McAccess::McAccess(int port, int slot) {
_port = port;
_slot = slot;
ee_sema_t newSema;
newSema.init_count = 1;
newSema.max_count = 1;
_sema = CreateSema(&newSema);
assert(mcInit(MC_TYPE_MC) >= 0);
}
void init_basic_modules(const char *path)
{
char *gz;
int gz_size;
module_t basic_modules[7] =
{
{ "sio2man", "freesio2.irx", NULL, 0, 0 },
{ "mcman", "mcman.irx", NULL, 0, 0 },
{ "mcserv", "mcserv.irx", NULL, 0, 0 },
{ "mtapman", "freemtap.irx", NULL, 0, 0 },
{ "padman", "freepad.irx", NULL, 0, 0 },
{ "IOX/File_Manager", "iomanX.irx", NULL, 0, 0 },
{ "IOX/File_Manager_Rpc", "fileXio.irx", NULL, 0, 0 }
};
gz = init_modules_tgz(path,&gz_size);
init_load_irx(gz, gz_size, basic_modules, 7);
// Init various libraries
mcInit(MC_TYPE_MC);
mtapInit();
padInit(0);
mtapPortOpen(0);
mtapPortOpen(1);
if (!basic_modules[6].result)
{
fileXioInit();
}
else
{
// Problem initializing fileXio modules
fioInit();
}
if (gz != (char*)modules_tgz)
{
free(gz);
}
}
int main() {
int fd, ret;
int i;
// Initialise
SifInitRpc(0);
LoadModules();
#ifdef TYPE_MC
if(mcInit(MC_TYPE_MC) < 0) {
printf("Failed to initialise memcard server!\n");
SleepThread();
}
#else
if(mcInit(MC_TYPE_XMC) < 0) {
printf("Failed to initialise memcard server!\n");
SleepThread();
}
#endif
printf("\nMemory card library example code - by Sjeep\n\n");
// int mcGetInfo(int port, int slot, int* type, int* free, int* format);
//
// mcGetInfo retrieves memcard state info, such as the memcard type, free blocks and
// the format status.
//
// mcGetInfo is passed pointers to three variables, which are filled upon completion
// of the getinfo rpc command. The mcGetInfo return values are as follows:
//
// 0 : The same memory card has been connected since the last mcGetInfo call.
// -1 : Switched to a formatted memory card.
// -2 : Switched to an unformatted memory card.
// -10 or less : The memory card could not be detected.
//
// NOTE: With the MCMAN/MCSERV, *format is always returned as 0 regardless of if
// if the memcard is formatted or not.
// Since this is the first call, -1 should be returned.
mcGetInfo(0, 0, &mc_Type, &mc_Free, &mc_Format);
mcSync(0, NULL, &ret);
printf("mcGetInfo returned %d\n",ret);
printf("Type: %d Free: %d Format: %d\n\n", mc_Type, mc_Free, mc_Format);
// Assuming that the same memory card is connected, this should return 0
mcGetInfo(0,0,&mc_Type,&mc_Free,&mc_Format);
mcSync(0, NULL, &ret);
printf("mcGetInfo returned %d\n",ret);
printf("Type: %d Free: %d Format: %d\n\n", mc_Type, mc_Free, mc_Format);
// int mcGetDir(int port, int slot, char *name, unsigned mode, int maxent, mcTable* table);
//
// mcGetDir retrieves the directory structure of a specific path on the memory card.
//
// The filename is relative to the root of the memory card. Wildcards such as '*' and '?'
// may be used. "maxent" is the maximum number of mcTable elements your array specified
// by "table" can hold. The mc_getdir return values are as follows:
//
// 0 or more : The number of file entries that were obtained.
// -2 : The memory card is unformatted
// -4 : A non-existant path was specified in the "name" parameter
// -10 or less : The memory card could not be detected.
