/
minc_1_rw.cpp
1438 lines (1245 loc) · 43.7 KB
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minc_1_rw.cpp
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/* ----------------------------- MNI Header -----------------------------------
@NAME :
@DESCRIPTION: Primitive" interface to minc files, using minctoraw and rawtominc programs
does not require linking with minc2 library.
Created during the days when minc2 didn't compile on 64bit architecture
@COPYRIGHT :
Copyright 2007 Vladimir Fonov, McConnell Brain Imaging Centre,
Montreal Neurological Institute, McGill University.
Permission to use, copy, modify, and distribute this
software and its documentation for any purpose and without
fee is hereby granted, provided that the above copyright
notice appear in all copies. The author and McGill University
make no representations about the suitability of this
software for any purpose. It is provided "as is" without
express or implied warranty.
---------------------------------------------------------------------------- */
#include <stdio.h>
#include <iostream>
#include <sstream>
#include <string.h>
//minc stuff
#include <math.h>
#include <limits.h>
#include "minc_1_rw.h"
namespace minc
{
dim_info::dim_info(int l, double sta,
double spa,dimensions d,
bool hd):
length(l),start(sta),step(spa),dim(d),have_dir_cos(hd)
{
switch(dim)
{
case dim_info::DIM_X:name=MIxspace;break;
case dim_info::DIM_Y:name=MIyspace;break;
case dim_info::DIM_Z:name=MIzspace;break;
case dim_info::DIM_TIME:name=MItime;break;
case dim_info::DIM_VEC:name=MIvector_dimension;break;
default: REPORT_ERROR("Unknown Dimension!");
}
}
minc_1_base::minc_1_base():
_dims(3,0),
_map_to_std(5,-1),
_mincid(MI_ERROR),
_imgid(MI_ERROR),
_icvid(MI_ERROR),
_cur(MAX_VAR_DIMS,0),
_slab(MAX_VAR_DIMS,1),
_last(false),
_datatype(MI_ORIGINAL_TYPE),
_io_datatype(MI_ORIGINAL_TYPE),
_slab_len(0),
_positive_directions(true),
_minc2(false)
{
_icvid=miicv_create();
}
//! destructor, closes minc file
minc_1_base::~minc_1_base()
{
close();
}
void minc_1_base::close(void)
{
if(_icvid!=MI_ERROR)
{
miicv_free(_icvid);
_icvid=MI_ERROR;
}
if(_mincid!=MI_ERROR) miclose(_mincid);
_mincid=MI_ERROR;
}
std::string minc_1_base::history(void) const
{
nc_type datatype;
int att_length;
#ifndef WIN32
int op=ncopts;
#endif //WIN32
//ncopts=0;
if ((ncattinq(_mincid, NC_GLOBAL, MIhistory, &datatype,&att_length) == MI_ERROR) ||
(datatype != NC_CHAR))
{
//ncopts=op;
return "";
}
char* str = new char[att_length+1];
str[0] = '\0';
miattgetstr(_mincid, NC_GLOBAL, (char*)MIhistory, att_length,str);
//ncopts=op;
std::string r(str);
delete [] str;
return r;
}
//code from mincinfo
int minc_1_base::var_number(void) const
{
int nvars;
if(ncinquire(_mincid, NULL, &nvars, NULL, NULL)!=MI_ERROR)
return nvars;
return 0;
}
std::string minc_1_base::var_name(int no) const
{
char name[MAX_NC_NAME];
if(ncvarinq(_mincid, no, name, NULL, NULL, NULL, NULL)!=MI_ERROR)
return name;
}
int minc_1_base::att_number(const char *var_name) const
{
int varid;
int natts;
if (*var_name=='\0') {
varid = NC_GLOBAL;
} else {
if((varid = ncvarid(_mincid, var_name))==MI_ERROR)
return 0;
}
return att_number(varid);
}
int minc_1_base::var_id(const char *var_name) const
{
return ncvarid(_mincid, var_name);
}
long minc_1_base::var_length(const char *var_name) const
{
int varid=var_id(var_name);
if(varid!=MI_ERROR)
return var_length(varid);
else
return 0;
}
long minc_1_base::var_length(int var_id) const
{
int vardims;
if(ncvarinq(_mincid, var_id, NULL, NULL, &vardims, NULL, NULL)!=MI_ERROR)
{
if(vardims==0) return 1;
int *dims=new int[vardims];
if(ncvarinq(_mincid, var_id, NULL, NULL, NULL, dims, NULL)!=MI_ERROR)
{
long varlength=1;
if(ncdiminq(_mincid,dims[0],NULL,&varlength)!=MI_ERROR)
{
delete[] dims;
return varlength;
}
delete[] dims;
return 1;
} else {
delete[] dims;
return 1;
}
}
return 0;
}
//! get the number of attributes associated with variable
int minc_1_base::att_number(int var_no) const
{
int natts;
if(ncvarinq(_mincid, var_no, NULL, NULL, NULL, NULL, &natts)!=MI_ERROR)
return natts;
return 0;
}
std::string minc_1_base::att_name(const char *var_name,int no) const
{
int varid;
int attid;
char name[MAX_NC_NAME];
if (*var_name=='\0')
varid = NC_GLOBAL;
else
{
if((varid = ncvarid(_mincid, var_name))==MI_ERROR)
return "";
}
return att_name(varid,no);
}
std::string minc_1_base::att_name(int varid,int no) const
{
int attid;
char name[MAX_NC_NAME];
if(ncattname(_mincid, varid, no, name)==MI_ERROR)
return "";
return name;
}
std::string minc_1_base::att_value_string(const char *var_name,const char *att_name) const
{
int varid;
int attid;
char name[MAX_NC_NAME];
if (*var_name=='\0')
varid = NC_GLOBAL;
else
{
if((varid = ncvarid(_mincid, var_name))==MI_ERROR)
return "";
}
return att_value_string(varid,att_name);
}
std::string minc_1_base::att_value_string(int varid,const char *att_name) const
{
int att_length;
nc_type datatype;
//TODO: make this handle other (double?) data types correctly
if ((ncattinq(_mincid, varid, (char *)att_name, &datatype,&att_length) == MI_ERROR) ||
(datatype != NC_CHAR))
{
//ncopts=op;
return "";
}
char* str = new char[att_length+1];
str[0] = '\0';
miattgetstr(_mincid, varid, (char *)att_name, att_length, str);
//ncopts=op;
std::string r(str);
delete [] str;
return r;
}
std::vector<double> minc_1_base::att_value_double(const char *var_name,const char *att_name) const
{
int varid;
if (*var_name=='\0')
varid = NC_GLOBAL;
else
{
if((varid = ncvarid(_mincid, var_name))==MI_ERROR)
return std::vector<double>(0);
}
return att_value_double(varid,att_name);
}
std::vector<short> minc_1_base::att_value_short(const char *var_name,const char *att_name) const
{
int varid;
if (*var_name=='\0')
varid = NC_GLOBAL;
else
{
if((varid = ncvarid(_mincid, var_name))==MI_ERROR)
return std::vector<short>(0);
}
return att_value_short(varid,att_name);
}
std::vector<unsigned char> minc_1_base::att_value_byte(const char *var_name,const char *att_name) const
{
int varid;
if (*var_name=='\0')
varid = NC_GLOBAL;
else
{
if((varid = ncvarid(_mincid, var_name))==MI_ERROR)
return std::vector<unsigned char>(0);
}
return att_value_byte(varid,att_name);
}
std::vector<int> minc_1_base::att_value_int(const char *var_name,const char *att_name) const
{
int varid;
if (*var_name=='\0')
varid = NC_GLOBAL;
else
{
if((varid = ncvarid(_mincid, var_name))==MI_ERROR)
return std::vector<int>(0);
