map.cpp 14.7 KB
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#include <fstream>
#include <iostream>
#include <stdio.h>
#include <stdlib.h>
#include <cstring>
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#include <math.h>
#include <fftw3.h>
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#include "map.h"
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#include "param.h"

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using namespace std;

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int bioem_RefMap::readRefMaps(bioem_param& param)
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{
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	//**************************************************************************************
	//***********************Reading reference Particle Maps************************
	//**************************************************************************************
	if (loadMap)
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	{
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		FILE* fp = fopen("maps.dump", "rb");
		if (fp == NULL)
		{
			cout << "Error opening dump file\n";
			exit(1);
		}
		fread(&ntotRefMap, sizeof(ntotRefMap), 1, fp);
		if (ntotRefMap > BIOEM_MAX_MAPS)
		{
			cout << "BIOEM_MAX_MAPS too small, some maps dropped\n";
			ntotRefMap = BIOEM_MAX_MAPS;
		}
		fread(&Ref[0], sizeof(Ref[0]), ntotRefMap, fp);
		fclose(fp);

		cout << "Particle Maps read from Map Dump \nTotal Number of particles: " << ntotRefMap ;
		cout << "\n+++++++++++++++++++++++++++++++++++++++ \n";
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	}
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	else
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	{
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		if(readMRC) {

			ntotRefMap = 0;

			if(readMultMRC)
			{

				ifstream input(filemap);

				if (!input.good())
				{
					cout << "Failed to open file contaning MRC names: " << filemap << "\n";
					exit(0);
				}

				char line[512] = {0};
				char mapname[100];
				char tmpm[10] = {0};
				const char* indifile;

				while (!input.eof())
				{
					input.getline(line, 512);
					char tmpVals[100]  = {' '};

					strncpy (tmpVals, line, 100);
					sscanf (tmpVals, "%99c", mapname);

					// Check for last line
					strncpy (tmpm, mapname, 3);
					if(strcmp(tmpm, "XXX") != 0) {
						indifile = mapname;
						//Reading Multiple MRC
						read_MRC(indifile, param);

					}
					for(int i = 0; i < 3; i++)mapname[i] = 'X';
					for(int i = 3; i < 100; i++)mapname[i] = {0};

				}
				cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";
				cout << "Particle Maps read from MULTIPLE MRC Files in: " << filemap << "\n" ;

			} else {

				read_MRC(filemap, param);
				cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
				cout << "Particle Maps read from ONE MRC File: " << filemap << "\n" ;

			}

		}
		else {

			int nummap = -1;
			int lasti = 0;
			int lastj = 0;
			ifstream input(filemap);
			if (!input.good())
			{
				cout << "Particle Maps Failed to open file" << endl ;
				exit(1);
			}

			char line[512] = {' '};
			char tmpLine[512] = {' '};

			while (!input.eof())
			{
				input.getline(line, 512);

				strncpy(tmpLine, line, strlen(line));
				char *token = strtok(tmpLine, " ");

				if (strcmp(token, "PARTICLE") == 0) // to count the number of maps
				{
					nummap++;
					if (nummap % 128 == 0)
					{
						cout << "..." << nummap << "\n";
					}
					if (nummap == BIOEM_MAX_MAPS)
					{
						cout << "BIOEM_MAX_MAPS too small\n";
						exit(1);
					}
					if(lasti != param.param_device.NumberPixels && lastj != param.param_device.NumberPixels && nummap > 0)
					{
						cout << "PROBLEM INCONSISTENT NUMBER OF PIXELS IN MAPS AND INPUTFILE ( " << param.param_device.NumberPixels << ", i " << lasti << ", j " << lastj << ")" << "\n";
						exit(1);
					}
				}
				else
				{
					int i, j;
					float z;

					char tmpVals[36]  = {' '};

					strncpy (tmpVals, line, 8);
					sscanf (tmpVals, "%d", &i);

