Repository: mahout Updated Branches: refs/heads/master 9df093c98 -> 4105063d8
MAHOUT-1838: Simple 2d plotting of a sampled DRM closes apache/mahout #229 Project: http://git-wip-us.apache.org/repos/asf/mahout/repo Commit: http://git-wip-us.apache.org/repos/asf/mahout/commit/4105063d Tree: http://git-wip-us.apache.org/repos/asf/mahout/tree/4105063d Diff: http://git-wip-us.apache.org/repos/asf/mahout/diff/4105063d Branch: refs/heads/master Commit: 4105063d87178c93fd216c8eaeac85b83f506e73 Parents: 9df093c Author: Andrew Palumbo <[email protected]> Authored: Fri Apr 29 18:00:52 2016 -0400 Committer: Andrew Palumbo <[email protected]> Committed: Fri Apr 29 18:00:52 2016 -0400 ---------------------------------------------------------------------- LICENSE.txt | 207 +++++++++++++++++++ examples/bin/spark-shell-plot.mscala | 19 ++ math-scala/pom.xml | 7 + .../org/apache/mahout/visualization/mlpot.scala | 24 +++ .../apache/mahout/visualization/mplot2d.scala | 69 +++++++ .../apache/mahout/visualization/mplot3d.scala | 24 +++ spark-shell/pom.xml | 1 + .../sparkbindings/shell/MahoutSparkILoop.scala | 5 + spark/pom.xml | 9 +- spark/src/main/assembly/dependency-reduced.xml | 1 + 10 files changed, 365 insertions(+), 1 deletion(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/mahout/blob/4105063d/LICENSE.txt ---------------------------------------------------------------------- diff --git a/LICENSE.txt b/LICENSE.txt index 92ceb9b..c88e7c0 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -812,3 +812,210 @@ The following license applies to the H2O package See the License for the specific language governing permissions and limitations under the License. +========================================================== +Smile Plot Library +========================================================== +The following applies to the Smile plot library: + +Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "{}" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright {yyyy} {name of copyright owner} + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + http://git-wip-us.apache.org/repos/asf/mahout/blob/4105063d/examples/bin/spark-shell-plot.mscala ---------------------------------------------------------------------- diff --git a/examples/bin/spark-shell-plot.mscala b/examples/bin/spark-shell-plot.mscala new file mode 100644 index 0000000..73578f7 --- /dev/null +++ b/examples/bin/spark-shell-plot.mscala @@ -0,0 +1,19 @@ +import org.apache.mahout.visualization.mplot2d + +val mxRnd = Matrices.symmetricUniformView(5000000, 2, 1234) +val drmRand = drmParallelize(mxRnd) + +val drmSin = drmRand.mapBlock() {case (keys, block) => + val blockB = block.like() + for (i <- 0 until block.nrow) { + blockB(i, 0) = block(i, 0) + blockB(i, 1) = Math.sin((block(i, 0) * 8)) + } + keys -> blockB +} + +new mplot2d(drmRand, samplePercent = 1) +new mplot2d(drmSin, samplePercent = 1) + + + http://git-wip-us.apache.org/repos/asf/mahout/blob/4105063d/math-scala/pom.xml ---------------------------------------------------------------------- diff --git a/math-scala/pom.xml b/math-scala/pom.xml index efb3792..d7ee17e 100644 --- a/math-scala/pom.xml +++ b/math-scala/pom.xml @@ -140,6 +140,13 @@ <version>3.3.0</version> </dependency> + + <dependency> + <groupId>com.github.haifengl</groupId> + <artifactId>smile-plot</artifactId> + <version>1.1.0</version> + </dependency> + <!-- scala stuff --> <dependency> <groupId>org.scalatest</groupId> http://git-wip-us.apache.org/repos/asf/mahout/blob/4105063d/math-scala/src/main/scala/org/apache/mahout/visualization/mlpot.scala ---------------------------------------------------------------------- diff --git a/math-scala/src/main/scala/org/apache/mahout/visualization/mlpot.scala b/math-scala/src/main/scala/org/apache/mahout/visualization/mlpot.scala new file mode 100644 index 0000000..18b692d --- /dev/null +++ b/math-scala/src/main/scala/org/apache/mahout/visualization/mlpot.scala @@ -0,0 +1,24 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + + +package org.apache.mahout.visualization + + +trait mlpot { + +} http://git-wip-us.apache.org/repos/asf/mahout/blob/4105063d/math-scala/src/main/scala/org/apache/mahout/visualization/mplot2d.scala ---------------------------------------------------------------------- diff --git a/math-scala/src/main/scala/org/apache/mahout/visualization/mplot2d.scala b/math-scala/src/main/scala/org/apache/mahout/visualization/mplot2d.scala new file mode 100644 index 0000000..20e2743 --- /dev/null +++ b/math-scala/src/main/scala/org/apache/mahout/visualization/mplot2d.scala @@ -0,0 +1,69 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.mahout.visualization + +import java.awt.