.0f;
        for (unsigned int i = 0; i < 14; i++) senses[i] = 0.0f;
        for (unsigned int i = 0; i < 20; i++) drives[i] = 0.0f;

        for (unsigned int i = 0; i < 8; i++) involactionlatency[i] = 0;

        halflives = 0;

        if (!catalogue.hasTag("Action Script To Neuron Mappings"))
                throw creaturesException("c2eCreature was unable to read the 'Action Script To Neuron Mappings' catalogue tag");
        const std::vector<std::string> &mappinginfotag = catalogue.getTag("Action Script To Neuron Mappings");
        for (std::vector<std::string>::const_iterator i = mappinginfotag.begin(); i != mappinginfotag.end(); i++)
                mappinginfo.push_back(atoi(i->c_str()));

        // TODO: should we really hard-code this?
        chosenagents.resize(40);

        brain = new c2eBrain(this);
        finishInit();
        brain->init();  
}

unsigned int c1Creature::getGait() {
        unsigned int gait = 0;

        for (unsigned int i = 1; i < 8; i++)
                if (gaitloci[i] > gaitloci[gait])
                        gait = i;

        return gait;
}

unsigned int c2Creature::getGait() {
        return 0; // TODO
}

void c1Creature::tick() {
        // TODO: should we tick some things even if dead?
        if (!alive) return;

        senses[0] = 255; // always-on
        senses[1] = (asleep ? 255 : 0); // asleep

        tickBrain();
        tickBiochemistry();

        // lifestage checks
        for (unsigned int i = 0; i < 7; i++) {
                if ((lifestageloci[i] != 0) && (stage == (lifestage)i))
                        ageCreature();
        }

        if (dead != 0) die();

        Creature::tick();
}

void oldCreature::tickBrain() {
        // TODO

        brain->tick();
        
        // TODO
}

unsigned int c2eCreature::getGait() {
        unsigned int gait = 0;

        for (unsigned int i = 1; i < 16; i++)
                if (gaitloci[i] > gaitloci[gait])
                        gait = i;

        return gait;
}

void c2eCreature::tick() {
        // TODO: should we tick some things even if dead?
        if (!alive) return;

        // TODO: update muscleenergy

        senses[0] = 1.0f; // always-on
        senses[1] = (asleep ? 1.0f : 0.0f); // asleep
        // space for old C2 senses: hotness, coldness, light level
        senses[5] = 0.0f; // crowedness (TODO)
        // space for old C2 senses: radiation, time of day, season
        senses[9] = 1.0f; // air quality (TODO)
        senses[10] = 0.0f; // steepness of upcoming slope (up) (TODO)
        senses[11] = 0.0f; // steepness of upcoming slope (down) (TODO)
        // space for old C2 senses: oncoming wind, wind from behind

        tickBrain();
        tickBiochemistry();

        // lifestage checks
        for (unsigned int i = 0; i < 7; i++) {
                if ((lifestageloci[i] != 0.0f) && (stage == (lifestage)i))
                        ageCreature();
        }

        if (dead != 0.0f) die();
        
        Creature::tick();
}

void c2eCreature::tickBrain() {
        if (asleep) {
                attn = -1;
                decn = -1;
                attention.clear(); // TODO: doesn't belong here
                if (!dreaming) return; // TODO
        }

        // TODO: correct timing?
        if ((ticks % 4) != 0)
                return;

        if (dreaming) {
                // TODO: this returns a bool (whether it did an instinct or not), shouldn't we do non-instinct dreaming or something if it's false?
                // .. if not, make it a void ;p
                processInstinct();
                return;
        }

        c2eLobe *drivlobe = brain->getLobeById("driv");
        if (drivlobe) {
                for (unsigned int i = 0; i < 20 && i < drivlobe->getNoNeurons(); i++) {
                        drivlobe->setNeuronInput(i, drives[i]);
                }
        }

        /*c2eLobe *verblobe = brain->getLobeById("verb");
        if (verblobe) {
                for (unsigned int i = 0; i < verblobe->getNoNeurons(); i++) {
                        verblobe->setNeuronInput(i, 0.0f); // TODO
                }
        }
        
        c2eLobe *nounlobe = brain->getLobeById("noun");
        if (nounlobe) {
                for (unsigned int i = 0; i < nounlobe->getNoNeurons(); i++) {
                        nounlobe->setNeuronInput(i, 0.0f); // TODO
                }       
        }*/

#ifndef _CREATURE_STANDALONE    
        // TODO: situ, detl
        
        chooseAgents();
        
        c2eLobe *visnlobe = brain->getLobeById("visn");
        if (visnlobe) {
                for (unsigned int i = 0; i < visnlobe->getNoNeurons() && i < chosenagents.size(); i++) {
                        AgentRef a = chosenagents[i];
                        if (!a) continue;

                        // TODO: use eye position? see Creature::agentInSight
                        float ourxpos = parent->x + (parent->getWidth() / 2.0f);
                        float theirxpos = a->x + (a->getWidth() / 2.0f);
                        float distance = theirxpos - ourxpos;

