@log_call
def selected_data(self):
if self.index_cursor in range(-self.n_data, self.n_data):
debug("retriving data at index=%s" %self.index_cursor)
return self.parent.request_data(Hdf5DataSpec, index=self.index_cursor)
else:
warning('Index cursor is set to wrong value.')
return None
def request_data(self, spec, **kwargs):
if spec is Hdf5DataSpec:
return self.selected_data
return None
register_pipeline_node(SequentialHdf5SelectorNode)
class SequentialHdf5SelectorInspector(InspectorPage):
"""Sequential hdf5 selector inspector.
"""
def __init__(self, *args, **kwargs):
"""Initializer.
"""
InspectorPage.__init__(self, *args, **kwargs)
n_data_label = wx.StaticText(self, -1, 'Number of data')
n_data = wx.TextCtrl(self, -1, "%s" %self.target.n_data, style=wx.TE_READONLY)
cursor_label = wx.StaticText(self, -1, 'Current Index')
cursor_spin = wx.SpinCtrl(self, -1, min=0, max=self.target.n_data, initial=self.target.index_cursor)
self.Bind(wx.EVT_SPINCTRL, self.OnCursorSpin)
data_label = wx.StaticText(self, -1, 'Selected data')
return None
species_section = self.hdf5_data.get('/species', None)
if species_section is None:
return None
return dict((id, dict(name=name, radius=radius, D=D))
for id, name, radius, D in species_section.value)
@property
def world_size(self):
"""Property getter for world size.
"""
if self.data_section is None:
return None
attrs = self.data_section.attrs
if bool(attrs) == False:
return None
return attrs.get('world_size', None)
def request_data(spec, **kwargs):
"""Provides data for children.
"""
if spec is ParticlesSpec:
return self.particles
elif spec is SpeciesTableSpec:
return self.species_table
elif spec is WorldSizeSpec:
return self.world_size
register_pipeline_node(ParticleConstructorNode)
"""
# examine cache
if self._particle_data:
pass
else: # self._particle_data is None
uri = self.parent.request_data(UriSpec)
if isinstance(uri, str):
parsed = urlparse(uri)
fullpath = parsed.netloc+parsed.path
if os.path.exists(fullpath):
pass #TBDDDDDDD
# self._particle_data is left None if something wrong in loading data.
return self._particle_data
def request_data(self, spec, **params):
"""Provides particle data.
"""
if spec is ParticleDataSpec:
return self.particle_data # this may be None if datasource is not valid.
return None
# Finally, register node to registry.
register_pipeline_node(SimpleParticleLoaderNode)
# You may write doctests, which runs on executing this module.
if __name__=='__main__':
# TBD
from doctest import testmod, ELLIPSIS
testmod(optionflags=ELLIPSIS)
warning('Failed to open %s: %s', fullpath, str(e))
pass
# self._particle_space is left None if something wrong in loading data.
return self._particle_space
@log_call
def request_data(self, spec, **kwargs):
"""Provides particle data.
"""
if spec == NumberOfItemsSpec:
debug('Serving NumberOfItemsSpec')
if self.fetch_particle_space(**kwargs) is None:
return 0
else:
return 1
elif spec == ParticleSpaceSpec:
debug('Serving ParticleSpaceSpec')
# this may be None if datasource is not valid.
return self.fetch_particle_space(**kwargs)
return None
register_pipeline_node(ParticleCSVLoaderNode)
if __name__=='__main__':
# TBD
from doctest import testmod, ELLIPSIS
testmod(optionflags = ELLIPSIS)
return
# otherwise: reset node cursor
self.node_cursor = '/'
debug('%s' % self.hdf5_data)
@property
@log_call
def hdf5_data(self):
"""Property getter for had5_data
"""
if self.parent:
return self.parent.request_data(Hdf5DataSpec)
debug('No parent.')
register_pipeline_node(SimpleHdf5TreeVisualizerNode)
class Hdf5TreeCtrl(TreeCtrlPlus):
"""Tree ctrl for simple hdf5 tree visualizer.
"""
def __init__(self, *args, **kwargs):
"""Initializer.