}
return att_value_int(varid,att_name);
}
std::vector<int> minc_1_base::att_value_int(int varid,const char *att_name) const
{
int att_length;
nc_type datatype;
if ((ncattinq(_mincid, varid, (char *)att_name, &datatype,&att_length) == MI_ERROR) ||
(datatype != NC_INT))
{
//ncopts=op;
return std::vector<int>(0);
}
std::vector<int> r(att_length);
miattget(_mincid, varid, (char*)att_name, NC_INT, att_length,&r[0], NULL) ;
//ncopts=op;
return r;
}
std::vector<double> minc_1_base::att_value_double(int varid,const char *att_name) const
{
int att_length;
nc_type datatype;
//TODO: make this handle other (double?) data types correctly
if ((ncattinq(_mincid, varid, (char *)att_name, &datatype,&att_length) == MI_ERROR) ||
(datatype != NC_DOUBLE))
{
//ncopts=op;
return std::vector<double>(0);
}
std::vector<double> r(att_length);
miattget(_mincid, varid, (char*)att_name, NC_DOUBLE, att_length,&r[0], NULL) ;
//ncopts=op;
return r;
}
std::vector<short> minc_1_base::att_value_short(int varid,const char *att_name) const
{
int att_length;
nc_type datatype;
//TODO: make this handle other (double?) data types correctly
if ((ncattinq(_mincid, varid, (char *)att_name, &datatype,&att_length) == MI_ERROR) ||
(datatype != NC_SHORT))
{
//ncopts=op;
return std::vector<short>(0);
}
std::vector<short> r(att_length);
miattget(_mincid, varid, (char*)att_name, NC_SHORT, att_length,&r[0], NULL) ;
//ncopts=op;
return r;
}
std::vector<unsigned char> minc_1_base::att_value_byte(int varid,const char *att_name) const
{
int att_length;
nc_type datatype;
//TODO: make this handle other (double?) data types correctly
if ((ncattinq(_mincid, varid, (char *)att_name, &datatype,&att_length) == MI_ERROR) ||
(datatype != NC_BYTE))
{
//ncopts=op;
return std::vector<unsigned char>(0);
}
std::vector<unsigned char> r(att_length);
miattget(_mincid, varid, (char*)att_name, NC_BYTE, att_length,&r[0], NULL) ;
//ncopts=op;
return r;
}
nc_type minc_1_base::att_type(const char *var_name,const char *att_name) const
{
int varid;
if (*var_name=='\0')
varid = NC_GLOBAL;
else
{
if((varid = ncvarid(_mincid, var_name))==MI_ERROR)
return MI_ORIGINAL_TYPE;
}
return att_type(varid,att_name);
}
nc_type minc_1_base::att_type(int varid,const char *att_name) const
{
int att_length;
nc_type datatype;
if(ncattinq(_mincid, varid, (char *)att_name, &datatype,&att_length) == MI_ERROR)
return MI_ORIGINAL_TYPE;
return datatype;
}
int minc_1_base::att_length(const char *var_name,const char *att_name) const
{
int varid;
if (*var_name=='\0')
varid = NC_GLOBAL;
else
{
if((varid = ncvarid(_mincid, var_name))==MI_ERROR)
return 0;
}
return att_length(varid,att_name);
}
int minc_1_base::att_length(int varid,const char *att_name) const
{
int att_length;
nc_type datatype;
if(ncattinq(_mincid, varid, (char *)att_name, &datatype,&att_length) == MI_ERROR)
return 0;
return att_length;
}
minc_1_reader::minc_1_reader(const minc_1_reader&):_metadate_only(false),_have_temp_file(false),_read_prepared(false)
{
}
minc_1_reader::minc_1_reader():_metadate_only(false),_have_temp_file(false),_read_prepared(false)
{
}
//based on the code from mincextract
void minc_1_reader::open(const char *path,bool positive_directions/*=true*/,bool metadate_only/*=false*/,bool rw/*=false*/)
