STYLE: Add "Segment Statistics" module documentation

Docs/user_guide/module_segmentstatistics.rst

@@ -0,0 +1,70 @@
+==================
+Segment statistics
+==================
+
+This is a module for the calculation of statistics related to the structure of segmentations, such as volume, surface area, mean intensity, and various other metrics for each segment.
+
+Labelmap statistics
+-------------------
+
+Labelmap statistics are calculated using the binary labelmap representation of the segment.
+
+- Voxel count: the number of voxels in the segment
+- Volume mm\ :sup:`3`: the volume of the segment in mm\ :sup:`3`
+- Volume cm\ :sup:`3`: the volume of the segment in cm\ :sup:`3`
+- Centroid: the center of mass of the segment in RAS coordinates
+- Feret diameter: the diameter of a sphere that can encompass the entire segment
+- Surface area mm\ :sup:`2`: the volume of the segment in mm\ :sup:`2`
+- Roundness: the roundness of the segment. Calculated from ratio of the area of the sphere calculated from the feret diameter by the actual area. Value of 1 represents a spherical structure. (http://hdl.handle.net/1926/584)
+- Flatness: the flatness of the segment. Calculated from square root of the ratio of the second smallest principal moment by the smallest. Value of 0 represents a flat structure. (http://hdl.handle.net/1926/584)
+- Elongation: the elongation of the segment. Calculated from square root of the ratio of the second largest principal moment by the second smallest. (http://hdl.handle.net/1926/584)
+- Principal moments: the principal moments of inertia for each axes of the segment
+- Principal axes: the principal axes of rotation of the segment
+- Oriented bounding box: the non-axis aligned bounding box that encompasses the segment
+
+Scalar volume statistics
+------------------------
+
+- Voxel count: the number of voxels in the segment
+- Volume mm\ :sup:`3`: the volume of the segment in mm\ :sup:`3`
+- Volume cm\ :sup:`3`: the volume of the segment in cm\ :sup:`3`
+- Minimum: the minimum scalar value behind the segment
+- Maximum: the maximum scalar value behind the segment
+- Mean: the mean scalar value behind the segment
+- Median: the median scalar value behind the segment
+- Standard deviation: the standard deviation of scalar values behind the segment
+
+Closed surface statistics
+-------------------------
+
+- Surface area mm\ :sup:`2`: the volume of the segment in mm\ :sup:`2`
+- Volume mm\ :sup:`3`: the volume of the segment in mm\ :sup:`3`
+- Volume cm\ :sup:`3`: the volume of the segment in cm\ :sup:`3`
+
+Related Modules
+---------------
+
+- :ref:`module_segmentations` module allows changing visualization options, exporting/importing segments to/from other nodes (models, labelmap volumes), and moving or copying segments between segmentation nodes.
+- :ref:`module_segment_editor` module for segmentation of volumes using tools for editing (paint, draw, erase, level tracing, grow from seeds, threshold, etc.)
+
+Information for Developers
+--------------------------
+
+See examples for calculating statistics from your own modules in the `Slicer script repository <https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Quantifying_segments>`_.
+Additional plugins for computation of other statistical measurements may be registered by subclassing `SegmentStatisticsPluginBase.py <https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/SegmentStatistics/SegmentStatisticsPlugins/SegmentStatisticsPluginBase.py>`_, and registering the plugin with SegmentStatisticsLogic.
+
+Contributors
+------------
+
+- Contributors: Csaba Pinter (PerkLab, Queen's University), Andras Lasso (PerkLab, Queen's University), Christian Bauer (University of Iowa), Steve Pieper (Isomics Inc.)
+- Contact: Csaba Pinter, csaba.pinter@queensu.ca; Andras Lasso, lasso@queensu.ca
+
+Acknowledgements
+----------------
+
+This module is partly funded by an Applied Cancer Research Unit of Cancer Care Ontario with funds provided by the Ministry of Health and Long-Term Care and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.
+The work is part of the `National Alliance for Medical Image Computing <http://www.na-mic.org/>`_ (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.
+
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+|  |isomics_logo|  |  |namic_logo|  |  |nac_logo|  |  |ge_logo|  |
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Docs/user_guide/modules.rst

@@ -62,6 +62,7 @@ Segmentation
 - :doc:`module_emsegment`
 - :doc:`module_emsegmentquick`
 - :doc:`module_segmenteditor`
+- :doc:`module_segmentstatistics`
 - :doc:`module_simpleregiongrowingsegmentation`
 - Specialized: