static char *merge_input(char *input, char **buf, size_t *buflen)
{
char *p, *ip;
size_t offset = 0;
offset = strlen(*buf);
if (offset <= 0)
return NULL;
ip = input;
while ((*buf)[offset - 1] == '\n' && (*ip == '\t' || *ip == ' ')) {
while (*ip == '\t' || *ip == ' ')
++ip;
(*buf)[offset - 1] = ' ';
p = cgetline(ip, buf, offset, buflen);
if (!p)
return NULL;
if (p == ip)
break;
offset += p - ip;
ip = p;
}
return ip;
}
char *parse_header(char *input, struct MailHeader *mh)
{
static char *buf = NULL;
static size_t buflen = BUF_LEN;
char *next_line = NULL;
int i;
int (*cmpfun)(const char *, const char *, size_t);
if (!input || !mh)
return NULL;
/*
* Set default value
*/
memset(mh, 0, sizeof(struct MailHeader));
strcpy(mh->content_type, "text/plain");
strcpy(mh->charset, "iso-8859-1");
strcpy(mh->transenc, "7bit");
if (!buf)
buf = (char *)malloc(buflen);
if (!buf)
return NULL;
memset(buf, 0, buflen);
next_line = cgetline(input, &buf, 0, &buflen);
while (buf[0] && buf[0] != '\n') {
for (i = 0 ; hh[i].header ; ++i) {
cmpfun = (hh[i].casesence) ? strncmp : strncasecmp;
if (!cmpfun(buf, hh[i].header, strlen(hh[i].header))) {
if (hh[i].multiline)
next_line = merge_input(next_line, &buf, &buflen);
if (hh[i].hdl(buf + strlen(hh[i].header) + 1, mh)) {
next_line = NULL;
dbg("Error at %s %30.30s\n", hh[i].header, buf + strlen(hh[i].header) + 1);
goto out;
}
break;
}
}
next_line = cgetline(next_line, &buf, 0, &buflen);
}
out:
return next_line;
}
static int print_simple_content(char *input, FILE *output, char *errmsg, struct MailHeader *mh, char **next_line)
{
static char *buf = NULL;
static size_t buflen = BUF_LEN;
char *ptr;
iconv_t tobig5 = (iconv_t) -1;
size_t offset;
unsigned char isbase64 = 0, isqp = 0;
int rt = 0;
dbg("In print_simple_content.\n");
if (output) {
if (is_notmycharset(mh->charset))
tobig5 = iconv_open("big5//TRANSLIT//IGNORE", mh->charset);
if (!strncasecmp(mh->transenc, "base64", 6))
isbase64 = 1;
else if (!strncasecmp(mh->transenc, "quoted-printable", 16))
isqp = 1;
}
if (!buf)
buf = malloc(buflen);
if (!buf) {
rt = ERROR;
goto out;
}
*next_line = cgetline(input, &buf, 0, &buflen);
while (buf[0]) {
offset = strlen(mh->boundary);
if (offset && (ptr = strstr(buf, mh->boundary)) != NULL) {
if (ptr[offset] == '\n')
rt = HIT_BOUNDARY;
else
rt = HIT_END_BOUNDARY;
break;
}
if (isbase64) {
offset = mmdecode((unsigned char *)buf, 'b', (unsigned char *)buf);
buf[offset] = '\0';
} else if (isqp) {
str_deqp(buf, buf);
}
if (tobig5 != (iconv_t)-1) {
if (!str_conv(tobig5, buf, buflen)) {
sprintf(errmsg, "%s CONVERR(%s)", mh->charset, strerror(errno));
rt = ERROR;
break;
}
}
if (output)
fputs(buf, output);
*next_line = cgetline(*next_line, &buf, 0, &buflen);
}
if (tobig5 != (iconv_t)-1)
iconv_close(tobig5);
out:
return rt;
}
int main()
{
int dir,m,i,j,k,n,num_line, Symmetry1;
int num_images, *pa,sx; /* Prepare for merge Nimages images together into a stack of num_images patches*/
FILE *input;
char oneline[100];
char *c;
char *tmpstring;
char *SYMname;
char *imagename, *profilename, *resultsfilename, *imagenumber, *temp_imagename;
int oversizexy[2], realcellxy[2], realcellxy1[2];
float angle[3];
tmpstring=(char *)calloc(200,sizeof(char));
SYMname=(char *)calloc(200,sizeof(char));
imagename=(char *)calloc(400,sizeof(char));
profilename=(char *)calloc(400,sizeof(char));
imagenumber=(char *)calloc(200,sizeof(char));
temp_imagename=(char *)calloc(200,sizeof(char));
resultsfilename=(char *)calloc(200,sizeof(char));
printf("\n2dx_ML: Performs Maximum Likelihood processing. \n");
scanf("%d",&doMLorCC);
if(doMLorCC==0)
printf("Weights for ref calculation... = from Maximum Likelihood estimate\n");
else
printf("Weights for ref calculation... = from Cross-Correlation between particle and old reference\n");
scanf("%s",resultsfilename);
printf("Results File Name............. = %s \n",resultsfilename);
input=fopen("2dx_image.cfg" ,"r");
/* input parameters from 2dx_image.cfg to generate stacks*/
