Xmipp  v3.23.11-Nereus
Public Member Functions | Public Attributes | List of all members
ProgKenderSOM Class Reference
Inheritance diagram for ProgKenderSOM:
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Public Member Functions

void defineParams ()
 
void readParams ()
 
void show ()
 
void run ()
 
- Public Member Functions inherited from XmippProgram
const char * getParam (const char *param, int arg=0)
 
const char * getParam (const char *param, const char *subparam, int arg=0)
 
int getIntParam (const char *param, int arg=0)
 
int getIntParam (const char *param, const char *subparam, int arg=0)
 
double getDoubleParam (const char *param, int arg=0)
 
double getDoubleParam (const char *param, const char *subparam, int arg=0)
 
float getFloatParam (const char *param, int arg=0)
 
float getFloatParam (const char *param, const char *subparam, int arg=0)
 
void getListParam (const char *param, StringVector &list)
 
int getCountParam (const char *param)
 
bool checkParam (const char *param)
 
bool existsParam (const char *param)
 
void addParamsLine (const String &line)
 
void addParamsLine (const char *line)
 
ParamDef * getParamDef (const char *param) const
 
virtual void quit (int exit_code=0) const
 
virtual int tryRun ()
 
void initProgress (size_t total, size_t stepBin=60)
 
void setProgress (size_t value=0)
 
void endProgress ()
 
void processDefaultComment (const char *param, const char *left)
 
void setDefaultComment (const char *param, const char *comment)
 
virtual void initComments ()
 
void setProgramName (const char *name)
 
void addUsageLine (const char *line, bool verbatim=false)
 
void clearUsage ()
 
void addExampleLine (const char *example, bool verbatim=true)
 
void addSeeAlsoLine (const char *seeAlso)
 
void addKeywords (const char *keywords)
 
const char * name () const
 
virtual void usage (int verb=0) const
 
virtual void usage (const String &param, int verb=2)
 
int version () const
 
virtual void show () const
 
virtual void read (int argc, const char **argv, bool reportErrors=true)
 
virtual void read (int argc, char **argv, bool reportErrors=true)
 
void read (const String &argumentsLine)
 
 XmippProgram ()
 
 XmippProgram (int argc, const char **argv)
 
virtual ~XmippProgram ()
 

Public Attributes

FileName fn_in
 
FileName fn_root
 
FileName tmpN
 
double eps
 
unsigned iter
 
bool norm
 
size_t xdim
 
size_t ydim
 
double reg0
 
double reg1
 
std::string layout
 
unsigned annSteps
 
- Public Attributes inherited from XmippProgram
bool doRun
 
bool runWithoutArgs
 
int verbose
 Verbosity level. More...
 
int debug
 

Additional Inherited Members

- Protected Member Functions inherited from XmippProgram
void defineCommons ()
 
- Protected Attributes inherited from XmippProgram
int errorCode
 
ProgramDef * progDef
 Program definition and arguments parser. More...
 
std::map< String, CommentList > defaultComments
 
int argc
 Original command line arguments. More...
 
const char ** argv
 

Detailed Description

Definition at line 32 of file classify_kerdensom.cpp.

Member Function Documentation

◆ defineParams()

void ProgKenderSOM::defineParams ( )
inlinevirtual

Function in which the param of each Program are defined.

Reimplemented from XmippProgram.

Definition at line 50 of file classify_kerdensom.cpp.

