int main(int ac, char **av, char **env)
{
char *line2;
t_e e;
(void)ac;
(void)av;
e.list = ft_env_cpy(env);
signal(SIGQUIT, ft_signal);
show_prompt(e.list);
while (get_next_line(0, &(e.line)) == 1)
{
line2 = exange_tab_or_space(e.line);
e.args = ft_strsplit(line2, ' ');
if (e.args && e.args[0])
{
if (ft_strchr(e.args[0], '/'))
exec_absolu(e.line, e.list);
else
do_command(&(e.list), e.line);
}
free(e.line);
show_prompt(e.list);
free_char_array(e.args);
}
ft_putchar('\n');
return (0);
}
int main(void)
{
char *line;
char *line2;
t_list *list;
char **args;
list = ft_env_cpy();
signal(SIGINT, ft_signal);
show_prompt(list);
while (get_next_line(0, &line) == 1)
{
line2 = exchange_tab_for_space(line);
args = ft_strsplit(line2, ' ');
if (args && args[0])
{
if (ft_strchr(args[0], '/'))
exec_absolu(line, list);
else
do_command(&list, line);
}
free(line);
show_prompt(list);
free_char_array(args);
}
ft_putchar('\n');
return (0);
}
const char *xml_get_string_value(xmlDoc *doc, char *format, ...)
{
va_list ap;
char str[4096];
va_start(ap, format);
vsnprintf(str, 4095, format, ap);
va_end(ap);
int i,n;
char **arr;
int found = TRUE;
split_into_array(str, '.', &n, &arr);
xmlNode *cur = xmlDocGetRootElement(doc);
// first item much match the name of the root
if (strcmp(arr[0], (char*)cur->name)!=0) {
// root node doesn't match -- return empty string
strcpy(buf, "");
}
else {
// subsequent items specify the search path through the xml tree
for (i=1; i<n; ++i) {
char *elem;
int k;
extract_array_specifier(arr[i], &elem, &k);
xmlNode *next = findNode(doc, cur, elem, k);
if (!next) {
// not found -- return NULL
found = FALSE;
strcpy(buf, "");
FREE(elem);
break;
}
FREE(elem);
cur = next;
}
}
if (found) {
assert(cur != NULL);
xmlChar *ret = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
strncpy_safe(buf, (char*)ret, MAX_LEN-1);
xmlFree(ret);
}
else {
strcpy(buf, MAGIC_UNSET_STRING);
}
free_char_array(&arr, n);
return buf;
}
static void exec_absolu(char *line, t_list *list)
{
char **str;
str = ft_strsplit(line, ' ');
if (check_cmd(str[0]))
ft_execve(str[0], str, list);
else
ft_erreur(line, ERR_NO_SUCH_FILE, 0);
free_char_array(str);
}
void ft_unsetenv(t_list **list, char *line)
{
char **cmp;
cmp = ft_strsplit(line, ' ');
if (char_array_size(cmp) >= 2)
{
list_remove(list, cmp[1]);
}
else
ft_erreur(BUILTIN_UNSETENV, ERR_NOT_ENOUGH_ARGS, 0);
free_char_array(cmp);
}
void ft_cd(t_list **list, char *line)
{
char *pwd;
char **argum;
char *cwd;
pwd = search(*list, "PWD=");
argum = ft_strsplit(line, ' ');
if (char_array_size(argum) == 1)
ft_oldpwd(list, "HOME=", "PWD=");
else if (char_array_size(argum) == 2)
{
if (ft_strcmp(argum[1], "-") == 0)
{
ft_putendl(search(*list, "OLDPWD=") + 7);
ft_oldpwd(list, "OLDPWD=", "PWD=");
}
else
reduc_cd(list, argum[1], pwd, cwd);
}
free_char_array(argum);
}
void show_prompt(t_list *list)
{
char *pwd;
char **path_components;
char *prompt;
int component_count;
pwd = search(list, "PWD=") + 4;
path_components = ft_strsplit(pwd, '/');
write(1, "[POKEMON] ", 10);
component_count = char_array_size(path_components);
if (component_count < 2)
ft_putstr(pwd);
else
{
prompt = join(path_components[component_count - 2], "/",
path_components[component_count - 1]);
ft_putstr(prompt);
free(prompt);
}
write(1, " > ", 3);
free_char_array(path_components);
}
void free_base_tree_node(struct base_tree_node *n)
{
free_char_array(n->base_list);
free(n);
}
const char *xml_get_string_attribute(xmlDoc *doc, char *format, ...)
