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http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testGroupWiseEml.eml ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testGroupWiseEml.eml b/tika-parsers/src/test/resources/test-documents/testGroupWiseEml.eml new file mode 100644 index 0000000..a6d2398 --- /dev/null +++ b/tika-parsers/src/test/resources/test-documents/testGroupWiseEml.eml @@ -0,0 +1,58 @@ +Mime-Version: 1.0 +X-Mailer: GroupWise 2012 +Subject: test333 +Date: Thu, 27 Jun 2013 13:29:57 +0200 +Message-ID: <51CC3E55020000000000000F@$$$> +References: <51CC3DB00200000000000003@$$$> +In-Reply-To: <51CC3DB00200000000000003@$$$> +From: "Novell GroupWise" <$$$.$$$.$$$> +Content-Type: multipart/mixed; boundary="____LPHMXLZMXOMRLFKSEJCW____" + + +--____LPHMXLZMXOMRLFKSEJCW____ +Content-Type: multipart/alternative; boundary="____WHPEPQYSAQXEHDGESJXG____" + + +--____WHPEPQYSAQXEHDGESJXG____ +Content-Type: text/plain; charset=utf-8 +Content-Transfer-Encoding: base64 +Content-Disposition: inline + +dGVzdA== +--____WHPEPQYSAQXEHDGESJXG____ +Content-Type: text/html; charset=utf-8 +Content-Transfer-Encoding: quoted-printable + += +<HTML><HEAD> +<META content=3D"text/html; charset=3Dutf-8" http-equiv=3DContent-Type> +<META name=3DGENERATOR content=3D"MSHTML 8.00.7601.17699"></HEAD> +<BODY style=3D"MARGIN: 4px 4px 1px; FONT: 10pt Segoe UI">test</BODY></HTML> +--____WHPEPQYSAQXEHDGESJXG____-- + +--____LPHMXLZMXOMRLFKSEJCW____ +Content-Type: message/rfc822 +Content-Transfer-Encoding: base64 +Content-Disposition: attachment; filename="test.eml" + +TWltZS1WZXJzaW9uOiAxLjANClgtTWFpbGVyOiBHcm91cFdpc2UgMjAxMg0KU3ViamVjdDogdGVz +dA0KRGF0ZTogVGh1LCAyNyBKdW4gMjAxMyAxMzoyNzoxMiArMDIwMA0KTWVzc2FnZS1JRDogPDUx +Q0MzREIwMDIwMDAwMDAwMDAwMDAwM0AkJCQ+DQpGcm9tOiAiTm92ZWxsIEdyb3VwV2lzZSIgPCQk +JC4kJCQuJCQkPg0KQ29udGVudC1UeXBlOiBtdWx0aXBhcnQvYWx0ZXJuYXRpdmU7IGJvdW5kYXJ5 +PSJfX19fTFBITVhMWk1YT01STEZLU0VKQ1dfX19fIg0KDQoNCi0tX19fX0xQSE1YTFpNWE9NUkxG +S1NFSkNXX19fXw0KQ29udGVudC1UeXBlOiB0ZXh0L3BsYWluOyBjaGFyc2V0PXV0Zi04DQpDb250 +ZW50LVRyYW5zZmVyLUVuY29kaW5nOiBiYXNlNjQNCkNvbnRlbnQtRGlzcG9zaXRpb246IGlubGlu +ZQ0KDQpkR1Z6ZEE9PQ0KLS1fX19fTFBITVhMWk1YT01STEZLU0VKQ1dfX19fDQpDb250ZW50LVR5 +cGU6IHRleHQvaHRtbDsgY2hhcnNldD11dGYtOA0KQ29udGVudC1UcmFuc2Zlci1FbmNvZGluZzog +cXVvdGVkLXByaW50YWJsZQ0KDQo8SFRNTD48SEVBRD4NCjxNRVRBIGNvbnRlbnQ9M0QidGV4dC9o +dG1sOyBjaGFyc2V0PTNEdXRmLTgiIGh0dHAtZXF1aXY9M0RDb250ZW50LVR5cGU+DQo8TUVUQSBu +YW1lPTNER0VORVJBVE9SIGNvbnRlbnQ9M0QiTVNIVE1MIDguMDAuNzYwMS4xNzY5OSI+PC9IRUFE +Pg0KPEJPRFkgc3R5bGU9M0QiTUFSR0lOOiA0cHggNHB4IDFweDsgRk9OVDogMTBwdCBTZWdvZSBV +SSI+dGVzdDwvQk9EWT48L0hUTUw+DQotLV9fX19MUEhNWExaTVhPTVJMRktTRUpDV19fX18tLQ0K +--____LPHMXLZMXOMRLFKSEJCW____ +Content-Type: text/plain; charset=us-ascii +Content-Transfer-Encoding: quoted-printable +Content-Disposition: attachment; filename="Neues Textdokument.txt" + +ssssssssssssssssssssss +--____LPHMXLZMXOMRLFKSEJCW____-- http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testH.h ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testH.h b/tika-parsers/src/test/resources/test-documents/testH.h new file mode 100644 index 0000000..43002be --- /dev/null +++ b/tika-parsers/src/test/resources/test-documents/testH.h @@ -0,0 +1,5 @@ +#ifndef TIKA_HELLO_WORLD +#define TIKA_HELLO_WORLD + +#define HELLO "world" +#endif http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testHTML_utf8.html ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testHTML_utf8.html b/tika-parsers/src/test/resources/test-documents/testHTML_utf8.html new file mode 100644 index 0000000..310181f --- /dev/null +++ b/tika-parsers/src/test/resources/test-documents/testHTML_utf8.html @@ -0,0 +1,25 @@ +<!-- + 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. +--> +<html> + <head> + <title>Title : Tilte with UTF-8 chars öäå</title> + </head> + <body> + <h1>Content with UTF-8 chars</h1> + <p>åäö</p> + </body> +</html> \ No newline at end of file http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testHWP_3.0.hwp ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testHWP_3.0.hwp b/tika-parsers/src/test/resources/test-documents/testHWP_3.0.hwp new file mode 100644 index 0000000..6436bff Binary files /dev/null and b/tika-parsers/src/test/resources/test-documents/testHWP_3.0.hwp differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testHWP_5.0.hwp ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testHWP_5.0.hwp b/tika-parsers/src/test/resources/test-documents/testHWP_5.0.hwp new file mode 100644 index 0000000..a430016 Binary files /dev/null and b/tika-parsers/src/test/resources/test-documents/testHWP_5.0.hwp differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testINDD.indd ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testINDD.indd b/tika-parsers/src/test/resources/test-documents/testINDD.indd new file mode 100644 index 0000000..b455f1a Binary files /dev/null and b/tika-parsers/src/test/resources/test-documents/testINDD.indd differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testIPA.ipa ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testIPA.ipa b/tika-parsers/src/test/resources/test-documents/testIPA.ipa new file mode 100644 index 0000000..a0d13db Binary files /dev/null and b/tika-parsers/src/test/resources/test-documents/testIPA.ipa differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testJAR.jar ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testJAR.jar b/tika-parsers/src/test/resources/test-documents/testJAR.jar new file mode 100644 index 0000000..4677a62 Binary files /dev/null and b/tika-parsers/src/test/resources/test-documents/testJAR.jar differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testJAR_with_HTML.jar ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testJAR_with_HTML.jar b/tika-parsers/src/test/resources/test-documents/testJAR_with_HTML.jar new file mode 100644 index 0000000..c1a1ecf Binary files /dev/null and b/tika-parsers/src/test/resources/test-documents/testJAR_with_HTML.jar differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testJAR_with_PEHDR.jar ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testJAR_with_PEHDR.jar b/tika-parsers/src/test/resources/test-documents/testJAR_with_PEHDR.jar new file mode 100644 index 0000000..1cc1bfb Binary files /dev/null and b/tika-parsers/src/test/resources/test-documents/testJAR_with_PEHDR.jar differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testJAVAPROPS.properties ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testJAVAPROPS.properties b/tika-parsers/src/test/resources/test-documents/testJAVAPROPS.properties new file mode 100644 index 0000000..aa85928 --- /dev/null +++ b/tika-parsers/src/test/resources/test-documents/testJAVAPROPS.properties @@ -0,0 +1,22 @@ +# 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. +org.apache.tika=great +file.content.detection=often.hard +properties\:files=fun with special characters... + +# Logs please! +log4j.appender.stdout=org.apache.log4j.ConsoleAppender +log4j.appender.stdout.layout=org.apache.log4j.PatternLayout +log4j.appender.stdout.layout.ConversionPattern=%5p [%t] (%F:%L) - %m%n http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testJNILIB.jnilib ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testJNILIB.jnilib b/tika-parsers/src/test/resources/test-documents/testJNILIB.jnilib new file mode 100644 index 0000000..2b10f10 Binary files /dev/null and b/tika-parsers/src/test/resources/test-documents/testJNILIB.jnilib differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testJPEG.jp2 ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testJPEG.jp2 b/tika-parsers/src/test/resources/test-documents/testJPEG.jp2 new file mode 100644 index 0000000..ad74cf3 Binary files /dev/null and b/tika-parsers/src/test/resources/test-documents/testJPEG.jp2 differ http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testJS.js ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testJS.js b/tika-parsers/src/test/resources/test-documents/testJS.js new file mode 100644 index 0000000..c45b97d --- /dev/null +++ b/tika-parsers/src/test/resources/test-documents/testJS.js @@ -0,0 +1,53 @@ +/* + * 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. + */ +function selectProvider(form) { + provider = form.elements['searchProvider'].value; + if (provider == "any") { + if (Math.random() > 0.5) { + provider = "lucid"; + } else { + provider = "sl"; + } + } + if (provider == "lucid") { + form.action = "http://search.lucidimagination.com/p:tika";; + } else if (provider == "sl") { + form.action = "http://search-lucene.com/tika";; + } + days = 90; + date = new Date(); + date.setTime(date.getTime() + (days * 24 * 60 * 60 * 1000)); + expires = "; expires=" + date.toGMTString(); + document.cookie = "searchProvider=" + provider + expires + "; path=/"; +} +function initProvider() { + if (document.cookie.length>0) { + cStart=document.cookie.indexOf("searchProvider="); + if (cStart!=-1) { + cStart=cStart + "searchProvider=".length; + cEnd=document.cookie.indexOf(";", cStart); + if (cEnd==-1) { + cEnd=document.cookie.length; + } + provider = unescape(document.cookie.substring(cStart,cEnd)); + document.forms['searchform'].elements['searchProvider'].value = provider; + } + } + document.forms['searchform'].elements['q'].focus(); +} http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testKML.kml ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testKML.kml b/tika-parsers/src/test/resources/test-documents/testKML.kml new file mode 100644 index 0000000..5f17f62 --- /dev/null +++ b/tika-parsers/src/test/resources/test-documents/testKML.kml @@ -0,0 +1,917 @@ +<?xml version="1.0" encoding="UTF-8"?> +<kml xmlns="http://www.opengis.net/kml/2.2";> + <!-- Provided by Google as part of their KML Documentation --> + <!-- Available at https://developers.google.com/kml/documentation/KML_Samples.kml --> + <Document> + <name>KML Samples</name> + <open>1</open> + <description>Unleash your creativity with the help of these examples!</description> + <Style id="downArrowIcon"> + <IconStyle> + <Icon> + <href>http://maps.google.com/mapfiles/kml/pal4/icon28.png</href> + </Icon> + </IconStyle> + </Style> + <Style id="globeIcon"> + <IconStyle> + <Icon> + <href>http://maps.google.com/mapfiles/kml/pal3/icon19.png</href> + </Icon> + </IconStyle> + <LineStyle> + <width>2</width> + </LineStyle> + </Style> + <Style id="transPurpleLineGreenPoly"> + <LineStyle> + <color>7fff00ff</color> + <width>4</width> + </LineStyle> + <PolyStyle> + <color>7f00ff00</color> + </PolyStyle> + </Style> + <Style id="yellowLineGreenPoly"> + <LineStyle> + <color>7f00ffff</color> + <width>4</width> + </LineStyle> + <PolyStyle> + <color>7f00ff00</color> + </PolyStyle> + </Style> + <Style id="thickBlackLine"> + <LineStyle> + <color>87000000</color> + <width>10</width> + </LineStyle> + </Style> + <Style id="redLineBluePoly"> + <LineStyle> + <color>ff0000ff</color> + </LineStyle> + <PolyStyle> + <color>ffff0000</color> + </PolyStyle> + </Style> + <Style id="blueLineRedPoly"> + <LineStyle> + <color>ffff0000</color> + </LineStyle> + <PolyStyle> + <color>ff0000ff</color> + </PolyStyle> + </Style> + <Style id="transRedPoly"> + <LineStyle> + <width>1.5</width> + </LineStyle> + <PolyStyle> + <color>7d0000ff</color> + </PolyStyle> + </Style> + <Style id="transBluePoly"> + <LineStyle> + <width>1.5</width> + </LineStyle> + <PolyStyle> + <color>7dff0000</color> + </PolyStyle> + </Style> + <Style id="transGreenPoly"> + <LineStyle> + <width>1.5</width> + </LineStyle> + <PolyStyle> + <color>7d00ff00</color> + </PolyStyle> + </Style> + <Style id="transYellowPoly"> + <LineStyle> + <width>1.5</width> + </LineStyle> + <PolyStyle> + <color>7d00ffff</color> + </PolyStyle> + </Style> + <Style id="noDrivingDirections"> + <BalloonStyle> + <text><![CDATA[ + <b>$[name]</b> + <br /><br /> + $[description] + ]]></text> + </BalloonStyle> + </Style> + <Folder> + <name>Placemarks</name> + <description>These are just some of the different kinds of placemarks with + which you can mark your favorite places</description> + <LookAt> + <longitude>-122.0839597145766</longitude> + <latitude>37.42222904525232</latitude> + <altitude>0</altitude> + <heading>-148.4122922628044</heading> + <tilt>40.5575073395506</tilt> + <range>500.6566641072245</range> + </LookAt> + <Placemark> + <name>Simple placemark</name> + <description>Attached to the ground. Intelligently places itself at the + height of the underlying terrain.</description> + <Point> + <coordinates>-122.0822035425683,37.42228990140251,0</coordinates> + </Point> + </Placemark> + <Placemark> + <name>Floating placemark</name> + <visibility>0</visibility> + <description>Floats a defined distance above the ground.