Merge pull request #8 from petermr/dev

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petermr · May 18, 2015 · 70459ce · 70459ce
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diff --git a/docs/CREATING_CM.md b/docs/CREATING_CM.md
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+# CREATING CM directories
+
+*** BY FAR THE SAFEST WAY IS TO USE QUICKSCRAPE ***
+
+Any other method is likely to lead to fies out of sync unless you are acreful with what you are doing.
+However it can be sometimes useful to create CMDirs from single files.
+This documentation may not have been thoroughly checked.
+
+## Input
+
+For a command: 
+
+``` norma -i foo/bar/a12345.suffix -o plugh/xyzzy```
+
+the system will create a CMDir of the form:
+
+``` plugh/xyzzy/a12345```
+
+It will then use ```suffix``` to create either reserved files (e.g. ```fulltext.xml```) in the CMDir or reserved subdirectories
+of the form:
+
+``` plugh/xyzzy/a12345/image```
+
+to hold the images. As there can be several images (e.g.  ```plugh/xyzzy/a12345.png``` ) we use the given names, such as:
+
+``` plugh/xyzzy/a12345/image/a12345.png```
+
+This is verbose and also leads to a separate CMDir for each image.
+
+## File types
+
+The following suffixes are supported:
+
+### Single reserved files
+
+The CMDir is generated from the ```-o mydir``` parameter and the input baseNames ```(FilenameUtile.getBaseName())```
+
+```mydir/bar``` is the CMDir.
+
+```foo/bar.xml``` is copied to ```mydir/bar/fulltext.xml```
+```foo/bar.html``` is copied to ```mydir/bar/fulltext.html```
+```foo/bar.pdf``` is copied to ```mydir/bar/fulltext.pdf```
+```foo/bar.epub``` is copied to ```mydir/bar/fulltext.epub```
+```foo/bar.txt``` is copied to ```mydir/bar/fulltext.txt```
+
+### Image files
+
+```foo/bar.png``` is copied to ```mydir/bar/image/bar.png```
+
+Analogous copies for:
+ ```gif```, ```jpg```, ```tif```
+
+### Supplemental Data files
+
+```foo/bar.doc``` is copied to ```mydir/bar/supplement/bar.png```
+
+Analogous copies for:
+ ```docx```, ```csv```, ```tex```, ```ppt```, ```pptx```, ...
+
+### SVG Data files
+
+```foo/bar.svg``` is copied to ```mydir/bar/svg/bar.svg```
+
+
+
diff --git a/examples/hocr-tesseract-ijsem-140.zip b/examples/hocr-tesseract-ijsem-140.zip
diff --git a/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000026-0-000.pbm2.png b/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000026-0-000.pbm2.png
diff --git a/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000026-0-000.pbm2.png.hocr b/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000026-0-000.pbm2.png.hocr
diff --git a/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000109-0-000.pbm.png b/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000109-0-000.pbm.png
diff --git a/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000109-0-000.pbm.png.hocr b/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000109-0-000.pbm.png.hocr
diff --git a/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000117-0-000.pbm.png b/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000117-0-000.pbm.png
diff --git a/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000117-0-000.pbm.png.hocr b/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000117-0-000.pbm.png.hocr
diff --git a/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000158-0-000.pbm.png b/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000158-0-000.pbm.png
diff --git a/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000158-0-000.pbm.png.hocr b/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000158-0-000.pbm.png.hocr
diff --git a/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000174-0-000.pbm.png b/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000174-0-000.pbm.png
diff --git a/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000174-0-000.pbm.png.hocr b/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000174-0-000.pbm.png.hocr
