IMP  2.0.1
The Integrative Modeling Platform
SpiderReaderWriter.h
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1 /**
2  * \file IMP/em/SpiderReaderWriter.h
3  * \brief Management of Spider Headers Electron Microscopy. Compatible with
4  * Spider and Xmipp formats
5  * Copyright 2007-2013 IMP Inventors. All rights reserved.
6 */
7 
8 #ifndef IMPEM_SPIDER_READER_WRITER_H
9 #define IMPEM_SPIDER_READER_WRITER_H
10 
11 #include "IMP/em/em_config.h"
12 #include "IMP/em/ImageHeader.h"
13 #include "IMP/em/header_converters.h"
14 #include "IMP/em/MapReaderWriter.h"
15 #include "IMP/em/DensityHeader.h"
16 #include <IMP/algebra/utility.h>
17 #include <IMP/algebra/endian.h>
18 #include <IMP/exception.h>
19 #include <IMP/log.h>
20 #include <typeinfo>
21 #include <complex>
22 #include <string>
23 #include <cstdio>
24 #include <iostream>
25 #include <fstream>
26 #include <cstring>
27 
28 IMPEM_BEGIN_NAMESPACE
29 
30 //! Class to read EM maps (3D) in Spider and Xmipp formats
31 /**
32  * \note: Compatible only with Xmipp 2.2 and Spider floating point maps
33  * \note: A DensityHeader class must be provided
34  */
35 class IMPEMEXPORT SpiderMapReaderWriter : public MapReaderWriter {
36 public:
37  String filename_;
38  bool skip_type_check_;
39  bool force_reversed_;
40  bool skip_extra_checkings_;
41 
42  //! Empty constructor. It does not force reversed header and does not
43  //! skip any of the tests
44  SpiderMapReaderWriter() {
45  skip_type_check_=false;
46  force_reversed_=false;
47  skip_extra_checkings_=false;
48  }
49 
50  //! Full constructor.
51  /**
52  * \param[in] filename file to read
53  * \param[in] skip_type_check if true, the check for type of image is skipped
54  * \param[in] force_reversed if true, the reverse mode is enforced
55  * for reading and writting
56  * \param[in] skip_extra_checkings if true, the most stringent
57  * tests for consistency of images are skipped when reading
58  */
59  SpiderMapReaderWriter(String filename,bool skip_type_check,
60  bool force_reversed,bool skip_extra_checkings) {
61  filename_=filename;
62  skip_type_check_=skip_type_check;
63  force_reversed_=force_reversed;
64  skip_extra_checkings_=skip_extra_checkings;
65  }
66 #if !defined(DOXYGEN) && !defined(SWIG)
67  //! Reads a map in Spider format and transfers the data and header.
68  /**
69  * \param[in] filename file to read
70  * \param[in] data pointer to the structure where to store the data
71  * \param[in] header DensityHeader class where to store the info
72  * from the header.
73  */
74  void read(const char *filename, float **data, DensityHeader &header);
75 
76  //! Writes a map in Spider format from data and header.
77  /**
78  * \param[in] filename file to write
79  * \param[in] data pointer to the structure where data are stored
80  * \param[in] header DensityHeader class where the header info is stored
81  * data from the header.
82  */
83  void write(const char *filename,
84  const float *data,const DensityHeader &header);
85 #endif
86  IMP_OBJECT_INLINE(SpiderMapReaderWriter,
87  {out << "SpiderMapReaderWriter";}, {});
88 };
89 
90 IMPEM_END_NAMESPACE
91 
92 #endif /* IMPEM_SPIDER_READER_WRITER_H */