{
#ifndef WIN32
ncopts = 0;
#endif
_metadate_only=metadate_only;
_read_prepared=false;
int element_size;
int idim;
int nstart, ncount;
_positive_directions=positive_directions;
//ncopts = 0;
// Open the file
// Expand file
if(_metadate_only)
{
int created_tempfile;
char * tempfile = miexpand_file((char*)path, NULL, true, &created_tempfile);
if (tempfile == NULL) REPORT_ERROR("Error expanding minc file");
_tempfile=tempfile;
path=_tempfile.c_str();
_have_temp_file=created_tempfile;
}
_mincid = miopen((char*)path, rw?NC_WRITE:NC_NOWRITE);
if(_mincid == MI_ERROR) REPORT_ERROR("Can't open minc file for reading!");
#ifdef MINC2
if (MI2_ISH5OBJ(_mincid)) {
_minc2 = true;
}
#endif
/* Inquire about the image variable */
_imgid = ncvarid(_mincid, MIimage);
if(_imgid == MI_ERROR) REPORT_ERROR("Can't get Image ID");
ncvarinq(_mincid, _imgid, NULL, NULL, &_ndims, mdims, NULL);
//get image data type... not used for now
miget_datatype(_mincid, _imgid, &_datatype, &_is_signed);
//dir_cos.SetIdentity();
int dim_cnt=0;
miget_image_range(_mincid, _image_range);
//go through dimensions , calculating parameters for reshaping into ZYX array if needed
_info.resize(_ndims);
_world_matrix.resize(_ndims*4,0.0);
_voxel_matrix.resize(_ndims*4,0);
//_dir_cos.resize(_ndims*_ndims,0.0);
for(int i=_ndims-1;i>=0;i--)
{
//_world_matrix[i*(_ndims+1)]=1.0;
//_voxel_matrix[i*(_ndims+1)]=1.0;
char dimname[MAX_NC_NAME];
long dimlength;
//get dimensions info
ncdiminq(_mincid, mdims[i], dimname, &dimlength);
_info[i].name=dimname;
_info[i].length=dimlength;
_info[i].have_dir_cos=false;
int axis=-1;
unsigned int sz=0;
if(!strcmp(dimname,MIxspace))
{
_dims[0]=dimlength;axis=0;
_info[i].dim=dim_info::DIM_X;
_map_to_std[1]=i;
} else if(!strcmp(dimname,MIyspace)) {
_dims[1]=dimlength;axis=1;
_info[i].dim=dim_info::DIM_Y;
_map_to_std[2]=i;
} else if(!strcmp(dimname,MIzspace)) {
_dims[2]=dimlength;axis=2;
_info[i].dim=dim_info::DIM_Z;
_map_to_std[3]=i;
} else if(!strcmp(dimname,MIvector_dimension)) {
axis=-1;
_info[i].dim=dim_info::DIM_VEC;
_map_to_std[0]=i;
} else if(!strcmp(dimname,MItime)) {
axis=3;
_info[i].dim=dim_info::DIM_TIME;
_map_to_std[4]=i;
} else {
REPORT_ERROR ("Unknown dimension");
_info[i].dim=dim_info::DIM_UNKNOWN;
}
if(_info[i].dim!=dim_info::DIM_VEC)
{
//ncopts = 0;
int dimid = ncvarid(_mincid, dimname);
//ncopts = NC_VERBOSE | NC_FATAL;
if (dimid == MI_ERROR) continue;
// Get dimension attributes
//ncopts = 0;
miattget1(_mincid, dimid, (char*)MIstep, NC_DOUBLE, &_info[i].step);
if(_info[i].step == 0.0)
_info[i].step = 1.0;
miattget1(_mincid, dimid, (char*)MIstart, NC_DOUBLE, &_info[i].start);
if(_positive_directions && _info[i].step<0.0)
{
_info[i].start+=_info[i].step*(dimlength-1);
_info[i].step=-_info[i].step;
}
if(miattget(_mincid, dimid, (char*)MIdirection_cosines, NC_DOUBLE, 3, &_info[i].dir_cos[0], NULL)!= MI_ERROR)
{
_info[i].have_dir_cos=true;
/* Normalize the direction cosine */
double len=sqrt(_info[i].dir_cos[0]*_info[i].dir_cos[0]+
_info[i].dir_cos[1]*_info[i].dir_cos[1]+
_info[i].dir_cos[2]*_info[i].dir_cos[2]);
if(len>1e-6 && fabs(len-1.0)>1e-6) //TODO: use some epsiolon here?