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+    "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+ <head>
+  <title>
+</title>
+<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
+  <meta name='ocr-system' content='tesseract 3.03' />
+  <meta name='ocr-capabilities' content='ocr_page ocr_carea ocr_par ocr_line ocrx_word'/>
+</head>
+<body>
+  <div class='ocr_page' id='page_1' title='image "ijs.0.000174-0-000.pbm.png"; bbox 0 0 994 516; ppageno 0'>
+   <div class='ocr_carea' id='block_1_1' title="bbox 273 4 951 34">
+    <p class='ocr_par' dir='ltr' id='par_1_1' title="bbox 273 4 951 34">
+     <span class='ocr_line' id='line_1_1' title="bbox 273 4 951 34; baseline 0 -7"><span class='ocrx_word' id='word_1_1' title='bbox 273 4 448 34; x_wconf 78' lang='eng' dir='ltr'><em>‘Rhodoplanes</em></span> <span class='ocrx_word' id='word_1_2' title='bbox 458 4 616 34; x_wconf 77' lang='eng' dir='ltr'><em>cryptolactis’</em></span> <span class='ocrx_word' id='word_1_3' title='bbox 633 5 701 27; x_wconf 91' lang='eng' dir='ltr'><em>DSM</em></span> <span class='ocrx_word' id='word_1_4' title='bbox 711 5 773 27; x_wconf 84' lang='eng'><em>9987</em></span> <span class='ocrx_word' id='word_1_5' title='bbox 791 5 951 33; x_wconf 88' lang='eng' dir='ltr'>(AB087718)</span> 
+     </span>
+    </p>
+   </div>
+   <div class='ocr_carea' id='block_1_2' title="bbox 0 9 324 504">
+    <p class='ocr_par' dir='ltr' id='par_1_2' title="bbox 0 9 324 504">
+     <span class='ocr_line' id='line_1_2' title="bbox 165 9 272 51; baseline 0 -1"><span class='ocrx_word' id='word_1_6' title='bbox 165 9 272 51; x_wconf 95' lang='eng' dir='ltr'><em>  </em></span> 
+     </span>
+     <span class='ocr_line' id='line_1_3' title="bbox 138 51 272 120; baseline 0 -4"><span class='ocrx_word' id='word_1_7' title='bbox 138 51 272 120; x_wconf 95' lang='eng' dir='ltr'><em>  </em></span> 
+     </span>
+     <span class='ocr_line' id='line_1_4' title="bbox 63 120 251 187; baseline 0.027 -4"><span class='ocrx_word' id='word_1_8' title='bbox 63 120 251 187; x_wconf 95' lang='eng' dir='ltr'><em>  </em></span> 
+     </span>
+     <span class='ocr_line' id='line_1_5' title="bbox 0 187 303 321; baseline 0.02 -70"><span class='ocrx_word' id='word_1_9' title='bbox 0 187 303 321; x_wconf 95' lang='eng' dir='ltr'><em>   </em></span> 
+     </span>
+     <span class='ocr_line' id='line_1_6' title="bbox 0 321 324 461; baseline 0 0"><span class='ocrx_word' id='word_1_10' title='bbox 0 321 324 461; x_wconf 95' lang='eng' dir='ltr'><em>  </em></span> 
+     </span>
+     <span class='ocr_line' id='line_1_7' title="bbox 0 461 275 504; baseline 0 12"><span class='ocrx_word' id='word_1_11' title='bbox 0 461 275 504; x_wconf 95' lang='eng' dir='ltr'><em> </em></span> 
+     </span>
+    </p>
+   </div>
+   <div class='ocr_carea' id='block_1_3' title="bbox 244 67 990 445">
+    <p class='ocr_par' dir='ltr' id='par_1_3' title="bbox 244 67 844 168">
+     <span class='ocr_line' id='line_1_8' title="bbox 288 67 844 100; baseline 0.002 -7"><span class='ocrx_word' id='word_1_12' title='bbox 288 70 455 100; x_wconf 81' lang='eng' dir='ltr'><em>Rhodoplanes</em></span> <span class='ocrx_word' id='word_1_13' title='bbox 465 78 547 93; x_wconf 77' lang='eng' dir='ltr'><em>roseus</em></span> <span class='ocrx_word' id='word_1_14' title='bbox 557 72 624 94; x_wconf 92' lang='eng' dir='ltr'><em>DSM</em></span> <span class='ocrx_word' id='word_1_15' title='bbox 635 67 710 94; x_wconf 86' lang='eng' dir='ltr'><em>5909T</em></span> <span class='ocrx_word' id='word_1_16' title='bbox 721 70 844 100; x_wconf 83' lang='eng' dir='ltr'>(D25313)</span> 
+     </span>
+     <span class='ocr_line' id='line_1_9' title="bbox 244 136 758 168; baseline 0 -6"><span class='ocrx_word' id='word_1_17' title='bbox 244 139 410 168; x_wconf 80' lang='eng' dir='ltr'><em>Rhodoplanes</em></span> <span class='ocrx_word' id='word_1_18' title='bbox 420 139 517 168; x_wconf 83' lang='eng' dir='ltr'><em>elegans</em></span> <span class='ocrx_word' id='word_1_19' title='bbox 527 136 628 162; x_wconf 80' lang='eng' dir='ltr'><em>A8130T</em></span> <span class='ocrx_word' id='word_1_20' title='bbox 635 139 728 167; x_wconf 88' lang='eng' dir='ltr'>(D2531</span> <span class='ocrx_word' id='word_1_21' title='bbox 737 139 758 168; x_wconf 94' lang='eng'><em>1)</em></span> 