mcGetDir(0, 0, "/*", 0, ARRAY_ENTRIES - 10, mcDir);
mcSync(0, NULL, &ret);
printf("mcGetDir returned %d\n\nListing of root directory on memory card:\n\n", ret);
for(i=0; i < ret; i++)
{
if(mcDir[i].attrFile & MC_ATTR_SUBDIR)
printf("[DIR] %s\n", mcDir[i].name);
else
printf("%s - %d bytes\n", mcDir[i].name, mcDir[i].fileSizeByte);
}
// Check if existing save is present
fd = fioOpen("mc0:PS2DEV/icon.sys", O_RDONLY);
if(fd <= 0) {
printf("\nNo previous save exists, creating...\n");
if((ret = CreateSave()) < 0) {
printf("Failed to create save! Errorno: %d\n",ret);
SleepThread();
}
} else {
printf("\nPrevious save exists, listing directory\n\n");
ret = mcGetDir(0, 0, "/PS2DEV/*", 0, ARRAY_ENTRIES, mcDir);
printf("mcGetDir returned %d\n\n", ret);
for(i=0; i < ret; i++)
{
if(mcDir[i].attrFile & MC_ATTR_SUBDIR)
printf("[DIR] %s\n", mcDir[i].name);
else
printf("%s - %d bytes\n", mcDir[i].name, mcDir[i].fileSizeByte);
}
}
// Return to the browser, so you can see the PS2Dev icon :)
SifExitRpc();
return 0;
}
static void frontend_ps2_init(void *data)
{
char cwd[FILENAME_MAX];
int bootDeviceID;
SifInitRpc(0);
#if !defined(DEBUG)
/* Comment this line if you don't wanna debug the output */
while(!SifIopReset(NULL, 0)){};
#endif
while(!SifIopSync()){};
SifInitRpc(0);
sbv_patch_enable_lmb();
/* I/O Files */
SifExecModuleBuffer(&iomanX_irx, size_iomanX_irx, 0, NULL, NULL);
SifExecModuleBuffer(&fileXio_irx, size_fileXio_irx, 0, NULL, NULL);
SifExecModuleBuffer(&freesio2_irx, size_freesio2_irx, 0, NULL, NULL);
/* Memory Card */
SifExecModuleBuffer(&mcman_irx, size_mcman_irx, 0, NULL, NULL);
SifExecModuleBuffer(&mcserv_irx, size_mcserv_irx, 0, NULL, NULL);
/* Controllers */
SifExecModuleBuffer(&freemtap_irx, size_freemtap_irx, 0, NULL, NULL);
SifExecModuleBuffer(&freepad_irx, size_freepad_irx, 0, NULL, NULL);
/* USB */
SifExecModuleBuffer(&usbd_irx, size_usbd_irx, 0, NULL, NULL);
SifExecModuleBuffer(&usbhdfsd_irx, size_usbhdfsd_irx, 0, NULL, NULL);
/* Audio */
SifExecModuleBuffer(&freesd_irx, size_freesd_irx, 0, NULL, NULL);
SifExecModuleBuffer(&audsrv_irx, size_audsrv_irx, 0, NULL, NULL);
/* CDVD */
SifExecModuleBuffer(&cdvd_irx, size_cdvd_irx, 0, NULL, NULL);
if (mcInit(MC_TYPE_XMC)) {
RARCH_ERR("mcInit library not initalizated\n");
}
/* Initializes audsrv library */
if (audsrv_init()) {
RARCH_ERR("audsrv library not initalizated\n");
}
/* Initializes pad libraries
Must be init with 0 as parameter*/
if (mtapInit() != 1) {
RARCH_ERR("mtapInit library not initalizated\n");
}
if (padInit(0) != 1) {
RARCH_ERR("padInit library not initalizated\n");
}
if (mtapPortOpen(0) != 1) {
RARCH_ERR("mtapPortOpen library not initalizated\n");
}
/* Initializes CDVD library */
/* SCECdINoD init without check for a disc. Reduces risk of a lockup if the drive is in a erroneous state. */
