Merge branch 'dev'

.travis.yml

@@ -6,6 +6,7 @@ branches:
     - travis-ci
     - dev
     - master
+    - camdev
 
 matrix:
   include:
@@ -109,7 +110,7 @@ script:
   # 2. build Galaxy image writing interface
   # 3. run gold image tests
   - scripts/travis-ci-build.sh
-  - if [ -z ${GXY_REBUILDING_CACHE} ] && [ -f install/bin/gxywriter ]; then tests/image-gold-tests.sh; fi
+  - if [ -z ${GXY_REBUILDING_CACHE} ] && [ -f install/bin/gxywriter ] && [ "${TRAVIS_OS_NAME}" == "linux" ]; then tests/image-gold-tests.sh; fi
   - if [ -z ${GXY_REBUILDING_CACHE} ] && [ -d install/tests ]; then tests/unit-tests.sh; fi
   - echo $(date) > .galaxy/last_build
 

RELEASE_NOTES.md

@@ -1,5 +1,19 @@
 # Galaxy Release Notes
 
+## version 0.4.0 - pending
+
+* *TODO* - reorganize `src` directory to: framework, data, filters, apps
+* *TODO* - singularity recipe for multi-node distributed testing on TACC systems
+
+## version 0.3.1 - 20190930
+
+* added examples for Schlieren renderer in `examples/schlieren`
+* added examples for various data samplers in `examples/sampletrace`
+* added second, energy-accumulation schlieren algorithm
+* added 'data.state' argument to `sampletrace` to track data
+* moved image resolution specification to Camera
+* added Cinema database example of Water in the Universe data in `examples/WitU`
+* added 'data range' to visualizations to select range of interest
 
 ## version 0.3.0 - 20190821
 
@@ -12,7 +26,7 @@
 * Support for vector-valued volumes
   - added JSON format for volume description files that implements 'number of components' field
 * Initial implementation of RungeKutta operator to trace streamlines in vector volumes
-  - also 'TraceToPathLines' opewrtor to convert RungeKutta results to path lines for rendering
+  - also 'TraceToPathLines' operator to convert RungeKutta results to path lines for rendering
 * Added `schlieren` to provide multi-hued Schlieren and shadowgraph-style rendering
   - also implemented 'float-image' output (in FITS format)
 * Added `ospray` modules for class overrides to the underlying [OSPRay][1] rendering engine

examples/WitU/cinema/compare/1.0/copyright.md

@@ -0,0 +1,20 @@
+Copyright (c) 2018-2019, Triad National Security, LLC. All rights reserved.
+
+This software was produced under U.S. Government contract 89233218CNA000001 for 
+Los Alamos National Laboratory (LANL), which is operated by Triad National 
+Security, LLC for the U.S. Department of Energy/National Nuclear Security 
+Administration.
+
+All rights in the program are reserved by Triad National Security, LLC, and the 
+U.S. Department of Energy/National Nuclear Security Administration. The 
+Government is granted for itself and others acting on its behalf a nonexclusive,
+paid-up, irrevocable worldwide license in this material to reproduce, prepare 
+derivative works, distribute copies to the public, perform publicly and display 
+publicly, and to permit others to do so. 
+
+This is open source software; you can redistribute it and/or modify it under the
+terms of the "3-Clause BSD License". If software is modified to produce 
+derivative works, such modified software should be clearly marked, so as not to 
+confuse it with the version available from LANL. Full text of the "3-Clause BSD 
+License" can be found in the License file in the main development branch of the 
+repository.

