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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi there,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m having an issue trying to use the GDAL Polygonize feature in QGIS.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">My aim is to clip out or mask the background of some hyperspectral data of some diseased Cocoa leaves for my research masters project. My background up until this project with GIS has been fairly rudimentary GUI use of ArcGIS and QGIS.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">My attempted workflow involves using a k-means classifier to classify the HSI raster files, then convert to vector to edit out background and use result to clip out or mask the background of my HSI data. However, when I run GDAL Polygonize
the output is inverted above the input raster. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’ve tried adding a coordinate projection to the input raster data prior to converting, but this didn’t work.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The input file info is: <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<table class="MsoNormalTable" border="0" cellspacing="0" cellpadding="0" style="background:white;border-collapse:collapse">
<tbody>
<tr>
<td width="142" valign="top" style="width:106.35pt;padding:.75pt 11.25pt .75pt 15.0pt">
<p class="MsoNormal" align="right" style="text-align:right"><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif">CRS<o:p></o:p></span></b></p>
</td>
<td width="630" valign="top" style="width:472.2pt;padding:.75pt .75pt .75pt .75pt;word-wrap: break-word">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">EPSG:4326 - WGS 84 - Geographic</span><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></p>
</td>
</tr>
<tr>
<td width="142" valign="top" style="width:106.35pt;padding:.75pt 11.25pt .75pt 15.0pt;word-wrap: break-word">
<p class="MsoNormal" align="right" style="text-align:right"><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">Extent</span></b><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></b></p>
</td>
<td width="630" valign="top" style="width:472.2pt;padding:.75pt .75pt .75pt .75pt;word-wrap: break-word">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">0.0000000000000000,-696.0000000000000000 : 520.0000000000000000,0.0000000000000000</span><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></p>
</td>
</tr>
<tr>
<td width="142" valign="top" style="width:106.35pt;padding:.75pt 11.25pt .75pt 15.0pt;word-wrap: break-word">
<p class="MsoNormal" align="right" style="text-align:right"><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">Unit</span></b><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></b></p>
</td>
<td width="630" valign="top" style="width:472.2pt;padding:.75pt .75pt .75pt .75pt;word-wrap: break-word">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">degrees</span><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></p>
</td>
</tr>
<tr>
<td width="142" valign="top" style="width:106.35pt;padding:.75pt 11.25pt .75pt 15.0pt;word-wrap: break-word">
<p class="MsoNormal" align="right" style="text-align:right"><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">Width</span></b><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></b></p>
</td>
<td width="630" valign="top" style="width:472.2pt;padding:.75pt .75pt .75pt .75pt;word-wrap: break-word">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">520</span><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></p>
</td>
</tr>
<tr>
<td width="142" valign="top" style="width:106.35pt;padding:.75pt 11.25pt .75pt 15.0pt;word-wrap: break-word">
<p class="MsoNormal" align="right" style="text-align:right"><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">Height</span></b><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></b></p>
</td>
<td width="630" valign="top" style="width:472.2pt;padding:.75pt .75pt .75pt .75pt;word-wrap: break-word">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">696</span><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></p>
</td>
</tr>
<tr>
<td width="142" valign="top" style="width:106.35pt;padding:.75pt 11.25pt .75pt 15.0pt;word-wrap: break-word">
<p class="MsoNormal" align="right" style="text-align:right"><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">Data type</span></b><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></b></p>
</td>
<td width="630" valign="top" style="width:472.2pt;padding:.75pt .75pt .75pt .75pt;word-wrap: break-word">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">Byte - Eight bit unsigned integer</span><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></p>
</td>
</tr>
<tr>
<td width="142" valign="top" style="width:106.35pt;padding:.75pt 11.25pt .75pt 15.0pt;word-wrap: break-word">
<p class="MsoNormal" align="right" style="text-align:right"><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">GDAL Driver