					strncpy (tmpVals, line + 8, 8);
					sscanf (tmpVals, "%d", &j);

					strncpy (tmpVals, line + 16, 12);
					sscanf (tmpVals, "%f", &z);
					//checking for Map limits
					if(i > 0 && i - 1 < BIOEM_MAP_SIZE_X && j > 0 && j - 1 < BIOEM_MAP_SIZE_Y && nummap < BIOEM_MAX_MAPS)
					{
						Ref[nummap].points[i - 1][j - 1] = (myfloat_t) z;
						lasti = i;
						lastj = j;
					}
					else
					{
						cout << "PROBLEM READING MAP (Map number " << nummap << ", i " << i << ", j " << j << ")" << "\n";
						exit(1);
					}
				}
			}
			cout << ".";
			ntotRefMap = nummap + 1;
			cout << "\n++++++++++++++++++++++++++++++++++++++++++ \n";
			cout << "Particle Maps read from Standard File\n" ;
		}
		cout << "Total Number of particles: " << ntotRefMap ;
		cout << "\n+++++++++++++++++++++++++++++++++++++++++++ \n";

		if (dumpMap)
		{
			FILE* fp = fopen("maps.dump", "w+b");
			if (fp == NULL)
			{
				cout << "Error opening dump file\n";
				exit(1);
			}
			fwrite(&ntotRefMap, sizeof(ntotRefMap), 1, fp);
			fwrite(&Ref[0], sizeof(Ref[0]), ntotRefMap, fp);
			fclose(fp);
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		}
	}

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	return(0);
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}

int bioem_RefMap::PreCalculateMapsFFT(bioem_param& param)
{
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	//**************************************************************************************
	//********** Routine that pre-calculates Kernels for Convolution ***********************
	//**************************************************************************************
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	myfloat_t* localMap;
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	localMap = (myfloat_t *) myfftw_malloc(sizeof(myfloat_t) * param.param_device.NumberPixels * param.param_device.NumberPixels);
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	RefMapsFFT = new mycomplex_t[ntotRefMap * param.RefMapSize];
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	mycomplex_t* localout;
	localout = (mycomplex_t *) myfftw_malloc(sizeof(mycomplex_t) * param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D);
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	for (int iRefMap = 0; iRefMap < ntotRefMap ; iRefMap++)
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	{
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		//Assigning localMap values to padded Map
		for(int i = 0; i < param.param_device.NumberPixels; i++)
		{
			for(int j = 0; j < param.param_device.NumberPixels; j++)
			{
				localMap[i * param.param_device.NumberPixels + j] = Ref[iRefMap].points[i][j];
			}
		}
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		//Calling FFT_Forward
		myfftw_execute_dft_r2c(param.fft_plan_r2c_forward, localMap, localout);
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		// Normalizing and saving the Reference CTFs
		mycomplex_t* RefMap = &RefMapsFFT[iRefMap * param.RefMapSize];
		for(int i = 0; i < param.param_device.NumberPixels * param.param_device.NumberFFTPixels1D ; i++ )
		{
			RefMap[i][0] = localout[i][0];
			RefMap[i][1] = localout[i][1];
		}
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	}

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	myfftw_free(localMap);
	myfftw_free(localout);
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	return(0);
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}

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int bioem_RefMap::read_MRC(const char* filename, bioem_param& param)
{
	myfloat_t st, st2;
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	unsigned long count;
	FILE *fin;
	float currfloat;
	int nc, nr, ns, swap, header_ok = 1;
	float xlen, ylen, zlen;
	int mode, ncstart, nrstart, nsstart, ispg, nsymbt, lskflg;
	float a_tmp, b_tmp, g_tmp;
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	int  mx, my, mz, mapc, mapr, maps;
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	float dmin, dmax, dmean;
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	int n_range_viol0, n_range_viol1;
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	fin = fopen(filename, "rb");
	if( fin == NULL ) {
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		cout << "ERROR opening MRC: " << filename;
		exit(1);
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	}
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	n_range_viol0 = test_mrc(filename, 0);
	n_range_viol1 = test_mrc(filename, 1);