51  {
52  addUsageLine("Purpose: Kernel Density Estimator Self-Organizing Map");
53  addUsageLine("+KerDenSOM stands for Kernel Probability Density Estimator Self-Organizing Map.");
54  addUsageLine("+It maps a set of high dimensional input vectors into a two-dimensional grid. ");
55  addUsageLine("+For more information, please see the following [[http://www.ncbi.nlm.nih.gov/pubmed/11472094][reference]].");
56  addUsageLine("+");
57  addUsageLine("+The topology of the network can be hexagonal or rectangular (see below). ");
58  addUsageLine("+It is advised to design maps with one of its sides larger than the other (e.g. 10x5).");
59  addUsageLine("+ Xdim is ------>",true);
60  addUsageLine("+ HEXAGONAL:",true);
61  addUsageLine("+ O O O O O O O O O",true);
62  addUsageLine("+O O O & & & O O O",true);
63  addUsageLine("+ O O & @ @ & O O O",true);
64  addUsageLine("+O O & @ + @ & O O",true);
65  addUsageLine("+ O O & @ @ & O O O",true);
66  addUsageLine("+O O O & & & O O O",true);
67  addUsageLine("+ O O O O O O O O O",true);
68  addUsageLine("+ RECTANGULAR:",true);
69  addUsageLine("+O O O O O O O O O",true);
70  addUsageLine("+0 O O O & O O O O",true);
71  addUsageLine("+O O O & @ & O O O",true);
72  addUsageLine("+O O & @ + @ & O O",true);
73  addUsageLine("+O O O & @ & O O O",true);
74  addUsageLine("+O O O O & O O O O",true);
75  addUsageLine("+O O O O O O O O O",true);
76  addSeeAlsoLine("image_vectorize");
77  addParamsLine(" -i <file_in> : Input data file");
78  addParamsLine(" : This file is generated by [[image_vectorize_v3][image_vectorize]]");
79  addParamsLine(" --oroot <rootname> : rootname_classes.xmd, rootname_images.xmd and rootname_vectors.xmd will be created");
80  addParamsLine(" : This file mst be read by [[image_vectorize_v3][image_vectorize]]");
81  addParamsLine(" [--xdim <Hdimension=10>] : Horizontal size of the map");
82  addParamsLine(" [--ydim <Vdimension=5>] : Vertical size of the map");
83  addParamsLine(" [--topology <topology=RECT>] : Lattice topology");
84  addParamsLine(" :+The following picture will help in understanding the differences ");
85  addParamsLine(" :+between both topologies and the map axis convention:");
86  addParamsLine(" where <topology> RECT HEXA");
87  addParamsLine(" [--deterministic_annealing <steps=10> <Initial_reg=1000> <Final_reg=100>] : Deterministic annealing");
88  addParamsLine(" : controls the smoothness regularization");
89  addParamsLine(" : Set it to 0 0 0 for Kernel C-means");
90  addParamsLine(" [--eps <epsilon=1e-7>] : Stopping criteria");
91  addParamsLine(" [--iter <N=200>] : Number of iterations");
92  addParamsLine(" [--norm] : Normalize input data");
93  addExampleLine("xmipp_image_vectorize -i images.stk -o vectors.xmd");
94  addExampleLine("xmipp_classify_kerdensom -i vectors.xmd -o kerdensom.xmd");
95  }
XmippProgram::addSeeAlsoLine
void addSeeAlsoLine(const char *seeAlso)
Definition: xmipp_program.cpp:290
XmippProgram::addExampleLine
void addExampleLine(const char *example, bool verbatim=true)
Definition: xmipp_program.cpp:286
XmippProgram::addUsageLine
void addUsageLine(const char *line, bool verbatim=false)
Definition: xmipp_program.cpp:282
XmippProgram::addParamsLine
void addParamsLine(const String &line)
Definition: xmipp_program.cpp:305

◆ readParams()

void ProgKenderSOM::readParams ( )
inlinevirtual

Function in which each program will read parameters that it need. If some error occurs the usage will be printed out.

Reimplemented from XmippProgram.

Definition at line 98 of file classify_kerdensom.cpp.