                        // TODO: squash result into appropriate range?
                        visnlobe->setNeuronInput(i, distance / parent->range.getFloat());
                }
        }

        c2eLobe *smellobe = brain->getLobeById("smel");
        if (smellobe) {
                // TODO
        }
#endif

        brain->tick();
        
#ifndef _CREATURE_STANDALONE    
        AgentRef oldattn = attention;
        int olddecn = decn;

        c2eLobe *attnlobe = brain->getLobeById("attn");
        if (attnlobe) {
                attn = attnlobe->getSpareNeuron();
        }

        c2eLobe *decnlobe = brain->getLobeById("decn");
        if (decnlobe) {
                // TODO: check bounds of mappinginfo
                decn = mappinginfo[decnlobe->getSpareNeuron()];
        }

        // TODO: doesn't belong here
        if (attn >= 0 && attn < (int)chosenagents.size())
                attention = chosenagents[attn];

        if (zombie) return; // TODO: docs say zombies "don't process decision scripts", correct?

        // fire scripts as needed
        // TODO: doesn't belong here
        // TODO: deal with decisions which don't have agents attached
        // TODO: deal with moving between ATTNs which don't have a choseagent right now (eg, nothing in sight)
        if (parent->vmStopped() || oldattn != attention || olddecn != decn) {
                if (attention && dynamic_cast<CreatureAgent *>(attention.get())) {
                        parent->queueScript(decn + 32); // 'on creatures'
                } else {
                        parent->queueScript(decn + 16); // 'on agents'
                }
        }

        // involuntary actions
        for (unsigned int i = 0; i < 8; i++) {
                if (involactionlatency[i] > 0) {
                        involactionlatency[i]--;
                        continue;
                }

                if (involaction[i] > 0.0f) {
                        parent->queueScript(i + 64);
                }
        }
#endif
}

bool c2eCreature::processInstinct() {
        if (unprocessedinstincts.empty()) return false;

        creatureInstinctGene *g = unprocessedinstincts.front();
        unprocessedinstincts.pop_front();

        // *** work out which verb neuron to fire by reverse-mapping from the mapping table
        int actualverb = reverseMapVerbToNeuron(g->action);
        // we have no idea which verb neuron to use, so no instinct processing
        if (actualverb == -1) return false;

        // *** debug output

        /*std::cout << "*** processing instinct for verb #" << actualverb << std::endl;
        std::cout << "reinforce using drive #" << (int)g->drive << " at level " << ((int)g->level - 128) / 128.0f << std::endl;
        for (unsigned int i = 0; i < 3; i++) {
                if (g->lobes[i] != 255) {
                        std::cout << "input: lobe tissue #" << (int)(g->lobes[i] - 1) << ", neuron #" << (int)g->neurons[i] << std::endl;
                }
        }*/

        /*
         * instinct processing! a production by fuzzie in conjunction with coffee
         *
         * this is mostly guesswork because instincts seem to take place in a single tick in the engine,
         * making them pretty difficult to observe
         *
         * we reset the brain by setting pre-REM chemical to full and ticking it once, then we set REM to full
         * and perform two ticks: one with just the inputs set, and once with a response in the 'resp' lobe
         */

        // *** sanity checks/setup

        c2eLobe *resplobe = brain->getLobeById("resp");
        c2eLobe *verblobe = brain->getLobeById("verb");
        // no response/verb lobe? no instincts for you, then..
        if (!resplobe || !verblobe) return false;

        // if action/drive are beyond the size of the relevant lobe, can't process instinct
        if ((unsigned int)actualverb >= verblobe->getNoNeurons()) return false;
        if (g->drive >= resplobe->getNoNeurons()) return false;

        c2eLobe *inputlobe[3] = { 0, 0, 0 };

        for (unsigned int i = 0; i < 3; i++) {
                // TODO: what about unused?
                uint8 lobetissueid = g->lobes[i];
                if (lobetissueid == 255) continue;
                /* fuzzie would like to take this opportunity to quote from the pygenes source:
                 * Apparently, someone decided that because the rows are 1 above the lobe IDs, they should write the ROW NUMBER into the file, instead. Someone, somewhere, needs SHOOTING. */
                lobetissueid -= 1;
                inputlobe[i] = brain->getLobeByTissue(lobetissueid);
                // TODO: should we really barf out if this happens?
                if (!inputlobe[i]) return false;
                if (g->neurons[i] >= inputlobe[i]->getNoNeurons()) return false;
        }

        // *** reset brain
        
        // TODO: is this a sensible place to wipe the lobes?
        for (std::map<std::string, c2eLobe *>::iterator i = brain->lobes.begin(); i != brain->lobes.end(); i++)
                i->second->wipe();

        // TODO: non-hardcode 212/213? they seem to be in "Brain Parameters" catalogue tag
        // TODO: won't learning be sort of ruined by the repeated application of pre-REM?
        chemicals[212] = 1.0f; // pre-REM to full
        chemicals[213] = 0.0f; // REM to null
        brain->tick();
        chemicals[212] = 0.0f; // pre-REM to null
        chemicals[213] = 1.0f; // REM to full