{
va_list ap;
char str[4096];
va_start(ap, format);
vsnprintf(str, 4095, format, ap);
va_end(ap);
int i,n;
char **arr;
int found = TRUE;
split_into_array(str, '.', &n, &arr);
xmlNode *cur = xmlDocGetRootElement(doc);
// first item much match the name of the root
if (strcmp(arr[0], (char*)cur->name)!=0) {
// root node doesn't match -- return empty string
strcpy(buf, "");
}
else {
// subsequent items specify the search path through the xml tree
// all except the last one -- that is the attribute name
for (i=1; i<n-1; ++i) {
char *elem;
int k;
extract_array_specifier(arr[i], &elem, &k);
xmlNode *next = findNode(doc, cur, elem, k);
if (!next) {
// not found -- return NULL
found = FALSE;
strcpy(buf, "");
FREE(elem);
break;
}
FREE(elem);
cur = next;
}
}
if (found) {
assert(cur != NULL);
xmlChar *val = xmlGetProp(cur, (xmlChar*)(arr[n-1]));
if (val) {
strncpy_safe(buf, (char*)val, MAX_LEN-1);
xmlFree(val);
}
else {
// found the node, but it did not have the requested attribute
found = FALSE;
}
}
if (!found) {
strcpy(buf, MAGIC_UNSET_STRING);
}
free_char_array(&arr, n);
return buf;
}
static void rgps_grid2cell(char *line, rgps_grid_t *grid, int nGrids,
rgps_cell_t *cell, int nCells, dbf_header_t *dbf, FILE *fpOut)
{
char **col;
int ii, nCols, nCoords=0, cell_id=0, obs_year;
double obs_time, x_disp, y_disp;
// Extract information from line
split_into_array(line, ',', &nCols, &col);
for (ii=0; ii<nCols; ii++) {
if (dbf[ii].format == CSV_STRING)
dbf[ii].sValue = STRDUP(col[ii]);
else if (dbf[ii].format == CSV_DOUBLE)
dbf[ii].fValue = atof(col[ii]);
else if (dbf[ii].format == CSV_INTEGER)
dbf[ii].nValue = atoi(col[ii]);
if (strcmp_case(dbf[ii].shape, "CELL_ID") == 0)
cell_id = dbf[ii].nValue;
else if (strcmp_case(dbf[ii].shape, "OBS_YEAR") == 0)
obs_year = dbf[ii].nValue;
else if (strcmp_case(dbf[ii].shape, "OBS_TIME") == 0) {
obs_time = dbf[ii].fValue;
if (obs_year > grid[0].obs_year)
obs_time += date_getDaysInYear(grid[0].obs_year);
}
else if (strcmp_case(dbf[ii].shape, "X_DISP") == 0)
x_disp = dbf[ii].fValue;
else if (strcmp_case(dbf[ii].shape, "Y_DISP") == 0)
y_disp = dbf[ii].fValue;
}
free_char_array(&col, nCols);
// Extract information from connectivity table
int *grid_id = (int *) MALLOC(sizeof(int)*50);
double *grid_order = (double *) MALLOC(sizeof(double)*50);
size_t *p = (size_t *) MALLOC(sizeof(size_t)*50);
for (ii=0; ii<nCells; ii++) {
if (cell_id == cell[ii].cell_id) {
grid_id[nCoords] = cell[ii].grid_id;
grid_order[nCoords] = cell[ii].cell_id + (double) cell[ii].order / 100;
nCoords++;
}
}
gsl_sort_index(p, grid_order, 1, nCoords);
double disp_mag = sqrt(x_disp*x_disp + y_disp*y_disp);
// Extract grid information from motion product
int kk, index;
double diff, grid_time, birth_time, death_time;
char image_id[30];
char *tmp = (char *) MALLOC(sizeof(char)*25);
char *coordStr = (char *) MALLOC(sizeof(char)*50*nCoords);
strcpy(coordStr, "");
for (kk=0; kk<nCoords; kk++) {
index = -1;
for (ii=0; ii<nGrids; ii++) {
grid_time = grid[ii].obs_time;
if (grid[ii].obs_year > grid[0].obs_year)
grid_time += date_getDaysInYear(grid[0].obs_year);
diff = fabs(grid_time - obs_time);
if ((grid_id[p[kk]] == grid[ii].gpid) && (diff < 0.01)) {
birth_time = grid[ii].birth_time;
if (grid[ii].birth_year > grid[0].obs_year)
birth_time += date_getDaysInYear(grid[0].obs_year);
index = ii;
}
}
if (index > 0 && birth_time <= grid_time) {