99  {
100  fn_in = getParam("-i");
101  if (checkParam("--oroot"))
102  fn_root=getParam("--oroot");
103  ydim = getIntParam("--ydim");
104  xdim = getIntParam("--xdim");
105  layout = getParam("--topology");
106  annSteps = getIntParam("--deterministic_annealing",0);
107  reg0 = getDoubleParam("--deterministic_annealing",1);
108  reg1 = getDoubleParam("--deterministic_annealing",2);
109  eps = getDoubleParam("--eps");
110  iter = getIntParam("--iter");
111  norm = checkParam("--norm");
112 
113  // Some checks
114  if (iter < 1)
115  REPORT_ERROR(ERR_ARG_INCORRECT,"iter must be > 1");
116 
117  if ((reg0 <= reg1) && (reg0 != 0) && (annSteps > 1))
118  REPORT_ERROR(ERR_ARG_INCORRECT,"reg0 must be > reg1");
119  if (reg0 == 0)
120  annSteps = 0;
121  if (reg0 < 0)
122  REPORT_ERROR(ERR_ARG_INCORRECT,"reg0 must be > 0");
123  if (reg1 < 0)
124  REPORT_ERROR(ERR_ARG_INCORRECT,"reg1 must be > 0");
125  if (xdim < 1)
126  REPORT_ERROR(ERR_ARG_INCORRECT,"xdim must be >= 1");
127  if (ydim < 1)
128  REPORT_ERROR(ERR_ARG_INCORRECT,"ydim must be >= 1");
129  }
XmippProgram::getDoubleParam
double getDoubleParam(const char *param, int arg=0)
Definition: xmipp_program.cpp:341
REPORT_ERROR
#define REPORT_ERROR(nerr, ErrormMsg)
Definition: xmipp_error.h:211
XmippProgram::getParam
const char * getParam(const char *param, int arg=0)
Definition: xmipp_program.cpp:321
ERR_ARG_INCORRECT
Incorrect argument received.
Definition: xmipp_error.h:113
XmippProgram::checkParam
bool checkParam(const char *param)
Definition: xmipp_program.cpp:379
XmippProgram::getIntParam
int getIntParam(const char *param, int arg=0)
Definition: xmipp_program.cpp:331

◆ run()

void ProgKenderSOM::run ( )
inlinevirtual

This function will be start running the program. it also should be implemented by derived classes.

Reimplemented from XmippProgram.

Definition at line 153 of file classify_kerdensom.cpp.