{BorderLayout, Color} +import java.io.File +import javax.swing.JFrame + +import org.apache.mahout.math._ +import scalabindings._ +import RLikeOps._ +import drm._ +import smile.plot._ + +import scala.collection.JavaConversions._ + + +/** + * Create a s scatter plot of a DRM by sampling a given percentage + * and plotting corresponding points of (drmXY(::,0),drmXY(::,2)) + * + * @param drmXY an m x 2 Drm drm to plot + * @param samplePercent the percentage the drm to sample + * @tparam K + */ +class mplot2d[K](drmXY: DrmLike[K], samplePercent: Int = 1, setVisible: Boolean = true) { + val drmSize = drmXY.checkpoint().numRows() + val sampleDec: Double = (samplePercent.toDouble / 100.toDouble) + + val numSamples: Int = (drmSize * sampleDec).toInt + + val mPlotMatrix: Matrix = drmSampleKRows(drmXY, numSamples, false) + val arrays: Array[Array[Double]] = Array.ofDim[Double](mPlotMatrix.numRows(), 2) + for (i <- 0 until mPlotMatrix.numRows()) { + arrays(i)(0) = mPlotMatrix(i, 0) + arrays(i)(1) = mPlotMatrix(i, 1) + } + + val canvas: PlotCanvas = ScatterPlot.plot(arrays,Color.BLUE) + canvas.setTitle("2d Plot: " + samplePercent + " % sample of " + drmSize +" points") + canvas.setAxisLabels("x_0", "x_1") + + val plotPanel: PlotPanel = new PlotPanel(canvas) + + val plotFrame: JFrame = new JFrame("2d Plot") + plotFrame.setLayout(new BorderLayout()) + plotFrame.add(plotPanel) + plotFrame.setSize(300,300) + if (setVisible) { + plotFrame.setVisible(true) + plotFrame.show() + } + +} http://git-wip-us.apache.org/repos/asf/mahout/blob/4105063d/math-scala/src/main/scala/org/apache/mahout/visualization/mplot3d.scala ---------------------------------------------------------------------- diff --git a/math-scala/src/main/scala/org/apache/mahout/visualization/mplot3d.scala b/math-scala/src/main/scala/org/apache/mahout/visualization/mplot3d.scala new file mode 100644 index 0000000..24e2415 --- /dev/null +++ b/math-scala/src/main/scala/org/apache/mahout/visualization/mplot3d.scala @@ -0,0 +1,24 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one or more + * contributor license agreements. See the NOTICE file distributed with + * this work for additional information regarding copyright ownership. + * The ASF licenses this file to You under the Apache License, Version 2.0 + * (the "License"); you may not use this file except in compliance with + * the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + + +package org.apache.mahout.visualization + + +class mplot3d { + +} http://git-wip-us.apache.org/repos/asf/mahout/blob/4105063d/spark-shell/pom.xml ---------------------------------------------------------------------- diff --git a/spark-shell/pom.xml b/spark-shell/pom.xml index 763fc38..f62aee9 100644 --- a/spark-shell/pom.xml +++ b/spark-shell/pom.xml @@ -163,6 +163,7 @@ <artifactId>scalatest_${scala.compat.version}</artifactId> </dependency> + </dependencies> <profiles> http://git-wip-us.apache.org/repos/asf/mahout/blob/4105063d/spark-shell/src/main/scala/org/apache/mahout/sparkbindings/shell/MahoutSparkILoop.scala ---------------------------------------------------------------------- diff --git a/spark-shell/src/main/scala/org/apache/mahout/sparkbindings/shell/MahoutSparkILoop.scala b/spark-shell/src/main/scala/org/apache/mahout/sparkbindings/shell/MahoutSparkILoop.scala index dfce339..7a8f60e 100644 --- a/spark-shell/src/main/scala/org/apache/mahout/sparkbindings/shell/MahoutSparkILoop.scala +++ b/spark-shell/src/main/scala/org/apache/mahout/sparkbindings/shell/MahoutSparkILoop.scala @@ -86,6 +86,11 @@ class MahoutSparkILoop extends SparkILoop { conf.set("spark.executor.memory", "1g") } + // set default if not already set- this is useful in local mode + if(!conf.contains("spark.kryoserializer.buffer.max")) { + conf.set("spark.kryoserializer.buffer.max", "1g") + } + sdc = mahoutSparkContext( masterUrl = master, appName = "Mahout Spark Shell", http://git-wip-us.apache.org/repos/asf/mahout/blob/4105063d/spark/pom.xml ---------------------------------------------------------------------- diff --git a/spark/pom.xml b/spark/pom.xml index d5c7c36..420c40d 100644 --- a/spark/pom.xml +++ b/spark/pom.xml @@ -171,7 +171,14 @@ <scope>test</scope> </dependency> - <!-- 3rd-party --> + <dependency> + <groupId>com.github.haifengl</groupId> + <artifactId>smile-plot</artifactId> + <version>1.1.0</version> + </dependency> + + + <!-- 3rd-party --> <!-- scala stuff --> <dependency> http://git-wip-us.apache.org/repos/asf/mahout/blob/4105063d/spark/src/main/assembly/dependency-reduced.xml ---------------------------------------------------------------------- diff --git a/spark/src/main/assembly/dependency-reduced.xml b/spark/src/main/assembly/dependency-reduced.xml index a3044da..660d031 100644 --- a/spark/src/main/assembly/dependency-reduced.xml +++ b/spark/src/main/assembly/dependency-reduced.xml @@ -42,6 +42,7 @@ <include>com.tdunning:t-digest</include> <include>org.apache.commons:commons-math3</include> <include>it.unimi.dsi:fastutil</include> + <include>com.github.haifengl:smile-plot</include> </includes> </dependencySet> </dependencySets>
