1. CoGAPS
  2. Commit 7c2dde8cfef53ddaaeca3a3309ded5a4b376a79b
Browse code

Merge pull request #19 from FertigLab/add_index_sampler

Add index sampler

Tom Sherman authored on 06/06/2018 16:19:26 • GitHub committed on 06/06/2018 16:19:26
Showing 3 changed files
src/GapsRunner.cpp
History View file @ 7c2dde8cf
... ... 
@@ -1,10 +1,84 @@
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 #include "GapsRunner.h"
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 #include "math/SIMD.h"
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+#include "math/Random.h"
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+#include "GapsAssert.h"
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+#include <algorithm>
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 #ifdef __GAPS_OPENMP__
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     #include <omp.h>
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 #endif
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+// create "nSets" vectors where each vector contains a vector of indices in the
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+// range [0,n)
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+// see createGWCoGAPSSets.R - here we just sample indices, that function
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+// samples gene names as well
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+static std::vector< std::vector<unsigned> > sampleIndices(unsigned n, unsigned nSets)
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+{
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+    unsigned setSize = (int) n / nSets;
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+    std::vector< std::vector<unsigned> > sampleIndices;
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+    std::vector<unsigned> toBeSampled;
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+    for (unsigned i = 1; i < n; ++i)
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+    {
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+        toBeSampled.push_back(i);
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+    }
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+
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+    for (unsigned i = 0; i < (nSets - 1); ++i)
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+    {
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+        sampleIndices.push_back(gaps::random::sample(toBeSampled, setSize));
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+    }
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+
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+    GAPS_ASSERT(!toBeSampled.empty());
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+
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+    sampleIndices.push_back(toBeSampled);
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+
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+    return sampleIndices;
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+
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+    /*
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+    std::vector< std::vector<unsigned> > sampleIndices;
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+    std::vector<unsigned> sampled;
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+
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+    for (unsigned i = 0; i < (n - 1) % nSets; ++i)
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+    {
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+        std::vector<unsigned> set;
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+        for (unsigned i = 0; i < ((unsigned) (n - 1) / nSets) + 1; ++i)
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+        {
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+            while(true)
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+            {
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+                unsigned sample = gaps::random::uniform64(1, n);
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+                if (find(sampled.begin(), sampled.end(), sample) == sampled.end())
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+                {
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+                    set.push_back(sample);
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+                    sampled.push_back(sample);
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+                    break;
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+                }
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+            }
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+        }
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+        sampleIndices.push_back(set);
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+    }
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+
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+    for (unsigned i = (n - 1) % nSets; i < nSets; ++i)
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+    {
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+        std::vector<unsigned> set;
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+        for (unsigned i = 0; i < (unsigned) (n - 1) / nSets; ++i)
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+        {
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+            while(true)
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+            {
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+                unsigned sample = gaps::random::uniform64(1, n);
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+                if (find(sampled.begin(), sampled.end(), sample) == sampled.end())
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+                {
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+                    set.push_back(sample);
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+                    sampled.push_back(sample);
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+                    break;
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+                }
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+            }
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+        }
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+        sampleIndices.push_back(set);
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+    }
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+
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+    return sampleIndices;
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+    */
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+}
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+
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 GapsRunner::GapsRunner(const Rcpp::NumericMatrix &D, const Rcpp::NumericMatrix &S,
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 unsigned nFactor, unsigned nEquil, unsigned nCool, unsigned nSample,
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 unsigned nOutputs, unsigned nSnapshots, float alphaA, float alphaP,
... ... 
@@ -276,4 +350,4 @@ void GapsRunner::makeCheckpointIfNeeded()
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         createCheckpoint();
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         mLastCheckpoint = bpt_now();
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     }
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-}
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\ No newline at end of file
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+}
src/math/Random.cpp
History View file @ 7c2dde8cf
... ... 
@@ -21,6 +21,7 @@
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 #include <boost/random/uniform_real_distribution.hpp>
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 #include <stdint.h>
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+#include <algorithm>
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 #ifdef __GAPS_OPENMP__
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     #include <omp.h>
... ... 
@@ -178,4 +179,37 @@ float gaps::random::inverseGammaSample(float a, float b, float mean, float sd)
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         u = gaps::random::uniform(a, b);
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     }
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     return gaps::random::q_gamma(u, mean, sd);
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-}
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\ No newline at end of file
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+}
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+
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+std::vector<unsigned> sample(std::vector<unsigned> &elements, unsigned n) {
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+    std::vector<unsigned> sampleVect;
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+    for (unsigned i = 0; i < n; ++i)
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+    {
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+        GAPS_ASSERT(n <= elements.size());
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+        unsigned sampleIndex = gaps::random::uniform64(0, elements.size());
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+        sampleVect.push_back(elements.at(sampleIndex));
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+
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+        elements[sampleIndex] = elements.back();
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+        elements.pop_back();
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+    }
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+    return sampleVect;
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+
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+    /*
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+    std::vector<unsigned> sampleVect;
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+    std::vector<unsigned> sampledIndices;
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+    for (unsigned i = 0; i < n; ++i)
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+    {
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+        while(true)
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+        {
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+            unsigned sampleIndex = gaps::random::uniform64(0, elements.size());
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+            if (find(sampledIndices.begin(), sampledIndices.end(), sampleIndex) == sampledIndices.end())
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+            {
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+                sampleVect.push_back(elements.at(sampleIndex));
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+                sampledIndices.push_back(sampleIndex);
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+                break;
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+            }
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+        }
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+    }
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+    return sampleVect;
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+    */
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+}
src/math/Random.h
History View file @ 7c2dde8cf
... ... 
@@ -34,7 +34,9 @@ namespace gaps
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         void save(Archive &ar);
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         void load(Archive &ar);
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+
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+        std::vector<unsigned> sample(const std::vector<unsigned> &elements, unsigned n);
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     } // namespace random
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 } // namespace gaps
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-#endif
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\ No newline at end of file
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+#endif