154  {
155  FileName fnClasses=fn_root+"_classes.xmd";
156  MetaDataVec dummy;
157  dummy.write(formatString("classes@%s",fnClasses.c_str()));
158 
159  /* Open training vector ================================================= */
160  ClassicTrainingVectors ts(0, true);
161  std::cout << std::endl << "Reading input data file " << fn_in << "....." << std::endl;
162  ts.read(fn_in);
163 
164  /* Real stuff ============================================================== */
165  if (norm)
166  {
167  std::cout << "Normalizing....." << std::endl;
168  ts.normalize(); // Normalize input data
169  }
170 
171  auto *myMap = new FuzzyMap(layout, xdim, ydim, ts);
172 
173  KerDenSOM *thisSOM= new GaussianKerDenSOM(reg0, reg1, annSteps, eps, iter); // Creates KerDenSOM Algorithm
174 
175  TextualListener myListener; // Define the listener class
176  myListener.setVerbosity() = verbose; // Set verbosity level
177  thisSOM->setListener(&myListener); // Set Listener
178  thisSOM->train(*myMap, ts, fnClasses); // Train algorithm
179 
180  // Test algorithm
181  double dist = thisSOM->test(*myMap, ts);
182  std::cout << std::endl << "Quantization error : " << dist << std::endl;
183 
184  // Classifying
185  std::cout << "Classifying....." << std::endl;
186  myMap->classify(&ts);
187 
188  // Calibrating
189  std::cout << "Calibrating....." << std::endl;
190  myMap->calibrate(ts);
191 
192  /*******************************************************
193  Saving all kind of Information
194  *******************************************************/
195  // Save map size
196  MetaDataVec MDkerdensom;
197  size_t id=MDkerdensom.addObject();
198  MDkerdensom.setValue(MDL_XSIZE,xdim,id);
199  MDkerdensom.setValue(MDL_YSIZE,ydim,id);
200  MDkerdensom.setValue(MDL_MAPTOPOLOGY,layout,id);
201  MDkerdensom.write(formatString("KerDenSOM_Layout@%s",fnClasses.c_str()),MD_APPEND);
202 
203  // save intracluster distance and number of vectors in each cluster
204  MetaDataVec MDsummary;
205  for (unsigned i = 0; i < myMap->size(); i++)
206  {
207  id=MDsummary.addObject();
208  MDsummary.setValue(MDL_REF,(int)i+1,id);
209  MDsummary.setValue(MDL_CLASSIFICATION_INTRACLASS_DISTANCE,myMap->aveDistances[i],id);
210  MDsummary.setValue(MDL_CLASS_COUNT,(size_t)myMap->classifSizeAt(i),id);
211  }
212  MDsummary.write(formatString("classes@%s",fnClasses.c_str()),MD_APPEND);
213 
214  // assign data to clusters according to fuzzy threshold
215  std::cout << "Saving neurons assigments ....." << std::endl;
216  MetaDataVec vectorContentIn, MDimages;
217  vectorContentIn.read(formatString("vectorContent@%s",fn_in.c_str()));
218  std::vector<size_t> objIds;
219  vectorContentIn.findObjects(objIds);
220  for (unsigned i = 0; i < myMap->size(); i++)
221  {
222  MetaDataVec MD;
223  for (size_t j = 0; j < myMap->classifAt(i).size(); j++)
224  {
225  MDRowVec row;
226  size_t order=myMap->classifAt(i)[j];
227  vectorContentIn.getRow(row,objIds[order]);
228  row.setValue(MDL_REF,(int) i+1);
229  MDimages.addRow(row);
230  MD.addRow(row);
231  }
232  if (MD.size()>0)
233  {
234  MD.removeLabel(MDL_ORDER);
235  MD.write(formatString("class%06d_images@%s",i+1,fnClasses.c_str()),MD_APPEND);
236  }
237  }
238  MDimages.removeLabel(MDL_ORDER);
239  MDimages.write((String)"images@"+fn_root+"_images.xmd");
240 
241  // Save code vectors
242  if (norm)
243  {
244  std::cout << "Denormalizing code vectors....." << std::endl;
245  myMap->unNormalize(ts.getNormalizationInfo()); // de-normalize codevectors
246  }
247  MetaDataVec vectorHeaderIn, vectorHeaderOut, vectorContentOut;
248  vectorHeaderIn.read(formatString("vectorHeader@%s",fn_in.c_str()));
249  vectorHeaderOut.setColumnFormat(false);
250  size_t size, vectorSize;
251  size_t idIn=vectorHeaderIn.firstRowId();
252  size_t idOut=vectorHeaderOut.addObject();
253  vectorHeaderIn.getValue(MDL_XSIZE,size,idIn);
254  vectorHeaderOut.setValue(MDL_XSIZE,size,idOut);
255  vectorHeaderIn.getValue(MDL_YSIZE,size,idIn);
256  vectorHeaderOut.setValue(MDL_YSIZE,size,idOut);
257  vectorHeaderIn.getValue(MDL_ZSIZE,size,idIn);
258  vectorHeaderOut.setValue(MDL_ZSIZE,size,idOut);
259  vectorHeaderOut.setValue(MDL_COUNT,myMap->size(),idOut);
260  vectorHeaderIn.getValue(MDL_CLASSIFICATION_DATA_SIZE,vectorSize,idIn);
