/* -------------------------------------------------------------------- */
void BLBRotate(char *base, char *ext, int *reg, int *ansi)
{
char fn[15];
char ext2[4];
int *num;
strcpy(ext2, ext);
/*
* Are we doing ansi or normal
*/
if (changedir(cfg.helppath) == -1 ) return;
sprintf(fn, "%s.%2.2s@", base, ext);
if(*term.bold && filexists(fn))
{
ext2[2] = '@';
num = ansi;
}
else
{
num = reg;
}
if(*num == 0)
{
sprintf(fn, "%s.%s", base, ext2);
dumpf(fn);
}
else
{
sprintf(fn, "%s%d.%s", base, *num, ext2);
if (!filexists(fn))
{
sprintf(fn, "%s.%s", base, ext2);
dumpf(fn);
*num = 0;
}
else
{
dumpf(fn);
}
}
(*num)++;
changedir(cfg.homepath);
}
void TERMWINDOWMEMBER showRoomDescription(void)
{
OC.SetOutFlag(OUTOK);
label DescFile;
CurrentRoom->GetDescFile(DescFile, sizeof(DescFile));
if (CurrentUser->IsViewRoomDesc() && *DescFile && !Talley->Visited(thisRoom) && IsFilenameLegal(DescFile, NULL))
{
char pathToRoomDesc[128];
sprintf(pathToRoomDesc, sbs, cfg.roompath, DescFile);
if (filexists(pathToRoomDesc))
{
if (!CurrentUser->IsExpert())
{
CRmPrintfCR(getmsg(577));
}
dumpf(pathToRoomDesc, TRUE, 0);
doCR();
OC.SetOutFlag(OUTOK);
}
else
{
mPrintfCR(getmsg(427), cfg.Lroom_nym, DescFile);
}
doCR();
}
}
/* -------------------------------------------------------------------- */
void tutorial(char *filename)
{
int i;
char temp[14];
char oldverbose;
outFlag = OUTOK;
setio(whichIO, echo, outFlag);
if (!expert) mPrintf("\n <3J0>ump <3N0>ext <3P0>ause <3S0>top\n");
/* doCR(); */
if (changedir(cfg.helppath) == -1 ) return;
/* no bad files */
if (checkfilename(filename, 0) == ERROR)
{
mPrintf(" No helpfile %s", filename);
changedir(cfg.homepath);
return;
}
if (ambig(filename))
{
/* fill our directory array according to filename */
oldverbose = verbose;
verbose = FALSE;
filldirectory(filename);
verbose = oldverbose;
/* print out all the files */
for (i = 0; filedir[i].entry[0] &&
( dumpf(filedir[i].entry) != ERROR) ; i++);
if ( !i) mPrintf(" No helpfile %s", filename);
/* free file directory structure */
if(filedir != NULL)
_ffree((void *)filedir);
}
else
{
strcpy(temp, filename);
temp[strlen(temp)-1] = '@';
if (filexists(temp) && *term.bold)
dump(temp);
else
dumpf(filename);
}
/* go to our home-path */
changedir(cfg.homepath);
}
void CreateConfigurationFile(int FileNameIndex, int FileDataIndex, Bool PrintStuff)
{
discardable *d;
if (!filexists(citfiles[FileNameIndex]))
{
if ((d = readData(16, FileDataIndex, FileDataIndex)) != NULL)
{
FILE *File;
if ((File = fopen(citfiles[FileNameIndex], FO_W)) != NULL)
{
if (PrintStuff)
{
#ifndef WINCIT
cPrintf(getcfgmsg(133), citfiles[FileNameIndex]);
doccr();
#endif
}
const char **Data = (const char **) d->aux;
for (int i = 0; !SameString(Data[i], getcfgmsg(244)); i++)
{
fprintf(File, getmsg(472), Data[i], bn);
}
fclose(File);
}
else
{
if (PrintStuff)
{
#ifndef WINCIT
cPrintf(getcfgmsg(134), citfiles[FileNameIndex]);
doccr();
#endif
}
}
discardData(d);
}
else
{
if (PrintStuff)
{
cOutOfMemory(51);
}
}
}
}
void about_callb(GtkWidget *wdg, gpointer app) {
GtkWidget *content=NULL, *lbl;
gchar *fname = NULL,*utf8_msg=NULL;
gsize br,bw;
GError *ger;
static gchar *f1=NULL;
static gchar *f2 = "splash.jpg";
static gchar *msg = "\nGEOMORPH 0.6\nhttp://geomorph.sourceforge.net\n\n(c) Patrice St-Gelais 2003-2009 (GPL)\[email protected]\n\nGerman translation by\nSimon Donike (2005-2008) and Tim Schuermann (2004)";
if (!f1) {
f1 = x_malloc(2+strlen(PKGDATADIR)+strlen(VERSION)+strlen(f2), "Splash image");
strcpy(f1,PKGDATADIR);
strcat(f1,VERSION);
strcat(f1,"/");
strcat(f1,f2);
}
if (!utf8_msg) {
utf8_msg = g_locale_to_utf8(msg,-1,&br,&bw,&ger);
}
if (!utf8_msg)
utf8_msg = msg;
if (filexists(f1))
fname = f1;
else
if (filexists(f2))
fname = f2;
if (fname) {
content = gtk_vbox_new(FALSE,0);
gtk_container_add(GTK_CONTAINER(content),gtk_image_new_from_file(fname));
lbl = gtk_label_new(utf8_msg);
gtk_label_set_justify(GTK_LABEL(lbl),GTK_JUSTIFY_CENTER);
gtk_container_add(GTK_CONTAINER(content),lbl);
gtk_widget_show_all(content);
}
if (content)
modal_dialog (content, " ", NULL, NULL, NULL, GTK_WIN_POS_CENTER, TRUE);
else
my_msg(utf8_msg,INFO);
}
/* -------------------------------------------------------------------- */
static void reciveFiles(void)
{
cPrintf(" Receiving mail and rooms.");
doccr();
wxrcv(cfg.temppath, roomdatain,
(char)strpos((char)tolower(node.ndprotocol[0]), extrncmd));
if (!filexists(roomdatain))
{
drop_dtr();
netFailed = TRUE;
}
}
/* -------------------------------------------------------------------- */
static void reciveRequest(void)
{
cPrintf(" Receiving room request file.");
doccr();
wxrcv(cfg.temppath, roomreqin,
(char)strpos((char)tolower(node.ndprotocol[0]), extrncmd));
if (!filexists(roomreqin))
{
drop_dtr();
netFailed = TRUE;
}
}
void TERMWINDOWMEMBER receiveFiles(const protocols *theProt)
{
cPrintf(getnetmsg(101));
doccr();
wxrcv(LocalTempPath, roomdataIn, theProt);
if (!filexists(roomdataIn))
{
CITWINDOW *w = ScreenSaver.IsOn() ? NULL : CitWindowsMsg(NULL, getmsg(685), getmsg(74));
Hangup();
netFailed = TRUE;
if (w)
{
destroyCitWindow(w, FALSE);
}
}
}
/* -------------------------------------------------------------------- */
void setfileinfo(void)
{
label filename;
label uploader;
char comments[64];
char path[80];
struct fInfo old;
getNormStr("filename", filename, FILESIZE, ECHO);
sprintf(path, "%s\\%s", roomBuf.rbdirname, filename);
/* no bad file names */
if (checkfilename(filename, 0) == ERROR) {
mPrintf("\n No file %s.\n ", filename);
return;
}
/* no file name? */
if (!filexists(path)) {
mPrintf("\n No file %s.\n ", filename);
return;
}
if (!getInfo(filename, &old)) {
strcpy(uploader, logBuf.lbname);
} else {
strcpy(uploader, old.uploader);
}
getString("comments", comments, 64, FALSE, TRUE, "");
entercomment(filename, uploader, comments);
sprintf(msgBuf->mbtext, "File info changed for file %s by %s",
filename, logBuf.lbname);
trap(msgBuf->mbtext, T_AIDE);
}
static void analyzeIdentifier(char **ch, int modelNumber, tree *tr)
{
char
ident[2048] = "",
model[2048] = "",
thisModel[2048] = "";
int
i = 0,
n,
j,
containsComma = 0;
while(**ch != '=')
{
if(**ch != ' ' && **ch != '\t')
{
ident[i] = **ch;
i++;
}
*ch = *ch + 1;
}
n = i;
i = 0;
for(i = 0; i < n; i++)
if(ident[i] == ',')
containsComma = 1;
if(!containsComma)
{
printf("Error, model file must have format: DNA or AA model, then a comma, and then the partition name\n");
exit(-1);
}
else
{
boolean
useProteinSubstitutionFile = FALSE,
found = FALSE;
int
openBracket = 0,
closeBracket = 0,
openPos = 0,
closePos = 0;
i = 0;
while(ident[i] != ',')
{
if(ident[i] == '[')
{
openPos = i;
openBracket++;
}
if(ident[i] == ']')
{
closePos = i;
closeBracket++;
}
model[i] = ident[i];
i++;
}
if(closeBracket > 0 || openBracket > 0)
{
if((closeBracket == 1) && (openBracket == 1) && (openPos < closePos))
useProteinSubstitutionFile = TRUE;
else
{
printf("\nError: Apparently you want to specify a user-defined protein substitution model that shall be read from file\n");
printf("It must be enclosed in opening and closing bracktes like this: [fileName]\n\n");
printf("you specified: %s\n\n", model);
exit(-1);
}
}
if(useProteinSubstitutionFile)
{
char
protFileName[2048] = "";
int
pos,
k,
lower = 0,
upper = i - 1;
while(model[lower] == '[' || model[lower] == ' ')
lower++;
while(model[upper] == ']' || model[upper] == ' ')
upper--;
assert(lower < upper);
for(k = lower, pos = 0; k <= upper; k++, pos++)
protFileName[pos] = model[k];
protFileName[pos] = '\0';
if(!filexists(protFileName))
{
printf("\n\ncustom protein substitution file [%s] you want to use does not exist!\n", protFileName);
printf("you need to specify the full path\n");