        // *** set inputs and tick

        for (unsigned int i = 0; i < 3; i++) {
                // TODO: eeeevil hack - it looks like this is required, but is there no better way?
                if (g->lobes[i] == 3) {
                        /*
                         * the visn lobe subtracts input from 1.0 to get distance of object, so 1.0 is no good
                         * we use 0.1, like c2e seems to feed it (the joys of hacked genetics and brain-in-a-vat!)
                         */
                        // TODO: shouldn't we check lobe size?
                        c2eLobe *visnlobe = brain->getLobeById("visn");
                        if (visnlobe)
                                visnlobe->setNeuronInput(g->neurons[i], 0.1f);
                }

                if (inputlobe[i])
                        inputlobe[i]->setNeuronInput(g->neurons[i], 1.0f);
        }
        verblobe->setNeuronInput(actualverb, 1.0f);
        brain->tick();

        // *** set response and tick

        // TODO: shouldn't we make sure that decn/attn achieved the desired result?
        // TODO: should we set the input neurons again here? (it seems to work without - fuzzie)

        // TODO: TODO: TODO: check division of g->level!!
        // g->drive seems to be a direct mapping
        resplobe->setNeuronInput(g->drive, ((int)g->level - 128) / 128.0f);
        brain->tick();

        // *** finish off and return

        // TODO: shouldn't REM be present throughout sleep?
        chemicals[213] = 0.0f; // REM to null

        // wipe the lobes again, to stop any issues with neurons being set which shouldn't be at the end of an instinct run
        // TODO: is wiping the lobes here truly what we should do?
        for (std::map<std::string, c2eLobe *>::iterator i = brain->lobes.begin(); i != brain->lobes.end(); i++)
                i->second->wipe();

        //std::cout << "*** instinct done" << std::endl;
        //std::cout << std::endl;

        return true;
}

void oldCreature::addGene(gene *g) {
        Creature::addGene(g);
        if (typeid(*g) == typeid(bioInitialConcentrationGene)) {
                // initialise chemical levels
                bioInitialConcentrationGene *b = (bioInitialConcentrationGene *)(g);
                chemicals[b->chemical] = b->quantity;
        } else if (typeid(*g) == typeid(bioHalfLivesGene)) {
                bioHalfLivesGene *d = dynamic_cast<bioHalfLivesGene *>(g);
                assert(d);
                halflives = d;
        }       
}

void c1Creature::addGene(gene *g) {
        oldCreature::addGene(g);

        if (typeid(*g) == typeid(bioReactionGene)) {
                reactions.push_back(shared_ptr<c1Reaction>(new c1Reaction()));
                reactions.back()->init((bioReactionGene *)(g));
        } else if (typeid(*g) == typeid(bioEmitterGene)) {
                emitters.push_back(c1Emitter());
                emitters.back().init((bioEmitterGene *)(g), this);
        } else if (typeid(*g) == typeid(bioReceptorGene)) {
                receptors.push_back(c1Receptor());
                receptors.back().init((bioReceptorGene *)(g), this);
        }
}

void c2eCreature::addGene(gene *g) {
        Creature::addGene(g);

        if (typeid(*g) == typeid(bioInitialConcentrationGene)) {
                // initialise chemical levels
                bioInitialConcentrationGene *b = (bioInitialConcentrationGene *)(g);
                chemicals[b->chemical] = b->quantity / 255.0f; // TODO: correctness unchecked
        } else if (typeid(*g) == typeid(organGene)) {
                // create organ
                organGene *o = dynamic_cast<organGene *>(g);
                assert(o);
                if (!o->isBrain()) { // TODO: handle brain organ
                        organs.push_back(shared_ptr<c2eOrgan>(new c2eOrgan(this, o)));
                }
        } else if (typeid(*g) == typeid(bioHalfLivesGene)) {
                bioHalfLivesGene *d = dynamic_cast<bioHalfLivesGene *>(g);
                assert(d);
                halflives = d;
        }
}

void oldCreature::addChemical(unsigned char id, unsigned char val) {
        if (id == 0) return;

        // clipping..
        if ((int)chemicals[id] + val > 255) chemicals[id] = 255;
        else chemicals[id] += val;
}

void oldCreature::subChemical(unsigned char id, unsigned char val) {
        if (id == 0) return;

        // clipping..
        if ((int)chemicals[id] - val < 0) chemicals[id] = 0;
        else chemicals[id] -= val;
}

void c2eCreature::adjustChemical(unsigned char id, float value) {
        if (id == 0) return;
        
        chemicals[id] += value;

        if (chemicals[id] < 0.0f) chemicals[id] = 0.0f;
        else if (chemicals[id] > 1.0f) chemicals[id] = 1.0f;
}

void c2eCreature::adjustDrive(unsigned int id, float value) {
        assert(id < 20);
        drives[id] += value;

        if (drives[id] < 0.0f) drives[id] = 0.0f;
        else if (drives[id] > 1.0f) drives[id] = 1.0f;
}

// lookup table, snaffled from real creatures
// TODO: work out if these are meaningful values :)
unsigned int c1rates[32] = {
        0, 0x32A5, 0x71DD, 0xAABB, 0xD110, 0xE758, 0xF35C,
        0xF999, 0xF999, 0xF999, 0xF999, 0xF999, 0xF999, 0xF999, 0xF999,
        0xF999, 0xF999, 0xF999, 0xF999, 0xF999, 0xF999, 0xF999, 0xF999,
        0xF999, 0xF999, 0xF999, 0xF999, 0xF999, 0xF999, 0xF999, 0xF999,
        0xFFFF
};

inline unsigned int oldCreature::calculateMultiplier(unsigned char rate) {
        return c1rates[rate];
}

inline unsigned int oldCreature::calculateTickMask(unsigned char rate) {
        if (rate < 7) return 0;
        else return (1 << ((unsigned int)rate - 7)) - 1;
}

void c1Creature::tickBiochemistry() {
        // TODO: untested

        if ((ticks % 5) != 0) return;

        // process emitters
        for (std::vector<c1Emitter>::iterator i = emitters.begin(); i != emitters.end(); i++) {
                processEmitter(*i);
        }

        // process receptors
        for (std::vector<c1Receptor>::iterator i = receptors.begin(); i != receptors.end(); i++) {
                processReceptor(*i);
        }

        // process reactions
        for (std::vector<shared_ptr<c1Reaction> >::iterator i = reactions.begin(); i != reactions.end(); i++) {
                processReaction(**i);
        }

        oldCreature::tickBiochemistry();
}

void oldCreature::tickBiochemistry() {
        // process half-lives
        if (!halflives) return; // TODO: correct?
        for (unsigned int i = 0; i < 256; i++) {
                // TODO: this code hasn't been tested thoroughly, but seems to agree with basic testing

                // work out which rate we're dealing with
                unsigned char rate = halflives->halflives[i] / 8;
        
                // if the tickmask doesn't want us to change things this tick, don't!
                if ((biochemticks & calculateTickMask(rate)) != 0) continue;

                // do the actual adjustment
                chemicals[i] = (chemicals[i] * calculateMultiplier(rate)) / 65536;
        }
        
        biochemticks++;
}

void c2eCreature::tickBiochemistry() {
        // only process biochem every 4 ticks
        // TODO: correct? should probably apply to brain too, at least
        if ((ticks % 4) != 0) return;
        
        // tick organs
        for (std::vector<shared_ptr<c2eOrgan> >::iterator x = organs.begin(); x != organs.end(); x++) {
                (*x)->tick();
        }

        // process half-lives for chemicals
        if (!halflives) return; // TODO: correct?
        for (unsigned int x = 0; x < 256; x++) {
                if (halflives->halflives[x] == 0) {
                        // 0 is a special case for half-lives
                        chemicals[x] = 0.0f;
                } else {
                        // reaction rate = 1.0 - 0.5**(1.0 / 2.2**(rate * 32.0 / 255.0))
                        float rate = 1.0 - powf(0.5, 1.0 / powf(2.2, (halflives->halflives[x] * 32.0) / 255.0));

                        chemicals[x] -= chemicals[x] * rate;
                }
        }
}

unsigned char *c1Creature::getLocusPointer(bool receptor, unsigned char o, unsigned char t, unsigned char l) {
        switch (o) {
                case 0: // brain
                        return 0; // TODO

                case 1: // creature
                        switch (t) {
                                case 0: // somantic
                                        if (receptor) {
                                                if (l > 7) break;
                                                return &lifestageloci[l];
                                        } else if (l == 0) return &muscleenergy;
                                        break;

                                case 1: // circulatory
                                        if (l > 8) break;
                                        return &floatingloci[l];
                                
                                case 2: // reproductive
                                        if (receptor) {
                                                if (l == 0) return &fertile;
                                                else if (l == 1) return &receptive;
                                        } else {
                                                if (l == 0) return &fertile;
                                                else if (l == 1) return &pregnant;
                                        }
                                        break;

                                case 3: // immune
                                        if (l == 0) return &dead;
                                        break;

                                case 4: // sensorimotor
                                        if (receptor) {
                                                if (l < 8) return &involaction[l];
                                                else if (l < 16) return &gaitloci[l - 8];
                                        } else {
                                                if (l < 6) return &senses[l];
                                        }
                                        break; // TODO: should this break be here? added it, but can't check, no internet

                                case 5: // drive levels
                                        if (l < 16) return &drives[l];
                        }
        }

        std::cout << "c1Creature::getLocusPointer failed to interpret locus (" << (int)o << ", "
                << (int)t << ", " << (int)l << ") of " << (receptor ? "receptor" : "emitter")
                << std::endl;

        return 0;
}

float *c2eCreature::getLocusPointer(bool receptor, unsigned char o, unsigned char t, unsigned char l) {
        switch (o) {
                case 0: // brain
                        {
                        c2eLobe *lobe = brain->getLobeByTissue(t);
                        if (!lobe) break;

                        unsigned int neuronid = o/3, stateno = o%3;
                        if (neuronid >= lobe->getNoNeurons()) break;
                        return &lobe->getNeuron(neuronid)->variables[stateno];
                        }

                case 1: // creature
                        switch (t) {
                                case 0: // somatic
                                        if (receptor) {
                                                if (l > 6) break;
                                                return &lifestageloci[l];
                                        } else if (l == 0) return &muscleenergy;
                                        break;

                                case 1: // circulatory
                                        if (l > 31) break;
                                        return &floatingloci[l];

                                case 2: // reproductive
                                        { int val = l;