sprintf(tmp, ",%.4f,%.4f", grid[index].x, grid[index].y);
strcat(coordStr, tmp);
strcpy(image_id, grid[index].image_id);
}
}
// Check cell death time
int n, cell_death_year;
double cell_death_time;
split_into_array(line, ',', &n, &col);
for (ii=0; ii<nCells; ii++) {
if (cell[ii].cell_id == atoi(col[0])) {
cell_death_time = death_time = cell[ii].death_time;
cell_death_year = cell[ii].death_year;
if (cell[ii].death_year > cell[0].birth_year)
death_time += date_getDaysInYear(cell[0].birth_year);
if (cell[ii].death_year == -1)
death_time = -1;
}
}
if (death_time < 0 || obs_time < (death_time + 0.01)) {
fprintf(fpOut, "%.6f,%s,%s,%s", obs_time, col[0], col[1], col[2]);
fprintf(fpOut, ",%s,%d,%.6f", col[3], cell_death_year, cell_death_time);
for (kk=4; kk<n; kk++)
fprintf(fpOut, ",%s", col[kk]);
fprintf(fpOut, ",%s,%.6f%s\n", image_id, disp_mag, coordStr);
}
free_char_array(&col, n);
// Clean up
FREE(grid_id);
FREE(grid_order);
FREE(p);
FREE(tmp);
FREE(coordStr);
return;
}
int main(int argc, char **argv)
{
dbf_header_t *header;
extern int currArg; // Pre-initialized to 1
int n=0;
char motion[512], deformation[512], connectivity[512], definition[512];
char cell[512], shape_type[25], line[1024], **col;
// Parse command line
if ((argc-currArg)<1) {
printf("Insufficient arguments.\n");
usage();
}
strcpy(motion, argv[currArg]);
strcpy(deformation, argv[currArg+1]);
strcpy(connectivity, argv[currArg+2]);
strcpy(definition, argv[currArg+3]);
strcpy(cell, argv[currArg+4]);
asfSplashScreen(argc, argv);
// Reading cell connectivity file
asfPrintStatus("Reading cell connectivity file ...\n");
FILE *fp = FOPEN(connectivity, "r");
int ii, kk, nCells = 0;
fgets(line, 1024, fp);
while (fgets(line, 1024, fp))
nCells++;
FCLOSE(fp);
rgps_cell_t *cells = (rgps_cell_t *) MALLOC(sizeof(rgps_cell_t)*nCells);
fp = FOPEN(connectivity, "r");
fgets(line, 1024, fp);
for (ii=0; ii<nCells; ii++) {
fgets(line, 1024, fp);
chomp(line);
split_into_array(line, ',', &n, &col);
cells[ii].cell_id = atoi(col[0]);
cells[ii].grid_id = atoi(col[1]);
cells[ii].order = atoi(col[2]);
free_char_array(&col, n);
}
FCLOSE(fp);
// Reading cell definition file
asfPrintStatus("Reading cell definition file ...\n");
fp = FOPEN(definition, "r");
fgets(line, 1024, fp);
while (fgets(line, 1024, fp)) {
chomp(line);
split_into_array(line, ',', &n, &col);
for (ii=0; ii<nCells; ii++)
if (cells[ii].cell_id == atoi(col[0])) {
cells[ii].birth_year = atoi(col[3]);
cells[ii].birth_time = atof(col[4]);
cells[ii].death_year = atoi(col[5]);
cells[ii].death_time = atof(col[6]);
}
free_char_array(&col, n);
}
FCLOSE(fp);
// Reading ice motion file
asfPrintStatus("Reading ice motion file ...\n");
read_header_config("RGPS_LP_GRID", &header, &n, shape_type);
fp = FOPEN(motion, "r");
int nGrids = 0;
fgets(line, 1024, fp);
chomp(line);
while (fgets(line, 1024, fp))
nGrids++;
FCLOSE(fp);
rgps_grid_t *grid = (rgps_grid_t *) MALLOC(sizeof(rgps_grid_t)*nGrids);
fp = FOPEN(motion, "r");
fgets(line, 1024, fp);
for (ii=0; ii<nGrids; ii++) {
fgets(line, 1024, fp);
chomp(line);
split_into_array(line, ',', &n, &col);
for (kk=0; kk<n; kk++) {
if (strcmp_case(header[kk].shape, "IMAGE_ID") == 0)
strcpy(grid[ii].image_id, col[kk]);
else if (strcmp_case(header[kk].shape, "GPID") == 0)
grid[ii].gpid = atoi(col[kk]);
else if (strcmp_case(header[kk].shape, "OBS_YEAR") == 0)