sceCdInit(SCECdINoD);
if (CDVD_Init() != 1) {
RARCH_ERR("CDVD_Init library not initalizated\n");
}
_init_ps2_io();
/* Prepare device */
getcwd(cwd, sizeof(cwd));
bootDeviceID=getBootDeviceID(cwd);
waitUntilDeviceIsReady(bootDeviceID);
#if defined(HAVE_FILE_LOGGER)
retro_main_log_file_init("retroarch.log");
verbosity_enable();
#endif
}
void InitPS2()
{
int i, sometime;
static char hddarg[] = "-o" "\0" "4" "\0" "-n" "\0" "20";
static char pfsarg[] = "-m" "\0" "4" "\0" "-o" "\0" "10" "\0" "-n" "\0" "40";
SifInitRpc(0);
// Reset IOP borrowed from uLaunchelf
while (!SifIopReset(NULL, 0)){};
while (!SifIopSync()){};
SifInitRpc(0);
sbv_patch_enable_lmb();
SifExecModuleBuffer(&iomanX_irx, size_iomanX_irx, 0, NULL, NULL);
SifExecModuleBuffer(&fileXio_irx, size_fileXio_irx, 0, NULL, NULL);
SifExecModuleBuffer(&freesio2_irx, size_freesio2_irx, 0, NULL, NULL);
/* SifLoadModule("rom0:XSIO2MAN", 0, NULL);
SifLoadModule("rom0:XMCMAN", 0, NULL);
SifLoadModule("rom0:XMCSERV", 0, NULL);
SifLoadModule("rom0:XMTAPMAN", 0, NULL);
SifLoadModule("rom0:XPADMAN", 0, NULL); */
SifExecModuleBuffer(&mcman_irx, size_mcman_irx, 0, NULL, NULL);
SifExecModuleBuffer(&mcserv_irx, size_mcserv_irx, 0, NULL, NULL);
SifExecModuleBuffer(&freemtap_irx, size_freemtap_irx, 0, NULL, NULL);
SifExecModuleBuffer(&freepad_irx, size_freepad_irx, 0, NULL, NULL);
#ifdef SOUND_ON
SifExecModuleBuffer(&freesd_irx, size_freesd_irx, 0, NULL, NULL);
SifExecModuleBuffer(&audsrv_irx, size_audsrv_irx, 0, NULL, NULL);
#endif
SifExecModuleBuffer(&SMSUTILS_irx, size_SMSUTILS_irx, 0, NULL, NULL);
SifExecModuleBuffer(&usbd_irx, size_usbd_irx, 0, NULL, NULL);
SifExecModuleBuffer(&usbhdfsd_irx, size_usbhdfsd_irx, 0, NULL, NULL);
for (i = 0; i < 3; i++) { // Taken from ulaunchelf
sometime = 0x01000000;
while (sometime--) asm("nop\nnop\nnop\nnop");
}
SifExecModuleBuffer(&poweroff_irx, size_poweroff_irx, 0, NULL, NULL);
SifExecModuleBuffer(&ps2dev9_irx, size_ps2dev9_irx, 0, NULL, NULL);
SifExecModuleBuffer(&ps2atad_irx, size_ps2atad_irx, 0, NULL, NULL);
SifExecModuleBuffer(&ps2hdd_irx, size_ps2hdd_irx, sizeof(hddarg), hddarg, NULL);
SifExecModuleBuffer(&ps2fs_irx, size_ps2fs_irx, sizeof(pfsarg), pfsarg, NULL);
mcInit(MC_TYPE_XMC);
#ifdef CDSUPPORT
SifExecModuleBuffer(&cdvd_irx, size_cdvd_irx, 0, NULL, NULL);
cdInit(CDVD_INIT_INIT);
CDVD_Init();
#endif
#ifdef SOUND_ON
audsrv_init();
#endif
mtapInit();
padInit(0);
mtapPortOpen(0);
}
void mcMigrate (char const **paramFile, int *nrFiles, char const *inputDir, char const *outputDir)
{
int i, j, k, RepLoop, envChgStep, dispStep, loopID, simulTime,last, action;
bool advOutput, habIsSuitable, cellInDispDist, tempResilience, tail;
char fileName[128], simulName2[128];
FILE *fp = NULL, *fp2 = NULL;
double lddSeedProb;
time_t startTime;
/*
** These variables are not (yet) used.
**
** int vegResTime, seedBankResTime, *seedBank, tSinceDecol, tWhenCol;
*/
/*
** Pixel counter variables. These variables allow us to record interesting
** values to be printed into the output file:
**
** ==> Many of these aren't used yet. <==
**
** - nrColonized: The number of pixels in "Colonized" state at
** any given time.
** - nrAbsent: The number of pixels in "Absent" state at any
** given time.
** - nrDecolonized: The number of pixels in "Decolonized" state at
** any given time.
** - nrTmpResilient: The number of pixels that in "Temporary
** Resilience" state at any given time.
** - nrVegResilient: The number of pixels that are in "Vegetative
** Resilience" state at any given time.
** - nrSeedBank: The number of pixels that are in Seed Bank
** Resilience state at any given time.
** - nrStepColonized: The number of pixels which changed to
** "Colonized" state during a given step.
** - nrStepDecolonized: The number of pixels which changed to
** "Decolonized" state during a given step.
** - nrStepTmpResilient: The number of pixels that which changed to
** "Temporary Resilience" state during a given
** step.
** - nrStepVegResilient: The number of pixels that are which changed to
** "Vegetative Resilience" state during a given
** step.
** - nrStepSeedBank: The number of pixels that are which changed to
** "Seed Bank Resilience" state during a given
** step.
** - nrStepLostUnsuit: The number of pixels that were lost due to
** unsuitable habitat conditons during a given
** dispersal step.
** - nrStepLostExtreme: The number of pixels that were lost due to
** "Extreme Event" during a given dispersal step.
** - nrStepLDDSuccess: The number of LDD events that were successful
** (can be any of a "normal" LDD or a River or
** Road LDD).
** - nrStepVegResRecover: The number of "Vegetative Resilience" recovery
** events that occured within a given dispersal
** step.
** - nrStepSeedBankRecover: The number of "Seed Bank Resilience" recovery
** events that occured within a given dispersal
** step.
** - nrTotColonized: \
** - nrTotLostUnsuit: |
** - nrTotLostExtreme: | Same as above but over the total
** - nrTotLostNatural: > simulation instead of one step.
** - nrTotLDDSuccess: |
** - nrTotVegResRecover: |
** - nrTotSeedBankRecover: /
** - nrInitial: The number of initial pixels that are occupied
** by the species.
** - nrNoDispersal: The number of pixels that would be colonized at
** the end of the simulation under the
** "no-dispersal" hypothesis.
** - nrUnivDispersal: The number of pixels that would be colonized
** at the end of the simulation under the
** "unlimited-dispersal" hypothesis.
*/
int nrColonized, nrAbsent, nrStepColonized, nrStepDecolonized, nrStepLDDSuccess,
nrTotColonized, nrTotLDDSuccess, nrInitial, nrNoDispersal, nrUnivDispersal, nrTotDecolonized;
/* As of yet unused count variables:
** int nrTotVegResRecover, nrTotSeedBankRecover, nrStepVegResilient,
** nrStepSeedBank, nrVegResilient, nrStepSeedBankRecover,
** nrStepVegResRecover, nrSeedBank, nrDecolonized; */
/* Matrices:
** - currentState: Values in [-32768;32767]. NoData values are represented by -9999
** - habSuitability: Values in [0;1000].
** - barriers: Values in [0;255].
** - pixelAge: Values in [0;255].
** - noDispersal: Values in [0;255].
*/
int **currentState, **habSuitability, **barriers, **pixelAge, **noDispersal;
/* Initialize the variables. */
advOutput = false;
currentState = NULL;
habSuitability = NULL;
barriers = NULL;
pixelAge = NULL;
noDispersal = NULL;
propaguleProd = NULL;
dispKernel = NULL;
if (mcInit(*paramFile) == -1) /* Reads the "_param.txt" file */
{
*nrFiles = -1;
goto End_of_Routine;
}
/* We'll use 'srand' and 'rand' here, as 'srandom' and 'random' do not work on Windows :-( */
srand (time (NULL)+procID);
/* Allocate the necessary memory. */
currentState = (int **)malloc (nrRows * sizeof (int *));
habSuitability = (int **)malloc (nrRows * sizeof (int *));
barriers = (int **)malloc (nrRows * sizeof (int *));
pixelAge = (int **)malloc (nrRows * sizeof (int *));
noDispersal = (int **)malloc (nrRows * sizeof (int *));
for (i = 0; i < nrRows; i++)
{
currentState[i] = (int *)malloc (nrCols * sizeof (int));
habSuitability[i] = (int *)malloc (nrCols * sizeof (int));
barriers[i] = (int *)malloc (nrCols * sizeof (int));
pixelAge[i] = (int *)malloc (nrCols * sizeof (int));
noDispersal[i] = (int *)malloc (nrCols * sizeof (int));
}
clock_t begin, end, total_begin, total_end;
double time_spent;
double total_time_spent;
total_begin = clock();
/* Replicate the simulation replicateNb times. If replicateNb > 1 then the
** simulation's output names are "simulName1", "simulName2", etc... */
for (RepLoop = 1; RepLoop <= replicateNb; RepLoop++)
{
/* Remember the current time */
startTime = time(NULL);
/* If replicateNb > 1 then we need to change the simulation name */
if (replicateNb == 1)
{
strcpy(simulName2, simulName);
}
else if (replicateNb > 1)
{
sprintf(simulName2, "%s%d", simulName, RepLoop); /* sprinf(): puts a string into variable simulName2 */
}
/* Load and prepare the data. */
/* Species initial distribution */
sprintf(fileName, "%s%s.tif", inputDir, iniDist); /* sprinf(): puts a string into variable fileName */
printf("%s", fileName);
if (readMat(fileName, currentState) == -1)
{
*nrFiles = -1;
goto End_of_Routine;
}
//remove initial occurences
/*removeInitial(currentState);*/
/* Barrier options */
for (i = 0; i < nrRows; i++)
{
for (j = 0; j < nrCols; j++)
{
barriers[i][j] = 0;
}
}
if (useBarrier)
{
sprintf(fileName, "%s.tif", barrier);
if (readMat(fileName, barriers) == -1)
{
*nrFiles = -1; /* if readMat() return -1, an error occured */
goto End_of_Routine;
}
}
/* Filter the barrier matrix in two ways:
** -> reclass any value < 0 as 0 (this is to remove NoData values of -9999).
** -> set the cells with NoData in 'currentState' to NoData in 'barriers'
** so that the NoData in 'currentState' and 'barriers' are identical */
mcFilterMatrix(barriers, currentState, true, false, true);
/* Filter the values of current state matrix by the barriers matrix
** (when barriers = 1 we set currentState = 0) */
if (useBarrier) mcFilterMatrix(currentState, barriers, false, true, false);
/* Time to reach dispersal maturity.