examples/WitU/cinema/compare/1.0/css/common.css

@@ -0,0 +1,29 @@
+* {
+    font-family: helvetica !important;
+}
+
+div.container {
+    width: 100%;
+    border: 1px solid gray;
+}
+
+body {
+    background-color: #f9f9f9;
+}
+
+header, footer {
+    padding-left:   1px;
+    padding-right:  1px;
+    padding-top:    10px;
+    padding-bottom: 10px;
+    color: white;
+    background-color: #373737;
+    clear: left;
+    text-align: center;
+}
+
+#header h2 {
+	display: inline-block;
+	margin: initial;
+}
+

examples/WitU/cinema/compare/1.0/css/compare.css

@@ -0,0 +1,26 @@
+#resultsArea {
+	float: left;
+	left: 0px;
+	right: 0px;
+	width: 100%;
+	padding: 10px;
+	background-color: white;
+}
+
+.imageArea {
+	float: left;
+	position: relative;
+	width: 75%;
+}
+
+.sliderArea {
+	float: left;
+	position: relative;
+	width: 20%;
+}
+
+.cinemaImage {
+	float: left;
+	position: relative;
+	padding: 2px;
+}

examples/WitU/cinema/compare/1.0/license.md

@@ -0,0 +1,28 @@
+Copyright (c) 2018-2019, Triad National Security, LLC. All rights reserved.
+
+Redistribution and use in source and binary forms, with or
+without modification, are permitted provided that the following conditions
+are met:
+
+    1. Redistributions of source code must retain the above copyright notice, 
+       this list of conditions and the following disclaimer.
+
+    2. Redistributions in binary form must reproduce the above copyright
+       notice, this list of conditions and the following disclaimer in the
+       documentation and/or other materials provided with the distribution.
+
+    3. Neither the name of Los Alamos National Security, LLC, Los Alamos
+       National Laboratory, LANL, the U.S. Government, nor the names of its
+       contributors may be used to endorse or promote products derived from 
+       this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL LOS ALAMOS NATIONAL SECURITY, LLC OR CONTRIBUTORS 
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE 
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) 
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF
+THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