+     </span>
+    </p>
+
+    <p class='ocr_par' dir='ltr' id='par_1_4' title="bbox 263 203 670 235">
+     <span class='ocr_line' id='line_1_10' title="bbox 263 203 670 235; baseline 0.002 -6"><span class='ocrx_word' id='word_1_22' title='bbox 263 207 345 230; x_wconf 82' lang='eng' dir='ltr'><strong>Strain</strong></span> <span class='ocrx_word' id='word_1_23' title='bbox 356 203 499 230; x_wconf 86' lang='eng' dir='ltr'><em>TUT3530T</em></span> <span class='ocrx_word' id='word_1_24' title='bbox 509 207 670 235; x_wconf 87' lang='eng' dir='ltr'><strong>(AB087717)</strong></span> 
+     </span>
+    </p>
+
+    <p class='ocr_par' dir='ltr' id='par_1_5' title="bbox 281 273 990 445">
+     <span class='ocr_line' id='line_1_11' title="bbox 303 273 889 305; baseline 0.002 -7"><span class='ocrx_word' id='word_1_25' title='bbox 303 276 473 298; x_wconf 77' lang='eng' dir='ltr'><em>Blastochlaris</em></span> <span class='ocrx_word' id='word_1_26' title='bbox 484 276 563 298; x_wconf 82' lang='eng' dir='ltr'><em>viridis</em></span> <span class='ocrx_word' id='word_1_27' title='bbox 573 277 657 299; x_wconf 91' lang='eng' dir='ltr'>ATCC</span> <span class='ocrx_word' id='word_1_28' title='bbox 671 273 889 305; x_wconf 71' lang='eng' dir='ltr'>19567T(D25314)</span> 
+     </span>
+     <span class='ocr_line' id='line_1_12' title="bbox 336 343 937 375; baseline 0.002 -7"><span class='ocrx_word' id='word_1_29' title='bbox 336 345 506 368; x_wconf 80' lang='eng' dir='ltr'><em>Blastochloris</em></span> <span class='ocrx_word' id='word_1_30' title='bbox 516 345 659 374; x_wconf 76' lang='eng' dir='ltr'><em>sulfoviridis</em></span> <span class='ocrx_word' id='word_1_31' title='bbox 671 346 736 369; x_wconf 88' lang='eng' dir='ltr'><em>DSM</em></span> <span class='ocrx_word' id='word_1_32' title='bbox 748 343 807 369; x_wconf 84' lang='eng' dir='ltr'><em>729T</em></span> <span class='ocrx_word' id='word_1_33' title='bbox 815 346 937 375; x_wconf 88' lang='eng' dir='ltr'>(D86514)</span> 
+     </span>
+     <span class='ocr_line' id='line_1_13' title="bbox 281 412 990 445; baseline 0 -7"><span class='ocrx_word' id='word_1_34' title='bbox 281 415 538 444; x_wconf 79' lang='eng' dir='ltr'><em>Rhodopseudomonas</em></span> <span class='ocrx_word' id='word_1_35' title='bbox 545 415 659 444; x_wconf 81' lang='eng' dir='ltr'><em>palustris</em></span> <span class='ocrx_word' id='word_1_36' title='bbox 674 416 758 439; x_wconf 90' lang='eng' dir='ltr'>ATCC</span> <span class='ocrx_word' id='word_1_37' title='bbox 771 412 990 445; x_wconf 75' lang='eng' dir='ltr'>17001T(D25312)</span> 
+     </span>
+    </p>
+   </div>
+   <div class='ocr_carea' id='block_1_4' title="bbox 293 481 956 513">
+    <p class='ocr_par' dir='ltr' id='par_1_6' title="bbox 293 481 956 513">
+     <span class='ocr_line' id='line_1_14' title="bbox 293 481 956 513; baseline 0 -6"><span class='ocrx_word' id='word_1_38' title='bbox 293 484 465 507; x_wconf 76' lang='eng' dir='ltr'><em>Rhodoblastus</em></span> <span class='ocrx_word' id='word_1_39' title='bbox 476 484 625 513; x_wconf 74' lang='eng' dir='ltr'><em>acidophilus</em></span> <span class='ocrx_word' id='word_1_40' title='bbox 634 485 718 508; x_wconf 88' lang='eng' dir='ltr'>ATCC</span> <span class='ocrx_word' id='word_1_41' title='bbox 728 481 820 508; x_wconf 90' lang='eng' dir='ltr'><em>25092T</em></span> <span class='ocrx_word' id='word_1_42' title='bbox 828 484 956 513; x_wconf 85' lang='eng' dir='ltr'>(M34128)</span> 
+     </span>
+    </p>
+   </div>
+  </div>
+ </body>
+</html>
diff --git a/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000257-0-000.pbm.png b/examples/hocr-tesseract-ijsem-140/sourceimages/ijs.0.000257-0-000.pbm.png