</description> + <LookAt> + <longitude>-122.0839597145766</longitude> + <latitude>37.42222904525232</latitude> + <altitude>0</altitude> + <heading>-148.4122922628044</heading> + <tilt>40.5575073395506</tilt> + <range>500.6566641072245</range> + </LookAt> + <styleUrl>#downArrowIcon</styleUrl> + <Point> + <altitudeMode>relativeToGround</altitudeMode> + <coordinates>-122.084075,37.4220033612141,50</coordinates> + </Point> + </Placemark> + <Placemark> + <name>Extruded placemark</name> + <visibility>0</visibility> + <description>Tethered to the ground by a customizable + "tail"</description> + <LookAt> + <longitude>-122.0845787421525</longitude> + <latitude>37.42215078737763</latitude> + <altitude>0</altitude> + <heading>-148.4126684946234</heading> + <tilt>40.55750733918048</tilt> + <range>365.2646606980322</range> + </LookAt> + <styleUrl>#globeIcon</styleUrl> + <Point> + <extrude>1</extrude> + <altitudeMode>relativeToGround</altitudeMode> + <coordinates>-122.0857667006183,37.42156927867553,50</coordinates> + </Point> + </Placemark> + </Folder> + <Folder> + <name>Styles and Markup</name> + <visibility>0</visibility> + <description>With KML it is easy to create rich, descriptive markup to + annotate and enrich your placemarks</description> + <LookAt> + <longitude>-122.0845787422371</longitude> + <latitude>37.42215078726837</latitude> + <altitude>0</altitude> + <heading>-148.4126777488172</heading> + <tilt>40.55750733930874</tilt> + <range>365.2646826292919</range> + </LookAt> + <styleUrl>#noDrivingDirections</styleUrl> + <Document> + <name>Highlighted Icon</name> + <visibility>0</visibility> + <description>Place your mouse over the icon to see it display the new + icon</description> + <LookAt> + <longitude>-122.0856552124024</longitude> + <latitude>37.4224281311035</latitude> + <altitude>0</altitude> + <heading>0</heading> + <tilt>0</tilt> + <range>265.8520424250024</range> + </LookAt> + <Style id="highlightPlacemark"> + <IconStyle> + <Icon> + <href>http://maps.google.com/mapfiles/kml/paddle/red-stars.png</href> + </Icon> + </IconStyle> + </Style> + <Style id="normalPlacemark"> + <IconStyle> + <Icon> + <href>http://maps.google.com/mapfiles/kml/paddle/wht-blank.png</href> + </Icon> + </IconStyle> + </Style> + <StyleMap id="exampleStyleMap"> + <Pair> + <key>normal</key> + <styleUrl>#normalPlacemark</styleUrl> + </Pair> + <Pair> + <key>highlight</key> + <styleUrl>#highlightPlacemark</styleUrl> + </Pair> + </StyleMap> + <Placemark> + <name>Roll over this icon</name> + <visibility>0</visibility> + <styleUrl>#exampleStyleMap</styleUrl> + <Point> + <coordinates>-122.0856545755255,37.42243077405461,0</coordinates> + </Point> + </Placemark> + </Document> + <Placemark> + <name>Descriptive HTML</name> + <visibility>0</visibility> + <description><![CDATA[Click on the blue link!<br><br> +Placemark descriptions can be enriched by using many standard HTML tags.<br> +For example: +<hr> +Styles:<br> +<i>Italics</i>, +<b>Bold</b>, +<u>Underlined</u>, +<s>Strike Out</s>, +subscript<sub>subscript</sub>, +superscript<sup>superscript</sup>, +<big>Big</big>, +<small>Small</small>, +<tt>Typewriter</tt>, +<em>Emphasized</em>, +<strong>Strong</strong>, +<code>Code</code> +<hr> +Fonts:<br> +<font color="red">red by name</font>, +<font color="#408010">leaf green by hexadecimal RGB</font> +<br> +<font size=1>size 1</font>, +<font size=2>size 2</font>, +<font size=3>size 3</font>, +<font size=4>size 4</font>, +<font size=5>size 5</font>, +<font size=6>size 6</font>, +<font size=7>size 7</font> +<br> +<font face=times>Times</font>, +<font face=verdana>Verdana</font>, +<font face=arial>Arial</font><br> +<hr> +Links: +<br> +<a href="http://earth.google.com/";>Google Earth!</a> +<br> + or: Check out our website at www.google.com +<hr> +Alignment:<br> +<p align=left>left</p> +<p align=center>center</p> +<p align=right>right</p> +<hr> +Ordered Lists:<br> +<ol><li>First</li><li>Second</li><li>Third</li></ol> +<ol type="a"><li>First</li><li>Second</li><li>Third</li></ol> +<ol type="A"><li>First</li><li>Second</li><li>Third</li></ol> +<hr> +Unordered Lists:<br> +<ul><li>A</li><li>B</li><li>C</li></ul> +<ul type="circle"><li>A</li><li>B</li><li>C</li></ul> +<ul type="square"><li>A</li><li>B</li><li>C</li></ul> +<hr> +Definitions:<br> +<dl> +<dt>Google:</dt><dd>The best thing since sliced bread</dd> +</dl> +<hr> +Centered:<br><center> +Time present and time past<br> +Are both perhaps present in time future,<br> +And time future contained in time past.<br> +If all time is eternally present<br> +All time is unredeemable.<br> +</center> +<hr> +Block Quote: +<br> +<blockquote> +We shall not cease from exploration<br> +And the end of all our exploring<br> +Will be to arrive where we started<br> +And know the place for the first time.<br> +<i>-- T.S. Eliot</i> +</blockquote> +<br> +<hr> +Headings:<br> +<h1>Header 1</h1> +<h2>Header 2</h2> +<h3>Header 3</h3> +<h3>Header 4</h4> +<h3>Header 5</h5> +<hr> +Images:<br> +<i>Remote image</i><br> +<img src="//developers.google.com/kml/documentation/images/googleSample.png"><br> +<i>Scaled image</i><br> +<img src="//developers.google.com/kml/documentation/images/googleSample.png" width=100><br> +<hr> +Simple Tables:<br> +<table border="1" padding="1"> +<tr><td>1</td><td>2</td><td>3</td><td>4</td><td>5</td></tr> +<tr><td>a</td><td>b</td><td>c</td><td>d</td><td>e</td></tr> +</table> +<br> +[Did you notice that double-clicking on the placemark doesn't cause the viewer to take you anywhere? This is because it is possible to directly author a "placeless placemark". If you look at the code for this example, you will see that it has neither a point coordinate nor a LookAt element.]]]></description> + </Placemark> + </Folder> + <Folder> + <name>Ground Overlays</name> + <visibility>0</visibility> + <description>Examples of ground overlays</description> + <GroundOverlay> + <name>Large-scale overlay on terrain</name> + <visibility>0</visibility> + <description>Overlay shows Mount Etna erupting on July 13th, 2001.</description> + <LookAt> + <longitude>15.02468937557116</longitude> + <latitude>37.67395167941667</latitude> + <altitude>0</altitude> + <heading>-16.5581842842829</heading> + <tilt>58.31228652890705</tilt> + <range>30350.36838438907</range> + </LookAt> + <Icon> + <href>http://developers.google.com/kml/documentation/images/etna.jpg</href> + </Icon> + <LatLonBox> + <north>37.91904192681665</north> + <south>37.46543388598137</south> + <east>15.35832653742206</east> + <west>14.60128369746704</west> + <rotation>-0.1556640799496235</rotation> + </LatLonBox> + </GroundOverlay> + </Folder> + <Folder> + <name>Screen Overlays</name> + <visibility>0</visibility> + <description>Screen overlays have to be authored directly in KML. These + examples illustrate absolute and dynamic positioning in screen space.