	if (n_range_viol0 < n_range_viol1) { //* guess endianism
		swap = 0;
		if (n_range_viol0 > 0) {
			printf(" Warning: %i header field range violations detected in file %s \n", n_range_viol0, filename);
		}
	} else {
		swap = 1;
		if (n_range_viol1 > 0) {
			printf("Warning: %i header field range violations detected in file %s \n", n_range_viol1, filename);
		}
	}
	printf("\n+++++++++++++++++++++++++++++++++++++++++++\n");
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	printf("Reading Information from MRC: %s \n", filename);
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	header_ok *= read_int(&nc, fin, swap);
	header_ok *= read_int(&nr, fin, swap);
	header_ok *= read_int(&ns, fin, swap);
	header_ok *= read_int(&mode, fin, swap);
	header_ok *= read_int(&ncstart, fin, swap);
	header_ok *= read_int(&nrstart, fin, swap);
	header_ok *= read_int(&nsstart, fin, swap);
	header_ok *= read_int(&mx, fin, swap);
	header_ok *= read_int(&my, fin, swap);
	header_ok *= read_int(&mz, fin, swap);
	header_ok *= read_float(&xlen, fin, swap);
	header_ok *= read_float(&ylen, fin, swap);
	header_ok *= read_float(&zlen, fin, swap);
	header_ok *= read_float(&a_tmp, fin, swap);
	header_ok *= read_float(&b_tmp, fin, swap);
	header_ok *= read_float(&g_tmp, fin, swap);
	header_ok *= read_int(&mapc, fin, swap);
	header_ok *= read_int(&mapr, fin, swap);
	header_ok *= read_int(&maps, fin, swap);
	header_ok *= read_float(&dmin, fin, swap);
	header_ok *= read_float(&dmax, fin, swap);
	header_ok *= read_float(&dmean, fin, swap);
	header_ok *= read_int(&ispg, fin, swap);
	header_ok *= read_int(&nsymbt, fin, swap);
	header_ok *= read_int(&lskflg, fin, swap);

	printf("Number Columns  = %8d \n", nc);
	printf("Number Rows     = %8d \n", nr);
	printf("Number Sections = %8d \n", ns);
	printf("MODE = %4d (only data type mode 2: 32-bit)\n", mode);
	printf("NSYMBT = %4d (# bytes symmetry operators)\n", nsymbt);
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	/* printf("  NCSTART = %8d  (index of first column, counting from 0)\n",ncstart);
	   printf(">  NRSTART = %8d  (index of first row, counting from 0)\n",nrstart);
	   printf("  NSSTART = %8d  (index of first section, counting from 0)\n",nsstart);
	   printf("       MX = %8d  (# of X intervals in unit cell)\n",mx);
	   printf("       MY = %8d  (# of Y intervals in unit cell)\n",my);
	   printf("       MZ = %8d  (# of Z intervals in unit cell)\n",mz);
	   printf(" X length = %8.3f  (unit cell dimension)\n",xlen);
	   printf(" Y length = %8.3f  (unit cell dimension)\n",ylen);
	   printf(" Z length = %8.3f  (unit cell dimension)\n",zlen);
	   printf("    Alpha = %8.3f  (unit cell angle)\n",a_tmp);
	   printf("     Beta = %8.3f  (unit cell angle)\n",b_tmp);
	   printf("    Gamma = %8.3f  (unit cell angle)\n",g_tmp);
	   printf("     MAPC = %8d  (columns axis: 1=X,2=Y,3=Z)\n",mapc);
	   printf("     MAPR = %8d  (rows axis: 1=X,2=Y,3=Z)\n",mapr);
	   printf("     MAPS = %8d  (sections axis: 1=X,2=Y,3=Z)\n",maps);
	   printf("     DMIN = %8.3f  (minimum density value - ignored)\n",dmin);
	   printf("     DMAX = %8.3f  (maximum density value - ignored)\n",dmax);
	   printf("    DMEAN = %8.3f  (mean density value - ignored)\n",dmean);
	   printf("     ISPG = %8d  (space group number - ignored)\n",ispg);
	   printf("   NSYMBT = %8d  (# bytes storing symmetry operators)\n",nsymbt);
	   printf("   LSKFLG = %8d  (skew matrix flag: 0:none, 1:follows)\n",lskflg);*/