printf("\nReading Parameters for ML:\n");
strcpy(tmpstring,"imagename");
imagename=cgetline(input,tmpstring);
strcpy(temp_imagename, imagename);
strcat(imagename,".mrc");
printf("Image Name..................... = %s \n",imagename);
strcpy(tmpstring,"imagenumber");
imagenumber=cgetline(input,tmpstring);
printf("Image Number................... = %s \n",imagenumber);
strcpy(profilename,"image_ctfcor_profile.dat");
printf("Profile Name................... = %s \n",profilename);
strcpy(tmpstring,"CS");
if(fgetline(input,tmpstring,&CS)==0)
printf("CS............................. = %f \n",CS);
else
printf(":: ERROR in CS assignment.");
strcpy(tmpstring,"KV");
if(fgetline(input,tmpstring, &KV )==0)
printf("KV............................. = %f \n",KV);
else
printf(":: ERROR in KV assignment.");
strcpy(tmpstring,"RESMIN");
if(fgetline(input,tmpstring, &RESMIN )==0)
printf("RESMIN......................... = %f \n",RESMIN);
else
printf(":: ERROR in RESMIN assignment.");
strcpy(tmpstring,"RESMAX");
if(fgetline(input,tmpstring,&RESMAX )==0)
printf("RESMAX......................... = %f \n",RESMAX);
else
printf(":: ERROR in RESMAX assignment.");
strcpy(tmpstring,"defocus");
if(fgetline(input,tmpstring, defocus)==0)
{
DIFMID1=defocus[0];
DIFMID2=defocus[1];
ANGAST=defocus[2];
printf("DFMID1,DFMID2,ANGAST........... = %f,%f,%f\n",DIFMID1,DIFMID2, ANGAST);
}
strcpy(tmpstring,"ML_do_whiten");
if(*(cgetline(input,tmpstring))=='y')
{ do_whiten =1;
printf("do_whiten...................... = yes \n");
}
else
{ do_whiten=0;
printf("do_whiten...................... = no \n");
}
strcpy(tmpstring,"ML_correct_CTF");
if(*(cgetline(input,tmpstring))=='y')
{ correct_CTF =1;
printf("correct_CTF.................... = yes \n");
}
else
{ correct_CTF=0;
printf("correct_CTF.................... = no \n");
}
strcpy(tmpstring,"stepdigitizer");
if(fgetline(input,tmpstring,&DSTEP )==0)
printf("DSTEP.......................... = %f\n",DSTEP);
strcpy(tmpstring,"magnification");
if(fgetline(input,tmpstring, &XMAG)==0)
printf("Magnification (XMAG)........... = %f \n",XMAG);
/*
if(igetline(input, "ML_oversizexy", oversizexy)==0)
{ oversized_x=oversizexy[0];
oversized_y=oversizexy[1];
printf("ML_oversizexy................. = %d,%d\n",oversized_x,oversized_y);
}
else printf("parameter ML_oversizexy does not exists \n");
*/
strcpy(tmpstring,"ML_realcellxy_outer");
if(igetline(input,tmpstring, realcellxy)==0)
{ realcell_x=realcellxy[0];
realcell_y=realcellxy[1];
printf("ML_realcellxy_outer............ = %d,%d\n",realcell_x,realcell_y);
}
else printf("parameter ML_realcellxy_outer does not exists \n");
/*
if(igetline(input, "ML_realcellxy_inner", realcellxy1)==0)
{ realcell_x1=realcellxy1[0];
realcell_y1=realcellxy1[1];
printf("ML_realcellxy_inner............ = %d,%d\n",realcell_x1,realcell_y1);
}
else printf("parameter ML_realcell_xy1 does not exists \n");
*/
realcell_x1=realcell_x;
realcell_y1=realcell_y;
strcpy(tmpstring,"ML_mask_radius");
if(igetline(input,tmpstring, &mask_radius)==0)
printf("Mask radius.................... = %d \n",mask_radius);
else printf("parameter ML_mask_radius does not exists \n");
strcpy(tmpstring,"ML_iteration");
if(igetline(input,tmpstring, &Iteration)==0)
printf("Iteration...................... = %d \n",Iteration);
else printf("parameter ML_iteration does not exists \n");
strcpy(tmpstring,"ML_threshold_method");
if(igetline(input,tmpstring, &threshold_method)==0)
{
if(threshold_method==0)
{
strcpy(tmpstring,"ML_absolute_threshold");
if(fgetline(input,tmpstring, &threshold)==0)
printf("Absolute Threshold value....... = %f \n",threshold);
else printf("parameter ML_absolute_threshold does not exists \n");
}
else
{
strcpy(tmpstring,"ML_relative_threshold");
if(fgetline(input,tmpstring, &relative_threshold)==0)
printf("Percentage of peaks to use..... = %.2f\n",relative_threshold);
else printf("parameter ML_relative_threshold does not exists \n");
}
}