**
** Before a pixel (= a population) can disperse, it needs to reach a certain
** user-defined age. The "age" is a matrix that keeps track of the age
** of all pixels:
** 0 = pixel is not colonized.
** 1 = pixel is colonized since 1 "dispersal event".
** 2 = pixel is colonized since 2 "dispersal event".
** 3 = etc...
** Fill the "age" to reflect the initial distribution of the species:
** where the species is present, pixels get a value of 'FullMaturity', where
** the species is absent, pixels get a value of 0. */
for (i = 0; i < nrRows; i++)
{
for (j = 0; j < nrCols; j++)
{
if (currentState[i][j] == 1)
{
pixelAge[i][j] = fullMatAge;
}
else
{
pixelAge[i][j] = 0;
}
}
}
/* The "no dispersal" matrix.
** This Matrix will keep track of the species distribution under the
** "no dispersal" scenario. */
for (i = 0; i < nrRows; i++)
{
for (j = 0; j < nrCols; j++)
{
noDispersal[i][j] = currentState[i][j];
}
}
/* Initialize counter variables.
** Reset pixel counters to zero before we start the dispersal simulation. */
nrInitial = 0;
nrColonized = 0;
nrAbsent = 0;
nrNoDispersal = 0;
nrUnivDispersal = 0;
nrTotColonized = 0;
nrTotDecolonized = 0;
nrTotLDDSuccess = 0;
tempResilience = true;
nrStepColonized = 0;
nrStepDecolonized = 0;
nrStepLDDSuccess = 0;
/* Currently unused counters:
** nrVegResilient = 0;
** nrSeedBank = 0;
** nrTotVegResRecover = 0;
** nrTotSeedBankRecover = 0; */
/* Count the number of initially colonized pixels (i.e. initial species distribution)
** as well as the number of empty (absence) cells. */
for (i = 0; i < nrRows; i++)
{
for (j = 0; j < nrCols; j++)
{
if (currentState[i][j] == 1) nrInitial++;
if (currentState[i][j] == 0) nrAbsent++;
}
}
nrColonized = nrInitial;
nrNoDispersal = nrInitial;
nrUnivDispersal = nrInitial;
/* Write the initial state to the data file. */
sprintf(fileName, "%s/%s_stats%d.txt", outputDir, simulName2,procID);
if ((fp = fopen (fileName, "w")) != NULL)
{
fprintf (fp, "envChgStep\tdispStep\tstepID\tunivDispersal\tNoDispersal\toccupied\tabsent\tstepColonized\tstepDecolonized\tstepLDDsuccess\n");
fprintf (fp, "0\t0\t1\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", nrUnivDispersal, nrNoDispersal,
nrColonized, nrAbsent, nrStepColonized, nrStepDecolonized, nrStepLDDSuccess);
}
else
{
*nrFiles = -1;
printf ("Could not open statistics file for writing.\n");
goto End_of_Routine;
}
/* **************************************************************** */
/* Simulate plant dispersal and migration (the core of the method). */
/* **************************************************************** */
printf("Running MigClim simulation %s.\n", simulName2);
/* Start of environmental change step loop (if simulation is run without change in environment this loop runs only once). */
for (envChgStep = 1; envChgStep <= envChgSteps; envChgStep++)
{
/* Print the current environmental change iteration. */
printf (" %d...\n", envChgStep);
/* Load the habitat suitability layer for the current envChgStep. */
sprintf (fileName, "%s%s%d.tif", inputDir, hsMap, envChgStep);
if (readMat (fileName, habSuitability) == -1)
{
*nrFiles = -1;
goto End_of_Routine;
}
/* if the user chose a rcThreshold > 0, reclass the habitat suitability into 0 or 1000
** if rcThreshold == 0 then suitability values are left unchanged. */
if (rcThreshold > 0)
{
for (i = 0; i < nrRows; i++)
{
for (j = 0; j < nrCols; j++)
{
if (habSuitability[i][j] < rcThreshold)
{
habSuitability[i][j] = 0;
}
else
{
habSuitability[i][j] = 1000;
}
}
}
}
/* Filter the habitat suitability matrix in three ways:
** -> replace any value < 0 by 0 (this removes NoData).
** -> set habitat suitability to 0 where barrier = 1.
** -> set habitat suitability values to NoData where barrier = NoData.
** and also */
mcFilterMatrix(habSuitability, barriers, true, true, true);