	if (header_ok == 0) {
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		cout << "ERROR reading MRC header: " << filename;
		exit(1);
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	}

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	if(nr != param.param_device.NumberPixels || nc != param.param_device.NumberPixels )
	{
		cout << "PROBLEM INCONSISTENT NUMBER OF PIXELS IN MAPS AND INPUTFILE ( " << param.param_device.NumberPixels << ", i " << nc << ", j " << nr << ")" << "\n";
		exit(1);
	}
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	if(mode != 2)
	{
		cout << "ERROR with MRC mode " << mode << "\n";
		cout << "Currently mode 2 is the only one allowed" << "\n";
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		exit(1);
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	} else
	{
		rewind (fin);
		for (count = 0; count < 256; ++count) if (read_float_empty(fin) == 0) {
				cout << "ERROR Converting Data: " <<  filename;
				exit(1);
			}

		for (count = 0; count < (unsigned long)nsymbt; ++count) if (read_char_float(&currfloat, fin) == 0) {
				cout << "ERROR Converting Data: " <<  filename;
				exit(1);
			}

		for ( int nmap = 0 ; nmap < ns ; nmap ++ )
		{

			st = 0.0;
			st2 = 0.0;
			for ( int j = 0 ; j < nr ; j ++ )
				for ( int i = 0 ; i < nc ; i ++ )
				{
					if (read_float(&currfloat, fin, swap) == 0) {
						cout << "ERROR Converting Data: " <<  filename;
						exit(1);
					} else {
						Ref[nmap + ntotRefMap].points[i][j] = currfloat;
						st += currfloat;
						st2 += currfloat * currfloat;

					}
				}

			//Normaling maps to zero mean and unit standard deviation
			st /= float(nr * nc);
			st2 = sqrt(st2 / float(nr * nc) - st * st);
			for ( int j = 0 ; j < nr ; j ++ ) for ( int i = 0 ; i < nc ; i ++ ) {
					Ref[nmap + ntotRefMap].points[i][j] =  Ref[nmap + ntotRefMap].points[i][j] / st2 - st / st2;
					//    if(nmap+ntotRefMap==300)cout << i << " " << j << " " << nmap+ntotRefMap << " " <<  Ref[nmap+ntotRefMap].points[i][j]  << "\n";
				}
		}
		ntotRefMap += ns ;
		//  cout << ntotRefMap << "\n";
	}
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	fclose (fin);
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	return(0);
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}

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int bioem_RefMap::read_float(float *currfloat, FILE *fin, int swap) {
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	unsigned char *cptr, tmp;

	if (fread(currfloat, 4, 1, fin) != 1) return 0;
	if (swap == 1) {
		cptr = (unsigned char *)currfloat;
		tmp = cptr[0];
		cptr[0] = cptr[3];
		cptr[3] = tmp;
		tmp = cptr[1];
		cptr[1] = cptr[2];
		cptr[2] = tmp;
	}
	return 1;
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}
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int  bioem_RefMap::read_int(int *currlong, FILE *fin, int swap) {
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	unsigned char *cptr, tmp;