</description> + <ScreenOverlay> + <name>Simple crosshairs</name> + <visibility>0</visibility> + <description>This screen overlay uses fractional positioning to put the + image in the exact center of the screen</description> + <Icon> + <href>http://developers.google.com/kml/documentation/images/crosshairs.png</href> + </Icon> + <overlayXY x="0.5" y="0.5" xunits="fraction" yunits="fraction"/> + <screenXY x="0.5" y="0.5" xunits="fraction" yunits="fraction"/> + <rotationXY x="0.5" y="0.5" xunits="fraction" yunits="fraction"/> + <size x="0" y="0" xunits="pixels" yunits="pixels"/> + </ScreenOverlay> + <ScreenOverlay> + <name>Absolute Positioning: Top left</name> + <visibility>0</visibility> + <Icon> + <href>http://developers.google.com/kml/documentation/images/top_left.jpg</href> + </Icon> + <overlayXY x="0" y="1" xunits="fraction" yunits="fraction"/> + <screenXY x="0" y="1" xunits="fraction" yunits="fraction"/> + <rotationXY x="0" y="0" xunits="fraction" yunits="fraction"/> + <size x="0" y="0" xunits="fraction" yunits="fraction"/> + </ScreenOverlay> + <ScreenOverlay> + <name>Absolute Positioning: Top right</name> + <visibility>0</visibility> + <Icon> + <href>http://developers.google.com/kml/documentation/images/top_right.jpg</href> + </Icon> + <overlayXY x="1" y="1" xunits="fraction" yunits="fraction"/> + <screenXY x="1" y="1" xunits="fraction" yunits="fraction"/> + <rotationXY x="0" y="0" xunits="fraction" yunits="fraction"/> + <size x="0" y="0" xunits="fraction" yunits="fraction"/> + </ScreenOverlay> + <ScreenOverlay> + <name>Absolute Positioning: Bottom left</name> + <visibility>0</visibility> + <Icon> + <href>http://developers.google.com/kml/documentation/images/bottom_left.jpg</href> + </Icon> + <overlayXY x="0" y="-1" xunits="fraction" yunits="fraction"/> + <screenXY x="0" y="0" xunits="fraction" yunits="fraction"/> + <rotationXY x="0" y="0" xunits="fraction" yunits="fraction"/> + <size x="0" y="0" xunits="fraction" yunits="fraction"/> + </ScreenOverlay> + <ScreenOverlay> + <name>Absolute Positioning: Bottom right</name> + <visibility>0</visibility> + <Icon> + <href>http://developers.google.com/kml/documentation/images/bottom_right.jpg</href> + </Icon> + <overlayXY x="1" y="-1" xunits="fraction" yunits="fraction"/> + <screenXY x="1" y="0" xunits="fraction" yunits="fraction"/> + <rotationXY x="0" y="0" xunits="fraction" yunits="fraction"/> + <size x="0" y="0" xunits="fraction" yunits="fraction"/> + </ScreenOverlay> + <ScreenOverlay> + <name>Dynamic Positioning: Top of screen</name> + <visibility>0</visibility> + <Icon> + <href>http://developers.google.com/kml/documentation/images/dynamic_screenoverlay.jpg</href> + </Icon> + <overlayXY x="0" y="1" xunits="fraction" yunits="fraction"/> + <screenXY x="0" y="1" xunits="fraction" yunits="fraction"/> + <rotationXY x="0" y="0" xunits="fraction" yunits="fraction"/> + <size x="1" y="0.2" xunits="fraction" yunits="fraction"/> + </ScreenOverlay> + <ScreenOverlay> + <name>Dynamic Positioning: Right of screen</name> + <visibility>0</visibility> + <Icon> + <href>http://developers.google.com/kml/documentation/images/dynamic_right.jpg</href> + </Icon> + <overlayXY x="1" y="1" xunits="fraction" yunits="fraction"/> + <screenXY x="1" y="1" xunits="fraction" yunits="fraction"/> + <rotationXY x="0" y="0" xunits="fraction" yunits="fraction"/> + <size x="0" y="1" xunits="fraction" yunits="fraction"/> + </ScreenOverlay> + </Folder> + <Folder> + <name>Paths</name> + <visibility>0</visibility> + <description>Examples of paths. Note that the tessellate tag is by default + set to 0. If you want to create tessellated lines, they must be authored + (or edited) directly in KML.</description> + <Placemark> + <name>Tessellated</name> + <visibility>0</visibility> + <description><![CDATA[If the <tessellate> tag has a value of 1, the line will contour to the underlying terrain]]></description> + <LookAt> + <longitude>-112.0822680013139</longitude> + <latitude>36.09825589333556</latitude> + <altitude>0</altitude> + <heading>103.8120432044965</heading> + <tilt>62.04855796276328</tilt> + <range>2889.145007690472</range> + </LookAt> + <LineString> + <tessellate>1</tessellate> + <coordinates> -112.0814237830345,36.10677870477137,0 + -112.0870267752693,36.0905099328766,0 </coordinates> + </LineString> + </Placemark> + <Placemark> + <name>Untessellated</name> + <visibility>0</visibility> + <description><![CDATA[If the <tessellate> tag has a value of 0, the line follow a simple straight-line path from point to point]]></description> + <LookAt> + <longitude>-112.0822680013139</longitude> + <latitude>36.09825589333556</latitude> + <altitude>0</altitude> + <heading>103.8120432044965</heading> + <tilt>62.04855796276328</tilt> + <range>2889.145007690472</range> + </LookAt> + <LineString> + <tessellate>0</tessellate> + <coordinates> -112.080622229595,36.10673460007995,0 + -112.085242575315,36.09049598612422,0 </coordinates> + </LineString> + </Placemark> + <Placemark> + <name>Absolute</name> + <visibility>0</visibility> + <description>Transparent purple line</description> + <LookAt> + <longitude>-112.2719329043177</longitude> + <latitude>36.08890633450894</latitude> + <altitude>0</altitude> + <heading>-106.8161545998597</heading> + <tilt>44.60763714063257</tilt> + <range>2569.386744398339</range> + </LookAt> + <styleUrl>#transPurpleLineGreenPoly</styleUrl> + <LineString> + <tessellate>1</tessellate> + <altitudeMode>absolute</altitudeMode> + <coordinates> -112.265654928602,36.09447672602546,2357 + -112.2660384528238,36.09342608838671,2357 + -112.2668139013453,36.09251058776881,2357 + -112.2677826834445,36.09189827357996,2357 + -112.2688557510952,36.0913137941187,2357 + -112.2694810717219,36.0903677207521,2357 + -112.2695268555611,36.08932171487285,2357 + -112.2690144567276,36.08850916060472,2357 + -112.2681528815339,36.08753813597956,2357 + -112.2670588176031,36.08682685262568,2357 + -112.2657374587321,36.08646312301303,2357 </coordinates> + </LineString> + </Placemark> + <Placemark> + <name>Absolute Extruded</name> + <visibility>0</visibility> + <description>Transparent green wall with yellow outlines</description> + <LookAt> + <longitude>-112.2643334742529</longitude> + <latitude>36.08563154742419</latitude> + <altitude>0</altitude> + <heading>-125.7518698668815</heading> + <tilt>44.61038665812578</tilt> + <range>4451.842204068102</range> + </LookAt> + <styleUrl>#yellowLineGreenPoly</styleUrl> + <LineString> + <extrude>1</extrude> + <tessellate>1</tessellate> + <altitudeMode>absolute</altitudeMode> + <coordinates> -112.2550785337791,36.07954952145647,2357 + -112.2549277039738,36.08117083492122,2357 + -112.2552505069063,36.08260761307279,2357 + -112.2564540158376,36.08395660588506,2357 + -112.2580238976449,36.08511401044813,2357 + -112.2595218489022,36.08584355239394,2357 + -112.2608216347552,36.08612634548589,2357 + -112.262073428656,36.08626019085147,2357 + -112.2633204928495,36.08621519860091,2357 + -112.2644963846444,36.08627897945274,2357 + -112.2656969554589,36.08649599090644,2357 </coordinates> + </LineString> + </Placemark> + <Placemark> + <name>Relative</name> + <visibility>0</visibility> + <description>Black