eerio.cpp File Reference

#include "eerio.h"
#include <tiffio.h>
#include <boost/property_tree/xml_parser.hpp>

Include dependency graph for eerio.cpp:

Go to the source code of this file.

Typedefs
typedef vector< pair< int, int > >	COORDS

Functions
auto	decode_eer_data (EerWord *data, Decoder &decoder)
void	TIFFOutputWarning (const char *module, const char *fmt, va_list ap)
string	read_acquisition_metadata (TIFF *tiff)
string	to_snake_case (const string &s)
Dict	parse_acquisition_data (string metadata)
auto	read_compression (TIFF *tiff)
auto	read_raw_data (TIFF *tiff)

Typedef Documentation

COORDS

typedef vector<pair<int, int> > COORDS

Definition at line 46 of file eerio.cpp.

Function Documentation

decode_eer_data()

auto decode_eer_data	(	EerWord *	data,
		Decoder &	decoder
	)

Definition at line 48 of file eerio.cpp.

                                                      {
        EerStream is((data));
        EerRle    rle;
        EerSubPix sub_pix;
 
        is >> rle >> sub_pix;
        int count = rle;
 
        COORDS coords;
 
        while (count < decoder.camera_size * decoder.camera_size) {
                coords.push_back(decoder(count, sub_pix));
 
                is >> rle >> sub_pix;
 
                count += rle+1;
        }
 
        return coords;
}

References EMAN::Decoder::camera_size.

parse_acquisition_data()

Dict parse_acquisition_data

(

string

metadata

)

Definition at line 104 of file eerio.cpp.

                                             {
        Dict dict;
        std::istringstream ins(metadata);
        ptree pt;
 
        read_xml(ins, pt);
 
        for(auto &v : pt.get_child("metadata")) {
                auto xml_item_name = v.second.get_child("<xmlattr>.name").data();
                auto xml_item_value = v.second.data();
 
                auto key = "EER." + to_snake_case(xml_item_name);
 
                dict[key] = xml_item_value;
        }
        
        return dict;
}

References to_snake_case().

Referenced by EMAN::EerIO::EerIO().

read_acquisition_metadata()

string read_acquisition_metadata

(

TIFF *

tiff

)

Definition at line 78 of file eerio.cpp.

                                             {
        char *metadata_c = nullptr;
        uint32_t count = 0;
 
        TIFFSetDirectory(tiff, 0);
        TIFFGetField(tiff, 65001, &count, &metadata_c);
 
        return string(metadata_c, count);
}

Referenced by EMAN::EerIO::EerIO().

read_compression()

auto read_compression

(

TIFF *

tiff

)

Definition at line 123 of file eerio.cpp.

                                  {
        uint16_t compression = 0;
 
        TIFFGetField(tiff, TIFFTAG_COMPRESSION, &compression);
 
        return compression;
}

read_raw_data()

auto read_raw_data

(

TIFF *

tiff

)

Definition at line 131 of file eerio.cpp.

                               {
        auto num_strips = TIFFNumberOfStrips(tiff);
        vector<unsigned int> strip_sizes(num_strips);
 
        for(size_t i=0; i<num_strips; ++i)
                strip_sizes[i] = TIFFRawStripSize(tiff, i);
 
        std::vector<unsigned char> data;
 
        for(size_t i=0; i<num_strips; ++i) {
                auto prev_size = data.size();
                data.resize(prev_size + strip_sizes[i]);
                TIFFReadRawStrip(tiff, i, data.data() + prev_size, strip_sizes[i]);
        }
 
        return data;
}

TIFFOutputWarning()

void TIFFOutputWarning	(	const char *	module,
		const char *	fmt,
		va_list	ap
	)

Definition at line 69 of file eerio.cpp.

{
#ifdef DEBUG
        cout << module << ": ";
        vprintf(fmt, ap);
        cout << endl;
#endif  //DEBUG
}

Referenced by EMAN::EerIO::EerIO().

to_snake_case()

string to_snake_case

(

const string &

s

)

Definition at line 88 of file eerio.cpp.

                                      {
        auto ret(s);
        int sh = 0;
        for(int i=0; i<s.size(); i++) {
                if(isupper(s[i])) {
                        if(!isupper(s[i-1])) {
                                ret.insert(i + sh, "_");
                                sh++;
                        }
                        ret[i + sh] = ::tolower(s[i]);
                }
        }
        
        return ret;
}

Referenced by parse_acquisition_data().