io API#

XML SmartRoot / RootNav / RootSystemTracker reader and writer

MTG writer:

  • Generate same file.

  • Manage an MTG with 2 scales: Plant, RootAxis

  • Manage an MTG with 3 scales: Plant, RootAxis, Segment

Visualisation: 1. PlantGL and Matplotlib 2. Time-series 3. Annotations

class openalea.rsml.io.Annotation(name)[source]#

Bases: object

class openalea.rsml.io.Dumper[source]#

Bases: object

Convert an MTG into RSML format

SubElement(parent, tag, text='', attrib={}, **kwds)[source]#
SubTree(parent, tag, tree)[source]#

recursively add tree to xml parent element

tree is a dictionary, for which a tag child is appended to parent Then recursively add:

  • a subtree for dictionary item

  • an element otherwise with text set to str(item-value)

accession = '{http://www.plantontology.org/xml-dtd/po.dtd}accession'#
dump(graph)[source]#
functions(axis, **props)[source]#

Set the root axis functions

axis is the xml element id of the root axis props ….

geometry(axis, **props)[source]#

Set the root axis geometry elements

axis is the xml element id of the root axis props should contain a suitable ‘geometry’ attribute

TODO: other geometry types?

image(metadata)[source]#

dump image element of metadata

metadata()[source]#
mtg()[source]#

Convert the MTG into a XML tree.

observation_hours(metadata)[source]#

dump observation-hours element of metadata

plant(vid)[source]#
properties(vid, axis)[source]#

set the axis properties

property_definitions(metadata)[source]#

dump property definitions of metadata

root(xml_parent, mtg_vid)[source]#
scene()[source]#
class openalea.rsml.io.Parser[source]#

Bases: object

Read an XML file an convert it into an MTG.

static add_field(elt, my_dict)[source]#

Update the properties in the MTG

annotation(elts, **properties)[source]#

Annotations attached to a part of the MTG.

annotations(elts, **properties)[source]#

Annotations attached to a part of the MTG.

dispatch(elt)[source]#

Call the suitable function to process elt w.r.t to elt.tag

function(elts, **properties)[source]#

A root axis with geometry, functions, properties.

function_definition(elts, **properties)[source]#

A plant with parameters and a recursive structure

functions(elts, **properties)[source]#

A root axis with geometry, functions, properties.

geometry(elts, **properties)[source]#

A root axis - geometry

image(elts, **properties)[source]#

A plant with parameters and a recursive structure.

metadata(elts, **properties)[source]#

Parse image information

parse(filename, debug=False)[source]#
plant(elts, **properties)[source]#

A plant with parameters and a recursive structure.

point(elts, **properties)[source]#
polyline(elts, **properties)[source]#

A root axis - geometry - polyline

properties(elts)[source]#

Update the tooy properties in the MTG

property_definition(elts, **properties)[source]#

A plant with parameters and a recursive structure

property_definitions(elts, **properties)[source]#

A plant with parameters and a recursive structure.

root(elts, **attrib)[source]#

A root axis with geometry, functions, properties

rsml(elts, **properties)[source]#

A RSA with attributes, parameters and a recursive structure.

sample(elt, domain)[source]#
scene(elts, **properties)[source]#

A plant with parameters and a recursive structure.

time_sequence(elts, **properties)[source]#

A plant with parameters and a recursive structure.

openalea.rsml.io.mtg2rsml(g, rsml_file)[source]#

Write continuous mtg g in rsml_file

See also:

Dumper, rsml.continuous

openalea.rsml.io.read_xml_tree(elt)[source]#

return xml tree elt

openalea.rsml.io.rsml2mtg(rsml_graph, debug=False)[source]#

Convert a rsml string, or file, to a MTG.

openalea.rsml.io.str2datetime(str_time)[source]#

convert datetime string to datetime object

Download the source file ../../src/openalea/rsml/io.py.