                                        if (!receptor) { // emitter
                                                if (l == 0) return &fertile;
                                                else if (l == 1) return &pregnant;
                                                val = l - 2;
                                        }

                                        switch (val) {
                                                case 0: return &ovulate;
                                                case 1: return &receptive;
                                                case 2: return &chanceofmutation;
                                                case 3: return &degreeofmutation;
                                        } }
                                        break;
                                        
                                case 3: // immune
                                        if (l == 0) return &dead;
                                        break;
                                
                                case 4: // sensorimotor
                                        { int val = l;

                                        if (!receptor) { // emitter
                                                if (val < 14) return &senses[val];
                                                val -= 14;
                                        }
                                        if (val < 8) return &involaction[val];
                                        val -= 8;
                                        if (val < 16) return &gaitloci[val];
                                        }
                                        break;

                                case 5: // drives
                                        if (l < 20) return &drives[l];
                                        break;
                        }

        }

        std::cout << "c2eCreature::getLocusPointer failed to interpret locus (" << (int)o << ", "
                << (int)t << ", " << (int)l << ") of " << (receptor ? "receptor" : "emitter")
                << std::endl;
        return 0;
}
 
/*****************************************************************************/

c2eOrgan::c2eOrgan(c2eCreature *p, organGene *g) {
        parent = p; assert(parent);
        ourGene = g; assert(ourGene);
        lifeforce = ourGene->lifeforce * (1000000.0f / 255.0f);
        longtermlifeforce = shorttermlifeforce = lifeforce;

        repairrate = 0.0f;
        clockrate = ourGene->clockrate / 255.0f;
        injurytoapply = 0.0f;
        damagerate = ourGene->damagerate / 255.0f;
        biotick = ourGene->biotickstart / 255.0f;
        atpdamagecoefficient = ourGene->atpdamagecoefficient * (lifeforce / (255.0f * 255.0f));

        // TODO: is genes.size() always the size we want?
        energycost = (1.0f / 128.0f) + ourGene->genes.size() * (0.1f / 255.0f);
}

void c2eOrgan::processGenes() {
        shared_ptr<c2eReaction> r; // we need to store the previous reaction for possible receptor use
        // TODO: should this cope with receptors created at other lifestages? i doubt it.. - fuzzie

        for (vector<gene *>::iterator i = ourGene->genes.begin(); i != ourGene->genes.end(); i++) {
                if (!parent->shouldProcessGene(*i)) continue;

                if (typeid(*(*i)) == typeid(bioReactionGene)) {
                        reactions.push_back(shared_ptr<c2eReaction>(new c2eReaction()));
                        r = reactions.back();
                        reactions.back()->init((bioReactionGene *)(*i));
                } else if (typeid(*(*i)) == typeid(bioEmitterGene)) {
                        emitters.push_back(c2eEmitter());
                        emitters.back().init((bioEmitterGene *)(*i), this);
                } else if (typeid(*(*i)) == typeid(bioReceptorGene)) {
                        receptors.push_back(c2eReceptor());
                        receptors.back().init((bioReceptorGene *)(*i), this, r);
                }
        }
}

void c2eOrgan::tick() {
        if (longtermlifeforce <= 0.5f) return; // We're dead!

        biotick += clockrate;

        bool ticked = false;
        
        // if it's our turn to tick..
        if (biotick >= 1.0f) {
                ticked = true;
                // .. push the biotick back down
                biotick -= 1.0f;

                // *** energy consumption
                // chem 35 = ATP, chem 36 = ADP (TODO: fix hardcoding)
                float atplevel = parent->getChemical(35);
                bool hadenergy = false;
                if (atplevel >= energycost) {
                        hadenergy = true;
                        parent->adjustChemical(35, -energycost);
                        parent->adjustChemical(36, energycost);
                        
                        // *** tick emitters
                        for (vector<c2eEmitter>::iterator i = emitters.begin(); i != emitters.end(); i++)
                                processEmitter(*i);
                        
                        // *** tick reactions
                        for (vector<shared_ptr<c2eReaction> >::iterator i = reactions.begin(); i != reactions.end(); i++)
                                processReaction(**i);
                } else {
                        // *** out of energy damage     
                        applyInjury(atpdamagecoefficient);
                }

                // *** long-term damage
                float diff = longtermlifeforce - shorttermlifeforce;
                longtermlifeforce = longtermlifeforce - (diff * damagerate); // damagerate always <= 1.0

                // *** repair injuries
                float repair = diff * repairrate; // repairrate always <= 1.00
                shorttermlifeforce += repair;
                // adjust Injury chemical (TODO: de-hardcode)
                parent->adjustChemical(127, -repair / lifeforce);

                if (injurytoapply)
                        applyInjury(injurytoapply);
        }
        
        // *** tick receptors   
        for (vector<shared_ptr<c2eReaction> >::iterator i = reactions.begin(); i != reactions.end(); i++) (*i)->receptors = 0;
        clockratereceptors = 0; repairratereceptors = 0; injuryreceptors = 0;
                
        for (vector<c2eReceptor>::iterator i = receptors.begin(); i != receptors.end(); i++)
                processReceptor(*i, ticked);
        
        for (vector<shared_ptr<c2eReaction> >::iterator i = reactions.begin(); i != reactions.end(); i++) if ((*i)->receptors > 0) (*i)->rate /= (*i)->receptors;
        if (clockratereceptors > 0) clockrate /= clockratereceptors;
        if (repairratereceptors > 0) repairrate /= repairratereceptors;
        if (injuryreceptors > 0) injurytoapply /= injuryreceptors;
        