else printf("parameter ML_threshold_method does not exists \n");
strcpy(tmpstring,"ML_ref_ind");
if(igetline(input,tmpstring, &ref_ind)==0)
{
if ( ref_ind == 0 )
printf("Initial Reference (ref_ind).... = average reference \n");
else if ( ref_ind == 1 )
printf("Initial Reference (ref_ind).... = random noise \n");
else if ( ref_ind == 2 )
printf("Initial Reference (ref_ind).... = random particle \n");
else
printf("::Initial Reference (ref_ind).... = ILLEGAL CHOICE !!!! \n");
}
else printf("parameter ML_ref_ind does not exists \n");
/*
if(igetline(input, "ML_DS_ratio", &DS_ratio)==0)
printf("DS_ratio............................ = %d \n",DS_ratio);
else printf("parameter DS_ratio does not exists \n");
*/
strcpy(tmpstring,"ML_rotational_symmetry");
if(igetline(input,tmpstring, &Symmetry1)==0)
{ if(Symmetry1==0) Symmetry=1;
else if(Symmetry1==1) Symmetry=2;
else if(Symmetry1==2) Symmetry=3;
else if(Symmetry1==3) Symmetry=4;
else if(Symmetry1==4) Symmetry=5;
else if(Symmetry1==5) Symmetry=6;
printf("Rotational Symmetry of Particle = %d \n",Symmetry);
}
else printf("parameter Symmetry does not exists \n");
strcpy(tmpstring,"ML_lp_method");
if(igetline(input,tmpstring, &lp_method)==0)
{
if(lp_method==1)
printf("Low-Pass filter................ = Gaussian \n");
else if(lp_method==2)
printf("Low-Pass filter................ = Sharp cutoff \n");
else
printf("Low-Pass filter................ = None \n");
}
else printf("parameter ML_lp_method does not exists \n");
strcpy(tmpstring,"ML_lp_radius");
if(fgetline(input,tmpstring,&lp_radius)==0)
printf("lp_radius...................... = %f \n",lp_radius);
else printf("paramter lp_radius does not exists \n");
strcpy(tmpstring,"ML_MinMaxStep_angle");
if(fgetline(input,tmpstring, angle)==0)
{
min_angle=angle[0];
max_angle=angle[1];
step_angle=angle[2];
printf("min_angle,max_angle,step_angle. = %f,%f,%f \n",min_angle, max_angle, step_angle);
}
else printf("Angle parameters do not exists \n");
strcpy(tmpstring,"ML_terminate_ML");
if(fgetline(input,tmpstring,&Terminate_ML)==0)
printf("Terminate_ML................... = %f \n",Terminate_ML);
else printf("paramter ML_terminate does not exists \n");
strcpy(tmpstring,"ML_B_factor");
if(fgetline(input,tmpstring,&B_fac)==0)
printf("B_factor....................... = %f \n",B_fac);
else printf("paramter B_factor does not exists \n");
strcpy(tmpstring,"ML_A_factor");
if(fgetline(input,tmpstring,&A)==0)
printf("A_factor....................... = %f \n",A);
else printf("paramter A_factor does not exists \n");
strcpy(tmpstring,"SYM");
SYMname=cgetline(input,tmpstring);
printf("Space Group.................... = %s \n",SYMname);
SYM=0;
if(strncmp(SYMname,"p12",3) == 0) SYM=1;
if(strncmp(SYMname,"p22",3) == 0) SYM=1;
if(strncmp(SYMname,"p42",3) == 0) SYM=1;
if(strncmp(SYMname,"p31",3) == 0) SYM=1;
if(strncmp(SYMname,"p32",3) == 0) SYM=1;
if(strncmp(SYMname,"p62",3) == 0) SYM=1;
strcpy(tmpstring,"ctfrev");
if(*(cgetline(input,tmpstring))=='y')
{ contrast=-1;
printf("Contrast of final map.......... = positive\n");
}
else
{ contrast=1;
printf("Contrast of final map.......... = negative\n");
}
strcpy(tmpstring,"phaori");
if(fgetline(input,tmpstring,phaori)==0)
{
printf("Phase Origin................... = %f %f\n",phaori[0],phaori[1]);
if(SYM==1)
{
printf(":: Adding 180deg phaseshift to phase origin, due to screw axis symmetry.\n");
phaori[0]+=180.0;
}
}
else
printf(":: ERROR in Phase Origin assignment.");
strcpy(tmpstring,"lattice");
if(fgetline(input,tmpstring,lattice)==0)
printf("Reciprocal Lattice............. = %f %f %f %f\n",lattice[0],lattice[1],lattice[2],lattice[3]);
else
printf(":: ERROR in Reciprocal Lattice assignment.");
fclose(input);
free(imagenumber);
free(temp_imagename);
printf("\n::Starting ML\n\n");
fflush(stdout);
/* ML main program */
ML(imagename, profilename,resultsfilename);
printf("\n::2dx_ML finished correctly\n\n");
fflush(stdout);
free(profilename);
free(imagename);
free(resultsfilename);
return 0;
}
