Changeset 605

Timestamp:

08/30/16 17:39:10 (8 years ago)

Author:

Maciej Komosinski

Message:

• Added 'fixedZaxis' option to paramtab (so that it is accessible from scripts)
• Variable renames, improvements in comments

Location:

cpp/frams

Files:

• _demos/simil_test.cpp (modified) (5 diffs)
• model/similarity/simil_model.cpp (modified) (4 diffs)
• model/similarity/simil_model.h (modified) (1 diff)

cpp/frams/_demos/simil_test.cpp

@@ -1 +1 @@
 // This file is a part of Framsticks SDK.  http://www.framsticks.com/
-// Copyright (C) 1999-2015  Maciej Komosinski and Szymon Ulatowski.
+// Copyright (C) 1999-2016  Maciej Komosinski and Szymon Ulatowski.
 // See LICENSE.txt for details.
 
@@ -17 +17 @@
 /** Computes a matrix of distances between all genotypes in the specified
     .gen file, using the matching and measure weights as specified in the
-    command line.
-
-    Command line parameters: [-names] <genotypesFile> <w_dP> <w_dDEG> <w_dNEU> <w_dGEO>
-
-    Parameters:
-      <genotypesFile> name of a file with genotypes
-      <w_dP> weight of the difference in the number of parts
-      <w_dDEG> weight of the difference in degrees of matched parts
-      <w_dNEU> weight of the difference in neurons of matched parts
-      <w_dGEO> weight of the distance between matched parts
-
-    Switches:
-      -names specifies that the number and names of genotypes are to be printed to output
-        before the distance matrix; by default the number and names are not printed
-
-    Outputs a distance matrix in the format:
-    <row_1> (columns in a row are separated by TABs)
-    ...
-    <row_n>
- */
+    command line. */
 int main(int argc, char *argv[])
 {
@@ -49 +30 @@
     if (argc < 7)
     {
-        // too few parameters
         printf("Too few parameters!\n");
-        printf("Command line: [-names] <genotypesFile> <w_dP> <w_dDEG> <w_dNEU> <w_dGEO> <isZfixed>\n\n");
+        printf("Command line: [-names] <genotypesFile> <w_dP> <w_dDEG> <w_dNEU> <w_dGEO> <fixZaxis?>\n\n");
         printf("Parameters:\n");
-        printf(" <genotypesFile> name of a file with genotypes\n");
-        printf(" <w_dP> weight of the difference in the number of parts\n");
-        printf(" <w_dDEG> weight of the difference in degrees of matched parts\n");
-        printf(" <w_dNEU> weight of the difference in neurons of matched parts\n");
-        printf(" <w_dGEO> weight of the distance of matched parts\n\n");
-        printf(" <isZFixed> should z cooridante be fixed during the alignment\n");
+        printf("  <genotypesFile> name of a file with genotypes\n");
+        printf("  <w_dP> weight of the difference in the number of parts\n");
+        printf("  <w_dDEG> weight of the difference in degrees of matched parts\n");
+        printf("  <w_dNEU> weight of the difference in neurons of matched parts\n");
+        printf("  <w_dGEO> weight of the distance of matched parts\n");
+        printf("  <fixZaxis?> should the 'z' (vertical) coordinate be fixed during the alignment? (0 or 1)\n\n");
         printf("Switches:\n");
-        printf(" -names specifies that the number and names of genotypes are to be printed to output\n");
-        printf("   before the distance matrix; by default the number and names are not printed\n\n");
+        printf("  -names specifies that the number and names of genotypes are to be printed to output\n");
+        printf("  before the distance matrix; by default the number and names are not printed\n\n");
 
         printf("Outputs a symmetric distance matrix in the format:\n");
-        printf(" <row_1> (columns in a row are separated by TABs)\n");
-        printf(" ...\n");
-        printf(" <row_n>\n");
+        printf("  <row_1> (columns in a row are separated by TABs)\n");
+        printf("  ...\n");
+        printf("  <row_n>\n");
 
         return -1;
@@ -130 +110 @@
         return -1;
     }
-    else if (M.zFixed != 0 && M.zFixed !=1)
-    {
-        printf("<isZFixed>=%d. <isZFixed> should be equal to 0 or 1\n", M.zFixed);
-        return -1;
+    else if (M.zFixed != 0 && M.zFixed != 1)
+    {
+        printf("<isZFixed>=%d. <isZFixed> should be equal to 0 or 1\n", M.zFixed);
+        return -1;
     }
     