printf("the file name shall not contain blanks!\n\n");
exit(0);
}
strcpy(tr->initialPartitionData[modelNumber].proteinSubstitutionFileName, protFileName);
/*printf("%s \n", tr->initialPartitionData[modelNumber].proteinSubstitutionFileName);*/
tr->initialPartitionData[modelNumber].protModels = PROT_FILE;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = TRUE;
tr->initialPartitionData[modelNumber].dataType = AA_DATA;
}
else
{
/* AA */
for(i = 0; i < NUM_PROT_MODELS && !found; i++)
{
strcpy(thisModel, protModels[i]);
if(strcasecmp(model, thisModel) == 0)
{
tr->initialPartitionData[modelNumber].protModels = i;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = TRUE;
tr->initialPartitionData[modelNumber].dataType = AA_DATA;
found = TRUE;
}
if(i != GTR && i != GTR_UNLINKED)
{
strcpy(thisModel, protModels[i]);
strcat(thisModel, "F");
if(strcasecmp(model, thisModel) == 0)
{
tr->initialPartitionData[modelNumber].protModels = i;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = AA_DATA;
found = TRUE;
}
}
if(found && (tr->initialPartitionData[modelNumber].protModels == GTR || tr->initialPartitionData[modelNumber].protModels == GTR_UNLINKED))
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
}
if(!found)
{
if(strcasecmp(model, "DNA") == 0)
{
tr->initialPartitionData[modelNumber].protModels = -1;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = DNA_DATA;
found = TRUE;
}
else
{
if(strcasecmp(model, "BIN") == 0)
{
tr->initialPartitionData[modelNumber].protModels = -1;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = BINARY_DATA;
found = TRUE;
}
else
{
if(strcasecmp(model, "MULTI") == 0)
{
tr->initialPartitionData[modelNumber].protModels = -1;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = GENERIC_32;
found = TRUE;
}
else
{
if(strcasecmp(model, "CODON") == 0)
{
tr->initialPartitionData[modelNumber].protModels = -1;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = GENERIC_64;
found = TRUE;
}
}
}
}
}
if(!found)
{
printf("ERROR: you specified the unknown model %s for partition %d\n", model, modelNumber);
exit(-1);
}
}
i = 0;
while(ident[i++] != ',');
tr->initialPartitionData[modelNumber].partitionName = (char*)rax_malloc((n - i + 1) * sizeof(char));
j = 0;
while(i < n)
tr->initialPartitionData[modelNumber].partitionName[j++] = ident[i++];
tr->initialPartitionData[modelNumber].partitionName[j] = '\0';
}
}
int main(int argc, char **argv)
{
/**************************************************************/
/************************** FROM previous version
CVBoardTypes VMEBoard;
short Device=0;
short Link=0;
int32_t BHandle;
VMEBoard=cvV1718;
Device=0;
if (CAENVME_Init( VMEBoard, Link, Device, &BHandle) != cvSuccess){
printf("error opening the device\n%s","");
//exit(1);
}
**************************************************/
// if (argc<=1){printf("%s\n"," ... consider \" ./gregory -r /tmp/lockfile\" for gregory.net");}
///////////////////////////////////// lockfile from argument (.net)
char lockfile[180]="";
Targs args;
parse_arguments(argc,argv, &args);//in main=normal var, outsourced with
if (args.rvalue!=NULL){strncpy( lockfile , args.rvalue, 180 );}
printf( "lockfile is ... %s\n", lockfile );
// ENVIRONMENT-------------
// char* BinPath, *DataPath;
BinPath = getenv ("GREGORY");
if (BinPath==NULL){
BinPath=new char[2]; strcpy(BinPath, "./");
}
DataPath = getenv ("GREGORY_DATA");
if (DataPath==NULL){
DataPath=new char[2]; strcpy(DataPath, "./");
}
// printf("%s\n"," export GREGORY=");
// printf("%s\n"," export GREGORY_DATA=");
// printf("%s\n","");
printf("%s\n","");
printf( "binary path: %s (not used yet...)\n",BinPath );
printf( "data path: %s\n",DataPath );
for (int ch=0;ch<8;ch++){
WaveBinfh[ch]=NULL;
}
// FILL THE TABLE OF FUNCTIONS ===========================TABLE
int ic=0;
sprintf( compile_table[ic].name, "%s", "get_status" );
compile_table[ic].addr=(functiontype_i)&vme_get_stat_reg;
ic++;
sprintf( compile_table[ic].name, "%s", "get_version" );
compile_table[ic].addr=(functiontype_i)&vme_get_version;
ic++;
/*
sprintf( compile_table[ic].name, "%s", "v1718_control" );
compile_table[ic].addr=(functiontype_i)&v1718_control;
ic++;
*/
//-----------------------------------------------------
// printf("\nlist of known functions\n%s" , "");
// for (icc=0;icc<ic;icc++){
// printf( " %s\n", compile_table[icc].name );
// }
printf("%50c\n",'-');
// END OF TABLE ==========================================TABLE
mmap_file=create_shared_memory( 1, "vme" );
mmap_file2=create_shared_memory( 1, "vmeOUT" );
mmap_fileS=create_shared_memory( 2, "socket" );
mmap_fileO=create_shared_memory( 3, "oscilo" );
mmap_fileC=create_shared_memory( 4, "counter" );
/*
//====================================== MMAP ====== communication
system("dd if=/dev/zero of=mmap.in bs=4096 count=1 2> /dev/null");
if ((mmapfd = open("mmap.in", O_RDWR, 0)) == -1) err(1, "open");
mmap_file=(char*)mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_FILE|MAP_SHARED, mmapfd, 0);
if (mmap_file == MAP_FAILED) errx(1, "either mmap");
strcpy(mmap_file, "... this is an initial input.\0\0\0" ); // "acq_setup.xml\nrun=1\n";
//====================================== MMAP ====== communication
//====================================== MMAP ====== communication
system("dd if=/dev/zero of=mmap.out bs=4096 count=1 2> /dev/null");
if ((mmapfd2 = open("mmap.out", O_RDWR, 0)) == -1) err(1, "open");
mmap_file2=(char*)mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_FILE|MAP_SHARED, mmapfd2, 0);
if (mmap_file2 == MAP_FAILED) errx(1, "either mmap2");
strcpy(mmap_file2, "... no output at the moment...\0\0\0" ); // "acq_setup.xml\nrun=1\n";
//====================================== MMAP ====== communication
//====================================== MMAP ====== communication server sock
system("dd if=/dev/zero of=mmap.socket bs=4096 count=1 2> /dev/null");
if ((mmapfdS = open("mmap.socket", O_RDWR, 0)) == -1) err(1, "open");
mmap_fileS=(char*)mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_FILE|MAP_SHARED, mmapfdS, 0);
if (mmap_fileS == MAP_FAILED) errx(1, "either mmapS");
strcpy(mmap_fileS, "...................o=ok;X=error...\0\0\0" ); // "acq_setup.xml\nrun=1\n";
//====================================== MMAP ====== communication
//====================================== MMAP ====== communication server OSCILO
system("dd if=/dev/zero of=mmap.oscilo bs=4096 count=1 2> /dev/null");
if ((mmapfdO = open("mmap.oscilo", O_RDWR, 0)) == -1) err(1, "open");
mmap_fileO=(char*)mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_FILE|MAP_SHARED, mmapfdO, 0);
if (mmap_fileO == MAP_FAILED) errx(1, "either mmapS");
strcpy(mmap_fileO, ".......no command to Oscilo...\0\0\0" ); // "acq_setup.xml\nrun=1\n";
//====================================== MMAP ====== communication
*/
/*
//====================================== MMAP ====== communication 4MB
char cmd3[100];
char fname3[100];
sprintf( cmd3,"dd if=/dev/zero of=%s/mmap.histo bs=4096 count=1024 2> /dev/null",
DataPath );
sprintf( fname3, "%s/mmap.histo", DataPath );
system( cmd3);
if ((mmapfd3 = open( fname3, O_RDWR, 0)) == -1) err(1, "open");
mmap_file3=(char*)mmap(NULL, 4194304 , PROT_READ|PROT_WRITE, MAP_FILE|MAP_SHARED, mmapfd3, 0);
if (mmap_file3 == MAP_FAILED) errx(1, "either mmap3");
*/
// strcpy(mmap_file3, "... no output at the moment...\0\0\0" ); // "acq_setup.xml\nrun=1\n";
//====================================== MMAP ====== communication
//===========histogram array
//http://root.cern.ch/root/roottalk/roottalk01/3614.html
//hclus[9] = new TH1F("name","descr",100,0,1000); hclus[9]->Fill(1);
//- BIG TRICK with allocation. We pray 4MB isok
// OBJECTS have to do TMapFile ... virtual classes etc.