        // *** decay life force
        shorttermlifeforce -= shorttermlifeforce * (1.0f / 1000000.0f);
        longtermlifeforce -= longtermlifeforce * (1.0f / 1000000.0f);
}

void c2eOrgan::applyInjury(float value) {
        shorttermlifeforce -= value;
        if (shorttermlifeforce < 0.0f)
                shorttermlifeforce = 0.0f;
        // adjust Injury chemical (TODO: de-hardcode)
        parent->adjustChemical(127, value / lifeforce);
}

void c1Creature::processReaction(c1Reaction &d) {
        // TODO: untested

        bioReactionGene &g = *d.data;

        // TODO: this might not all be correct

        // work out which rate we're dealing with
        unsigned char rate = g.rate / 8;
        
        // if the tickmask doesn't want us to change things this tick, don't!
        if ((biochemticks & calculateTickMask(rate)) != 0) return;

        unsigned char ratio = 255, ratio2 = 255;
        if (g.reactant[0] != 0) {
                assert(g.quantity[0] != 0); // TODO
                ratio = getChemical(g.reactant[0]) / g.quantity[0];
        }
        if (g.reactant[1] != 0) {
                assert(g.quantity[1] != 0); // TODO
                ratio2 = getChemical(g.reactant[1]) / g.quantity[1];
        }

        // pick lowest ratio, if zero then return
        if (ratio2 < ratio) ratio = ratio2;
        if (ratio == 0) return;
        
        // calculate the actual adjustment (can't go out of bounds)
        ratio = ratio - ((ratio * calculateMultiplier(rate)) / 65536);

        // change chemical levels
        subChemical(g.reactant[0], ratio * g.quantity[0]);
        subChemical(g.reactant[1], ratio * g.quantity[1]);
        addChemical(g.reactant[2], ratio * g.quantity[2]);
        addChemical(g.reactant[3], ratio * g.quantity[3]);
}

void c2eOrgan::processReaction(c2eReaction &d) {
        bioReactionGene &g = *d.data;
        
        // TODO: this might not all be correct

        float ratio = 1.0f, ratio2 = 1.0f;
        if (g.reactant[0] != 0) {
                assert(g.quantity[0] != 0); // TODO
                ratio = parent->getChemical(g.reactant[0]) / (float)g.quantity[0];
        }
        if (g.reactant[1] != 0) {
                assert(g.quantity[1] != 0); // TODO
                ratio2 = parent->getChemical(g.reactant[1]) / (float)g.quantity[1];
        }

        // pick lowest ratio, if zero then return
        if (ratio2 < ratio) ratio = ratio2;
        if (ratio == 0.0f) return;

        // calculate the actual adjustment
        float rate = 1.0 - powf(0.5, 1.0 / powf(2.2, (1.0 - d.rate) * 32.0));
        ratio = ratio * rate;

        // change chemical levels
        parent->adjustChemical(g.reactant[0], -(ratio * (float)g.quantity[0]));
        parent->adjustChemical(g.reactant[1], -(ratio * (float)g.quantity[1]));
        parent->adjustChemical(g.reactant[2], ratio * (float)g.quantity[2]);
        parent->adjustChemical(g.reactant[3], ratio * (float)g.quantity[3]);
}

void c1Creature::processEmitter(c1Emitter &d) {
        // TODO: untested

        bioEmitterGene &g = *d.data;

        if ((biochemticks % g.rate) != 0) return;

        if (!d.locus) return;
        unsigned char f = *d.locus;
        if (g.clear) *d.locus = 0;
        if (g.invert) f = 255 - f;

        if (g.digital) {
                if (f < g.threshold) return;
                addChemical(g.chemical, g.gain);
        } else {
                int r = (((int)f - g.threshold) * g.gain) / 255;
                
                // clip the result of the calculation to unsigned char, and reassign it
                if (r < 0) r = 0; else if (r > 255) r = 255;
                f = r;

                addChemical(g.chemical, f);
        }
}

void c2eOrgan::processEmitter(c2eEmitter &d) {
        bioEmitterGene &g = *d.data;
        
        if (d.sampletick != g.rate) {
                assert(d.sampletick < g.rate);
                d.sampletick++;
                return;
        }
        
        d.sampletick = 0;

        if (!d.locus) return;
        float f = *d.locus;
        if (g.clear) *d.locus = 0.0f;
        if (g.invert) f = 1.0f - f;

        if (g.digital) {
                if (f < d.threshold) return;
                parent->adjustChemical(g.chemical, d.gain);
        } else {
                f = (f - d.threshold) * d.gain;
                if (f > 0.0f) // TODO: correct check?
                        parent->adjustChemical(g.chemical, f);
        }
}

void c1Creature::processReceptor(c1Receptor &d) {
        // TODO: untested

        bioReceptorGene &g = *d.data;

