mthomure’s gists

mthomure / create_temp_dir.sh

Created November 8, 2017 02:08

Create temp dir in bash script

	#!/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 / pca.clj

Last active August 3, 2020 06:31

simple PCA implementation in clojure

	(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 / k_means.clj

Last active January 18, 2017 01:10

simple k-means in clojure

	(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 / learn_mallet.clj

Last active January 16, 2017 20:25

First steps at clojure idiomatic wrapper for mallet

	(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 / hdf5.clj

Last active May 9, 2017 15:40

Simple HDF5 reader in clojure

	(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 / read-excel-stream.clj

Created January 7, 2017 01:21

Read large excel files from clojure without killing the JVM

	(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 / ExampleDGELSrowmajor.clj

Created December 30, 2016 22:48

Using OpenBLAS from Clojure

	;; 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 / test_setulb.c

Last active May 25, 2017 18:13

LBFGS via JNR

	#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 / getpid.clj

Created June 26, 2016 07:39

	(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 / fuzzy_diff.clj

Created June 14, 2016 16:38

Approximate comparison of floating-point numbers for clojure.data/diff.

	(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

	#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");

Mick Thomure mthomure