261  vectorHeaderOut.setValue(MDL_CLASSIFICATION_DATA_SIZE,vectorSize,idOut);
262  vectorHeaderOut.write(formatString("vectorHeader@%s_vectors.xmd",fn_root.c_str()),MD_APPEND);
263  FileName fnVectorsRaw=fn_root+"_vectors.vec";
264  std::ofstream fhVectorsRaw(fnVectorsRaw.c_str(),std::ios::binary);
265  if (!fhVectorsRaw)
266  REPORT_ERROR(ERR_IO_NOWRITE,fnVectorsRaw);
267  for (size_t i = 0; i < myMap->size(); i++)
268  {
269  id=vectorContentOut.addObject();
270  vectorContentOut.setValue(MDL_REF,(int)i+1,id);
271  vectorContentOut.setValue(MDL_ORDER,i,id);
272  fhVectorsRaw.write((char*)&(myMap->theItems[i][0]),vectorSize*sizeof(float));
273  }
274  fhVectorsRaw.close();
275  vectorContentOut.write(formatString("vectorContent@%s_vectors.xmd",fn_root.c_str()),MD_APPEND);
276  delete myMap;
277  delete thisSOM;
278  }
MDL_ZSIZE
Z size (int)
Definition: metadata_label.h:516
MDL_ORDER
Definition: metadata_label.h:323
FuzzyMap
Definition: map.h:308
MetaDataVec::read
void read(const FileName &inFile, const std::vector< MDLabel > *desiredLabels=nullptr, bool decomposeStack=true) override
Definition: metadata_vec.cpp:120
REPORT_ERROR
#define REPORT_ERROR(nerr, ErrormMsg)
Definition: xmipp_error.h:211
ClassificationAlgorithm::setListener
void setListener(BaseListener *_listener)
Definition: base_algorithm.h:129
MD_APPEND
Definition: metadata_writemode.h:34
MetaDataVec::removeLabel
bool removeLabel(const MDLabel label) override
Definition: metadata_vec.cpp:414
ERR_IO_NOWRITE
Couldn&#39;t write to file.
Definition: xmipp_error.h:140
MDRowVec::setValue
void setValue(const MDObject &object) override
Definition: metadata_row_vec.cpp:199
MetaDataVec::write
void write(const FileName &outFile, WriteModeMetaData mode=MD_OVERWRITE) const
Definition: metadata_vec.cpp:140
KerDenSOM::test
virtual double test(const FuzzyMap &_som, const TS &_examples) const
Definition: kerdensom.cpp:74
MetaDataVec::getRow
std::unique_ptr< MDRow > getRow(size_t id) override
Definition: metadata_vec.cpp:310
KerDenSOM::train
virtual void train(FuzzyMap &_som, TS &_examples, FileName &_fn_vectors, bool _update=false, double _sigma=0, bool _saveIntermediate=false)=0
MetaDataVec::size
size_t size() const override
Definition: metadata_vec.cpp:393
i
#define i
Definition: numerical_recipes.cpp:2493
MetaDataVec::addRow
size_t addRow(const MDRow &row) override
Definition: metadata_vec.cpp:225
MDL_YSIZE
Y size (int)
Definition: metadata_label.h:502
MDL_COUNT
Number of elements of a type (int) [this is a genereic type do not use to transfer information to ano...
Definition: metadata_label.h:92
MetaDataVec::setValue
bool setValue(const MDObject &mdValueIn, size_t id)
Definition: metadata_vec.cpp:282
MetaDataVec::addObject
size_t addObject() override
Definition: metadata_vec.cpp:435
BaseListener::setVerbosity
virtual unsigned & setVerbosity()
Definition: xmipp_funcs.h:1072
MetaDataVec::firstRowId
size_t firstRowId() const override
Definition: metadata_vec.cpp:508
MetaDataVec::findObjects
void findObjects(std::vector< size_t > &objectsOut, const MDQuery &query) const override
Definition: metadata_vec.cpp:574
MDL_CLASSIFICATION_DATA_SIZE
Size of data vectors for classification (int)
Definition: metadata_label.h:84
XmippProgram::verbose
int verbose
Verbosity level.
Definition: xmipp_program.h:161
dummy
double dummy
Definition: numerical_recipes.cpp:4635
j
#define j
Definition: numerical_recipes.cpp:2493
MetaDataVec::getValue
bool getValue(MDObject &mdValueOut, size_t id) const override
Definition: metadata_vec.cpp:293
MDL_REF
Class to which the image belongs (int)
Definition: metadata_label.h:377
MetaData::setColumnFormat
virtual void setColumnFormat(bool column)
Definition: metadata_base.h:293
MDL_MAPTOPOLOGY
Magnification of microscope.
Definition: metadata_label.h:278
MDL_XSIZE
X size (int)
Definition: metadata_label.h:498
MDL_CLASS_COUNT
Number of images assigned to the same class as this image.
Definition: metadata_label.h:81
String
std::string String
Definition: xmipp_strings.h:34
formatString
String formatString(const char *format,...)
Definition: xmipp_strings.cpp:602
MDL_CLASSIFICATION_INTRACLASS_DISTANCE
Average intraclass distance (double)
Definition: metadata_label.h:86