line (10 pixels wide), height tracks terrain</description> + <LookAt> + <longitude>-112.2580438551384</longitude> + <latitude>36.1072674824385</latitude> + <altitude>0</altitude> + <heading>4.947421249553717</heading> + <tilt>44.61324882043339</tilt> + <range>2927.61105910266</range> + </LookAt> + <styleUrl>#thickBlackLine</styleUrl> + <LineString> + <tessellate>1</tessellate> + <altitudeMode>relativeToGround</altitudeMode> + <coordinates> -112.2532845153347,36.09886943729116,645 + -112.2540466121145,36.09919570465255,645 + -112.254734666947,36.09984998366178,645 + -112.255493345654,36.10051310621746,645 + -112.2563157098468,36.10108441943419,645 + -112.2568033076439,36.10159722088088,645 + -112.257494011321,36.10204323542867,645 + -112.2584106072308,36.10229131995655,645 + -112.2596588987972,36.10240001286358,645 + -112.2610581199487,36.10213176873407,645 + -112.2626285262793,36.10157011437219,645 </coordinates> + </LineString> + </Placemark> + <Placemark> + <name>Relative Extruded</name> + <visibility>0</visibility> + <description>Opaque blue walls with red outline, height tracks terrain</description> + <LookAt> + <longitude>-112.2683594333433</longitude> + <latitude>36.09884362144909</latitude> + <altitude>0</altitude> + <heading>-72.24271551768405</heading> + <tilt>44.60855445139561</tilt> + <range>2184.193522571467</range> + </LookAt> + <styleUrl>#redLineBluePoly</styleUrl> + <LineString> + <extrude>1</extrude> + <tessellate>1</tessellate> + <altitudeMode>relativeToGround</altitudeMode> + <coordinates> -112.2656634181359,36.09445214722695,630 + -112.2652238941097,36.09520916122063,630 + -112.2645079986395,36.09580763864907,630 + -112.2638827428817,36.09628572284063,630 + -112.2635746835406,36.09679275951239,630 + -112.2635711822407,36.09740038871899,630 + -112.2640296531825,36.09804913435539,630 + -112.264327720538,36.09880337400301,630 + -112.2642436562271,36.09963644790288,630 + -112.2639148687042,36.10055381117246,630 + -112.2626894973474,36.10149062823369,630 </coordinates> + </LineString> + </Placemark> + </Folder> + <Folder> + <name>Polygons</name> + <visibility>0</visibility> + <description>Examples of polygon shapes</description> + <Folder> + <name>Google Campus</name> + <visibility>0</visibility> + <description>A collection showing how easy it is to create 3-dimensional + buildings</description> + <LookAt> + <longitude>-122.084120030116</longitude> + <latitude>37.42174011925477</latitude> + <altitude>0</altitude> + <heading>-34.82469740081282</heading> + <tilt>53.454348562403</tilt> + <range>276.7870053764046</range> + </LookAt> + <Placemark> + <name>Building 40</name> + <visibility>0</visibility> + <styleUrl>#transRedPoly</styleUrl> + <Polygon> + <extrude>1</extrude> + <altitudeMode>relativeToGround</altitudeMode> + <outerBoundaryIs> + <LinearRing> + <coordinates> -122.0848938459612,37.42257124044786,17 + -122.0849580979198,37.42211922626856,17 + -122.0847469573047,37.42207183952619,17 + -122.0845725380962,37.42209006729676,17 + -122.0845954886723,37.42215932700895,17 + -122.0838521118269,37.42227278564371,17 + -122.083792243335,37.42203539112084,17 + -122.0835076656616,37.42209006957106,17 + -122.0834709464152,37.42200987395161,17 + -122.0831221085748,37.4221046494946,17 + 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</outerBoundaryIs> + </Polygon> + </Placemark> + <Placemark> + <name>Building 43</name> + <visibility>0</visibility> + <styleUrl>#transYellowPoly</styleUrl> + <Polygon> + <extrude>1</extrude> + <altitudeMode>relativeToGround</altitudeMode> + <outerBoundaryIs> + <LinearRing> + <coordinates> -122.0844371128284,37.42177253003091,19 + -122.0845118855746,37.42191111542896,19 + -122.0850470999805,37.42178755121535,19 + -122.0850719913391,37.42143663023161,19 + -122.084916406232,37.42137237822116,19 + -122.0842193868167,37.42137237801626,19 + -122.08421938659,37.42147617161496,19 + -122.0838086419991,37.4214613409357,19 + -122.0837899728564,37.42131306410796,19 + -122.0832796534698,37.42129328840593,19 + -122.0832609819207,37.42139213944298,19 + -122.0829373621737,37.42137236399876,19 + -122.0829062425667,37.42151569778871,19 + -122.0828502269665,37.42176282576465,19 + -122.0829435788635,37.42176776969635,19 + -122.083217411188,37.42179248552686,19 + -122.0835970430103,37.4217480074456,19 + 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+ -77.05315536854791,38.87053267794386,100 + -77.05552622493516,38.868757801256,100 + -77.05844056290393,38.86996206506943,100 + -77.05788457660967,38.87253259892824,100 </coordinates> + </LinearRing> + </outerBoundaryIs> + <innerBoundaryIs> + <LinearRing> + <coordinates> -77.05668055019126,38.87154239798456,100 + -77.05542625960818,38.87167890344077,100 + -77.05485125901024,38.87076535397792,100 + -77.05577677433152,38.87008686581446,100 + -77.05691162017543,38.87054446963351,100 + -77.05668055019126,38.87154239798456,100 </coordinates> + </LinearRing> + </innerBoundaryIs> + </Polygon> + </Placemark> + </Folder> + <Folder> + <name>Absolute and Relative</name> + <visibility>0</visibility> + <description>Four structures whose roofs meet exactly. 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CN=XXXX/OU=XX/OU=XXXX/O=XXX/C=XX; + flags=44; name=ForwardedFrom +X-Notes-Item: Thu, 4 Oct 2012 13:01:56 +0200; + type=400; name=ForwardedDate +X-Notes-Item: Thu, 4 Oct 2012 13:02:39 +0200; + type=400; name=OriginalModTime +X-Notes-Item: .; + name=$StorageTo +X-Notes-Item: 62AEA923:7CEE804A-C1257A8D:003C970D; + type=4; name=$Orig +X-Notes-Item: 2031619; + name=MIMEMailHeaderCharset +MIME-Version: 1.0 +X-Mailer: Lotus Notes Release 8.5.3 September 15, 2011 +Message-ID: <OF62AEA923.7CEE804A-ONC1257A8D.003C970D-C1257A8D.003CAB24@LocalDomain> +Date: Thu, 4 Oct 2012 13:02:39 +0200 +X-Notes-Item: 0; + name=MAILOPTIONS +X-Notes-Item: 1; + name=SaveOptions +X-Notes-Item: Memo; + name=Form +From: [email protected] +X-Notes-Item: CN=XXXX/OU=XX/OU=XXXX/O=XXX/C=XX; + name=AltFrom +X-Notes-Item: StdNotesLtr25; + name=Logo +X-Notes-Item: StdNotesLtr25; + name=dLogo +X-Notes-Item: True; + name=useApplet +X-Notes-Item: 1; + name=DefaultMailSaveOptions +X-Notes-Item: ; + name=Query_String 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http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testMATLAB.m ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testMATLAB.m b/tika-parsers/src/test/resources/test-documents/testMATLAB.m new file mode 100644 index 0000000..60871f7 --- /dev/null +++ b/tika-parsers/src/test/resources/test-documents/testMATLAB.m @@ -0,0 +1,4 @@ +function helloworld +fprintf('Hello, World!