@@ -194 +174 @@
     if (bPrintNames)
     {
-        // if "-names" switch was given,
-        // print the number of genotypes and their names
+        // if "-names" switch was given, print the number of genotypes and their names
         printf("%li\n", pvGenos.size());
                 for (unsigned int iGen = 0; iGen < pvNames.size(); iGen++)

cpp/frams/model/similarity/simil_model.cpp

@@ -34 +34 @@
 
 static ParamEntry MSparam_tab[] = {
-    {"Creature: Similarity", 1, 5, "ModelSimilarity", "Evaluates morphological dissimilarity. More information:\nhttp://www.framsticks.com/node/795\nhttp://www.framsticks.com/node/890", },
+    {"Creature: Similarity", 1, 6, "ModelSimilarity", "Evaluates morphological dissimilarity. More information:\nhttp://www.framsticks.com/node/795\nhttp://www.framsticks.com/node/890", },
     {"simil_parts", 0, 0, "Weight of parts count", "f 0 100 0", FIELD(m_adFactors[0]), "Differing number of parts is also handled by the 'part degree' similarity component.",},
     {"simil_partdeg", 0, 0, "Weight of parts' degree", "f 0 100 1", FIELD(m_adFactors[1]), "",},
     {"simil_neuro", 0, 0, "Weight of neurons count", "f 0 100 0.1", FIELD(m_adFactors[2]), "",},
     {"simil_partgeom", 0, 0, "Weight of parts' geometric distances", "f 0 100 0", FIELD(m_adFactors[3]), "",},
-    {"evaluateDistance", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "evaluate model dissimilarity", "p f(oGeno,oGeno)", PROCEDURE(p_evaldistance), "Calculates dissimilarity between two models created from Geno objects.",},
+        {"simil_fixedZaxis", 0, 0, "Fix 'z' (vertical) axis?", "d 0 1 0", FIELD(fixedZaxis), "", },
+        {"evaluateDistance", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "evaluate model dissimilarity", "p f(oGeno,oGeno)", PROCEDURE(p_evaldistance), "Calculates dissimilarity between two models created from Geno objects.", },
     {0,},
 };
@@ -1997 +1998 @@
             // get the position of the Part
             P1Pos = P1->p;
-            if (zFixed == 1)
+                        if (fixedZaxis == 1)
             {
-                P1Pos.z = 0;    
+                P1Pos.z = 0; //fixed vertical axis, so pretend all points are on the xy plane
             }
             for (iP2 = 0; iP2 < pModel->getPartCount(); iP2++)
@@ -2007 +2008 @@
                 // get the position of the Part
                 P2Pos = P2->p;
-                if (zFixed == 1)
+                                if (fixedZaxis == 1)
                 {
-                        P2Pos.z = 0;    
+                        P2Pos.z = 0; //fixed vertical axis, so pretend all points are on the xy plane
                 }
                 // compute the geometric (Euclidean) distance between the Parts
@@ -2019 +2020 @@
 
         MatrixTools::SVD(vEigenvalues, nSize, pDistances, m_aPositions[ iMod ]);
-        if (zFixed == 1)
+                if (fixedZaxis == 1) //restore the original vertical coordinate of each Part
         {
-                for (int coord = 0; coord < pModel->getPartCount(); coord++)
+                for (int part = 0; part < pModel->getPartCount(); part++)
                 {
-                        m_aPositions[ iMod ][coord].z = pModel->getPart(coord)->p.z;
+                        m_aPositions[iMod][part].z = pModel->getPart(part)->p.z;
                 }
         }

cpp/frams/model/similarity/simil_model.h

@@ -82 +82 @@
     double m_adFactors[4];
 
-    //Controls the depth of fuzzy neighbourhood 
+        //for Zfixed = 1, the "z" (vertical) coordinates are not taken into account during PCA alignment
+        int fixedZaxis;
+        
+        //Controls the depth of fuzzy neighbourhood 
     int fuzzyDepth;
     int isFuzzy;
-    //for Zfixed = 1 z coordinates are not taken into account during PCA alignment
-    int zFixed;
 
     /// Interface to local parameters