void sSCut(void)
{
dest=ATPOP;
len=ML(dest);
lens=ATPOP;
ML(dest)=max(0,len-lens);
}
P serialize_member( const T& t, P end, const member_if<ML, MR, RU>& memb )
{
typedef typename ML::type typeL;
if ( !( _get_value(t, ML()) == typeL() ) )
return serialize_member( t, end, ML() );
return serialize_member( t, end, MR() );
}
void sStSets(void)
{
dest=ATPOP;
len=ML(DBAdr+V_COUNT);
symb=(char)ATPOP;
ML(dest)=len;
dest=dest+(int32)DsspMem+4;
for (i=0;i<len;i++)
*(char*)(dest++)=symb;
//strnset((char*)dest,(char)symb,len);
}
void sStSet(void)
{
dest=ATPOP;
lend=ML(DBAdr+V_COUNT);
lens=ATPOP;
source=(int32)DsspMem+ATPOP;
len=min(lens,lend);
ML(dest)=len;
dest=dest+(int32)DsspMem+4;
strncpy((char*)dest,(char*)source,len);
}
void _VctrAllSet (void) { // Assign value to every item Vctr[i]
// Top= base address of Vector, SupTop = value to be assigned
int32 i,cnt,size,A,V;
cnt=ML(DBAdr+V_COUNT);
size=ML(DBAdr+V_SIZE);
DA_SETTYPEI;
A= ATPOP; V= ATPOP;
for (i=0; i<cnt; i++) {
APUSH(V); APUSH(A+i*size);
DA_EXEC(T_ALLSET); // !!! for Vctr[i]
}
}
void sSCmp(void)
{
dest=ATPOP;
len=ML(dest);
dest=dest+(int32)DsspMem+4;
lend=ML(DBAdr+V_COUNT);
lens=ATPOP;
source=ATPOP+(int32)DsspMem;
sEnd=*(char*)(source+lens); *(char*)(source+lens)=0;
dEnd=*(char*)(dest+len); *(char*)(dest+len)=0;
AINS; AT=-(int32)strcmp((char*)dest,(char*)source);
*(char*)(dest+len)=dEnd;
*(char*)(source+lens)=sEnd;
}
void sSAddB(void)
{
dest=ATPOP;
len=ML(dest);
lend=ML(DBAdr+V_COUNT);
if (len<lend)
{
ML(dest)++;
dest=dest+(int32)DsspMem+4+len;
*(char*)dest=(char)ATPOP;
}
else
{ADEL;}
}
void sSAdd(void)
{
dest=ATPOP;
len=ML(dest);
lend=ML(DBAdr+V_COUNT);
lens=ATPOP;
source=ATPOP+(int32)DsspMem;
ML(dest)=min(lend,len+lens);
dest=dest+(int32)DsspMem+4;
dest=dest+len;
for (i=0;i<(lend-len);i++)
{
*(char*)(dest++)=*(char*)(source++);
}
}
void sSSsb(void)
{
dest=ATPOP;
len=ML(dest);
dest=dest+(int32)DsspMem+4;
lend=ML(DBAdr+V_COUNT);
lens=ATPOP;
source=ATPOP+(int32)DsspMem;
sEnd=*(char*)(source+lens); *(char*)(source+lens)=0;
dEnd=*(char*)(dest+len); *(char*)(dest+len)=0;
result=strstr((char*)dest,(char*)source);
*(char*)(dest+len)=dEnd;
*(char*)(source+lens)=sEnd;
AINS; AT=(int32)result-dest;
AINS; if (result==NULL) AT=0; else AT=1;
}
void _VctrAdrI (void) { // Calculate Address of Vctr[i]
// AITEM(1) = index; AT= base address of Vector
_TstVctrInd();
AITEM(1)=AT+AITEM(1)*ML(DBAdr+V_SIZE);
ADEL;
// AT= address of item Vector[index]
}
void sStVal(void)
{
AT=AT+4;
APUSHCOPYn(1);
AT=AT-4;
AT=ML(AT);
}
void Riccati
( ElementalMatrix<F>& WPre,
ElementalMatrix<F>& X,
SignCtrl<Base<F>> ctrl )
{
DEBUG_CSE
DistMatrixReadProxy<F,F,MC,MR> WProx( WPre );
auto& W = WProx.Get();
const Grid& g = W.Grid();
Sign( W, ctrl );
const Int n = W.Height()/2;
DistMatrix<F> WTL(g), WTR(g),
WBL(g), WBR(g);
PartitionDownDiagonal
( W, WTL, WTR,
WBL, WBR, n );
// (ML, MR) = sgn(W) - I
ShiftDiagonal( W, F(-1) );
// Solve for X in ML X = -MR