{
for(int a=0;a<3;a++)
_info[i].dir_cos[a]/=len;
}
}
// fill voxel matrix
_voxel_matrix[i*4+axis]=1;
} else { //vectors don't have spatial component!
_info[i].start=0;
_info[i].step=0.0;
_info[i].dir_cos[0]=_info[i].dir_cos[1]=_info[i].dir_cos[2]=0.0;
_info[i].have_dir_cos=false;
}
//fill world matrix
for(int a=0;a<3;a++)
_world_matrix[i*4+a]=_info[i].dir_cos[a]*_info[i].step;
if(axis==3) //time
_world_matrix[i*4+3]=_info[i].step;
else
_world_matrix[i*4+3]=0.0;
}
//ncopts = NC_VERBOSE | NC_FATAL;
// now let's find out the slice dimensions
int idmax = ncvarid(_mincid, MIimagemax);
_slice_dimensions=0;
if(idmax != MI_ERROR)
{
int nmax_dims;
int mmax_dims[MAX_VAR_DIMS];
ncvarinq(_mincid, _imgid, NULL, NULL, &nmax_dims, mmax_dims, NULL);
if(nmax_dims>0)
_slice_dimensions=_ndims-nmax_dims;
}
if(_slice_dimensions<=0)
{
if(_info[_ndims-1].dim==dim_info::DIM_VEC || _info[_ndims-1].dim==dim_info::DIM_TIME)
_slice_dimensions=std::min(_ndims,3);
else
_slice_dimensions=std::min(_ndims,2);
}
std::fill(_slab.begin(),_slab.end(),1);
_slab_len=1;
for(int i=0;i<_slice_dimensions;i++)
{
_slab[_ndims-i-1]=_info[_ndims-i-1].length;
_slab_len*=_info[_ndims-i-1].length;
}
}
void minc_1_reader::close(void)
{
if(_have_temp_file)
remove(_tempfile.c_str());
_have_temp_file=false;
minc_1_base::close();
}
minc_1_reader::~minc_1_reader()
{
close();
}
minc_1_writer::minc_1_writer():
_set_image_range(false),_set_slice_range(false),
_calc_min_max(true),_write_prepared(false)
{
}
minc_1_writer::minc_1_writer(const minc_1_writer&):
_set_image_range(false),_set_slice_range(false),
_calc_min_max(true),_write_prepared(false)
{
}
void minc_1_writer::open(const char *path,const minc_info& inf,int slice_dimensions,nc_type datatype,int _s)
{
#ifndef WIN32
ncopts = 0;
#endif
_info=inf;
//int mdims[MAX_VAR_DIMS];
double vrange[2];
_write_prepared=false;
_mincid = micreate((char*)path, NC_CLOBBER/*|MI2_CREATE_V2*/); //TODO: add environment variable checking
#ifdef MINC2
if (MI2_ISH5OBJ(_mincid)) { //micreate might create MINC2 file if environment variable is set
_minc2 = true;
}
#endif
_ndims=_info.size();
_datatype=datatype;
_slice_dimensions=slice_dimensions;
_is_signed=_s;
fill(_map_to_std.begin(),_map_to_std.end(),-1);
for(int i=_ndims-1;i>=0;i--)
{
//just a precaution
switch(_info[i].dim)
{
case dim_info::DIM_X:_info[i].name=MIxspace;_map_to_std[1]=i;break;
case dim_info::DIM_Y:_info[i].name=MIyspace;_map_to_std[2]=i;break;
case dim_info::DIM_Z:_info[i].name=MIzspace;_map_to_std[3]=i;break;
case dim_info::DIM_TIME:_info[i].name=MItime;_map_to_std[4]=i;break;
default:
case dim_info::DIM_VEC:_info[i].name=MIvector_dimension;_map_to_std[0]=i;break;
//default: REPORT_ERROR("Unknown Dimension!");
}
mdims[i]=ncdimdef(_mincid, _info[i].name.c_str(), _info[i].length);
if(_info[i].dim!=dim_info::DIM_VEC)
{
int dimid=micreate_std_variable(_mincid,(char*)_info[i].name.c_str(),NC_INT, 0, NULL);
miattputdbl(_mincid, dimid, (char*)MIstep,_info[i].step);