	if (fread(currlong, 4, 1, fin) != 1) return 0;
	if (swap == 1) {
		cptr = (unsigned char *)currlong;
		tmp = cptr[0];
		cptr[0] = cptr[3];
		cptr[3] = tmp;
		tmp = cptr[1];
		cptr[1] = cptr[2];
		cptr[2] = tmp;
	}
	return 1;
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}
int  bioem_RefMap::read_float_empty (FILE *fin) {
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	float currfloat;
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	if (fread(&currfloat, 4, 1, fin) != 1) return 0;
	return 1;
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}

int  bioem_RefMap::read_char_float (float *currfloat, FILE *fin) {
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	char currchar;
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	if (fread(&currchar, 1, 1, fin) != 1) return 0;
	*currfloat = (float)currchar;
	return 1;
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}

int  bioem_RefMap::test_mrc (const char *vol_file, int swap) {
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	FILE *fin;
	int nc, nr, ns, mx, my, mz;
	int mode, ncstart, nrstart, nsstart;
	float xlen, ylen, zlen;
	int i, header_ok = 1, n_range_viols = 0;
	int mapc, mapr, maps;
	float alpha, beta, gamma;
	float dmin, dmax, dmean, dummy, xorigin, yorigin, zorigin;

	fin = fopen(vol_file, "rb");
	if( fin == NULL ) {
		cout << "ERROR opening MRC: " << vol_file;
		exit(1);
	}

//* read header info
	header_ok *= read_int(&nc, fin, swap);
	header_ok *= read_int(&nr, fin, swap);
	header_ok *= read_int(&ns, fin, swap);
	header_ok *= read_int(&mode, fin, swap);
	header_ok *= read_int(&ncstart, fin, swap);
	header_ok *= read_int(&nrstart, fin, swap);
	header_ok *= read_int(&nsstart, fin, swap);
	header_ok *= read_int(&mx, fin, swap);
	header_ok *= read_int(&my, fin, swap);
	header_ok *= read_int(&mz, fin, swap);
	header_ok *= read_float(&xlen, fin, swap);
	header_ok *= read_float(&ylen, fin, swap);
	header_ok *= read_float(&zlen, fin, swap);
	header_ok *= read_float(&alpha, fin, swap);
	header_ok *= read_float(&beta, fin, swap);
	header_ok *= read_float(&gamma, fin, swap);
	header_ok *= read_int(&mapc, fin, swap);
	header_ok *= read_int(&mapr, fin, swap);
	header_ok *= read_int(&maps, fin, swap);
	header_ok *= read_float(&dmin, fin, swap);
	header_ok *= read_float(&dmax, fin, swap);
	header_ok *= read_float(&dmean, fin, swap);
	for (i = 23; i < 50; ++i) header_ok *= read_float(&dummy, fin, swap);
	header_ok *= read_float(&xorigin, fin, swap);
	header_ok *= read_float(&yorigin, fin, swap);
	header_ok *= read_float(&zorigin, fin, swap);
	fclose (fin);
	if (header_ok == 0) {
		cout << "ERROR reading MRC header: " << vol_file;
		exit(1);
	}

	n_range_viols += (nc > 5000); n_range_viols += (nc < 0);
	n_range_viols += (nr > 5000); n_range_viols += (nr < 0);
	n_range_viols += (ns > 5000); n_range_viols += (ns < 0);
	n_range_viols += (ncstart > 5000); n_range_viols += (ncstart < -5000);
	n_range_viols += (nrstart > 5000); n_range_viols += (nrstart < -5000);
	n_range_viols += (nsstart > 5000); n_range_viols += (nsstart < -5000);
	n_range_viols += (mx > 5000); n_range_viols += (mx < 0);
	n_range_viols += (my > 5000); n_range_viols += (my < 0);
	n_range_viols += (mz > 5000); n_range_viols += (mz < 0);
	n_range_viols += (alpha > 360.0f); n_range_viols += (alpha < -360.0f);
	n_range_viols += (beta > 360.0f); n_range_viols += (beta < -360.0f);
	n_range_viols += (gamma > 360.0f); n_range_viols += (gamma < -360.0f);

	return n_range_viols;
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}