DistMatrix<F> ML(g), MR(g);
PartitionRight( W, ML, MR, n );
MR *= -1;
ls::Overwrite( NORMAL, ML, MR, X );
}
void _StructSt (void) { // Assign values to Structure from the address
int32 Adr;
Adr = AT; AT=ML(TypeAdr+T_SIZE);
APUSH(Adr);
// A-Astack contains now: [Address, Number of bytes, StructAddress ]
_MoveB (); // execute !!!SB
}
void _StructSt0 (void) { // Assign zero to every byte of Structure
int32 Adr;
Adr = AT; AT=0;
APUSH(Adr);
APUSH(ML(TypeAdr+T_SIZE));
// A-Astack contains now: [0, Address, Number of bytes ]
_SetB(); // execute !!!MB
}
void _ArrAdrI (void) { // Calculate Address of Arr[i1,..,ik]
// AITEM(p) = index (ip) of item, p=1,..,k
// AT= base address of Vector
int32 p,i,k;
k= ML(DBAdr+V_DIMENSION);
i=0; // calculate I= (...(I1*L2+I2)*L2+...)*Lk+Ik
for (p=1; p<=k; p++) {
i= i*ML(DBAdr+V_LIMITS+p-1)+AITEM(p);
// Test index out of range
if ( AITEM(p)>=ML(DBAdr+V_LIMITS+p-1) ) {
printf(" index out of range \n");
exit(77); // Wrong Index !!!!!
}//if
}//for
AITEM(k)=AT+i*ML(DBAdr+V_SIZE);
ADELn(k);
// AT= address of item Arr[i1,..,ik]
}
void _GTP (void) { // GTP
// Push to A-stack the following value in body
// of that procedure, from where the procedure,
// including GTP, was called.
lptr Rpc; int32 Val;
Rpc= (lptr)CT; Val=ML((bptr)Rpc);
Rpc++; CT=(int32)Rpc;
APUSH(Val);
}
//void sVDimQ(void)
//void sVSizeQ(void)
void sSDsb(void) // [N,I,A]
{
dest=ATPOP;
lend=ML(DBAdr+V_COUNT);
len=ML(dest);
if ((!(len<AT))&&(!(lend<AT)))
{
lens=ATPOP;
if (lend>0)
ML(dest)=max(0,len-AT);
dest=dest+(int32)DsspMem+4+lens;
j=ATPOP;
for (i=j;i<(lend-lens);i++)
*((char*)dest+i-j)=*((char*)dest+i);
}
else
{ ADEL;ADEL;}
}
void _Call (void)
{ // CALLTELO
// cmd-> CALLTELO
// +1 ADR // address of DSSP-procedure
// +2 ... // address of this position
// // will be in C-STACK
CPUSH(cmd+2);
cmd = (lptr)ML(cmd+1);
EXECMD;
}
void sSDel(void)
{
dest=ATPOP;
len=ML(DBAdr+V_COUNT);
lend=ML(dest);
if ((!(len<AT))&&(!(lend<AT)))
{
if (lend>0)
ML(dest)--;
dest=dest+(int32)DsspMem+4+AT;
j=ATPOP;
for (i=1;i<(lend-j);i++)
*((char*)dest+i-1)=*((char*)dest+i);
}
else
{
ADEL;
}
}
void _DOFor (void) { // DO- // DO- BODY
// N DO- P means execute [i] P for i=N,..,1
if (--AT>=0) { // decrement parameter and then test it
cmd= (lptr)ML(pc);
pc--; // so that pc points again to DO- position
EXECMD;
} else { // terminate loop, if AT became <0
pc++;
ADEL; // pop parameter
}
}
void sSIns(void)
{
dest=ATPOP;
len=ML(DBAdr+V_COUNT);
lend=ML(dest);
if (!(len<AT))
{
if (lend<len)
ML(dest)++;
dest=dest+(int32)DsspMem+4+AT;
j=ATPOP;
for (i=(lend-j);i>=1;i--)
*((char*)dest+i)=*((char*)dest+i-1);
*(char*)dest=(char)ATPOP;
}
else
{
ADEL;ADEL;
}
}
void sSIsb(void)
{
dest=ATPOP;
j=ATPOP;
len=ML(dest);
lend=ML(DBAdr+V_COUNT);
lens=ATPOP;
source=ATPOP+(int32)DsspMem;
if (!(len<j))
{
ML(dest)=min(lend,len+lens);
dest=dest+(int32)DsspMem+4;
dest=dest+j;
for (i=(lend-j-lens);i>1;i--)