/* Set the values that will keep track of pixels colonized during the next
** climate change loop.
** "loopID" is the value that will be given to the pixel colonized
** during the current loop. The pixels being decolonized during the
** current loop will be given a value of "-loopID". The limits in
** terms of number of dispersal events and environmental change
** events is the following:
** - Without environmental change, the maximum number of dispStep
** is 29'500.
** - With environmental change, the maximum number of dispStep is
** 98, the number of environmental change loops is limited to 250.
** The coding for the loopID is as follows: envChgStep * 100 + dispStep. */
if (envChgStep == 0)
{
loopID = 1;
}
else
{
loopID = envChgStep * 100;
}
/* "Unlimited" and "no dispersal" scenario pixel count. Here we compute the number of pixels
** that would be colonized if dispersal was unlimited or null. This is simply the sum of all
** potentially suitable habitats */
nrUnivDispersal = mcUnivDispCnt(habSuitability);
updateNoDispMat(habSuitability, noDispersal, &nrNoDispersal);
/* Reset number of decolonized cells within current dispersal step pixel counter */
nrStepDecolonized = 0;
/* Update for temporarily resilient pixels. */
for (i = 0; i < nrRows; i++)
{
for (j = 0; j < nrCols; j++)
{
/* Udate non-suitable pixels. If a pixel turned unsuitable, we update its status to "Temporarily Resilient". */
if ((habSuitability[i][j] == 0) && (currentState[i][j] > 0))
{
/* If the user selected TemporaryResilience==T, then the pixel is set to "Temporary Resilient" status. */
if (tempResilience == true)
{
currentState[i][j] = 29900;
}
else
{
/* If not temporary resilience was specified, then the pixel is set to "decolonized" status. */
currentState[i][j] = -1 - loopID;
pixelAge[i][j] = 0;
/* NOTE: Later we can add "Vegetative" and "SeedBank" resilience options at this location. */
}
/* The number of decolonized cells within current step is increased by one */
nrStepDecolonized++;
}
}
}
/* *************************************** */
/* Dispersal event step loop starts here. */
/* *************************************** */
for (dispStep = 1; dispStep <= dispSteps; dispStep++)
{
begin=clock();
/* Set the value of "loopID" for the current iteration of the dispersal loop. */
loopID++;
/* Reset pixel counters that count pixels within the current loop. */
nrStepColonized = 0;
nrStepLDDSuccess = 0;
if (dispStep > 1) nrStepDecolonized = 0;
/* Currently unused variables:
** nrStepVegResilient = 0;
** nrStepSeedBank = 0;
** nrStepVegResRecover = 0;
** nrStepSeedBankRecover = 0; */
removeInitial(currentState,dispStep);
/* Source cell search: Can the sink pixel be colonized? There are four
** conditions to be met for a sink pixel to become colonized:
** 1. Sink pixel is currently suitable and not already colonised.
** 2. Sink pixel is within dispersal distance of an already colonised
** and mature pixel.
** 3. Source pixel has reached dispersal maturity.
** 4. There is no obstacle (barrier) between the pixel to be colonised
** (sink pixel) and the pixel that is already colonised (source
** pixel).
**
** Loop through the cellular automaton. */
for (i = 0; i < nrRows; i++)
{
last = 0;
for (j = 0; j < nrCols; j++)
{
/* Reset variables. */
habIsSuitable = false;
cellInDispDist = false;
/* Remove mature cells for impact control */
if (pixelAge[i][j] >= iniMatAge) {
//determine the action for this cell
action = cellAction(i,j,dispStep);
if (action== IMPACT_CONTROL) {
//delete it?
double r = UNIF01;
if (r <= 0.7) {
currentState[i][j] = 0;
pixelAge[i][j] = 0;
if (aggregates[dispStep-1][i][j] > 0) {
aggregates[dispStep-1][i][j]--;
}
managementImpacts[dispStep-1][IMPACT_CONTROL][procID-1]++;
}
}
}
/* 1. Test whether the pixel is a suitable sink (i.e., its habitat
** is suitable, it's unoccupied and is not on a barrier or filter
** pixel). */
if ((habSuitability[i][j] > 0) && (currentState[i][j] <= 0) && checkSuitability(i,j,false)) habIsSuitable = true;
//set state from previous state
if (currentState[i][j] >= 1) {
aggregates[dispStep-1][i][j]++;
}
/* 2. Test whether there is a source cell within the dispersal
** distance. To be more time efficient, this code runs only if
** the answer to the first question is positive. Additionally,
** if there is a source cell within dispersion distance and if
** a barrier was asked for, then we also check that there is no
** barrier between this source cell and the sink cell (this
** verification is carried out in the "SearchSourceCell"
** function). */
if (habIsSuitable)
{
/* Now we search if there is a suitable source cell to colonize the sink cell. */
if (mcSrcCell (i, j, currentState, pixelAge, loopID, habSuitability[i][j], barriers, &last)) {
cellInDispDist = true;
//last=0;
} else {
//last++;
}
}
/* Update pixel status. */
if (habIsSuitable && cellInDispDist)
{
/* Only if the 2 conditions are fullfilled the cell's status is set to colonised. */
currentState[i][j] = loopID;
nrStepColonized++;
//printf("Step: %d, i: %d, j: %d\n",dispStep-1, i, j);
aggregates[dispStep-1][i][j]++;