        // TODO: same issues as c2eOrgan::processReceptor below, probably

        if (!d.locus) return;

        unsigned char f = chemicals[g.chemical];
        int r;
        if (g.digital)
                r = f > g.threshold ? g.gain : 0;
        else
                // TODO: int promotion correct to makke this work out?
                r = (((int)f - g.threshold) * g.gain) / 255;
        
        if (g.inverted) r = g.nominal - r;
        else r += g.nominal;
        
        // clip the result of the calculation to unsigned char, and reassign it
        if (r < 0) r = 0; else if (r > 255) r = 255;
        f = r;

        if (f == 0 && g.organ == 1 && g.tissue == 3 && g.locus == 0) // evil check for "Die if non-zero!" locus
                return;
        else
                *d.locus = f;
}

void c2eOrgan::processReceptor(c2eReceptor &d, bool checkchem) {
        bioReceptorGene &g = *d.data;
        
        /*
         * TODO: This code has issues..
         *
         * eg, if you have two receptors pointing at a non-local locus,
         * we just stomp over it in order, so the last receptor always get it
         * while c2e seems to alternate between them (possibly organ clockrate stuff)
         *
         */
        
        if (checkchem) {
                d.processed = true;
                d.lastvalue = parent->getChemical(g.chemical);
        }

        if (!d.processed) return;
        if (!d.locus) return;

        float f;
        if (g.digital)
                f = d.lastvalue > d.threshold ? d.gain : 0.0f;
        else
                f = (d.lastvalue - d.threshold) * d.gain;
        if (g.inverted) f *= -1.0f;
        f += d.nominal;

        if (f < 0.0f) f = 0.0f; else if (f > 1.0f) f = 1.0f; // TODO: correct?

        if (f == 0.0f && g.organ == 1 && g.tissue == 3 && g.locus == 0) // evil check for "Die if non-zero!" locus
                return;
        else if (d.receptors) {
                if (*d.receptors == 0) *d.locus = 0.0f;
                (*d.receptors)++;
                *d.locus += f;
        } else
                *d.locus = f;
}

float *c2eOrgan::getLocusPointer(bool receptor, unsigned char o, unsigned char t, unsigned char l, unsigned int**receptors) {
        if (receptors) *receptors = 0;

        switch (o) {
                case 2: // organ
                        if (t == 0)
                                switch (l) {
                                        case 0: // clock rate
                                                if (receptors) *receptors = &clockratereceptors;
                                                return &clockrate;
                                        case 1: // repair rate
                                                if (receptors) *receptors = &repairratereceptors;
                                                return &repairrate;
                                        case 2: // injury to apply
                                                if (receptors) *receptors = &injuryreceptors;
                                                return &injurytoapply;
                                }
                        break;
                case 3: // reaction
                        if (t == 0 && l == 0) { // reaction rate
                                shared_ptr<c2eReaction> r = reactions.back();
                                if (!r) {
                                        std::cout << "c2eOrgan::getLocusPointer failed to find a reaction" << std::endl;
                                        return 0;
                                } else {
                                        if (receptors) *receptors = &r->receptors;
                                        return &r->rate;
                                }
                        }
        }

        return parent->getLocusPointer(receptor, o, t, l);
}

void c1Reaction::init(bioReactionGene *g) {
        data = g;
}

void c2eReaction::init(bioReactionGene *g) {
        data = g;

        // rate is stored in genome as 0 fastest, 255 slowest
        // reversed in game, i think .. TODO: check this
        rate = 1.0 - (g->rate / 255.0);
}

void c1Receptor::init(bioReceptorGene *g, c1Creature *parent) {
        data = g;
        locus = parent->getLocusPointer(true, g->organ, g->tissue, g->locus);
}
        
void c2eReceptor::init(bioReceptorGene *g, c2eOrgan *parent, shared_ptr<c2eReaction> r) {
        data = g;
        processed = false;
        nominal = g->nominal / 255.0f;
        threshold = g->threshold / 255.0f;
        gain = g->gain / 255.0f;
        locus = parent->getLocusPointer(true, g->organ, g->tissue, g->locus, &receptors);
}

void c1Emitter::init(bioEmitterGene *g, c1Creature *parent) {
        data = g;
        locus = parent->getLocusPointer(false, g->organ, g->tissue, g->locus);
}

void c2eEmitter::init(bioEmitterGene *g, c2eOrgan *parent) {
        data = g;
        sampletick = 0;
        threshold = g->threshold / 255.0f;
        gain = g->gain / 255.0f;
        locus = parent->getLocusPointer(false, g->organ, g->tissue, g->locus, 0);
}

#include "AgentHelpers.h"

bool Creature::agentInSight(AgentRef a) {
#ifndef _CREATURE_STANDALONE    
        if (a->invisible()) return false;

        // TODO: specify x/y location for eyes
        // TODO: check open cabin?
        return agentIsVisible(parent, a);
#else
        return false;
#endif
}

void Creature::chooseAgents() {
#ifndef _CREATURE_STANDALONE    
        // zot any chosen agents which went out of range, went invisible or changed category
        for (unsigned int i = 0; i < chosenagents.size(); i++) {
                AgentRef a = chosenagents[i];
                if (a) {
                        if (a->category != (int)i || !agentInSight(a))
                                chosenagents[i].clear();
                }
        }

        std::vector<std::vector<AgentRef> > possibles(chosenagents.size());

        for (std::list<boost::shared_ptr<Agent> >::iterator i = world.agents.begin(); i != world.agents.end(); i++) {
                boost::shared_ptr<Agent> a = *i;
                if (!a) continue;