\n') +disp('Hello, World!'); +end http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testMATLAB_barcast.m ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testMATLAB_barcast.m b/tika-parsers/src/test/resources/test-documents/testMATLAB_barcast.m new file mode 100644 index 0000000..5cad76d --- /dev/null +++ b/tika-parsers/src/test/resources/test-documents/testMATLAB_barcast.m @@ -0,0 +1,383 @@ +%% CONTROL CODE FOR FULLY BAYESIAN SPATIO-TEMPORAL TEMPERATURE RECONSTRUCTION +%EVERYTHING IS MODULAR TO ALLOW FOR EASY DEBUGGING AND ADAPTATION +% _vNewModel_Oct08: change the formalism to reflect new model (Beta_1 now +% normal). Allows for multiple proxies +clear all; close all; +%SET MATLAB'S CURRENT DIRECTORY TO HERE. +% set the priors and the inital values for the MCMC sampler +Prior_pars_vNewModel +Initial_par_vals_vNewModel +%% Set the seed of the random number generators +randn('state', sum((1000+600)*clock)) +rand('state', sum((1000+800)*clock)) + +%% load the data +cd TestData +load BARCAST_INPUT_vNewMeth1 +%break it apart +Locs=BARCAST_INPUT.Master_Locs; +N_Locs=length(Locs(:,1)); %Number of locations: +timeline=[BARCAST_INPUT.Data_timeline(1)-1, BARCAST_INPUT.Data_timeline]; +N_Times=length(timeline)-1; %Number of DATA times +loc_areas=BARCAST_INPUT.Areas; +Inds_GridLocs_Central=BARCAST_INPUT.Inds_Central; + +%get the number of proxy types: +N_PT=length(fieldnames(BARCAST_INPUT))-5; + +%stack the three data matrices, one on top of the other +%the first N_Locs ROWS are the Inst, the next N_Locs ROWS the first proxy +%type, the next the third. . . . .. Each column a year. The first +%corresponds to the SECOND entry in timeline. +Data_ALL=BARCAST_INPUT.Inst_Data; +for kk=1:1:N_PT + tp=eval(['BARCAST_INPUT.Prox_Data', num2str(kk)]); + Data_ALL=[Data_ALL; tp]; +end + +% % % % All_locs_wInd=BARCAST_INPUT.All_locs_wInd; +% % % % lon_lat_area=BARCAST_INPUT.lon_lat_area; +% % % % DATA_Mat=BARCAST_INPUT.DATA_Mat; +% % % % DATA_Mat_locs=BARCAST_INPUT.DATA_Mat_locs; +% % % % Inds_GridLocs_Central=BARCAST_INPUT.Inds_GridLocs_Central; +% % % % timeline=BARCAST_INPUT.timeline; +% % % % clear BARCAST_INPUT + +%Priors and MH jumping parameters, from Prior_pars_vNewModel +load PRIORS_vNewMeth1 +load MHpars_vNewMeth1 +%Initial values from Initial_par_vals_vNewModel +load INITIAL_VALS_vNewMeth1 + +%The Order of THE SCALAR parameters WILL ALWAYS thus: +%1 = alpha, the AR(1) coefficient +%2 = mu, the constant par in the linear mean of the AR(1) process +%3 = sigma2, the partial sill in the spatial covariance matrix +%4 = phi, the range parameter in the spatial covariance matrix +%5 = tau2_I, the Inst measurement error +%6 = tau2_P, the measurement error, first PROX type +%7 = Beta_1, the scaling par in the first P observation equation +%8 = Beta_0, the additive par in the first P observation equation +%and, if there is second proxy type +%9 = tau2_P_2, the measurement error, second PROX type +%10 = Beta_1, the scaling par in the second P observation equation +%11 = Beta_0, the additive par in the second P observation equation +%and, if there is third proxy type . . . . + +%A NOTE ON GAMMA NOTATION. WE USE THE NOTATION OF Gelman et al, "Bayesian +%Data Analysis", WHERE GAMMA PARAMETERS ALPHA, BETA)==(SHAPE, INVERSE SCALE). +%THE RANDRAW.M CODE USES (A,B)==(SHAPE, SCALE), AND THE CALL IS RANDRAW('GAMMA', [M,B,A], SAMPLESIZE), +%WHERE M IS THE LOCATION (NOT NEEDED). SO IN THE NOTATION OF GELMAN ET AT, THE CALL IS +%RANDRAW('GAMMA', [0,1/BETA,ALPHA], SAMPLESIZE). +%For example, +%RANDRAW('GAMMA', [0,1/PRIORS.sigma2(2),PRIORS.sigma2(1)], 1), AND ETC. + +%switch back tot he main directory +cd .. +%% SET a few parameters +%Number of iterations of the complete sampler +Sampler_Its=2000; + +%Number of times to update only the temperature array before beginning to +%update the other parameters +pre_Sampler_Its=500; + + +%% Areal weights vector for averaging the temperatures at each year +%note that some of the elments of the temeprature are given 0 weight - +%outside the prediction bounds. This is based on an input of the area of +%each gridbox +SpaceWeight=loc_areas/sum(loc_areas); +%and for the central region/region of interest +Areas_Central=zeros(1,N_Locs); +Areas_Central(Inds_GridLocs_Central)=loc_areas(Inds_GridLocs_Central); +SpaceWeight_Central=Areas_Central/sum(Areas_Central); + +%(In some applications, the goal might be to estimate the block average +%over a subset of the locations in the reconstruction. For example, the +%goal might be to reconstruct temperatures in Maine, but proxy records from +%NH are incldued in the analysis, as they help to constrain temperatures in +%Maine. SO some of the weights are, in this case, set to zero). + + +%% CALCULATE FIXED QUANTITIES (DO NOT DEPEND ON UNKOWN PARAMETERS) + +%The matrix of distances between every possible pair of points, (I,P,R) +All_DistMat=EarthDistances(Locs); + +%The H(t) selection matrix. +%Basically, H(t) tells us which Inst and prox +%locations have measurements for a given year. So: define H(t) for each +%year as an indicator vector, and thus HH a matrix such that each column is +%the indicator vector for that year. In other words, this is the complete +%indicator matrix for the presence of data:: +%1=YES Measurement; +%0=NO Measurement +%Simply a ZERO wherever there is a NaN in Data_ALL, and a ONE whereever +%this is a value +HH_SelectMat=ones(size(Data_ALL))-isnan(Data_ALL); + +%The total number of Inst/Prox Observations are needed for several +%conditional posteriors, and can be calculated from the HH_SelectMat: +M_InstProx=NaN(1+N_PT,1); +%vectot: first the total number of inst obsm then the total number of each +%prox type, in order. +%Inst: +M_InstProx(1)=sum(sum(HH_SelectMat(1:1:N_Locs, :))); +%Prox: +for kk=1:1:N_PT + M_InstProx(kk+1)=sum(sum(HH_SelectMat(kk*N_Locs+1:1:(kk+1)*N_Locs, :))); +end + +%% Set the initial values of the Field matrix and Current Parameter Vector +% These will be updated and then saved at each iteration of the sampler. +% They are initially filled with the values from INITIAL_VALS. +% Paramter/field values at each step of the gibbs sampler are taken from +% these objects, and new draws override the current entries. This ensures +% that each step of the Gibbs sampler is ALWAYS using the most recent set of ALL +% parameters, without having to deal with +/-1 indices. + +%Array of the estimated true temperature values, set to the initial values: +Temperature_MCMC_Sampler=INITIAL_VALS.Temperature; +%Order: All I, P with locs common to I, Rest of the P, R. +%In other words, ordered the same as InstProx_locs, then with Rand_locs +%added on +%note that +%[Inst_locs; Prox_locs] = InstProx_locs([Inst_inds,Prox_inds],:) +%SO: Temperature_MCMC_Sampler([Inst_inds,Prox_inds], KK) extracts the +%elements that can be compared to the corresponding time of DATA_Mat + +% Current values of the scalar parameters +INITIAL_SCALAR_VALS=rmfield(INITIAL_VALS, 'Temperature'); +CURRENT_PARS=cell2mat(struct2cell(INITIAL_SCALAR_VALS)); + +% OR LOAD TRUE VALUES - FOR TESTING +% load TestData\Pars_TRUE +% CURRENT_PARS=Pars_TRUE'; +% +% load TestData\TrueTemps_v1 +% Temperature_MCMC_Sampler=Temperature_Matrix; + +%% DEFINE EMPTY MATRICES that will be filled with the sampler +%DEFINE the empty parameter matrix: +N_Pars=length(CURRENT_PARS); +Paramters_MCMC_Samples=NaN(N_Pars, Sampler_Its); +%The empty matrix of the samples of the blockaverage timeseries: +BlockAve_MCMC_Samples=NaN(N_Times+1, pre_Sampler_Its+Sampler_Its); +%and the central/target portion +BlockAve_Central_MCMC_Samples=NaN(N_Times+1, pre_Sampler_Its+Sampler_Its); +%NOTE the initial values of the parameters, field, and block averages will +%NOT be saved. So the first item in all matrices/arrays are the results +%after the first iteration of the sampler + +%IN this case, as the amount of data is small, we are able to deal +%with the whole array of space time draws. In applications with larger +%data, this is not possible (memory overflow). +Temperature_ARRAY=NaN(N_Locs, N_Times+1, pre_Sampler_Its+Sampler_Its); + + +%% CALCULATE PARAMETER DEPENDENT QUANTITIES +%that are used several times in the sampler +% +%The idea: calculate the quantities with the initial parameter values, then +%update as soon as possible, leaving the variablle name the same +% +%calculate the initial spatial correlation matrix, and its inverse +%these are needed several times. +%AS SOON as phi is updated, this is updated, ensuring that the +%correlation matrix and its inverse are always up to date, regardless of +%the order of the sampling below. +CURRENT_spatial_corr_mat=exp(-CURRENT_PARS(4)*All_DistMat); +CURRENT_inv_spatial_corr_mat=inv(CURRENT_spatial_corr_mat); + +%% To speed up the code +%1. Find the UNIQUE missing data patterns, number them. +%2. Index each year by the missing data pattern. +%3. For each missing data pattern, calculate the inverse and square root of +%the conditional posterior covariance of a T_k, and stack them +%4. Rewrite the T_k_Updater to simply call these matrices. +%This reduces the number of matrix inversions for each FULL iteration of +%the sampler to the number of UNIQUE data patterns, and reduces the number +%for the pre iterations to 2. + +U_Patterns=unique(HH_SelectMat', 'rows'); +%create an index vector that gices, for each year, the number of the +%corresponding pattern in U_Patterns +%Basically - HH_SelectMat can be represented by U_Patterns and this index vector: +Pattern_by_Year=NaN(N_Times,1); +for kk=1:1:length(U_Patterns(:,1)); + dummy=ismember(HH_SelectMat', U_Patterns(kk,:), 'rows'); + Pattern_by_Year(find(dummy==1))=kk; +end + +%Input the CURRENT_PARS vector and etc into Covariance_Patterns, which returns two 3d +%arrays: the covariance amtrix for each missing data patter (for +%the mean calculation) and the squre root of the covariance matrix (to make +%the draw). +[CURRENT_COV_ARRAY, CURRENT_SQRT_COV_ARRAY]=Covariance_Patterns(U_Patterns, CURRENT_PARS, CURRENT_inv_spatial_corr_mat, N_Locs, N_PT); + + + +%% In an attempt to speed convergence of the variance paramters +% we will uptate only the true temperature array for a number of +% iterations, and then add the updating of the other parameters. This is to +% prevent the model from requiring large variances to fit the observations +% to the data. +%timertimer=NaN; +for samples=1:1:pre_Sampler_Its + tic; + %% SAMPLE T(0): True temperature the year before the first measurement. + Temperature_MCMC_Sampler(:,1)=T_0_Updater_vNM(PRIORS.T_0, Temperature_MCMC_Sampler(:,2), CURRENT_PARS, CURRENT_inv_spatial_corr_mat); + + %% SAMPLE T(1), . . ., T(last-1). Recall that the T matrix starts at time=0, while the W matrix starts at time=1 + for Tm=2:1:N_Times + Temperature_MCMC_Sampler(:,Tm)=T_k_Updater_vFAST(Temperature_MCMC_Sampler(:, Tm-1), Temperature_MCMC_Sampler(:,Tm+1), Data_ALL(:,Tm-1), CURRENT_PARS, U_Patterns(Pattern_by_Year(Tm-1),:),CURRENT_COV_ARRAY(:,:,Pattern_by_Year(Tm-1)),CURRENT_SQRT_COV_ARRAY(:,:,Pattern_by_Year(Tm-1)),CURRENT_inv_spatial_corr_mat, N_Locs, N_PT); + end + %This is a SLOW step, because it is actually N_Times-1 steps. . . + + %% SAMPLE T(last) + Temperature_MCMC_Sampler(:,N_Times+1)=T_last_Updater_vNM(Temperature_MCMC_Sampler(:, N_Times), Data_ALL(:,N_Times), HH_SelectMat(:, N_Times), CURRENT_PARS, CURRENT_inv_spatial_corr_mat, N_Locs, N_PT); + + %% Fill in the next iteration of the BlockAve_MCMC_Samples matrix: + BlockAve_MCMC_Samples(:,samples)=(SpaceWeight*Temperature_MCMC_Sampler)'; + BlockAve_Central_MCMC_Samples(:, samples)=(SpaceWeight_Central*Temperature_MCMC_Sampler)'; + %Fill in the next slice of the space-time field draw array + Temperature_ARRAY(:,:,samples)=Temperature_MCMC_Sampler; + + %save the current draw of the space-time temp matrix + %save(['TestData\FieldDraws\Temp_MCMC_vNM_Test_PreStep' num2str(samples)],'Temperature_MCMC_Sampler'); + + timertimer=toc; + disp(['Working on pre-MCMC iteration ', num2str(samples), ' of ', num2str(pre_Sampler_Its), '. Last iteration took ', num2str(timertimer), ' seconds.']) + +end + +timertimer=NaN; +%% RUN THE SAMPLER +for samples=1:1:Sampler_Its + + tic + %% SAMPLE T(0): True temperature the year before the first measurement. + Temperature_MCMC_Sampler(:,1)=T_0_Updater_vNM(PRIORS.T_0, Temperature_MCMC_Sampler(:,2), CURRENT_PARS, CURRENT_inv_spatial_corr_mat); + + %% SAMPLE T(1), . . ., T(last-1). Recall that the T matrix starts at time=0, while the W matrix starts at time=1 + for Tm=2:1:N_Times + Temperature_MCMC_Sampler(:,Tm)=T_k_Updater_vFAST(Temperature_MCMC_Sampler(:, Tm-1), Temperature_MCMC_Sampler(:,Tm+1), Data_ALL(:,Tm-1), CURRENT_PARS, U_Patterns(Pattern_by_Year(Tm-1),:),CURRENT_COV_ARRAY(:,:,Pattern_by_Year(Tm-1)),CURRENT_SQRT_COV_ARRAY(:,:,Pattern_by_Year(Tm-1)),CURRENT_inv_spatial_corr_mat, N_Locs, N_PT); + end + %This is a SLOW step, because it is actually N_Times-1 steps. . . + + %% SAMPLE T(last) + Temperature_MCMC_Sampler(:,N_Times+1)=T_last_Updater_vNM(Temperature_MCMC_Sampler(:, N_Times), Data_ALL(:,N_Times), HH_SelectMat(:, N_Times), CURRENT_PARS, CURRENT_inv_spatial_corr_mat, N_Locs, N_PT); + + %% SAMPLE AR(1) coefficient + New_Alpha=Alpha_Updater_vNM(PRIORS.alpha, Temperature_MCMC_Sampler, CURRENT_PARS, CURRENT_inv_spatial_corr_mat); + CURRENT_PARS(1)=New_Alpha; + clear New_Alpha + + %% SAMPLE AR(1) mean constant parameter, mu: + New_mu=Mu_Updater_vNM(PRIORS.mu, Temperature_MCMC_Sampler, CURRENT_PARS, CURRENT_inv_spatial_corr_mat); + CURRENT_PARS(2)=New_mu; + clear New_AR_mean_mu + + %% SAMPLE Partial Sill of the spatial covaraince martrix + New_sigma2=Sigma2_Updater_vNM(PRIORS.sigma2, Temperature_MCMC_Sampler, CURRENT_PARS, CURRENT_inv_spatial_corr_mat); + %ARTIFICIALLY put a cieling at, say, 5. + %CHECK a posterior that, one the algorithm has converged, ALL draws are + %lower than this. + CURRENT_PARS(3)=min(5, New_sigma2); + clear New_sigma2 + + %% SAMPLE Range Parameter of the spatial covaraince martrix (METROPOLIS) + % This also updates the spatial corelation matrix and its inverse + [New_phi, New_scm, New_iscm]=Phi_Updater_vNM(PRIORS.phi, Temperature_MCMC_Sampler, CURRENT_PARS, CURRENT_spatial_corr_mat, CURRENT_inv_spatial_corr_mat, All_DistMat, MHpars.log_phi); + CURRENT_PARS(4)=New_phi; + CURRENT_spatial_corr_mat=New_scm; + CURRENT_inv_spatial_corr_mat=New_iscm; + clear New_phi New_iscm New_scm + + %% SAMPLE Instrumental measurement error + New_tau2_I=tau2_I_Updater_vNM(PRIORS.tau2_I, Temperature_MCMC_Sampler, Data_ALL, N_Locs, M_InstProx(1)); + %ARTIFICIALLY put a cieling at, say, 5. + %CHECK a posterior that, one the algorithm has converged, ALL draws are + %lower than this. + CURRENT_PARS(5)=min(5, New_tau2_I); + clear New_tau2_I + + + + %% NEED TO LOOP THE SAMPLING OF THESE THREE PARAMETERS + for Pnum=1:1:N_PT + %curtail the CURRENT_PARS vector to only include the pars for one + %proxy type at a time: + CURRENT_PARS_Brief=[CURRENT_PARS(1:1:5); CURRENT_PARS([6:1:8]+(Pnum-1)*3)]; + %Similarily exract each type of proxy data: + Prox_Data_Brief=eval(['BARCAST_INPUT.Prox_Data', num2str(Pnum)]); + + %% SAMPLE Proxy measurement error + New_tau2_P=tau2_P_Updater_vNM(eval(['PRIORS.tau2_P_', num2str(Pnum)]), Temperature_MCMC_Sampler, Prox_Data_Brief, CURRENT_PARS_Brief, M_InstProx(Pnum+1)); + %ARTIFICIALLY put a cieling at, say, 50. + %CHECK a posterior that, one the algorithm has converged, ALL draws are + %lower than this. + CURRENT_PARS_Brief(6)=min(10, New_tau2_P); + clear New_tau2_P + + %% SAMPLE Scaling constant in the proxy observation equation + New_beta_1=Beta_1_Updater_vNM(eval(['PRIORS.Beta_1_', num2str(Pnum)]), Temperature_MCMC_Sampler, Prox_Data_Brief, CURRENT_PARS_Brief); + CURRENT_PARS_Brief(7)=New_beta_1; + clear New_beta_1 + + %% SAMPLE Additive constant in the proxy observation equation + New_Beta_0=Beta_0_Updater_vNM(eval(['PRIORS.Beta_0_', num2str(Pnum)]), Temperature_MCMC_Sampler, Prox_Data_Brief, CURRENT_PARS_Brief, M_InstProx(Pnum+1)); + CURRENT_PARS_Brief(8)=New_Beta_0; + clear New_Beta_0 + + CURRENT_PARS([6:1:8]+(Pnum-1)*3)=CURRENT_PARS_Brief(6:1:8); + + end + + %% UPDATE the covariance arrays used in the T_k_Updater step + [CURRENT_COV_ARRAY, CURRENT_SQRT_COV_ARRAY]=Covariance_Patterns(U_Patterns, CURRENT_PARS, CURRENT_inv_spatial_corr_mat, N_Locs, N_PT); + + + %% UPDATE THE VARIOUS MATRICES, SAVE CURRENT TEMPERTAURE MATRIX + %update the Paramters_MCMC_Samples matrix: + Paramters_MCMC_Samples(:, samples)=CURRENT_PARS; + %CURRENT_PARS is not cleared: it is, after all, the current parameter + %vector. + + %Fill in the next iteration of the BlockAve_MCMC_Samples matrix: + BlockAve_MCMC_Samples(:, pre_Sampler_Its+samples)=(SpaceWeight*Temperature_MCMC_Sampler)'; + BlockAve_Central_MCMC_Samples(:, pre_Sampler_Its+samples)=(SpaceWeight_Central*Temperature_MCMC_Sampler)'; + + %add the new draw of the space-time temp matrix + Temperature_ARRAY(:,:,pre_Sampler_Its+samples)=Temperature_MCMC_Sampler; + %save the current draw of the space-time temp matrix + %save(['TestData\FieldDraws\Temp_MCMC_vNM_Test_Step' num2str(samples)],'Temperature_MCMC_Sampler'); + + %SAVE the matrix of parameter vector draws and the matrix of block + %average vectors. (This way, even if the code is stopped prematurely, + %we get something) + %cd TestData + %cd FieldDraws + %save TestData\FieldDraws\Paramters_MCMC_Samples_vNM Paramters_MCMC_Samples + %save TestData\FieldDraws\Temperature_ARRAY_vNM Temperature_ARRAY + %save TestData\FieldDraws\BlockAve_MCMC_Samples_vNM BlockAve_MCMC_Samples + %save TestData\FieldDraws\BlockAve_Central_MCMC_Samples_vNM BlockAve_Central_MCMC_Samples + %and back + %cd .. + %cd .. + timertimer=toc; + disp(['Finished MCMC iteration ', num2str(samples), ' of ', num2str(Sampler_Its), '. Last iteration took ', num2str(timertimer), ' seconds.']) +end + +%% SAVE the matrix of parameter vector draws and the matrix of block +%average vectors. +cd TestData +cd FieldDraws + save Paramters_MCMC_Samples_vNM Paramters_MCMC_Samples + save Temperature_ARRAY_vNM Temperature_ARRAY + save BlockAve_MCMC_Samples_vNM BlockAve_MCMC_Samples + save BlockAve_Central_MCMC_Samples_vNM BlockAve_Central_MCMC_Samples +%and back +cd .. +cd .. http://git-wip-us.apache.org/repos/asf/tika/blob/38916f89/tika-parsers/src/test/resources/test-documents/testMATLAB_wtsgaus.m ---------------------------------------------------------------------- diff --git a/tika-parsers/src/test/resources/test-documents/testMATLAB_wtsgaus.m b/tika-parsers/src/test/resources/test-documents/testMATLAB_wtsgaus.m new file mode 100644 index 0000000..f8943f2 --- /dev/null +++ b/tika-parsers/src/test/resources/test-documents/testMATLAB_wtsgaus.m @@ -0,0 +1,52 @@ +function b=wtsgaus(p,N) +% wtsgaus: weights for gaussian filter with specified frequency response +% b=wtsgaus(p,N); +% Last revised 2003-3-14 +% +% Weights for gaussian filter with specified frequency response +% Specify te wavelength for the 0.50 respons, and the length of series, get +% the coefficients, or weights +% +%*** INPUT +% +% p (1 x 1)i period (years) at which filter is to have amp frequency response of 0.5 +% N (1 x 1)i length of the time series (number of observations) +% +%*** OUTPUT +% +% b (1 x n)r computed weights +% +% +%*** REFERENCES +% +% WMO 1966, p. 47 +% +%*** UW FUNCTIONS CALLED -- NONE +%*** TOOLBOXES NEEDED -- stats +% +%*** NOTES +% +% Amplitude of frequency response drops to 0.50 at a wavelength of +% about 6 standard deviations of the appropriate guassian curve +% +% N is used as an input to restict the possible filter size (number of weights) to no larger than the sample length + +if p>N; + error(['Desired 50% period ' num2str(p) ' is greater than the sample length ' int2str(N)]); +end; + + +% Check that period of 50% response at least 5 yr +if p<5; + error('Period of 50% response must be at least 5 yr'); +end; + +sigma=p/6; % Gaussian curve should have this standard deviation + +x=-N:N; +b=normpdf(x/sigma,0,1); +bmax=max(b); +bkeep = b>=0.05*bmax; % keep weights at least 5% as big as central weight +b=b(bkeep); +b=b/sum(b); % force weights to sum to one +