//TH1F **harray;
// harray=new(mmap_file3) TH1F*[8];
//http://root.cern.ch/root/html/TMapFile.html#TMapFile:Add
//http://root.cern.ch/root/roottalk/roottalk98/2340.html
//http://root.cern.ch/root/roottalk/roottalk04/0352.html
//http://root.cern.ch/root/roottalk/roottalk04/0341.html
// initialize threads................................ALLOCATE
tinfo = (thread_info *)calloc(NTHREADS , sizeof(thread_info) );
if (tinfo == NULL) {printf("calloc failed%s\n", "");return 1;}
for (int tnum = 0; tnum < NTHREADS; tnum++) {tinfo[tnum].thread_num=-1;}
//==========================================CORE
int cmd_param[100]; //set of parameters// minimum 10!
int i=0; // CMD counter
int res;
printf("\n.h for help\n\n%s", "");
//---------------------infinite loop ----------------------------
char prefix[20]=" ";
char posfix[20]="...";
while(1==1){
i++;
usleep(100*1000); // 50ms is enough to finish thread..
cmd_line( i ); // shows PROMPT; reads INPUT to cmd_buffer;
res=get_cmd_name( cmd_param );// 1=quit; 2=list
if (res != 0 ){
// .n newrun? .r runnumber! .ls !
// .s status .l LOAD! .s save .c comment .f file .n numberrun ??
// filename send with 'start (maybe run and file commands before)'
if ( strcmp(cmd_buffer,".q")==0 ){ //.q
printf("%s quitting %s\n", prefix, posfix );
global_flag_quit=-1; // only LOOP itself
strcpy(mmap_file,"quit\0"); // send it to gregory.mmap
strcpy(mmap_fileO,"quit\0"); // send it oscilo
// strcpy(mmap_fileS,"quit\0"); // send it oscilo
strcpy(mmap_fileC,"quit\0"); // send it oscilo
// i will need to shutdown the socket
int socket_fd=atoi(mmap_fileS); // get (slowly) handle
shutdown( socket_fd, 2 );
break; // BREAK FROM WHILE 1==1 .... quit
} // .q
if ( strcmp(cmd_buffer,".s")==0 ){ //.s
if ( mmap_fileS[16] == 'o' ){
int socket_fd=atoi(mmap_fileS); // bad trick -get handle
printf("%s socket %d port %s %s\n", prefix,socket_fd,PORT,posfix);
// sprintf(outline,"%d %d %d\n%c", 1, 2 ,3 , '\0');
int socker[3]; // 32 bit ZH data for socket e0000001 e0010123 0xf0000000
socker[0]=0xe0010000;
socker[1]=0x000100ff;
// socker[2]=0x0001; //channel
// socker[3]=0x00ff; //value
socker[2]=0xf0000000;
// socker[5]=0x0000;
// int tmp=send(socket_fd, outline, strlen(outline), 0 );
int tmp=send(socket_fd, socker, sizeof(socker), 0 );
if (tmp < 0){
printf(" !...socket error ... i block mmap.socket from now\n");
mmap_fileS[16] = 'X';
//shutdown( socket_fd, 2 );
}
}else{ // socked_fd blocked [16]==X not "o"
printf(" !...socket blocked due to ealier error%s\n","");
}
} // .s
//--- exact match strcmp
//--- strstr means line start match
if ( strstr(cmd_buffer,".r")==cmd_buffer ){ // .r RUN number
char oldr[70];
int newri=1;
char cmdls[200];
sprintf( cmdls,"ls -1tr %s | grep run | grep \\.dat |tail -1 | awk -F _ '{sub(\"run\",\"\");print $1}' > RUNNUM ", DataPath );
system(cmdls);
sprintf( cmdls,"ls -ltrh %s/run*.dat 2>/dev/null | tail -1 | awk '{print $9,\" \",$5}' > RUNNAMELAST ", DataPath );
system(cmdls);
sprintf( cmdls,"ls -tr1 %s| grep -ie '^run[0-9]' | sed 's/run0*//' | cut -d. -f 1 | cut -d _ -f 1 | sort -n | tail -1 > RUNNEXT ", DataPath );
system(cmdls);
//============= read ll -h output with size ==========
FILE *frn=fopen("RUNNAMELAST","r");
if (frn!=NULL){
memset(&oldr[0], 0, sizeof(oldr));
fread( oldr, 1, sizeof(oldr), frn );
oldr[ strlen(oldr)-1 ]='\0';
fclose(frn);
printf("%s ... LAST SAVED ON DISK\n", oldr );
}
//----------------------------------
frn=fopen("RUNNUM","r");
if (frn!=NULL){
fread( oldr, 1, sizeof(oldr), frn );
fclose(frn);
if ( strlen(oldr)>0){
sscanf(oldr,"%d", &newri ); //from oldr => newri
printf("CURR /on disk/ RUN =%5d\n", newri );
//printf("NEXT proposed RUN =%5d\n", newri+1 );
}
}//no RUNNUM file
//-----------------------------
frn=fopen("RUNNEXT","r");
if (frn!=NULL){
fread( oldr, 1, sizeof(oldr), frn );
fclose(frn);
if ( strlen(oldr)>0){
sscanf(oldr,"%d", &newri ); //from oldr => newri
// printf("CURR /on disk/ RUN =%5d\n", newri );
printf("NEXT proposed RUN =%5d\n", newri+1 );
}else{ newri=1;}
}//no RUNNUM file
//-----------------------------
printf("%s to change the run number use run x %s\n",prefix,posfix);
printf("%s run 0 ... means no data file %s\n",prefix,posfix);
sprintf(cmdls,"run %d", newri+1 );
// strcpy( mmap_file, "run " );
strcpy( mmap_file, cmdls );
printf("%s run %d ... command was sent%s\n",prefix,newri+1, posfix);
} // .r RUN NUMBER
//means - '.ls' on the line start
if ( strstr(cmd_buffer,".ls")==cmd_buffer ){ // .ls
// printf("%s listing %s\n", prefix, posfix );
for (int tnum = 0; tnum < NTHREADS; tnum++) {
if ( (tnum==0) && (tinfo[tnum].thread_num==1) ){
printf("[--M--] process %d (of %d): measurement thread ACTIVE\n", tnum+1, NTHREADS);}
else if(tnum==0) {
printf("[--M--] process %d (of %d): measurement thread NOT LOADED\n", tnum+1, NTHREADS);}
if ( (tnum==1) && (tinfo[tnum].thread_num==2 )){
printf("[--M--] process %d (of %d): socket thread ACTIVE\n", tnum+1, NTHREADS);}
else if(tnum==1) {
printf("[--M--] process %d (of %d): socket thread NOT LOADED\n", tnum+1, NTHREADS);}
if ( (tnum==2) && (tinfo[tnum].thread_num==3 )){
printf("[--M--] process %d (of %d): oscilo thread ACTIVE\n", tnum+1, NTHREADS);}
else if(tnum==2) {
printf("[--M--] process %d (of %d): oscilo thread NOT LOADED\n", tnum+1, NTHREADS);}
if ( (tnum==3) && (tinfo[tnum].thread_num==4 )){
printf("[--M--] process %d (of %d): Countr thread ACTIVE\n", tnum+1, NTHREADS);}
else if(tnum==3) {
printf("[--M--] process %d (of %d): Countr thread NOT LOADED\n", tnum+1, NTHREADS);}
/*
if (tinfo[tnum].thread_num>0){
printf(" process %d (of %d): ACTIVE\n", tnum+1, NTHREADS);
// printf(" file size %d MB\n", 0 );
}else{
if (tinfo[tnum].thread_num==1){
printf(" process %d (of %d): measurement thread NOT LOADED\n", tnum+1, NTHREADS);}
else if (tinfo[tnum].thread_num==2){
printf(" process %d (of %d): socket thread NOT LOADED\n", tnum+1, NTHREADS);}
else {printf(" process %d (of %d): socket thread NOT LOADED\n", tnum+1, NTHREADS);}
}
*/
}// NTHREADS
printf("[--M--] last message:\n %s\n", mmap_file2 );
char text[100]; time_t now = time(NULL);
struct tm *t = localtime(&now);
strftime(text, sizeof(text)-1, "%Y/%m/%d_%H:%M:%S ", t);
printf("%s ...\n", text);
fflush(stdin);
global_flag_list=1;
/* //======= THIS IS A WAY TO PRINT ON PORT 7777 =======
int socket_fd=atoi(mmap_fileS);
if (socket_fd != -1) {
if (send(socket_fd, "\nAHOJ\n" , 6, 0) == -1) perror("ls");
}
*/
} // .ls list.............