                // if agent category is -1 or outside of our #categories, continue
                if (a->category < 0) continue;
                if (a->category >= (int)chosenagents.size()) continue;

                // if we already chose an agent from this category, continue
                if (chosenagents[a->category]) continue;

                if (!agentInSight(a)) continue;

                possibles[a->category].push_back(a);
        }

        for (unsigned int i = 0; i < chosenagents.size(); i++) {
                if (!chosenagents[i])
                        chosenagents[i] = selectRepresentativeAgent(i, possibles[i]);
        }
#endif
}

AgentRef c2eCreature::selectRepresentativeAgent(int type, std::vector<AgentRef> possibles) {
        // TODO: proper selection method

        if (possibles.size() > 0)
                return possibles[rand() % possibles.size()];
        else
                return AgentRef();
}

int c2eCreature::reverseMapVerbToNeuron(unsigned int verb) {
        // TODO: reverse-mapping like this seems utterly horrible, is it correct?
        int actualverb = -1;
        for (unsigned int i = 0; i < mappinginfo.size(); i++) {
                if (mappinginfo[i] == verb)
                        actualverb = (int)i;
        }
        return actualverb;
}

void c2eCreature::handleStimulus(c2eStim &stim) {
        // TODO: handle out-of-range verb_amount/noun_amount

        if (stim.verb_id >= 0) {
                c2eLobe *verblobe = brain->getLobeById("verb");
                if (verblobe) {
                        if ((unsigned int)stim.verb_id < verblobe->getNoNeurons())
                                verblobe->setNeuronInput(stim.verb_id, stim.verb_amount);
                }
        }

        if (stim.noun_id >= 0) {
                c2eLobe *nounlobe = brain->getLobeById("noun");
                if (nounlobe) {
                        if ((unsigned int)stim.noun_id < nounlobe->getNoNeurons())
                                nounlobe->setNeuronInput(stim.noun_id, stim.noun_amount);
                }
        }

        for (unsigned int i = 0; i < 4; i++) {
                if (stim.drive_id[i] >= 0) {
                        unsigned char chemno = stim.drive_id[i] + 148;
                        adjustChemical(chemno, stim.drive_amount[i]);
                        if (!stim.drive_silent[i]) {
                                c2eLobe *resplobe = brain->getLobeById("resp");
                                if (resplobe) {
                                        if ((unsigned int)stim.drive_id[i] < resplobe->getNoNeurons())
                                                resplobe->setNeuronInput(stim.drive_id[i], stim.drive_amount[i]);
                                }
                        }
                }
        }
}

// TODO: this needs to be passed noun details, it seems, judging by documentation
void c2eCreature::handleStimulus(unsigned int id, float strength) {
        // note that g->addoffset does not seem to exist in c2e
        
        c2eStim stim;
        creatureStimulusGene *g = 0;
        
        // TODO: generate the damn c2eStims in addGene, thus zapping a whole bunch of bugs
        for (vector<gene *>::iterator i = genome->genes.begin(); i != genome->genes.end(); i++) {
                if (typeid(*(*i)) == typeid(creatureStimulusGene)) {
                        creatureStimulusGene *x = (creatureStimulusGene *)(*i);
                        if (x->stim == id) {
                                g = x;
                                break;
                        }
                }
        }
        if (!g) return;

        // if we're asleep and the stimulus isn't to be processed when asleep, return
        if (!g->whenasleep && isAsleep()) return;

        // TODO: g->modulate
        
        // TODO: is multipler usage below okay?
        float multiplier = (strength == 0.0f ? 1.0f : strength);

        /*
         * TODO: what the heck does g->intensity do? it seems to almost entirely be 0
         * in the standard genomes (apart from a 255?) and it doesn't seem to change
         * anything - fuzzie
         */
        // TODO: grmph, g->sensoryneuron and g->significance make no sense to me right now
        // either, so commenting the verb_id setting out until someone works it out - fuzzie
        /*if (stim.verb_id != 0) // TODO: this is a guess to stop stuff from resting seemingly forever
                stim.verb_id = reverseMapVerbToNeuron(g->sensoryneuron); */
        // TODO: huh? gene kit has it in 255-ish steps
        stim.verb_amount = g->significance * (1.0f / 124.0f); /* multiply by 0.5? */
        for (unsigned int i = 0; i < 4; i++) {
                // TODO: ack, amount should be bound to range
                // TODO: fuzzie is suspicious about multiply/dividing on g->amounts here
                if (g->drives[i] != 255)
                        stim.setupDriveStim(i, g->drives[i], ((g->amounts[i] * (1.0f / 124.0f)) - 1.0f) * multiplier, g->silent[i]);
                
                if (strength == 0.0f)
                        stim.drive_silent[i] = true;
        }

        handleStimulus(stim);
}

/* vim: set noet: */