miattputdbl(_mincid, dimid, (char*)MIstart,_info[i].start);
if(_info[i].have_dir_cos)
ncattput(_mincid, dimid, (char*)MIdirection_cosines,NC_DOUBLE, 3, _info[i].dir_cos);
}
}
_slab_len=1;
for(int i=0;i<_slice_dimensions;i++)
{
_slab[_ndims-i-1]=_info[_ndims-i-1].length;
_slab_len*=_info[_ndims-i-1].length;
}
_icmax=_icmin=MI_ERROR;
//ncopts = NC_OPTS_VAL;
_imgid=micreate_std_variable(_mincid, (char*)MIimage, _datatype, _ndims, mdims);
_image_range[0]=DBL_MAX;_image_range[1]=-DBL_MAX;
switch(_datatype)
{
case NC_DOUBLE:
vrange[0]=-DBL_MAX;vrange[1]=DBL_MAX;
_is_signed=1;
break;
case NC_FLOAT:
vrange[0]=-FLT_MAX;vrange[1]=FLT_MAX;
_is_signed=1;
break;
case NC_SHORT:
if(_is_signed)
{
vrange[0]=SHRT_MIN;
vrange[1]=SHRT_MAX;
} else {
vrange[0]=0;vrange[1]=USHRT_MAX;
}
break;
case NC_BYTE:
if(_is_signed)
{
vrange[0]=-128;vrange[1]=127;
} else {
vrange[0]=0;vrange[1]=255;
}
break;
case NC_INT:
if(_is_signed)
{
vrange[0]=INT_MIN;vrange[1]=INT_MAX;
}else{
vrange[0]=0;vrange[1]=UINT_MAX;
}
break;
default:break;
};
miattputstr(_mincid, _imgid, (char*)MIcomplete, (char*)MI_FALSE);
miattputstr(_mincid, _imgid, (char*)MIsigntype, (char*)(_is_signed?MI_SIGNED:MI_UNSIGNED));
ncattput(_mincid, _imgid, (char*)MIvalid_range, NC_DOUBLE, 2, vrange);
miset_valid_range(_mincid, _imgid, vrange);
}
void minc_1_writer::open(const char *path,const minc_1_base& imitate)
{
open(path,imitate.info(),imitate.slice_dimensions(),
imitate.datatype(),imitate.is_signed());
copy_headers(imitate);
}
void minc_1_writer::open(const char *path,const char *imitate_file)
{
minc_1_reader rdr;
//open minc file in metadate mode
rdr.open(imitate_file,false,true);
open(path,rdr);
//copy_headers(rdr);
}
void minc_1_writer::setup_write_float()
{
_image_range[0]=DBL_MAX;_image_range[1]=-DBL_MAX;
switch(_datatype)
{
case NC_DOUBLE:
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, 0, NULL);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, 0, NULL);
_set_image_range=true;
_set_slice_range=false;
break;
case NC_FLOAT:
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, 0, NULL);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, 0, NULL);
_set_image_range=true;
_set_slice_range=false;
break;
case NC_SHORT:
_set_image_range=false;
_set_slice_range=true;
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
break;
case NC_BYTE:
_set_image_range=false;
_set_slice_range=true;
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
break;
case NC_INT:
_set_image_range=false;
_set_slice_range=true;
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
break;
default:
break;
};
ncendef(_mincid);
if(_datatype==NC_DOUBLE || _datatype==NC_FLOAT)
{
miicv_setstr(_icvid, MI_ICV_SIGN, (char*)MI_SIGNED);
miicv_setint(_icvid, MI_ICV_TYPE, NC_FLOAT);
miicv_setint(_icvid, MI_ICV_DO_NORM, true);
miicv_setint(_icvid, MI_ICV_USER_NORM, true);
miicv_setdbl(_icvid, MI_ICV_VALID_MIN, -FLT_MAX);
miicv_setdbl(_icvid, MI_ICV_VALID_MAX, FLT_MAX);
_calc_min_max=true;
} else { //do something smart here?