if ( strcmp(cmd_buffer,".l")==0 ){ // .l LOAD
// printf("%s LOADing %s\n", prefix, posfix );
int tnum, pth_res;
for (tnum = 0; tnum < NTHREADS; tnum++) {
if (tinfo[tnum].thread_num<0){
tinfo[tnum].thread_num = tnum + 1;
// if (tnum==0){
pth_res = pthread_create(&tinfo[tnum].thread_id, NULL,
&loop_thread, &tinfo[tnum] );
// }
// if (tnum==1){
// pth_res = pthread_create(&tinfo[tnum].thread_id, NULL,
// &loop_thread2, &tinfo[tnum] );
// }
if ( pth_res != 0){printf("pthread_create failed%s\n","");return 1;}
}// _num<0 == not active thread=> you can reload
else{
printf("%s thread %d is already active== %d %s no action\n", prefix,tnum, tinfo[tnum].thread_num, posfix );
// printf(" thread %d is already active== %d (no action)\n", tnum, tinfo[tnum].thread_num);
}// else already active
}//for all threads
} // .. LOAD
/* if ( strcmp(cmd_buffer,".s")==0 ){ // .s LOAD SERVER */
/* printf("%s loading network Server %s\n", prefix, posfix ); */
/* int tnum, pth_res; */
/* for (tnum = 0; tnum < NTHREADS; tnum++) { */
/* if (tinfo[tnum].thread_num<0){ */
/* tinfo[tnum].thread_num = tnum + 1; */
/* pth_res = pthread_create(&tinfo[tnum].thread_id, NULL, */
/* &loop_thread, &tinfo[tnum] ); */
/* if ( pth_res != 0){printf("pthread_create failed%s\n","");return 1;} */
/* }// _num<0 == not active thread=> you can reload */
/* else{ */
/* printf("%s thread %d is already active== %d %s no action\n", prefix,tnum, tinfo[tnum].thread_num, posfix ); */
/* // printf(" thread %d is already active== %d (no action)\n", tnum, tinfo[tnum].thread_num); */
/* }// else already active */
/* }//for all threads */
/* } // .. LOAD SERVER */
if ( strcmp(cmd_buffer,".h")==0 ){ // .h
// printf("%s help %s\n", prefix, posfix );
printf("%s .h %s help\n", prefix, posfix );
printf("%s .l %s LOAD ALL THREADS\n", prefix, posfix );
printf("%s .s %s TEST network server on port %s\n", prefix, posfix , PORT );
printf("%s .r %s look at run number\n", prefix, posfix );
printf("%s .ls %s list\n", prefix, posfix );
printf("%s .q %s QUIT\n", prefix, posfix );
printf("%s ------ %s measurement thread commands ------:\n" , prefix, posfix );
printf("%s qu %s quit \n" , prefix, posfix);
printf("%s sta %s start \n" , prefix, posfix );
printf("%s te %s test = start +no save\n" , prefix, posfix );
printf("%s sto %s STOP \n" , prefix, posfix );
printf("%s sts %s status \n" , prefix, posfix );
printf("%s cl %s clear histo \n" , prefix, posfix );
printf("%s hi %s histogram (save histogram to txt) \n" , prefix, posfix );
printf("%s wa %s waveform (save waveform to txt,mmap) \n" , prefix, posfix ); //not used anymore
printf("%s tr %s trigger \n" , prefix, posfix );
printf("%s in %s init \n" , prefix, posfix );
// printf("%s aon %s autosaveON \n" , prefix, posfix );
// printf("%s aof %s autosaveOFF\n" , prefix, posfix );
printf("%s won %s wavesaveON\n" , prefix, posfix );
printf("%s wof %s wavesaveOFF\n" , prefix, posfix );
printf("%s pd %s probe_down \n" , prefix, posfix );
printf("%s pu %s probe_up \n" , prefix, posfix );
printf("%s re %s restart \n" , prefix, posfix );
printf("%s don %s displayON \n" , prefix, posfix );
printf("%s dof %s displayOFF \n" , prefix, posfix );
} // .h ==============================================================HELP
} // was an internal command==============================
else{
if (DEBUGGREG>0)
printf(" cmd_name=%s\n", cmd_name);
// strcpy( mmap_file, cmd_buffer ); //command directly to mmap_file........
//translate to better phrases .....................
if (strstr(cmd_buffer,"qu")!=NULL) strcpy( mmap_file, "quit" );
if (strstr(cmd_buffer,"qu")!=NULL) strcpy( mmap_fileO, "quit" );
// if (strstr(cmd_buffer,"qu")!=NULL) strcpy( mmap_fileS, "quit" );
if (strstr(cmd_buffer,"qu")!=NULL) strcpy( mmap_fileC, "quit" );
if (strstr(cmd_buffer,"run")!=NULL) strcpy( mmap_file, cmd_buffer ); // send the number
if (strstr(cmd_buffer,"sta")!=NULL) strcpy( mmap_file, "start" );
if (strstr(cmd_buffer,"sta")!=NULL) strcpy( mmap_fileO, "start" ); //Oscilo
if (strstr(cmd_buffer,"sta")!=NULL) strcpy( mmap_fileC, "start" ); //Oscilo
if (strstr(cmd_buffer,"te")!=NULL) strcpy( mmap_file, "test" ); //must do wa
if (strstr(cmd_buffer,"te")!=NULL) strcpy( mmap_fileO, "test" ); //Oscilo
if (strstr(cmd_buffer,"te")!=NULL) strcpy( mmap_fileC, "test" ); //Oscilo
if (strstr(cmd_buffer,"go")!=NULL) printf(".. not programmed yet\n%s","");
if (strstr(cmd_buffer,"go")!=NULL) strcpy( mmap_fileO, "go" ); //Oscilo
if (strstr(cmd_buffer,"go")!=NULL) strcpy( mmap_fileC, "go" ); //Oscilo
if (strstr(cmd_buffer,"sto")!=NULL) strcpy( mmap_file, "STOP" );
if (strstr(cmd_buffer,"sto")!=NULL) strcpy( mmap_fileO, "stop" ); //Oscilo
if (strstr(cmd_buffer,"sto")!=NULL) strcpy( mmap_fileC, "stop" ); //Oscilo
if (strstr(cmd_buffer,"stat")!=NULL)strcpy( mmap_file, "status" );
if (strstr(cmd_buffer,"sts")!=NULL) strcpy( mmap_file, "status" );
if (strstr(cmd_buffer,"cl")!=NULL) strcpy( mmap_file, "clear" );
if (strstr(cmd_buffer,"hi")!=NULL) strcpy( mmap_file, "histogram" );
// not used anymore
if (strstr(cmd_buffer,"wa")!=NULL) strcpy( mmap_file, "waveform" ); // ? is it?
if (strstr(cmd_buffer,"tr")!=NULL) strcpy( mmap_file, "trigger" );
if (strstr(cmd_buffer,"in")!=NULL) strcpy( mmap_file, "init" );
//notused anymore ... autosave==1
if (strstr(cmd_buffer,"aon")!=NULL) strcpy( mmap_file, "autosaveON" );
if (strstr(cmd_buffer,"aof")!=NULL) strcpy( mmap_file, "autosaveOFF" );
//NOW autosave==111 ! wav file
if (strstr(cmd_buffer,"won")!=NULL) strcpy( mmap_file, "wavesaveON" );
if (strstr(cmd_buffer,"wof")!=NULL) strcpy( mmap_file, "wavesaveOFF" );
if (strstr(cmd_buffer,"pd")!=NULL) strcpy( mmap_file, "probe_down" );
if (strstr(cmd_buffer,"pu")!=NULL) strcpy( mmap_file, "probe_up" );
if (strstr(cmd_buffer,"re")!=NULL) strcpy( mmap_file, "restart" );
if (strstr(cmd_buffer,"don")!=NULL) strcpy( mmap_file, "displayON" );
if (strstr(cmd_buffer,"dof")!=NULL) strcpy( mmap_file, "displayOFF" );
if (strstr(cmd_buffer,"ac")!=NULL) strcpy( mmap_fileO, "accumulateXMGR" );
// if (strstr(cmd_buffer,"")!=NULL) strcpy( mmap_file, "" );
// if (strstr(cmd_buffer,"")!=NULL) strcpy( mmap_file, "" );
// NO this would spam the output printf("%s\n", mmap_file2 );
fflush(stdin);
/* for (icc=0;icc<ic;icc++){ */
/* if ( strcmp(cmd_name,compile_table[icc].name)==0){ */
/* if (DEBUGGREG>0) */
/* printf(" matches =%d\n", icc); */
/* compile_table[icc].addr( cmd_param[0] ); */
/* }//match */
/* } //for icc=0--- */
/* //PERFORM ON YOUR OWN */
}// else ===== real command
}// INF.WHILE.
//==========================================CORE
// NOW QUITTING ROUTINES ===========================
global_flag_quit=-1; // SEND SIGNAL TO THREAD
printf("[##M##] ........master is waiting for threads\n");fflush(stdin);
// printf("%s\n","------------------------------Thread-close-begin");fflush(stdin);
for (int tnum = 0; tnum < NTHREADS; tnum++) {
printf("[##M##]... waiting thread %d finish ...\n", tnum+1);fflush(stdin);
int pth_res = pthread_join(tinfo[tnum].thread_id, NULL );
if (pth_res != 0){printf("pthread_join failed%s'\n","");
//exit(1); // if no thread => quit to socat doesnot work
}
printf("[##M##] master join : thread %d (of %d) arrived\n",
tnum+1, NTHREADS);
// tinfo[tnum].thread_num, NTHREADS);
fflush(stdin);
// printf("thread %d/%d\n", tnum+1, NTHREADS);fflush(stdin);
}
if (tinfo!=NULL){ free(tinfo);}
printf("%s\n","------------------------------Thread-close-end");fflush(stdin);
// REMOVE LOCKFILE IS EXISTT ********************************
// this is important to let the script know "gregory has ended"
// ................................socat has a problem with kill
if ( filexists(lockfile)==1 ) {
printf("File %s exist\n", lockfile );fflush(stdin);
if( remove( lockfile ) != 0 ){
perror( "Error deleting file" );
}else{
puts( "File successfully deleted" );
}
}
exit(0);
}//===================================================================MAIN
static void get_args(int argc, char *argv[], parameters *params, int processID)
{
int i, k, res;
int number;
#define NUM_OPT 11
char *options[NUM_OPT]= {"-n1", "-n2", "-n3", "-n4", "-A", "-B", "-C", "-p", "-n", "-t", "-h"};
char fileName[1024];
char runName[1024];
int set[NUM_OPT];
/* init */
params->n1 = 0;
params->n2 = 0;
params->n3 = 0;
params->n4 = 0;
params->useExternalTraceFile = 0;
params->permutations = 0;
params->computeTracefileOnly = 0;
/*params->randomizedSelection = 0;*/
strcpy(params->outFileName, "outfile");
/***************/
for(i = 0; i < NUM_OPT; i++)
set[i] = 0;
for(i = 1; i < argc; i++)
{
int found = 0;
for(k = 0; k < NUM_OPT && !found; k++)
if(strcmp(options[k], argv[i]) == 0)
found = 1;
k--;
if(found)
{
switch(k)
{
case 0:
if(i == argc - 1)
{
printf("Error, argument expected after option %s\n", options[k]);
exit(-1);
}
else
{
res = sscanf(argv[++i],"%d", &number);
if(res == 0 || res == EOF)
{
printf("argument of %s must be an integer number\n", options[k]);
exit(-1);
}
}
params->n1 = number;
set[k] = 1;
break;
case 1:
if(i == argc - 1)
{
printf("Error, argument expected after option %s\n", options[k]);
exit(-1);
}
else
{
res = sscanf(argv[++i],"%d", &number);
if(res == 0 || res == EOF)
{
printf("argument of %s must be an integer number\n", options[k]);
exit(-1);
}
}
params->n2 = number;
set[k] = 1;
break;
case 2:
if(i == argc - 1)
{
printf("Error, argument expected after option %s\n", options[k]);
exit(-1);
}
else
{
res = sscanf(argv[++i],"%d", &number);
if(res == 0 || res == EOF)
{
printf("argument of %s must be an integer number\n", options[k]);
exit(-1);
}
}
params->n3 = number;
set[k] = 1;
break;
case 3:
if(i == argc - 1)
{
printf("Error, argument expected after option %s\n", options[k]);
exit(-1);
}
else
{
res = sscanf(argv[++i],"%d", &number);
if(res == 0 || res == EOF)
{
printf("argument of %s must be an integer number\n", options[k]);
exit(-1);
}
}
params->n4 = number;
set[k] = 1;
break;
case 4:
if(i == argc - 1)
{
printf("Error, argument expected after option %s\n", options[k]);
exit(-1);
}
else
{
strcpy(fileName, argv[++i]);
if(!filexists(fileName))
{
printf("file %s does not exist\n", fileName);
exit(-1);
}
}
strcpy(params->fileNameA, fileName);
set[k] = 1;
break;
case 5:
if(i == argc - 1)
{
printf("Error, argument expected after option %s\n", options[k]);
exit(-1);
}
else
{
strcpy(fileName, argv[++i]);
if(!filexists(fileName))
{
printf("file %s does not exist\n", fileName);
exit(-1);
}
}
strcpy(params->fileNameB, fileName);
set[k] = 1;
break;
case 6:
if(i == argc - 1)
{
printf("Error, argument expected after option %s\n", options[k]);
exit(-1);
}
else
{
strcpy(fileName, argv[++i]);
if(!filexists(fileName))
{
printf("file %s does not exist\n", fileName);
exit(-1);
}
}
strcpy(params->fileNameC, fileName);
set[k] = 1;
break;
case 7:
if(i == argc - 1)
{
printf("Error, argument expected after option %s\n", options[k]);
exit(-1);
}
else
{
res = sscanf(argv[++i],"%d", &number);
if(res == 0 || res == EOF)
{
printf("argument of %s must be an integer number\n", options[k]);
exit(-1);
}
}
params->permutations = number;
set[k] = 1;
break;
case 8:
if(i == argc - 1)
{
printf("Error, argument expected after option %s\n", options[k]);
exit(-1);
}
else
{
strcpy(runName, argv[++i]);
strcat(params->outFileName, ".");
strcat(params->outFileName, runName);
}
set[k] = 1;
break;
/*case 9:
if(i == argc - 1)
{
printf("Error, argument expected after option %s\n", options[k]);
exit(-1);
}
else
{
res = sscanf(argv[++i],"%d", &number);
if(res == 0 || res == EOF)
{
printf("argument of %s must be an integer number\n", options[k]);
exit(-1);
}
}
if(number <= 0)
{
printf("Randomized Selection must be a positive Integer Value\n");
exit(-1);
}
params->randomizedSelection = number;
break; */
case 9:
if(i == argc - 1)
{
printf("Error, argument expected after option %s\n", options[k]);
exit(-1);
}
else
{
strcpy(fileName, argv[++i]);
if(!filexists(fileName))
{
printf("file %s does not exist\n", fileName);
exit(-1);
}
}
strcpy(params->externalTraceFileName, fileName);
params->useExternalTraceFile = 1;
set[k] = 1;
break;
case 10:
if(processID == 0)
printHelp();
exit(0);
break;
default:
printf("unknown option %s\n", options[k]);
exit(-1);
}
}
else
{
printf("unknown option %s\n", argv[i]);
exit(-1);
}
}
for(i = 0; i < 10; i++)
{
if(set[i] == 0)
{
printf("Error option %s must be specified!\n", options[i]);
exit(-1);
}
}
if(params->useExternalTraceFile == 1 && params->computeTracefileOnly == 1)
{
printf("Conflicting Options, you are trying to read in a tracfile with \"-t\" while\n");
printf("you only want to compute the global significance with \"-g\" \n");
exit(-1);
}
if(processID == 0 && filexists(params->outFileName))
{
printf("Output File %s already exists\n", params->outFileName);
exit(-1);
}
}
/* -------------------------------------------------------------------- */
void doLogin(char moreYet)
{
int foundIt;
char InitPw[NAMESIZE+NAMESIZE+2];
char password[NAMESIZE+NAMESIZE+2];
char initials[NAMESIZE+NAMESIZE+2];
char *semicolon;
Mflush();
if (!CARRIER) return;
if (login_user || login_pw) /* handle command line log-ins */
{
if (!modStat)
if (cfg.offhook) offhook();
/* login using initials and pw */
if (login_pw)
{
normalizepw(cmd_login, initials, password);
login_pw = FALSE;
}
else
if (login_user)
{
normalizeString(cmd_login);
if (findPerson(cmd_login, &logBuf) != ERROR)
{
strcpy(initials, logBuf.lbin);
strcpy(password, logBuf.lbpw);
}
login_user = FALSE;
}
}
else /* ask user for initials and password */
{
if (moreYet == 2)
moreYet = FALSE;
else
{
/* dont print Login when hitting 'L' from console mode */
if (!(!moreYet && !loggedIn && !modStat))
{
mPrintf("Login ");
}
}
if (loggedIn)
{
mPrintf("\n Already logged in!\n ");
return;
}
if (!modStat)
if (cfg.offhook) offhook();
getNormStr((moreYet) ? "" : "your initials", InitPw, NAMESIZE+NAMESIZE+1, NO_ECHO);
if (!CARRIER) return;
dospCR();
semicolon = strchr(InitPw, ';');
if (!semicolon)
{
strcpy(initials, InitPw);
getNormStr( "password", password, NAMESIZE, NO_ECHO);
dospCR();
}
else
{
normalizepw(InitPw, initials, password);
}
/* dont allow anything over 19 characters */