examples/WitU/cinema/compare/1.0/version.md

@@ -0,0 +1 @@
+1.0

examples/WitU/cinema_compare.html

@@ -0,0 +1,191 @@
+<!doctype html>
+<html>
+
+<head>
+    <meta app="cinema:compare" version="1.0">
+    <meta charset="utf-8">
+    <link rel='stylesheet' href='cinema/compare/1.0/css/compare.css'>
+    <link rel='stylesheet' href='cinema/compare/1.0/css/common.css'>
+    <script src='cinema/lib/d3.v4.min.js'></script>
+</head>
+
+<body>
+<div class="container">
+<header>
+    <h2>CinemaCompare</h2>
+</header>
+
+<div id="resultsArea">
+    <div class="imageArea" id="imageArea"></div>
+    <div class="sliderArea">
+        <div id="sliderContainer" class="sliderContainer">
+            <div>
+                <div>Image Size</div>
+                <input type="range" min="1" max="100" id="imageSize" step="1">
+            </div>
+        </div>
+    </div>
+    </div>
+</div>
+
+<footer>&nbsp</footer>
+
+</div>
+
+   		<script>
+			function onlyUnique(value, index, self) {
+			    return self.indexOf(value) === index;
+			}
+
+			function getLookupKey(keys, query) {
+				var key = "";
+				keys.forEach(function(item, index) {
+					key += query[item] + "_";
+				});
+
+				return key;
+			}
+
+            var dataSets = ["data/test.cdb"];
+            // START: add code to manage databases to view 
+            var dataSets = [
+                "tmp/samples.cdb",
+                "tmp/visualization.cdb"
+            ];
+            // END:   add code to manage databases to view 
+
+   			var dataResults = null;
+   			var dataValues = null;
+   			var query = {};
+   			var images = [];
+
+   			var q = d3.queue();
+   			dataSets.forEach(function(item, index) {
+				q.defer(d3.csv, item + "/data.csv");
+			});
+			q.awaitAll(function(error, results) {
+				var values = {};
+				results.forEach(function(item, index) {
+					var keys = Object.keys(item[0]).filter(function(d) {
+						return !isNaN(+item[0][d]);
+					});
+
+					var lookup = {};
+
+					item.forEach(function(result, index) {
+						keys.forEach(function(key, index) {
+							if (!(key in values)) {
+								values[key] = [];
+							}
+
+							values[key].push(result[key]);
+						});
+
+						lookup[getLookupKey(keys, result)] = result;
+					})
+
+					results[index] = {keys: keys, results: results[index], lookup: lookup};
+				});
+
+				var keys = Object.keys(values);
+				keys.forEach(function(key, index) {
+					values[key] = values[key].filter(onlyUnique);
+					values[key] = values[key].sort(function(a, b){return (+a)-(+b)});
+				});
+
+				doneLoading(results, values);
+			});
+
+			function updateResults() {
+				dataResults.forEach(function(result, index) {
+		   						var imgSrcKey = getLookupKey(result.keys, query);
+		   						if (imgSrcKey in result.lookup) {
+			   						var imgSrc = dataSets[index] + "/" +result.lookup[imgSrcKey]["FILE"];
+				   					images[index].img.attr("src", imgSrc);
+		   						}
+		   						else {
+				   					images[index].img.attr("src", "images/empty.png");
+		   						}
+		   					});
+			}
+
+			function doneLoading(results, values) {
+				var imageSizeSlider = d3.select("#imageSize")
+					.property("value", (100/dataSets.length)-1)
+					.on("input", function() {
+						images.forEach(function(item, index) {
+							item.img.style("width","" + imageSizeSlider.node().value + "%");
+							item.img.attr("height", null);
+						});
+					});
+
+				dataResults = results;
+				dataValues = values;
+
+				var keys = Object.keys(values);
+				keys.forEach(function(key, index) {
+					var sliderDiv = d3.select("#sliderContainer").append("div");
+					sliderDiv.append("div")
+						.html(key)
+                        .style("padding", "5px");
+					var slider = sliderDiv.append("div")
+			   			.append("input")
+			   				.attr("type","range")
+			   				.attr("min", "0")
+			   				.attr("max", values[key].length - 1)
+			   				.property("value", "0")
+			   				.style("float", "left");
+			   		var sliderText = sliderDiv.append("input")
+			   				.attr("type","text")
+			   				.attr("value", values[key][0])
+			   				.style("width", "40px")
+			   				.on("input", function() {
+			   					query[key] = this.value;
+			   					var index = values[key].indexOf(this.value);
+			   					slider.property("value", index);
+		   						updateResults();
+			   				});
+
+			   		slider.on("input", function() {
+			   				var val = values[key][+this.value];
+				   			sliderText.property("value", val);
+		   					query[key] = val;
+		   					updateResults();
+			   			});
+
+			   		query[key] = values[key][0];
+				});
+
+				dataResults.forEach(function(result, index) {
+					var imgSrcKey = getLookupKey(result.keys, query);
+
+					var img = d3.select("#imageArea").append("img")
+						.attr("class", "cinemaImage")
+						.attr("src", "images/empty.png")
+						.style("width","" + imageSizeSlider.node().value + "%")
+						.on("load", function() {
+							if (this.src != "images/empty.png") {
+		   						images[index].height = this.height;
+							}
+		   				})
+						.on("error", function() {
+		   					this.src='images/empty.png';
+		   					this.height = images[index].height;
+		   				});
+
+					images.push({img: img});
+
+		   			if (imgSrcKey in result.lookup) {
+			   			var imgSrc = dataSets[index] + "/" + result.lookup[imgSrcKey]["FILE"];
+				   		images[index].img.attr("src", imgSrc);
+		   			}
+		   			else {
+				   		images[index].img.attr("src", "images/empty.png");
+		   			}
+
+				});
+			}
+
+   		</script>
+   </body>
+</html>

examples/WitU/cintools/__init__.py

@@ -0,0 +1,2 @@
+from . import install
+from . import cdb

examples/WitU/cintools/cdb/__init__.py

@@ -0,0 +1 @@
+from . import cdb