miicv_setstr(_icvid, MI_ICV_SIGN, (char*)MI_SIGNED);
miicv_setint(_icvid, MI_ICV_TYPE, NC_FLOAT);
miicv_setint(_icvid, MI_ICV_DO_NORM, false);
//miicv_setint(_icvid, MI_ICV_USER_NORM, false);
miicv_setdbl(_icvid, MI_ICV_VALID_MIN, -FLT_MAX);
miicv_setdbl(_icvid, MI_ICV_VALID_MAX, FLT_MAX);
_calc_min_max=true;
}
miicv_attach(_icvid, _mincid, _imgid);
_io_datatype=NC_FLOAT;
_write_prepared=true;
}
void minc_1_writer::setup_write_double()
{
_image_range[0]=DBL_MAX;_image_range[1]=-DBL_MAX;
switch(_datatype)
{
case NC_DOUBLE:
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, 0, NULL);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, 0, NULL);
_set_image_range=true;
_set_slice_range=false;
break;
case NC_FLOAT:
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, 0, NULL);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, 0, NULL);
_set_image_range=true;
_set_slice_range=false;
break;
case NC_SHORT:
_set_image_range=false;
_set_slice_range=true;
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
break;
case NC_BYTE:
_set_image_range=false;
_set_slice_range=true;
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
break;
case NC_INT:
_set_image_range=false;
_set_slice_range=true;
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, _ndims-_slice_dimensions, mdims);
break;
default:
break;
};
ncendef(_mincid);
if(_datatype==NC_DOUBLE)
{
miicv_setstr(_icvid, MI_ICV_SIGN, (char*)MI_SIGNED);
miicv_setint(_icvid, MI_ICV_TYPE, NC_DOUBLE);
miicv_setint(_icvid, MI_ICV_DO_NORM, true);
miicv_setint(_icvid, MI_ICV_USER_NORM, true);
miicv_setdbl(_icvid, MI_ICV_VALID_MIN, -DBL_MAX);
miicv_setdbl(_icvid, MI_ICV_VALID_MAX, DBL_MAX);
_calc_min_max=true;
} else if(_datatype==NC_FLOAT) {
miicv_setstr(_icvid, MI_ICV_SIGN, (char*)MI_SIGNED);
miicv_setint(_icvid, MI_ICV_TYPE, NC_DOUBLE);
miicv_setint(_icvid, MI_ICV_DO_NORM, true);
miicv_setint(_icvid, MI_ICV_USER_NORM, true);
miicv_setdbl(_icvid, MI_ICV_VALID_MIN, -DBL_MAX);
miicv_setdbl(_icvid, MI_ICV_VALID_MAX, DBL_MAX);
_calc_min_max=true;
} else { //do something smart here?