initials[NAMESIZE] = '\0';
}
/* reset transmitted & received */
transmitted = 0l;
received = 0l;
/* reset read & entered */
mread = 0;
entered = 0;
foundIt = ((pwslot(initials, password)) != ERROR);
if (foundIt && *password)
{
loggedIn = TRUE;
update25();
/* trap it */
if (!logBuf.lbflags.NODE)
{
sprintf( msgBuf->mbtext, "Login %s", logBuf.lbname);
if (onConsole)
strcat(msgBuf->mbtext, " (Console)");
trap(msgBuf->mbtext, T_LOGIN);
}
else
{
sprintf( msgBuf->mbtext, "NetLogin %s", logBuf.lbname);
trap(msgBuf->mbtext, T_NETWORK);
}
}
else
{
loginNew(initials, password);
}
if (!loggedIn)
return;
heldMessage = FALSE;
setsysconfig();
setgroupgen();
setroomgen();
setlbvisit();
slideLTab(thisSlot);
/* cant log in now. */
if (cfg.accounting && !logBuf.lbflags.NOACCOUNT)
{
negotiate();
logincrement();
if (!logincheck())
{
Hangup();
return;
}
}
/* can't log in now. */
if (logBuf.VERIFIED && !onConsole)
{
tutorial("verified.blb");
Hangup();
return;
}
if (logBuf.lbflags.NODE)
{
#ifdef TRASH
if (debug)
{
readnode();
cPrintf("Node: \"%s\" \"%s\"", node.ndname, node.ndregion); doccr();
cPrintf("Phone: \"%s\" %d", node.ndphone, node.nddialto); doccr();
cPrintf("Login: \"%s\" %d", node.ndlogin, node.ndwaitto); doccr();
cPrintf("Baud: %d Protocol: \"%s\"\n ", node.ndbaud, node.ndprotocol);
cPrintf("Expire:%d Waitout: %d", node.ndexpire, node.ndwaitto); doccr();
cPrintf("Network: %d ZIP: %s UNZIP: %s", node.network, node.zip, node.unzip); doccr();
}
#endif
time(&logtimestamp);
return;
}
if (logBuf.PSYCHO)
{
backout = TRUE;
}
/* reverse engineering Minibin?!?! */
if (logBuf.MINIBIN)
{
minibin();
}
changedir(cfg.helppath);
if ( filexists("bulletin.blb") )
{
tutorial("bulletin.blb");
}
gotodefaulthall();
roomtalley();
mf.mfLim = 0; /* just to make sure. */
mf.mfMai = 0;
mf.mfPub = 0;
mf.mfUser[0]=0;
nochat(TRUE); /* reset chats */
/* verbose = FALSE; */
verbose = logBuf.VERBOSE;
/* hmmm... where to put this */
if (roomBuf.rbflags.APLIC && roomBuf.rbflags.AUTOAPP )
ExeAplic();
showMessages(NEWoNLY, FALSE);
verbose = FALSE;
if (expert) listRooms(NEWRMS, FALSE);
else listRooms(OLDNEW, FALSE);
outFlag = OUTOK;
setio(whichIO, echo, outFlag);
/* record login time, date */
time(&logtimestamp);
cfg.callno++;
storeLog();
}
static char * EXTRACT_main( PLUGIN_interface * plint )
{
extract_data uda,*ud;
MRI_IMAGE * tsim;
MCW_idcode * idc ; /* input dataset idcode */
THD_3dim_dataset * old_dset , * new_dset ; /* input and output datasets */
char *tmpstr , * str , *nprfxstr;
int ntime, nvec ,nprfx, Err=0 , itmp;
float * vec , fs , T ;
char * tag; /* plugin option tag */
/* Allocate as much character space as Bob specifies in afni.h + a bit more */
tmpstr = (char *) calloc (PLUGIN_MAX_STRING_RANGE+10,sizeof(char));
nprfxstr = (char *) calloc (PLUGIN_MAX_STRING_RANGE+10,sizeof(char));
if (tmpstr == NULL || nprfxstr == NULL)
return "********************\n"
"Could not Allocate\n"
"a teeni weeni bit of\n"
"Memory ! Go complain\n"
"to yer Mamma ! \n"
"********************\n";
ud = &uda; /* ud now points to an allocated space */
ud->errcode = 0; /*reset error flag */
/*--------------------------------------------------------------------*/
/*----- Check inputs from AFNI to see if they are reasonable-ish -----*/
/*--------- go to first input line ---------*/
tag = PLUTO_get_optiontag(plint) ;
if (tag == NULL)
{
return "************************\n"
"Bad 1st line option \n"
"************************" ;
}
idc = PLUTO_get_idcode(plint) ; /* get dataset item */
old_dset = PLUTO_find_dset(idc) ; /* get ptr to dataset */
if( old_dset == NULL )
return "*************************\n"
"Cannot find Input Dataset\n"
"*************************" ;
ud->dsetname = DSET_FILECODE (old_dset);
ud->ignore = PLUTO_get_number(plint) ; /* get number item */
str = PLUTO_get_string(plint) ;
ud->dtrnd = (int)PLUTO_string_index( str , NUM_YN_STRINGS , yn_strings );
/*--------- loop over ramining options ---------*/
ud->iloc = -1;
ud->xloc = -1;
ud->yloc = -1;
ud->zloc = -1;
do
{
tag = PLUTO_get_optiontag(plint) ;
if (tag == NULL) break;
if (strcmp (tag, "Mask") == 0)
{
ud->strin = PLUTO_get_string(plint) ;
ud->ncols = PLUTO_get_number(plint) ;
ud->pass = PLUTO_get_number(plint) ;
ud->fail = 0; /* Set voxels that don't make it to 0 */
continue;
}
if (strcmp (tag, "Index") == 0)
{
ud->iloc = PLUTO_get_number(plint) ; /* get number item */
continue;
}
if (strcmp (tag, "XYZ") == 0)
{
ud->xloc = PLUTO_get_number(plint) ; /* get number item */
ud->yloc = PLUTO_get_number(plint) ; /* get number item */
ud->zloc = PLUTO_get_number(plint) ; /* get number item */
continue;
}
if (strcmp (tag, "Output") == 0)
{
ud->new_prefix = PLUTO_get_string(plint) ; /* get string item (the output prefix) */
/* check to see if the field is empty */
if (ud->new_prefix == NULL)
nprfx = 0;
else
nprfx = 1;
/* check if the size is larger than 0. I did not want to check for this unless it's allocated */
if (nprfx == 1 && (int)strlen (ud->new_prefix) == 0)
nprfx = 0;
if (nprfx == 0) /* now create the new name and make new_prefix point to it */
{
sprintf (nprfxstr,"%s.XTRCT",DSET_PREFIX (old_dset));
ud->new_prefix = nprfxstr;
/*printf ("New prefix is set to be : %s\n\a",ud->new_prefix);*/
}
if( ! PLUTO_prefix_ok(ud->new_prefix) ) /* check if it is OK */
return "************************\n"
"Output Prefix is illegal\n"
"************************" ;
ud->strout = PLUTO_get_string(plint) ;
str = PLUTO_get_string(plint) ;
ud->format = (int)PLUTO_string_index( str , NUM_FORMAT_STRINGS , format_strings );
continue;
}
} while (1);
/* ------------------ Check for some errorsor inconsistencies ------------- */
if (ud->iloc == -1 && ud->xloc == -1)
{
return "**************************\n"
"At least iloc or x/y/zloc\n"
"must be specified\n"
"**************************\n"
;
}
if (ud->iloc != -1 && ud->xloc != -1)
{
return "***************************\n"
"iloc AND x/y/zloc can not\n"
"be simultaneously specified\n"
"***************************\n"
;
}
/* ------------------Done with user parameters ---------------------------- */
/* Now loadup that index list or the xyz list */
if (ud->iloc != -1)
{
itmp = 0; /* might want to give option of setting it to number of rows if*/
/* the users know it, otherwise, it is automatically determined*/
ud->indvect = extract_index (ud->strin, ud->iloc, ud->ncols, &itmp, &Err);
}
else /* assuming the only other case is that x y z are specified */
{
itmp = 0;
ud->xyzvect = extract_xyz (ud->strin , ud->xloc , ud->yloc , ud->zloc , ud->ncols, &itmp, &Err);
}
ud->nrows = itmp;
switch (Err)
{
case (0):
break;
case (1):
return "****************************************\n"
"index location should be > 0 and < ncols\n"
"****************************************\n";
case (2):
return "********************************************\n"
"file size and number of columns do not match\n"
"********************************************\n";
case (3):
return "**********************\n"
"Can't find matrix file\n"
"**********************\n";
case (4):
return "*****************\n"
"ncols must be > 0\n"
"*****************\n";
case (5):
return "****************************************\n"
"x/y/z column numbers can NOT be the same\n"
"****************************************\n";
default:
return "****************************************\n"
"Should not have gotten here .....\n"
"****************************************\n";
}
if (strcmp (ud->strout,"") == 0) /* no output file is specified */
{
sprintf ( tmpstr , "%s" , ud->new_prefix);
ud->strout = tmpstr;
}
if (filexists(ud->strout) == 1)
{
return "*******************************\n"