grid[ii].obs_year = atoi(col[kk]);
else if (strcmp_case(header[kk].shape, "OBS_TIME") == 0)
grid[ii].obs_time = atof(col[kk]);
else if (strcmp_case(header[kk].shape, "BIRTH_YEAR") == 0)
grid[ii].birth_year = atoi(col[kk]);
else if (strcmp_case(header[kk].shape, "BIRTH_TIME") == 0)
grid[ii].birth_time = atof(col[kk]);
else if (strcmp_case(header[kk].shape, "DEATH_YEAR") == 0)
grid[ii].death_year = atoi(col[kk]);
else if (strcmp_case(header[kk].shape, "DEATH_TIME") == 0)
grid[ii].death_time = atof(col[kk]);
else if (strcmp_case(header[kk].shape, "X_MAP") == 0)
grid[ii].x = atof(col[kk]);
else if (strcmp_case(header[kk].shape, "Y_MAP") == 0)
grid[ii].y = atof(col[kk]);
}
free_char_array(&col, n);
}
FCLOSE(fp);
// Reading ice deformation file
asfPrintStatus("Converting ice deformation file ...\n");
read_header_config("RGPS_DP_GRID", &header, &n, shape_type);
fp = FOPEN(deformation, "r");
FILE *fpOut = FOPEN(cell, "w");
fprintf(fpOut, "CELL_TIME,CELL_ID,STREAM,BIRTH_YEAR,BIRTH_TIME,DEATH_YEAR,"
"DEATH_TIME,N_OBS,OBS_YEAR,OBS_TIME,X_MAP,Y_MAP,LAT,LON,X_DISP,Y_DISP,"
"C_AREA,D_AREA,DTP,DUDX,DUDY,DVDX,DVDY,IMAGE_ID,DISP_MAG\n");
fgets(line, 1024, fp); // header line
while (fgets(line, 1024, fp)) {
chomp(line);
rgps_grid2cell(line, grid, nGrids, cells, nCells, header, fpOut);
}
FCLOSE(fp);
FCLOSE(fpOut);
FREE(grid);
FREE(cells);
return(0);
}
int cycle()
{
xmachine_memory_keratinocyte * xmemory = current_xmachine->xmachine_keratinocyte;
char_array id_temp;
char buffer[10];
/* find number of contacts/bonds*/
int contacts = get_num_xy_bonds() + get_num_z_bonds();
/* touching a wall counts as two contacts*/
if (get_x() == 0 || get_x() == substrate_width) {
contacts += 2;
}
if (get_y() == 0 || get_y() == substrate_width) {
contacts += 2;
}
if (contacts <= get_max_num_bonds(calcium_level)) {
/* cell comes out of G0*/
set_cycle(get_cycle()+1);
set_contact_inhibited_ticks(0);
} else {
/* cell enters G0*/
set_contact_inhibited_ticks(get_contact_inhibited_ticks()+1);
}
/* check to see if enough time has elapsed as to whether cell can divide*/
if (divide(get_type(), get_cycle())) {
int new_cycle = start_new_cycle_postion();
double new_x = get_new_coord(get_x(), FALSE);
double new_y = get_new_coord(get_y(), FALSE);
double new_z = get_z();
double new_diff_noise_factor = 0.9 + (rnd()*0.2);
double new_dir = rnd() * 2 * PI;
double new_motility = (0.5 + (rnd() * 0.5)) * get_new_motility(get_type(), calcium_level);
last_agent_id ++; /* generate a new ID*/
if (can_stratify(get_type(), calcium_level) && get_num_xy_bonds() >= MAX_NUM_LATERAL_BONDS) {
new_z = get_new_coord(get_z(), TRUE);
}
xmemory->cycle = start_new_cycle_postion();
init_char_array(&id_temp);
copy_char_array(&ID_CHAR, &id_temp);
add_char(&id_temp, '.');
sprintf(buffer, "%d", SPLITS);
add_char(&id_temp, buffer[0]);
printf("new cell: %s\n", id_temp.array);
add_keratinocyte_agent(
/*get_id()+1,*/
ID,
&id_temp,
/*last_agent_id, id*/
0, /* splits*/
get_type(), /* type*/
new_x, /* x*/
new_y, /* y*/
new_z, /* z*/
0, /* force_x*/
0, /* force_y*/
0, /* force_z*/
0, /* num_xy_bonds*/
0, /* num_z_bonds*/
0, /* num_stem_bonds*/
new_cycle, /* cycle*/
new_diff_noise_factor, /* diff_noise_factor*/
0, /* dead_ticks*/
0, /* contact_inhibited_ticks*/
new_motility, /* motility*/
new_dir, /* dir*/
get_range() /* range */
);
xmemory->splits++;
free_char_array(&id_temp);
}
return 0;
}