*((char*)dest+i)=*((char*)dest+i-lens);
for (i=0;i<min(lens,lend-j);i++)
*((char*)dest+i)=*((char*)source+i);
}
}
void _arg2str(void) // ARG2STR
{
GETCMD;
DA_SETDB;
DA_GETADR;
DA_SETTYPE;
i=0;
dest=ATPOP;
lend=ML(DBAdr+V_COUNT);
ML(dest)=len=0;
dest+=((int32)DsspMem+4);
for (j=param_st;j<argc_gl;j++)
{
len=min((unsigned)(i+strlen(argv_gl[j])),(unsigned)lend);
strncpy((char*)(dest+i),argv_gl[j],len-i);
if ((i>=lend) || (j==argc_gl-1)) break;
i=len;*(char*)(dest+i)=' ';i++;
}
dest-=((int32)DsspMem+4);
ML(dest)=len;
}
void sSOvr(void)
{
dest=ATPOP;
len=ML(DBAdr+V_COUNT);
if (!(len<AT))
{
dest=dest+(int32)DsspMem+ATPOP+4;
*(char*)dest=(char)ATPOP;
}
else
{
ADEL;ADEL;
}
}
bool_t ML(divisor& x, const divisor& a, const ZZ& n)
// Montgomery's ladder: used to defend side channel attacks
// cf. Alg. 13.35 of HOEHCC
{
assert(a.is_valid_divisor());
bool_t OK = TRUE;
long nbits = NumBits(n);
divisor b1, b2;
if ( !nbits ) { // n = 0
x.set_unit();
return OK;
}
if ( n < 0) {
OK = OK && ML(x, a, -n);
OK = OK && dnegate(x, x);
return OK;
}
// Case n > 0
b1 = a; b2 = a + a;
for ( --nbits; OK && nbits > 0; --nbits) {
if ( !bit(n, nbits - 1) ) {
OK = OK && add(b2, b1, b2); // b2 = b1 + b2
OK = OK && add(b1, b1, b1); // b1 = [2]*b1
} else {
OK = OK && add(b1, b1, b2); // b1 = b1 + b2;
OK = OK && add(b2, b2, b2); // b2 = [2]*b2;
assert(OK);
}
}
assert(b1.is_valid_divisor());
x = b1;
return OK;
}
void _Br1 (void) { // BR1
CPOP(pc);
if (AITEM(1)==AT)
{ ADELn(2);
GETCMD;
// looking for ELSE
while (ML(pc)!=cmd_Else) pc++;
pc +=2; // so that pc points after P0
EXECMD;
} else {
ADEL;
pc++;
GETCMD;
CPUSH(pc);
pc=PCADR(cmd_BR1);
EXECMD;
}
}
}
}
}
#ifdef WIN32
#include <stdio.h>
#define ML(pn,sn) MAKELANGID(LANG_##pn, SUBLANG_##pn##_##sn)
#define MLN(pn) MAKELANGID(LANG_##pn, SUBLANG_DEFAULT)
#define RML(pn,sn) MAKELANGID(LANG_##pn, SUBLANG_##sn)
struct IDToCode {
LANGID id;
char* code;
};
static const IDToCode both_to_code[] = {
{ML(ENGLISH,US), "en_US.ISO_8859-1"},
{ML(ENGLISH,CAN), "en_CA"}, /* english / canadian */
{ML(ENGLISH,UK), "en_GB"},
{ML(ENGLISH,EIRE), "en_IE"},
{ML(ENGLISH,AUS), "en_AU"},
{MLN(GERMAN), "de_DE"},
{MLN(SPANISH), "es_ES"},
{ML(SPANISH,MEXICAN), "es_MX"},
{MLN(FRENCH), "fr_FR"},
{ML(FRENCH,CANADIAN), "fr_CA"},
{ML(FRENCH,BELGIAN), "fr_BE"}, /* ? */
{ML(DUTCH,BELGIAN), "nl_BE"}, /* ? */
{ML(PORTUGUESE,BRAZILIAN), "pt_BR"},
{MLN(PORTUGUESE), "pt_PT"},
{MLN(SWEDISH), "sv_SE"},
{ML(CHINESE,HONGKONG), "zh_HK"},
void R3DLuminance::calculateLuminance(std::list<double> *luminance)
{
std::list<R3DLight>::iterator light_it;
int N = m_triangles->size();
int Nsegm = m_Ntheta * m_Nphi + 2;
std::list<int> *segments = new std::list<int>[ Nsegm ];
bool *isVisible = new bool[N];
//LineSegment *rayList = new LineSegment[N];
R3DPoint *midPoint = new R3DPoint[N];
// initialize with zeros
int i;
luminance->clear();
for(i=0;i<N;i++)
luminance->push_back( 0 );