"Outfile exists, won't overwrite\n"
"*******************************\n";
}
ud->outwritets = fopen (ud->strout ,"w");
sprintf ( tmpstr , "%s.log" , ud->strout);
if (filexists(tmpstr) == 1)
{
return "*******************************\n"
"Outfile.log exists, won't overwrite\n"
"*******************************\n";
}
ud->outlogfile = fopen (tmpstr ,"w");
if ((ud->outwritets == NULL) || (ud->outlogfile == NULL) )
{
ud->errcode = ERROR_FILEWRITE;
return "***********************\n"
"Could Not Write Outfile\n"
"***********************\n";
}
ud->nxx = (int)old_dset->daxes->nxx; /* get data set dimensions */
ud->nyy = (int)old_dset->daxes->nyy;
ud->nzz = (int)old_dset->daxes->nzz;
/* ready to dump the log file */
write_ud (ud);
/*------------- ready to compute new dataset -----------*/
new_dset = PLUTO_4D_to_typed_fim( old_dset , /* input dataset */
ud->new_prefix , /* output prefix */
-1, /* negative value indicating data type is like original brick */
ud->ignore , /* ignore count */
ud->dtrnd , /* detrend */
EXTRACT_tsfunc , /* timeseries processor */
(void *)ud /* data for tsfunc */
) ;
PLUTO_add_dset( plint , new_dset , DSET_ACTION_MAKE_CURRENT ) ;
fclose (ud->outlogfile);
fclose (ud->outwritets);
free (tmpstr);
free (nprfxstr);
return NULL ; /* null string returned means all was OK */
}
BOOL fedit(char *filename)
{
FILE *fp;
char *buf;
unsigned int lim; /* can't edit more then a segment anyway */
long filesize;
int rc = FALSE;
int err;
char path[64];
getcwd(path,64);
err = errno = 0;
/* set the message entry flags and buffer */
clearmsgbuf();
setmem(msgBuf, sizeof(struct msgB), 0);
mailFlag = FALSE;
oldFlag = FALSE;
limitFlag = FALSE;
linkMess = FALSE;
if (loggedIn)
strcpy(msgBuf->mbauth,logBuf.lbname);
/* try to edit an existing file */
if (filexists(filename)) {
fp = fopen(filename,"rt");
if (fp) {
filesize = filelength(fileno(fp));
if ((unsigned int) (filesize + (long) cfg.maxtext) > UINT_MAX) {
err = -2;
cPrintf("\nFile too long\n");
} else {
lim = cfg.maxtext + (int) filesize;
buf = calloc(1,lim);
if (buf) {
errno = 0;
if (!fread(buf,1,lim,fp)) {
cPrintf("\nFile read error\n");
err = errno;
}
if (fclose(fp) && !err) {/* we need to 'recreate' later */
cPrintf("\nFile close error\n");
err = errno;
}
if (!err)
mFormat(buf); /* display the file */
oldFlag = TRUE;
}
}
} else {
lim = cfg.maxtext;
buf = calloc(1,lim);
oldFlag = FALSE;
}
}
if (buf && !err && editBuf(buf,lim)) {
changedir(path); /* because silly edit routines loose path */
if (!strblank(buf)) {
rc = TRUE;
lim = strlen(buf);
errno = 0; /* because silly video routines set it */
fp = fopen(filename,"wt");
if (!fp && !err) {
cPrintf("\nFile open error 2\n");
err = errno;
}
if (fp) {
/* because silly DOS doesn't 'error' on disk full */
if(!fwrite(buf,1,lim,fp) && !errno) {
cPrintf("\nFile write error\n");
err = -1;
}
errno = 0;
if (!fclose(fp)&& !err) {
cPrintf("\nFile close error 2\n");
err = errno;
}
}
} else { /* we won't save empty files */
rc = FALSE;
}
}
if (!buf) { /* out of memory condition */
mtPrintf(TERM_BOLD," \n Out of memory editing file %s.\n",filename);
rc = FALSE;
} else {
switch (err) {
case 0: /* no error */
break;
case -1: /* disk full condition */
mtPrintf(TERM_BOLD,
" \n Disk full saving %s, file truncated.\n",filename);
rc = FALSE;
break;
case -2: /* file >64k condition */
mtPrintf(TERM_BOLD,
" \n File %s is too large to edit.\n",filename);
rc = FALSE;
break;
default: /* DOS error condition */
mtPrintf(TERM_BOLD, " \n DOS error '%s' editing %s: \n",
strerror(err),filename);
rc = FALSE;
break;
}
}
if (buf) {
free(buf);
buf = NULL;
}
return rc;
}
static void analyzeIdentifier(char **ch, int modelNumber, tree *tr)
{
char
*start = *ch,
ident[2048] = "",
model[2048] = "",
thisModel[2048] = "";
int
i = 0,
n,
j,
containsComma = 0;
while(**ch != '=')
{
if(**ch == '\n' || **ch == '\r')
{
printf("\nPartition file parsing error!\n");
printf("Each line must contain a \"=\" character\n");
printf("Offending line: %s\n", start);
printf("RAxML will exit now.\n\n");
errorExit(-1);
}
if(**ch != ' ' && **ch != '\t')
{
ident[i] = **ch;
i++;
}
*ch = *ch + 1;
}
ident[i] = '\0';
n = i;
i = 0;
for(i = 0; i < n; i++)
if(ident[i] == ',')
containsComma = 1;
if(!containsComma)
{
printf("Error, model file must have format: Substitution model, then a comma, and then the partition name\n");
exit(-1);
}
else
{
boolean
analyzeRest = TRUE,
useExternalFile = FALSE,
found = FALSE;
int
openBracket = 0,
closeBracket = 0,
openPos = 0,
closePos = 0;
i = 0;
while(ident[i] != ',')
{
if(ident[i] == '[')
{
openPos = i;
openBracket++;
}
if(ident[i] == ']')
{
closePos = i;
closeBracket++;
}
model[i] = ident[i];
i++;
}
if(closeBracket > 0 || openBracket > 0)
{
if((closeBracket == 1) && (openBracket == 1) && (openPos < closePos))
useExternalFile = TRUE;
else
{
printf("\nError: Apparently you want to specify a user-defined protein substitution model\n");
printf("or ascertainment bias correction model that shall be read from file\n");
printf("It must be enclosed in opening and closing bracktes like this: [prot=fileName] or [asc=fileName]\n\n");
printf("you specified: %s\n\n", model);
exit(-1);
}
}
if(useExternalFile)
{
char
designator[2048] = "",
fileName[2048] = "";
int
pos,
index,
lower = 0,
upper = i - 1;
boolean
isProteinFile = TRUE;
while(model[lower] == '[')
lower++;
while(model[upper] == ']')
upper--;
assert(lower < upper);
index = lower;
pos = 0;
while(model[index] != '~')
{
designator[pos] = model[index];
pos++;
index++;
}
designator[pos] = '\0';
if(strcmp(designator, "asc") == 0)
isProteinFile = FALSE;
else
{
if(strcmp(designator, "prot") == 0)
isProteinFile = TRUE;
else
{
printf("Error external partition file type %s does not exist\n", designator);
printf("Available file types: asc and prot\n");
exit(-1);
}
}
while(model[index] == '~')
index++;
pos = 0;
while(model[index] != ']')
{
fileName[pos] = model[index];
index++;
pos++;
}
fileName[pos] = '\0';
if(!filexists(fileName))
{
printf("\n\ncustom protein substitution or ascertainment bias file [%s] you want to use does not exist!\n", fileName);
printf("you need to specify the full path\n");
printf("the file name shall not contain blanks!\n\n");
exit(-1);
}
if(isProteinFile)
{
strcpy(tr->initialPartitionData[modelNumber].proteinSubstitutionFileName, fileName);
/*printf("%s \n", tr->initialPartitionData[modelNumber].proteinSubstitutionFileName);*/
tr->initialPartitionData[modelNumber].protModels = PROT_FILE;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = TRUE;
tr->initialPartitionData[modelNumber].dataType = AA_DATA;
analyzeRest = FALSE;
}
else
{
int
newIndex = 0;
strcpy(tr->initialPartitionData[modelNumber].ascFileName, fileName);
i = 0;
while(ident[i] != ',')
{
if(ident[i] == '\0')
{
printf("Expecting two commas in string %s\n", ident);
exit(-1);
}
i++;
}
i++;
while(ident[i] != ',')
{
if(ident[i] == '\0')
{
printf("Expecting two commas in string %s\n", ident);
exit(-1);
}
model[newIndex] = ident[i];
i++;
newIndex++;
}
model[newIndex] = '\0';
}
}
if(analyzeRest)
{
/* AA */
tr->initialPartitionData[modelNumber].ascBias = FALSE;
for(i = 0; i < NUM_PROT_MODELS && !found; i++)
{
strcpy(thisModel, protModels[i]);
if(strcasecmp(model, thisModel) == 0)
{
tr->initialPartitionData[modelNumber].protModels = i;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = TRUE;
tr->initialPartitionData[modelNumber].dataType = AA_DATA;
found = TRUE;
}
if(!found)
{
if(i != GTR && i != GTR_UNLINKED)
{
strcpy(thisModel, protModels[i]);
strcat(thisModel, "F");
if(strcasecmp(model, thisModel) == 0)