/* If the pixel was in seed bank resilience state, then we
** update the corresponding counter. Currently not used.
** if (pixelAge[i][j] == 255) nrStepSeedBank--; */
/* Update "age" value. We do this only now because we needed the old "age" value just before
** to determine whether a pixel was in "Decolonized" or "SeedBank resilience" status. */
pixelAge[i][j] = 0;
}
}
}
/* If the LDD frequence is larger than zero, perform it. */
if (lddFreq > 0.0)
{
/* Loop through the entire cellular automaton. */
for (i = 0; i < nrRows; i++)
{
for (j = 0; j < nrCols; j++)
{
/* Check if the pixel is a source cell (i.e. is it colonised since at least 1 dispersal Loop)
** and check if the pixel has reached dispersal maturity. */
if ((currentState[i][j]) > 0 && (currentState[i][j] != loopID))
{
if (pixelAge[i][j] >= iniMatAge)
{
/* Set the probability of generating an LDD event. This
** probability is weighted by the age of the cell. */
if (pixelAge[i][j] >= fullMatAge)
{
lddSeedProb = lddFreq;
}
else
{
lddSeedProb = lddFreq * propaguleProd[pixelAge[i][j] - iniMatAge];
}
/* Now we can try to generate a LDD event with the calculated probability. */
if (UNIF01 < lddSeedProb || lddSeedProb == 1.0)
{
/* Randomly select a pixel within the distance "lddMinDist - lddMaxDist". */
mcRandomPixel (&rndPixel);
rndPixel.row = rndPixel.row + i;
rndPixel.col = rndPixel.col + j;
/* Now we check if this random cell is a suitable sink cell.*/
if (mcSinkCellCheck (rndPixel, currentState, habSuitability) && srcPixel(i,j,rndPixel.row,rndPixel.col,dispStep,true))
{
/* if condition is true, the pixel gets colonized.*/
currentState[rndPixel.row][rndPixel.col] = loopID;
//include ldd state
aggregates[dispStep-1][i][j]++;
nrStepColonized++;
nrStepLDDSuccess++;
/* If the pixel was in seed bank resilience state, then we
** update the corresponding counter. Currently not used.
** if (pixelAge[rndPixel.row][rndPixel.col] == 255) nrStepSeedBank--; */
/* Reset pixel age. */
pixelAge[rndPixel.row][rndPixel.col] = 0;
}
}
}
}
}
}
}
/* Update pixel age: At the end of a dispersal loop we want to
** increase the "age" of each colonized pixel.
**
** Reminder: pixel "age" structure is as follows:
** 0 = Pixel is either "Absent", "Decolonized" or has just been
** "Colonized" during this dispersal step.
** 1 to 250 = Pixel is in "Colonized" or "Temporarily Resilient"
** status. The value indicates the number of "dispersal events
** (usually years) since when the pixel was colonized.
** 255 = Pixel is in "SeedBank Resilience" state. */
for (i = 0; i < nrRows; i++)
{
for (j = 0; j < nrCols; j++)
{
/* If the pixel is in "Colonized" or "Temporarily Resilient" state, update it's age value. */
if (currentState[i][j] > 0) pixelAge[i][j] += 1;
/* If a pixel is in "Temporarily Resilient" state, we also increase its "currentState" value by 1
** so that the pixels gains 1 year of "Temporarily Resilience" age. */
if (currentState[i][j] >= 29900) currentState[i][j] += 1;
}
}
/* Update pixel counters. */
nrColonized = nrColonized + nrStepColonized - nrStepDecolonized;
nrAbsent = nrAbsent - nrStepColonized + nrStepDecolonized;
nrTotColonized += nrStepColonized;
nrTotDecolonized += nrStepDecolonized;
nrTotLDDSuccess += nrStepLDDSuccess;
/* Currently unused variables:
** nrTotVegResRecover += nrStepVegResRecover;
** nrTotSeedBankRecover += nrStepSeedBankRecover; */
/* Write current iteration data to the statistics file. */
fprintf(fp, "%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", envChgStep, dispStep, loopID, nrUnivDispersal,
nrNoDispersal, nrColonized, nrAbsent, nrStepColonized, nrStepDecolonized, nrStepLDDSuccess);
/* If the user has requested full output, also write the current state matrix to file. */
/*if (fullOutput)
{
sprintf (fileName, "%s/%s_step_%d.asc", outputDir, simulName2, loopID);
if (writeMat (fileName, currentState) == -1)
{
*nrFiles = -1;
goto End_of_Routine;
}
}*/
end = clock();
time_spent = (double)(end - begin) / CLOCKS_PER_SEC;
//fprintf(f,"%lf\n",time_spent);
//printf("Step %d completed by proc(%i) in %lf \n",dispStep,procID,time_spent);
//increment step tracker
if (incrementStepComplete(dispStep-1)) {