miicv_setstr(_icvid, MI_ICV_SIGN, (char*)MI_SIGNED);
miicv_setint(_icvid, MI_ICV_TYPE, NC_DOUBLE);
miicv_setint(_icvid, MI_ICV_DO_NORM, false);
//miicv_setint(_icvid, MI_ICV_USER_NORM, false);
miicv_setdbl(_icvid, MI_ICV_VALID_MIN, -DBL_MAX);
miicv_setdbl(_icvid, MI_ICV_VALID_MAX, DBL_MAX);
_calc_min_max=true;
}
miicv_attach(_icvid, _mincid, _imgid);
_io_datatype=NC_DOUBLE;
_write_prepared=true;
}
void minc_1_writer::setup_write_short(bool n)
{
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, 0, NULL);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, 0, NULL);
_set_image_range=true;
_set_slice_range=false;
ncendef(_mincid);
miicv_setint(_icvid, MI_ICV_TYPE, NC_SHORT);
miicv_setstr(_icvid, MI_ICV_SIGN, (char*)MI_SIGNED);
//miicv_setstr(_icvid, MI_ICV_SIGN, true);
/* Set range of values */ //TODO: set this to something sensible?
miicv_setint(_icvid, MI_ICV_VALID_MIN, SHRT_MIN);
miicv_setint(_icvid, MI_ICV_VALID_MAX, SHRT_MAX);
/* No normalization so that pixels are scaled to the slice */
miicv_setint(_icvid, MI_ICV_DO_NORM, false);
miicv_setint(_icvid, MI_ICV_DO_RANGE, false);
miicv_attach(_icvid, _mincid, _imgid);
_io_datatype=NC_SHORT;
_write_prepared=true;
}
void minc_1_writer::setup_write_ushort(bool n)
{
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, 0, NULL);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, 0, NULL);
_set_image_range=true;
_set_slice_range=false;
ncendef(_mincid);
miicv_setint(_icvid, MI_ICV_TYPE, NC_SHORT);
miicv_setstr(_icvid, MI_ICV_SIGN, (char*)MI_UNSIGNED);
miicv_setstr(_icvid, MI_ICV_SIGN, false);
/* Set range of values */ //TODO: set this to something sensible?
miicv_setint(_icvid, MI_ICV_VALID_MIN, 0);
miicv_setint(_icvid, MI_ICV_VALID_MAX, USHRT_MAX);
/* No normalization so that pixels are scaled to the slice */
miicv_setint(_icvid, MI_ICV_DO_NORM, false);
miicv_setint(_icvid, MI_ICV_DO_RANGE, false);
miicv_attach(_icvid, _mincid, _imgid);
_io_datatype=NC_SHORT;
_write_prepared=true;
}
void minc_1_writer::setup_write_byte(bool n)
{
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, 0, NULL);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, 0, NULL);
_set_image_range=true;
_set_slice_range=false;
ncendef(_mincid);
miicv_setint(_icvid, MI_ICV_TYPE, NC_BYTE);
miicv_setstr(_icvid, MI_ICV_SIGN, (char*)MI_UNSIGNED);
/* Set range of values */ //TODO: set this to something sensible?
miicv_setint(_icvid, MI_ICV_VALID_MIN, 0);
miicv_setint(_icvid, MI_ICV_VALID_MAX, UCHAR_MAX);
/* No normalization so that pixels are scaled to the slice */
miicv_setint(_icvid, MI_ICV_DO_NORM, false);
miicv_setint(_icvid, MI_ICV_DO_RANGE, false);
miicv_attach(_icvid, _mincid, _imgid);
_io_datatype=NC_BYTE;
_write_prepared=true;
}
void minc_1_writer::setup_write_int(bool n)
{
_icmax=micreate_std_variable(_mincid, (char*)MIimagemax, NC_DOUBLE, 0, NULL);
_icmin=micreate_std_variable(_mincid, (char*)MIimagemin, NC_DOUBLE, 0, NULL);
_set_image_range=true;
_set_slice_range=false;
ncendef(_mincid);
miicv_setint(_icvid, MI_ICV_TYPE, NC_INT);
miicv_setstr(_icvid, MI_ICV_SIGN, (char*)MI_SIGNED);
/* Set range of values */ //TODO: set this to something sensible?
miicv_setint(_icvid, MI_ICV_VALID_MIN, INT_MIN);
miicv_setint(_icvid, MI_ICV_VALID_MAX, INT_MAX);
/* No normalization so that pixels are scaled to the slice */
miicv_setint(_icvid, MI_ICV_DO_NORM, false);