{
tr->initialPartitionData[modelNumber].protModels = i;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = AA_DATA;
found = TRUE;
if(tr->initialPartitionData[modelNumber].protModels == AUTO)
{
printf("\nError: Option AUTOF has been deprecated, exiting\n\n");
errorExit(-1);
}
}
}
}
if(!found)
{
strcpy(thisModel, protModels[i]);
strcat(thisModel, "X");
if(strcasecmp(model, thisModel) == 0)
{
tr->initialPartitionData[modelNumber].protModels = i;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = AA_DATA;
tr->initialPartitionData[modelNumber].optimizeBaseFrequencies = TRUE;
found = TRUE;
if(tr->initialPartitionData[modelNumber].protModels == AUTO)
{
printf("\nError: Option AUTOX has been deprecated, exiting\n\n");
errorExit(-1);
}
}
}
if(found && (tr->initialPartitionData[modelNumber].protModels == GTR || tr->initialPartitionData[modelNumber].protModels == GTR_UNLINKED))
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
}
/* AA with Asc bias*/
if(!found)
{
for(i = 0; i < NUM_PROT_MODELS && !found; i++)
{
strcpy(thisModel, "ASC_");
strcat(thisModel, protModels[i]);
if(strcasecmp(model, thisModel) == 0)
{
tr->initialPartitionData[modelNumber].protModels = i;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = TRUE;
tr->initialPartitionData[modelNumber].dataType = AA_DATA;
found = TRUE;
}
if(!found)
{
if(i != GTR && i != GTR_UNLINKED)
{
strcpy(thisModel, protModels[i]);
strcat(thisModel, "F");
if(strcasecmp(model, thisModel) == 0)
{
tr->initialPartitionData[modelNumber].protModels = i;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = AA_DATA;
found = TRUE;
}
}
}
if(!found)
{
strcpy(thisModel, protModels[i]);
strcat(thisModel, "X");
if(strcasecmp(model, thisModel) == 0)
{
tr->initialPartitionData[modelNumber].protModels = i;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = AA_DATA;
tr->initialPartitionData[modelNumber].optimizeBaseFrequencies = TRUE;
found = TRUE;
}
}
if(found)
tr->initialPartitionData[modelNumber].ascBias = TRUE;
if(found && (tr->initialPartitionData[modelNumber].protModels == GTR || tr->initialPartitionData[modelNumber].protModels == GTR_UNLINKED))
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
}
}
if(!found)
{
if(strcasecmp(model, "DNA") == 0 || strcasecmp(model, "DNAX") == 0 || strcasecmp(model, "ASC_DNA") == 0 || strcasecmp(model, "ASC_DNAX") == 0)
{
tr->initialPartitionData[modelNumber].protModels = -1;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = DNA_DATA;
if(strcasecmp(model, "DNAX") == 0 || strcasecmp(model, "ASC_DNAX") == 0)
{
if(strcasecmp(model, "ASC_DNAX") == 0)
tr->initialPartitionData[modelNumber].ascBias = TRUE;
else
tr->initialPartitionData[modelNumber].ascBias = FALSE;
tr->initialPartitionData[modelNumber].optimizeBaseFrequencies = TRUE;
}
else
{
if(strcasecmp(model, "ASC_DNA") == 0)
tr->initialPartitionData[modelNumber].ascBias = TRUE;
else
tr->initialPartitionData[modelNumber].ascBias = FALSE;
tr->initialPartitionData[modelNumber].optimizeBaseFrequencies = FALSE;
}
found = TRUE;
}
else
{
if(strcasecmp(model, "BIN") == 0 || strcasecmp(model, "BINX") == 0 || strcasecmp(model, "ASC_BIN") == 0 || strcasecmp(model, "ASC_BINX") == 0)
{
tr->initialPartitionData[modelNumber].protModels = -1;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = BINARY_DATA;
if(strcasecmp(model, "BINX") == 0 || strcasecmp(model, "ASC_BINX") == 0)
{
if(strcasecmp(model, "ASC_BINX") == 0)
tr->initialPartitionData[modelNumber].ascBias = TRUE;
else
tr->initialPartitionData[modelNumber].ascBias = FALSE;
tr->initialPartitionData[modelNumber].optimizeBaseFrequencies = TRUE;
}
else
{
if(strcasecmp(model, "ASC_BIN") == 0)
tr->initialPartitionData[modelNumber].ascBias = TRUE;
else
tr->initialPartitionData[modelNumber].ascBias = FALSE;
tr->initialPartitionData[modelNumber].optimizeBaseFrequencies = FALSE;
}
found = TRUE;
}
else
{
if(strcasecmp(model, "MULTI") == 0 || strcasecmp(model, "MULTIX") == 0 || strcasecmp(model, "ASC_MULTI") == 0 || strcasecmp(model, "ASC_MULTIX") == 0)
{
tr->initialPartitionData[modelNumber].protModels = -1;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = GENERIC_32;
if(strcasecmp(model, "MULTIX") == 0 || strcasecmp(model, "ASC_MULTIX") == 0)
{
if(strcasecmp(model, "ASC_MULTIX") == 0)
tr->initialPartitionData[modelNumber].ascBias = TRUE;
else
tr->initialPartitionData[modelNumber].ascBias = FALSE;
tr->initialPartitionData[modelNumber].optimizeBaseFrequencies = TRUE;
}
else
{
if(strcasecmp(model, "ASC_MULTI") == 0)
tr->initialPartitionData[modelNumber].ascBias = TRUE;
else
tr->initialPartitionData[modelNumber].ascBias = FALSE;
tr->initialPartitionData[modelNumber].optimizeBaseFrequencies = FALSE;
}
found = TRUE;
}
else
{
if(strcasecmp(model, "CODON") == 0 || strcasecmp(model, "CODONX") == 0 || strcasecmp(model, "ASC_CODON") == 0 || strcasecmp(model, "ASC_CODONX") == 0)
{
tr->initialPartitionData[modelNumber].protModels = -1;
tr->initialPartitionData[modelNumber].usePredefinedProtFreqs = FALSE;
tr->initialPartitionData[modelNumber].dataType = GENERIC_64;
if(strcasecmp(model, "CODONX") == 0 || strcasecmp(model, "ASC_CODONX") == 0)
{
if(strcasecmp(model, "ASC_CODONX") == 0)
tr->initialPartitionData[modelNumber].ascBias = TRUE;
else
tr->initialPartitionData[modelNumber].ascBias = FALSE;
tr->initialPartitionData[modelNumber].optimizeBaseFrequencies = TRUE;
}
else
{
if(strcasecmp(model, "ASC_CODON") == 0)
tr->initialPartitionData[modelNumber].ascBias = TRUE;
else
tr->initialPartitionData[modelNumber].ascBias = FALSE;
tr->initialPartitionData[modelNumber].optimizeBaseFrequencies = FALSE;
}
found = TRUE;
}
}
}
}
}
if(!found)
{
printf("ERROR: you specified the unknown model %s for partition %d\n", model, modelNumber);
exit(-1);
}
}
i = 0;
while(ident[i++] != ',');
tr->initialPartitionData[modelNumber].partitionName = (char*)rax_malloc((n - i + 1) * sizeof(char));
j = 0;
while(i < n)
tr->initialPartitionData[modelNumber].partitionName[j++] = ident[i++];
tr->initialPartitionData[modelNumber].partitionName[j] = '\0';
}
}
main (int argc,char *argv[])
{/* Main */
char outfile[300];
int N_FaceSetList, *FaceSetList ,writeout,CountOnly,paramnum;
if (argc < 2)
{
usage ();
exit (1);
}
writeout = 0; /* check out second option */
CountOnly = 0; /* Set to 1 if you want to Count the number of triplets only */
paramnum = 2;
while (paramnum < argc)
{
if (equal_strings (argv[paramnum],"-o") == 1)
{
if ((paramnum + 1) >= argc)
{
SUMA_error_message ("SUMA_IV_FaceSetsextract","No Output file name specified with -o option",1);
exit (1);
}
if (filexists (argv[paramnum+1]) == 1)
{
SUMA_error_message ("SUMA_IV_FaceSetsextract","Output file exists, will not overwrite",1);
exit (1);
}
else
{
sprintf(outfile,"%s",argv[paramnum+1]);
writeout = 1;
}
++ paramnum;
}
if (equal_strings (argv[paramnum],"-co") == 1)
{
CountOnly = 1;
}
++ paramnum;
}
FaceSetList = SUMA_IV_FaceSetsextract (argv[1], &N_FaceSetList);
if (CountOnly)
printf ("%d FaceSets sets read\n",N_FaceSetList);
if (writeout == 1) {
FILE *outfid;
outfid = fopen (outfile, "w");
if (outfid == NULL) {
fprintf (SUMA_STDERR, "Error %s: Could not open %s for writing.\n", FuncName, outfile);
}else {
i = 0;
cntlim = N_FaceSetList*3;
while (i < cntlim) {
j = 0;
while (j < 3) {
fprintf (outfid, "%d\t", FaceSetList[i]);
++i;
++j;
}
fprintf (outfid, "\n");
}
fclose (outfid);
}
} else if (!CountOnly) {
i = 0;
cntlim = N_FaceSetList*3;
while (i < cntlim) {
j = 0;
while (j < 3) {
fprintf (SUMA_STDOUT, "%d\t", FaceSetList[i]);
++i;
++j;
}
fprintf (SUMA_STDOUT, "\n");
}
}
SUMA_free(FaceSetList);
}/* Main */