// calculate luminance: light by light
for(light_it = m_lights->begin();
light_it != m_lights->end();
light_it ++)
{
R3DPoint L = (*light_it).position;
double power = (*light_it).power;
for(i=0;i<Nsegm;i++) segments[i].clear();
for(i=0;i<N;i++) isVisible[i] = true;
std::set<int> S; //segment of triangles
std::set<int>::iterator set_it;
std::list<R3DTriangle>::iterator tri_it;
int tri_idx;
// add triangles to appropriate segments
for(tri_it = m_triangles->begin(), tri_idx = 0;
tri_it != m_triangles->end();
tri_it++, tri_idx ++ )
{
S.clear();
getSegments( *tri_it, //R3DTriangle &T,
L ,// R3DPoint &L, //light position
&S //std::set<int> *segment_set
);
if(DEBUG) std::cout<<"Triangle "<<*tri_it<<" SEGMENTS:"<<std::endl;
for( set_it = S.begin(); set_it!=S.end(); set_it ++ )
{
if(DEBUG)
{
std::cout<<*set_it;
}
segments[ *set_it ].push_back( tri_idx );
}
}// tri_it
if(DEBUG)
{
for(i=0;i<Nsegm;i++)
{
std::list<int>::iterator idx_it;
printf("SEGMENT %d:\n",i);
for( idx_it = segments[i].begin(); idx_it!=segments[i].end(); idx_it++)
{
std::cout<<"Triangle "<<*idx_it<<" : "<< *m_triIndex[ *idx_it ]<<std::endl;
}
}
}
// intersect triangles inside the segments
int segm_id;
for(segm_id = 0; segm_id < Nsegm; segm_id++)
{
// go through all the triangles in the segment
std::list<int>::iterator idx_it1,idx_it2;
for( idx_it1 = segments[ segm_id].begin();
idx_it1 != segments[ segm_id].end();
idx_it1++)
{
R3DTriangle T1 = *m_triIndex[ *idx_it1 ];
R3DPoint M = (T1.A + T1.B + T1.C)/3;
R3DLineSegment ML(M,L);
midPoint[ *idx_it1 ] = M;
// check if ML croses one of triangles in this segment
for(idx_it2 = segments[segm_id].begin();
idx_it2 != segments[segm_id].end();
idx_it2 ++ )
{
if ( *idx_it1 == *idx_it2) continue; //triangle coinside
R3DPoint X; //cross of the plane with
R3DPlane P2 = *m_planeIndex[ *idx_it2 ];
if(! intersect( ML, P2, &X)) continue; // ML does not intersect wuth the plane of second triangle
R3DTriangle T2 = *m_triIndex[ *idx_it2 ];
if( T2.isInside(X)) //croos point (X) is inside T2
{
isVisible[ *idx_it1 ] = false; // T2 covers T1
break;
}
}//idx_it2
}// idx_it1
} //segm_id
// std::list<double>::iterator lum_it;
std::list<double>::iterator lum_it;
for( i=0, lum_it = luminance->begin();
i<N;
i++, lum_it++)
{
if(!isVisible[i]) continue;
R3DPlane P = *m_planeIndex[i];
R3DLineSegment ML( midPoint[i], L);
double normML = ML.m_direction.norm();
double cos_phi = fabs( P.getNormal() * ML.m_direction )/normML;
if(DEBUG)
std::cout<<"M:"<<midPoint[i]<<" cos_phi="<<cos_phi<<" normML="<<normML<<std::endl;
// K = L.power / (normML * normML) * cos_phi;
*lum_it += power / (normML * normML) * cos_phi;
}
}// for light
delete [] segments;
delete [] isVisible;
delete [] midPoint;
}
P unserialize_member( T& t, P beg, P end, member_if<ML, MR, false>, bool& unserialized )
{
return unserialize_member(t, beg, end, ML(), unserialized);
}
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;
}