</span></b><b><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></b></p>
</td>
<td width="630" valign="top" style="width:472.2pt;padding:.75pt .75pt .75pt .75pt;word-wrap: break-word">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif;color:black">GTiff</span><span style="font-size:10.0pt;font-family:"Lucida Grande",sans-serif"><o:p></o:p></span></p>
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</table>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">And the output is: <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<table class="MsoNormalTable" border="0" cellpadding="0" style="margin-left:7.5pt">
<tbody>
<tr>
<td style="padding:0cm 11.25pt 0cm 15.0pt">
<p align="right" style="margin:0cm;margin-bottom:.0001pt;text-align:right"><b><span style="color:black">Storage</span></b><o:p></o:p></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm">
<p style="margin:0cm;margin-bottom:.0001pt;-qt-block-indent:0"><span style="color:black">ESRI Shapefile</span><o:p></o:p></p>
</td>
</tr>
<tr>
<td style="padding:0cm 11.25pt 0cm 15.0pt">
<p align="right" style="margin:0cm;margin-bottom:.0001pt;text-align:right;-qt-block-indent:0">
<b><span style="color:black">Comment</span></b><o:p></o:p></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm"></td>
</tr>
<tr>
<td style="padding:0cm 11.25pt 0cm 15.0pt">
<p align="right" style="margin:0cm;margin-bottom:.0001pt;text-align:right;-qt-block-indent:0">
<b><span style="color:black">Encoding</span></b><o:p></o:p></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm">
<p style="margin:0cm;margin-bottom:.0001pt;-qt-block-indent:0"><span style="color:black">macintosh</span><o:p></o:p></p>
</td>
</tr>
<tr>
<td style="padding:0cm 11.25pt 0cm 15.0pt">
<p align="right" style="margin:0cm;margin-bottom:.0001pt;text-align:right;-qt-block-indent:0">
<b><span style="color:black">Geometry</span></b><o:p></o:p></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm">
<p style="margin:0cm;margin-bottom:.0001pt;-qt-block-indent:0"><span style="color:black">Polygon (MultiPolygon)</span><o:p></o:p></p>
</td>
</tr>
<tr>
<td style="padding:0cm 11.25pt 0cm 15.0pt">
<p align="right" style="margin:0cm;margin-bottom:.0001pt;text-align:right;-qt-block-indent:0">
<b><span style="color:black">CRS</span></b><o:p></o:p></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm">
<p style="margin:0cm;margin-bottom:.0001pt;-qt-block-indent:0"><span style="color:black">EPSG:4326 - WGS 84 - Geographic</span><o:p></o:p></p>
</td>
</tr>
<tr>
<td style="padding:0cm 11.25pt 0cm 15.0pt">
<p align="right" style="margin:0cm;margin-bottom:.0001pt;text-align:right;-qt-block-indent:0">
<b><span style="color:black">Extent</span></b><o:p></o:p></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm">
<p style="margin:0cm;margin-bottom:.0001pt;-qt-block-indent:0"><span style="color:black">0.0000000000000000,0.0000000000000000 : 520.0000000000000000,696.0000000000000000</span><o:p></o:p></p>
</td>
</tr>
<tr>
<td style="padding:0cm 11.25pt 0cm 15.0pt">
<p align="right" style="margin:0cm;margin-bottom:.0001pt;text-align:right;-qt-block-indent:0">
<b><span style="color:black">Unit</span></b><o:p></o:p></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm">
<p style="margin:0cm;margin-bottom:.0001pt;-qt-block-indent:0"><span style="color:black">degrees</span><o:p></o:p></p>
</td>
</tr>
<tr>
<td style="padding:0cm 11.25pt 0cm 15.0pt">
<p align="right" style="margin:0cm;margin-bottom:.0001pt;text-align:right;-qt-block-indent:0">
<b><span style="color:black">Feature count</span></b><o:p></o:p></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm">
<p style="margin:0cm;margin-bottom:.0001pt;-qt-block-indent:0"><span style="color:black">761</span><o:p></o:p></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The log from processing reads:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p style="margin:0cm;margin-bottom:.0001pt"><span style="color:white">2020-04-05T13:21:51 INFO </span>gdal_polygonize.py /Users/user/Documents/qgis_test/kmns/c1a_kmns.tif /Users/user/Documents/qgis_test/c1a_vctr.shp -b 1 -f "ESRI Shapefile" c1a_vctr
Class<o:p></o:p></p>
<p class="MsoNormal" style="-qt-block-indent:0"><span style="color:white">2020-04-05T13:21:51 INFO </span>GDAL execution console output<br>
0...10...20...30...40...50...60...70...80...90...Creating output /Users/user/Documents/qgis_test/c1a_vctr.shp of format ESRI Shapefile.<br>
<br>
100 - done.<o:p></o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">I’ve read a few forum posts on some similar issues, but solutions seem aimed at raster projections. It’s clear the extents are inversed, but I can’t figure out how to change them.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Any input would be gratefully received,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Richard<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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