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Merge pull request #1773 from lixun910/master
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V1.12.1.179
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@lixun910
lixun910 committed Dec 3, 2018
2 parents b295f99 + ff64fd0 commit b4a9b63
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Showing 133 changed files with 7,639 additions and 3,606 deletions.
12 changes: 6 additions & 6 deletions Algorithms/DataUtils.h
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Original file line number Diff line number Diff line change
Expand Up @@ -17,20 +17,20 @@ using namespace std;

class DataUtils {
public:
static double ManhattanDistance(double* x1, double* x2, size_t size)
static double ManhattanDistance(double* x1, double* x2, size_t size, double* weight)
{
double d =0;
for (size_t i =0; i<size; i++ ) {
d += fabs(x1[i] - x2[i]);
d += fabs(x1[i] - x2[i]) * weight[i];
}
return d;
}

static double EuclideanDistance(double* x1, double* x2, size_t size)
static double EuclideanDistance(double* x1, double* x2, size_t size, double* weight)
{
double d =0,tmp=0;
for (size_t i =0; i<size; i++ ) {
tmp = x1[i] - x2[i];
tmp = (x1[i] - x2[i]) * weight[i];
d += tmp * tmp;
}
return d;
Expand Down Expand Up @@ -285,7 +285,7 @@ class DataUtils {
}

// upper triangular part of a symmetric matrix
static double* getPairWiseDistance(double** matrix, int n, int k, double dist(double* , double* , size_t))
static double* getPairWiseDistance(double** matrix, double* weight, int n, int k, double dist(double* , double* , size_t, double*))
{
unsigned long long _n = n;

Expand All @@ -294,7 +294,7 @@ class DataUtils {
double* result = new double[nn];
for (int i=0; i<n; i++) {
for (int j=i+1; j<n; j++) {
result[cnt++] = dist(matrix[i], matrix[j], k);
result[cnt++] = dist(matrix[i], matrix[j], k, weight);
}
}
return result;
Expand Down
11 changes: 8 additions & 3 deletions Algorithms/cluster.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2977,7 +2977,7 @@ number of clusters is larger than the number of elements being clustered,
/* *********************************************************************** */

void kmedoids (int nclusters, int nelements, double** distmatrix,
int npass, int clusterid[], double* error, int* ifound, double bound_vals[], double min_bound, int s1, int s2)
int npass, int n_maxiter, int clusterid[], double* error, int* ifound, double bound_vals[], double min_bound, int s1, int s2)
/*
Purpose
=======
Expand Down Expand Up @@ -3092,8 +3092,13 @@ to 0. If kmedoids fails due to a memory allocation error, ifound is set to -1.

if (npass!=0)
randomassign (nclusters, nelements, tclusterid, _s1, _s2);
while(1)
{ double previous = total;

int iter = 0;

while(iter < n_maxiter)
{
iter ++;
double previous = total;
total = 0.0;

if (counter % period == 0) /* Save the current cluster assignments */
Expand Down
2 changes: 1 addition & 1 deletion Algorithms/cluster.h
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ void kcluster (int nclusters, int ngenes, int ndata, double** data,
int** mask, double weight[], int transpose, int npass, int n_maxiter, char method, char dist,
int clusterid[], double* error, int* ifound, double bound_vals[], double min_bound, int s1, int s2);
void kmedoids (int nclusters, int nelements, double** distance,
int npass, int clusterid[], double* error, int* ifound, double bound_vals[], double min_bound, int s1, int s2);
int npass, int n_maxiter, int clusterid[], double* error, int* ifound, double bound_vals[], double min_bound, int s1, int s2);

void test (int nclusters, int nrows, int ncolumns, double** data, int** mask, double weight[], int transpose, int npass, int n_maxiter, char a);

Expand Down
2 changes: 1 addition & 1 deletion Algorithms/hdbscan.h
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@
#include <algorithm>
#include <vector>

#include "../kNN/ANN.h"
#include "../kNN/ANN/ANN.h"
#include "redcap.h"

using namespace SpanningTreeClustering;
Expand Down
5 changes: 4 additions & 1 deletion BuildTools/macosx/GNUmakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ default: compile-geoda

app: build-geoda-mac

compile-geoda: ogl-target io-target algorithms-target dataviewer-target dialogtools-target \
compile-geoda: weights-target ogl-target io-target algorithms-target dataviewer-target dialogtools-target \
knn-target explore-target libgdiam-target regression-target \
shapeoperations-target resource-target varcalc-target \
geoda-target
Expand All @@ -22,6 +22,9 @@ test:
resource-target:
(cd $(GeoDa_ROOT)/rc; $(MAKE) xrc; $(MAKE))

weights-target:
(cd $(GeoDa_ROOT)/Weights; $(MAKE))

ogl-target:
(cd $(GeoDa_ROOT)/ogl; $(MAKE))

Expand Down
62 changes: 50 additions & 12 deletions BuildTools/macosx/GeoDa.xcodeproj/project.pbxproj
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,15 @@
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Expand Down Expand Up @@ -124,7 +133,6 @@
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Expand Down Expand Up @@ -324,6 +332,18 @@
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Expand Down Expand Up @@ -510,17 +530,12 @@
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Expand Down Expand Up @@ -886,6 +901,15 @@
path = visualization;
sourceTree = "<group>";
};
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);
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sourceTree = "<group>";
};
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isa = PBXGroup;
children = (
Expand Down Expand Up @@ -1067,6 +1091,16 @@
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isa = PBXGroup;
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A14735B421A65F1700CA69B2 /* bd_tree.h */,
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Expand All @@ -1076,15 +1110,10 @@
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A4ED7D4B2097F113008685D6 /* kd_util.h */,
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A4ED7D422097EC54008685D6 /* ANNperf.h */,
A4ED7D402097EC54008685D6 /* ANNx.h */,
);
path = kNN;
sourceTree = "<group>";
Expand All @@ -1101,6 +1130,7 @@
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Expand Down Expand Up @@ -1818,6 +1848,7 @@
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Expand Down Expand Up @@ -1851,15 +1882,18 @@
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Expand All @@ -1869,7 +1903,6 @@
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Expand All @@ -1892,15 +1925,18 @@
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Expand All @@ -1912,6 +1948,7 @@
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DD3082B319F709BB001E5E89 /* WebViewHelpWin.cpp in Sources */,
Expand Down Expand Up @@ -1946,6 +1983,7 @@
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DDFFC7F21AC1C7CF00F7DD6D /* HighlightState.cpp in Sources */,
DD9373F71AC1FEAA0066AF21 /* PolysToContigWeights.cpp in Sources */,
DDCCB5CC1AD47C200067D6C4 /* SimpleBinsHistCanvas.cpp in Sources */,
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