Gamera XML format (version 2.0)

Last modified: May 11, 2016

Contents

Introduction

The Gamera XML format is used to store sets of small ONEBIT (binary) images. This is most commonly used to store training data for a classifier.

Since these files tend to be quite large, Gamera supports loading and saving of gzipped XML files.

XML format

Below is an informal description on the XML format. A more formal definition is given in the DTD.

Gamera uses Unicode internally to store symbol names, so the XML file can be encoded in most standard encodings that Python can automatically convert to Unicode. (See the Python documentation for the codecs module).

All XML files created directly from Gamera are encoded in UTF-8.

<?xml version="1.0" encoding="utf-8"?>

gamera-database (Toplevel)

At the top level is the gamera-database element. A version must be specified. Note that the version refers to the "Gamera XML file format" version which does not correspond to the version of Gamera. The version documented here is 2.0. Version 1.0 was a weak first attempt and is no longer supported. We plan to make future versions backward and forward compatible whenever possible.

<gamera-database version="2.0">
  ...
</gamera-database>

glyphs

The glyphs element simply contains glyph elements.

<glyphs>
  ...
</glyphs>

glyph

Each glyph element represents a small ONEBIT (binary) image.

It has the following attributes that specify the bounding box, and are directly equivalent to the members on the image object itself: uly, ulx, nrows and ncols.

<glyph uly="242" ulx="1758" nrows="26" ncols="18">
  ...
</glyph>
ids

Each glyph contains an ids element which contains all of the class names that define the glyph. Since some classifiers will return multiple class names with different confidences, ids is actually a set of id elements.

ids has an attribute state that defines how the glyph was classified. It can be one of {UNCLASSIFIED, AUTOMATIC, HEURISTIC, MANUAL}.

Each id element within ids has two attributes:

name
The class name, which is period-delimited by category.
confidence
A confidence value represented how sure the classifier was about the identity of this glyph. The value is in the range 0 (not at all confident) to 1 (very confident).
<ids state="AUTOMATIC">
  <id name="number.three" confidence="1.000000"/>
</ids>
data

Data contains a run-length encoded representation of the image itself. This data is used to reconstruct the image when loading. It consists of decimal numbers separated by whitespace. The numbers alternate between the length of white runs and the length of black runs. Runs "wrap-over" the right side of the image to the next row on the left side of the image. Systems that work on Gamera XML should take care not to modify the data block, as it is very easy to corrupt and there is only minimal error checking upon reloading.

<data>
  6 4 12 9 8 12 5 6 1 7 4 5 3 7 2 6 4 6 2 7 3 6 2 7 3 6 3 6 3 6 3 4 5 6
  4 3 4 7 5 3 2 6 7 11 7 11 8 11 6 5 1 7 2 6 4 6 2 6 4 15 3 14 4 14 4 6
  2 6 3 7 2 15 4 12 7 10 11 3 9 0
</data>
features

The features element contains a set of feature elements, one for each feature function.

Note

When Gamera XML files are loaded into Gamera, the features information is discarded and regenerated. This is so the classifier has complete control over what features are used and how they are used. The feature values are dumped to the XML file only for the benefit of third-party applications that may wish to use the features without using Gamera code itself.

The features element has one attribute, scaling, which is used to define how the features should be scaled (if at all).

Each feature element has one attribute, name, which is the feature function that generated the values. More feature functions can be added by creating plugin methods in the category Features.

The CDATA block of the feature element contains a list of floating point numbers (in decimal) that were generated by the given feature function.

<features scaling="1.0">
  <feature name="area">
    468.0
  </feature>
  <feature name="aspect_ratio">
    0.692307692308
  </feature>
  <feature name="black_area">
    294.0
  </feature>
  <feature name="compactness">
    0.428571428571
  </feature>
  <feature name="moments">
    0.302825261159 0.307856673241 0.0657821501667 0.149170828096
    0.0533051094428 0.008619818861 -0.000427188837948 0.000613411663867
    0.0317229010445
  </feature>
  <feature name="nholes">
    0.944444444444 0.615384615385
  </feature>
  <feature name="nholes_extended">
    3.0 6.0 4.0 2.0 3.0 6.0 4.0 3.0
  </feature>
  <feature name="skeleton_features">
    3.0 10.0 0.206349206349 6.0 4.0 3.0
  </feature>
  <feature name="volume">
    0.628205128205
  </feature>
  <feature name="volume16regions">
    0.485714285714 0.514285714286 0.457142857143 0.8 0.771428571429
    0.685714285714 0.828571428571 0.8 0.657142857143 0.571428571429
    0.714285714286 0.685714285714 0.657142857143 0.885714285714
    0.857142857143 0.771428571429
  </feature>
  <feature name="volume64regions">
    0.0833333333333 0.5 0.5 0.0833333333333 0.0 0.583333333333
    0.916666666667 0.416666666667 0.5 1.0 1.0 0.583333333333 0.25
    0.833333333333 1.0 0.916666666667 0.833333333333 1.0 0.916666666667
    0.833333333333 0.916666666667 1.0 1.0 1.0 0.916666666667 0.5 0.5
    0.333333333333 1.0 0.583333333333 0.416666666667 0.833333333333
    0.833333333333 0.25 0.0 0.5 0.916666666667 0.166666666667
    0.0833333333333 0.833333333333 0.75 0.833333333333 0.666666666667
    0.916666666667 1.0 0.75 0.75 1.0 0.583333333333 1.0 1.0 1.0 1.0 1.0
    1.0 0.75 0.25 0.916666666667 1.0 0.666666666667 0.583333333333 1.0
    1.0 0.416666666667
  </feature>
  <feature name="zernike_moments">
    -10.6511384992 6.48862460298 -29.6215265124 21.4915669267
    -4.95741930842 9.70917594801 -41.1062437889 61.7375776134
    5.72778404882 5.31916863982 -16.2283589874 87.6140952777
    0.148787539745 -2.75048482171 -4.19045628996 74.7653517483
    0.403589004311 -0.403486704972 -4.89682421377 61.1321737136
    -1.01342510763 -0.526430778878 -13.8421959343 63.5845586372
    -0.188701625589 0.697880091555
  </feature>
</features>

symbols

The symbols element contains a set of symbol names. This is used to import/export symbol tables without the expense of loading glyphs.

Each symbol element contains one attribute name which defines a period-delimited class name.

<symbols>
  <symbol name="notehead.half.ledger.middle" />
  <symbol name="dot" />
  <symbol name="clef.bass" />
  <symbol name="accidental.doubleflat" />
  <symbol name="notehead.triangle.hollow" />
  <symbol name="bracket" />
  <symbol name="brace" />
</symbols>

DTD

This is the formal definition of the Gamera XML Format.

<!-- DTD for gamera glyph database files
  11/18/02 Michael Droettboom
-->

<!ELEMENT gamera-database (symbols*,glyphs*)>
<!ATTLIST gamera-database version CDATA #REQUIRED>

<!ELEMENT symbols (symbol*)>

<!ELEMENT symbol EMPTY>
<!ATTLIST symbol name CDATA #REQUIRED>

<!ELEMENT glyphs (glyph*)>

<!ELEMENT glyph (ids,data,features?)>
<!ATTLIST glyph uly CDATA #REQUIRED>
<!ATTLIST glyph ulx CDATA #REQUIRED>
<!ATTLIST glyph nrows CDATA #REQUIRED>
<!ATTLIST glyph ncols CDATA #REQUIRED>

<!ELEMENT ids (id*)>
<!ATTLIST ids state
  (UNCLASSIFIED|HEURISTIC|AUTOMATIC|MANUAL) "UNCLASSIFIED">

<!ELEMENT id EMPTY>
<!ATTLIST id name CDATA "UNKNOWN">
<!ATTLIST id confidence CDATA "1.0">

<!ELEMENT data (#PCDATA)>

<!ELEMENT features (feature*)>
<!ATTLIST features scaling CDATA "1.0">

<!ELEMENT feature (#PCDATA)>
<!ATTLIST feature name CDATA #REQUIRED>

Saving and loading Gamera XML files

The code for saving and loading Gamera XML files is in gamera/gamera_xml.py.

Use the following functions to save and load Gamera XML files:

glyphs_from_xml

glyphs_from_xml (filename, feature_functions = None)

Return a list of glyphs from a Gamera XML file.

glyphs_with_features_from_xml

glyphs_with_features_from_xml (filename, feature_functions = None)

Loads glyphs from a Gamera XML file, and then generates features for all of those glyphs. The set of features can be specified with the feature_functions argument (which defaults to all features).

glyphs_to_xml

glyphs_to_xml (filename, glyphs, with_features = True)

Saves the given list of glyphs to a Gamera XML file.

with_features
When set to True, features generated on the image are saved to the XML file.

strip_features

strip_features (input_filename, output_filename)

Strips the features from a Gamera XML file. Provided mainly to reduce filesizes for files created before saving features was an option.

input_filename
The input Gamera XML filename
output_filename
The output Gamera XML filename