//print summary
int avgColonised = sum(dispStep-1);
int d_range=0, p_range=0, r_range=0, c_range=0, ic_range=0, ap_range=0;
int proc;
for (proc = 0; proc < NUMPROC; proc++) {
d_range += managementImpacts[dispStep-1][DELIMITATION][proc];
p_range += managementImpacts[dispStep-1][PREVENTION][proc];
r_range += managementImpacts[dispStep-1][REMOVAL][proc];
c_range += managementImpacts[dispStep-1][CONTAINMENT][proc];
ic_range += managementImpacts[dispStep-1][IMPACT_CONTROL][proc];
ap_range += managementImpacts[dispStep-1][ASSET_PROTECTION][proc];
//printf("IC%i: %i\n",proc,managementImpacts[dispStep-1][ASSET_PROTECTION][proc]);
}
d_range = d_range / NUMPROC;
p_range = p_range / NUMPROC;
r_range = r_range / NUMPROC;
c_range = c_range / NUMPROC;
ic_range = ic_range / NUMPROC;
ap_range = ap_range / NUMPROC;
//printf("IC: %i : %i\n",managementImpacts[dispStep-1][IMPACT_CONTROL][procID-1], procID-1);
//printf("IC Averaged: %i\n",ic_range);
char impactStr[128];
sprintf(impactStr,"\"d_range\":%i,\"p_range\":%i,\"r_range\":%i,\"c_range\":%i,\"ic_range\":%i,\"ap_range\":%i",d_range,p_range,r_range,c_range,ic_range,ap_range);
//printf("%s",impactStr);
printf("StepComplete %i : {\"time\":%lf,\"occupied\":%i,\"new\":%i,%s}\n",dispStep,time_spent,avgColonised,nrStepColonized,impactStr);
}
} /* END OF: dispStep */
/* Update temporarily resilient pixels.
** Temporarily resilient pixels can be distinguished by:
** -> CurrentState_Matrix = 29'900 to 29'999. Increases by 1 at each year.
** -> Age_Matrix has a positive value. */
for (i = 0; i < nrRows; i++)
{
for (j = 0; j < nrCols; j++)
{
if (currentState[i][j] >= 29900)
{
currentState[i][j] = dispSteps - loopID - 1;
pixelAge[i][j] = 0;
}
}
}
} /* END OF: envChgStep loop */
printf("All dispersal steps completed. Final output in progress...\n");
/* Update currentState matrix for pixels that are suitable but
** could not be colonized due to dispersal limitations.
** These pixels are assigned a value of 30'000 */
for (i = 0; i < nrRows; i++)
{
for (j = 0; j < nrCols; j++)
{
if ((habSuitability[i][j] > 0) && (currentState[i][j] <= 0)) currentState[i][j] = 30000;
}
}
/* Write the final state matrix to file. */
/* sprintf(fileName, "%s/%s_raster.asc", simulName, simulName2);
if (writeMat (fileName, currentState) == -1)
{
*nrFiles = -1;
goto End_of_Routine;
}*/
/* Write summary output to file. */
simulTime = time (NULL) - startTime;
total_end = clock();
time_spent = (double)(total_end - total_begin) / CLOCKS_PER_SEC;
printf("Process Completed after %lf \n",time_spent);
sprintf(fileName, "%s/%s_summary.txt", outputDir, simulName2);
if ((fp2 = fopen (fileName, "w")) != NULL)
{
fprintf(fp2, "simulName\tiniCount\tnoDispCount\tunivDispCount\toccupiedCount\tabsentCount\ttotColonized\ttotDecolonized\ttotLDDsuccess\trunTime\n");
fprintf(fp2, "%s\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\n", simulName2, nrInitial, nrNoDispersal, nrUnivDispersal,
nrColonized, nrAbsent, nrTotColonized, nrTotDecolonized, nrTotLDDSuccess, simulTime);
fclose (fp2);
}
else
{
*nrFiles = -1;
printf ("Could not write summary output to file.\n");
goto End_of_Routine;
}
/* Close the data file. */
if (fp != NULL) fclose (fp);
fp = NULL;
} /* end of "RepLoop" */
/* Set the number of output files created. */
*nrFiles = envChgSteps;
End_of_Routine:
/* Close the data file. */
if (fp != NULL) fclose (fp);
//fclose(f);
/* Free the allocated memory. */
if (currentState != NULL)
{
for (i = 0; i < nrRows; i++) free(currentState[i]);
free(currentState);
}
if (habSuitability != NULL)
{
for (i = 0; i < nrRows; i++) free(habSuitability[i]);
free(habSuitability);
}
if (barriers != NULL)
{
for (i = 0; i < nrRows; i++) free(barriers[i]);
free(barriers);
}
if (pixelAge != NULL)
{
for (i = 0; i < nrRows; i++) free(pixelAge[i]);
free(pixelAge);
}
if (noDispersal != NULL)
{
for (i = 0; i < nrRows; i++) free(noDispersal[i]);
free(noDispersal);
}
if (dispKernel != NULL) free(dispKernel);
if (propaguleProd != NULL) free(propaguleProd);
/* If an error occured, display failure message to the user... */
if (*nrFiles == -1) printf("MigClim simulation aborted...\n");
}