◆ show()

void ProgKenderSOM::show ( )
inline

Definition at line 131 of file classify_kerdensom.cpp.

132  {
133  std::cout << "Input data file : " << fn_in << std::endl;
134  std::cout << "Output rootname : " << fn_root << std::endl;
135  std::cout << "Horizontal dimension (Xdim) = " << xdim << std::endl;
136  std::cout << "Vertical dimension (Ydim) = " << ydim << std::endl;
137  if (layout == "HEXA")
138  std::cout << "Hexagonal topology " << std::endl;
139  else
140  std::cout << "Rectangular topology " << std::endl;
141  std::cout << "Initial smoothness factor (reg0) = " << reg0 << std::endl;
142  std::cout << "Final smoothness factor (reg1) = " << reg1 << std::endl;
143  std::cout << "Deterministic annealing steps = " << annSteps << std::endl;
144  std::cout << "Total number of iterations = " << iter << std::endl;
145  std::cout << "Stopping criteria (eps) = " << eps << std::endl;
146  if (norm)
147  std::cout << "Normalize input data" << std::endl;
148  else
149  std::cout << "Do not normalize input data " << std::endl;
150  }

Member Data Documentation

◆ annSteps

unsigned ProgKenderSOM::annSteps

Definition at line 47 of file classify_kerdensom.cpp.

◆ eps

double ProgKenderSOM::eps

Definition at line 39 of file classify_kerdensom.cpp.

◆ fn_in

FileName ProgKenderSOM::fn_in

Definition at line 36 of file classify_kerdensom.cpp.

◆ fn_root

FileName ProgKenderSOM::fn_root

Definition at line 37 of file classify_kerdensom.cpp.

◆ iter

unsigned ProgKenderSOM::iter

Definition at line 40 of file classify_kerdensom.cpp.

◆ layout

std::string ProgKenderSOM::layout

Definition at line 46 of file classify_kerdensom.cpp.

◆ norm

bool ProgKenderSOM::norm

Definition at line 41 of file classify_kerdensom.cpp.

◆ reg0

double ProgKenderSOM::reg0

Definition at line 44 of file classify_kerdensom.cpp.

◆ reg1

double ProgKenderSOM::reg1

Definition at line 45 of file classify_kerdensom.cpp.

◆ tmpN

FileName ProgKenderSOM::tmpN

Definition at line 38 of file classify_kerdensom.cpp.

◆ xdim

size_t ProgKenderSOM::xdim

Definition at line 42 of file classify_kerdensom.cpp.

◆ ydim

size_t ProgKenderSOM::ydim

Definition at line 43 of file classify_kerdensom.cpp.

The documentation for this class was generated from the following file:
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