mthomure

#!/bin/bash

# See also: https://stackoverflow.com/questions/10982911/creating-temporary-files-in-bash

# Create temporary directory.
mydir=$(mktemp -d "${TMPDIR:-/tmp/}$(basename $0).XXXXXXXXXXXX")

# Remove on exit.
trap "rm -rf $mydir" EXIT

mthomure

(ns pca
  (:require [clojure.core.matrix :as m]
            [clojure.core.matrix.linear :as ml]
            [clojure.core.matrix.utils :as mu]
            [clojure.core.matrix.stats :as ms]))

;; dependency: [net.mikera/core.matrix "0.57.0"]

(defn fit! [m & {:keys [num-components transform?]}]
  (let [mean (ms/mean m)  ;; per-column mean

mthomure

(ns k-means
  (:import [org.apache.commons.math3.ml.clustering
            Clusterable KMeansPlusPlusClusterer]
           [org.apache.commons.math3.ml.distance EuclideanDistance]))

;; dependency: [org.apache.commons/commons-math3 "3.6.1"]

(defrecord ClusterableWrapper [x]
  Clusterable
  (getPoint [this] x))

mthomure

(ns learn-mallet.core
  (:import [cc.mallet.optimize Optimizable$ByGradientValue
            ConjugateGradient GradientAscent LimitedMemoryBFGS
            OptimizerEvaluator$ByGradient]))

;; add dependency [cc.mallet/mallet "2.0.8"]

(defprotocol IProblem
  ;; returns map of problem's current state
  (problem-state [this]))

mthomure

(ns hdf5
  (:import [org.bytedeco.javacpp
            DoublePointer FloatPointer
            LongPointer IntPointer
            ShortPointer BytePointer]
           [org.bytedeco.javacpp hdf5 hdf5$H5File]))

;; Using maven dependency:
;; [org.bytedeco.javacpp-presets/hdf5-platform "1.10.0-patch1-1.3"]

mthomure

(ns read-excel-stream
  (:import [com.monitorjbl.xlsx StreamingReader]))

;; Remember to add the following maven dependency:
;;   [com.monitorjbl/xlsx-streamer "1.0.1"]
;; More info here:
;;   https://github.com/monitorjbl/excel-streaming-reader

(defn workbook
  "Open an Excel workbook, for example in a with-open form. This is lazy, and

mthomure

;; Port of https://github.com/bytedeco/javacpp-presets/tree/master/openblas
;; Requires openblas dependency:
;; [org.bytedeco.javacpp-presets/openblas-platform "0.2.19-1.3"]
(ns ExampleDGELSrowmajor
  (:import [org.bytedeco.javacpp openblas]))

(defn print-matrix-rowmajor [desc m n mat ldm]
  (println "\n " desc)
  (doseq [i (range m)]
    (doseq [j (range n)]

mthomure

#include "lbfgs.h"  // see https://github.com/stephenbeckr/L-BFGS-B-C/blob/master/src/lbfgsb.h
#include <stdio.h>

int test_setulb(integer *n, integer *m, double *x, double *l,
                double *u, integer *nbd, double *f,
                double *g, double *factr, double *pgtol, double *wa,
                integer *iwa, integer *task,
                integer *iprint, integer *csave,
                logical *lsave, integer *isave, double *dsave) {
    printf("test_setulb()\n");

mthomure

(ns getpid
  (:import [jnr.ffi.types pid_t]
           [jnr.ffi LibraryLoader]))

;; see https://github.com/jnr/jnr-ffi-examples/blob/master/getpid/src/main/java/getpid/Getpid.java
;; using dependency: [com.github.jnr/jnr-ffi "2.0.9"]

;; public interface LibC  {
;;   public @pid_t long getpid();
;;   public @pid_t long getppid();

mthomure

(ns fuzzy-diff
  "Approximate comparison of floating-point numbers for clojure.data/diff."
  (:require [clojure.data :refer [Diff]]))

(def ^:dynamic *fuzz* 0)

(defn fuzzy-float-diff [a b]
  (if (< (Math/abs (- a b)) *fuzz*) [nil nil a] [a b nil]))

(extend java.lang.Double