"""
style = kwargs.pop(
'style',
0) | wx.TR_NO_BUTTONS | wx.TR_HAS_BUTTONS | wx.SUNKEN_BORDER
kwargs['style'] = style
self.selection_callback = kwargs.pop('selection_callback', None)
TreeCtrlPlus.__init__(self, *args, **kwargs)
self._hdf5_file = None
if self.hdf5_data.get(self.node_cursor):
return
# otherwise: reset node cursor
self.node_cursor = '/'
debug('%s' %self.hdf5_data)
@property
@log_call
def hdf5_data(self):
"""Property getter for had5_data
"""
if self.parent:
return self.parent.request_data(Hdf5DataSpec)
debug('No parent.')
register_pipeline_node(SimpleHdf5TreeVisualizerNode)
class Hdf5TreeCtrl(TreeCtrlPlus):
"""Tree ctrl for simple hdf5 tree visualizer.
"""
def __init__(self, *args, **kwargs):
"""Initializer.
"""
style = kwargs.pop('style', 0)|wx.TR_NO_BUTTONS|wx.TR_HAS_BUTTONS|wx.SUNKEN_BORDER
kwargs['style'] = style
self.selection_callback = kwargs.pop('selection_callback', None)
TreeCtrlPlus.__init__(self, *args, **kwargs)
self._hdf5_file = None
def get_hdf5_file(self):
if particle_space is not None:
self.sid_list = particle_space.species
@log_call
def request_data(self, spec, **kwargs):
"""Provides particle data.
"""
if spec == NumberOfItemsSpec:
debug('Serving NumberOfItemsSpec')
return self.parent.request_data(NumberOfItemsSpec, **kwargs)
elif spec == ParticleSpaceSpec:
debug('Serving ParticleSpaceSpec')
return self.fetch_particle_space(**kwargs)
return None
register_pipeline_node(ParticleSpaceFilterNode)
class ParticleSpaceFilterInspector(InspectorPage):
"""Inspector page for ParticleSpaceFilter.
"""
# PROP_NAMES = ['filename', 'mode', 'driver', 'libver', 'userblock_size',
# 'name', 'id', 'ref', 'attrs']
def __init__(self, *args, **kwargs):
"""Initializer.
"""
InspectorPage.__init__(self, *args, **kwargs)
widgets = []
self.max_num_entry = wx.TextCtrl(
self, wx.ID_ANY, "10000", style=wx.TE_PROCESS_ENTER)
warning('Invalid timestamp/particles')
species_section = chunk.get('/species')
if species_section == None:
warning('No species table for index=%d' % (i))
continue
# iterate for species...
for id, name, radius, dvalue in species_section:
# count number of particles
n_particles = sum(particles['species_id'] == id)
bin_ = populations.setdefault(name, [])
bin_.append((ts, n_particles))
print populations
return populations
register_pipeline_node(TimecourseVisualizerNode)
class TimecourseVisualizer(VisualizerPage):
"""Simple timecourse visualizer.
"""
def __init__(self, *args, **kwargs):
"""
"""
VisualizerPage.__init__(self, *args, **kwargs)
figure = Figure()
figure.add_subplot('111')
canvas = FigureCanvasWxAgg(self, -1, figure)
self.sizer.Add(canvas, 1, wx.ALL | wx.EXPAND, 5)
self.figure = figure
self.canvas = canvas
if uri is None:
return
debug('hdf5 data uri=%s' % uri)
try:
parsed = urlparse(uri)
fullpath = parsed.netloc + parsed.path
if os.path.exists(fullpath):
self._hdf5_data = File(fullpath)
except IOError, e:
warning('Failed to open %s: %s', fullpath, str(e))
pass
# self._hdf5_data is left None if something wrong in loading data.
return self._hdf5_data
@log_call
def request_data(self, spec, **kwargs):
"""Provides particle data.
"""
if spec == Hdf5DataSpec:
debug('Serving Hdf5DataSpec')
return self.hdf5_data # this may be None if datasource is not valid.
return None
register_pipeline_node(SimpleHdf5LoaderNode)
if __name__ == '__main__':
# TBD
from doctest import testmod, ELLIPSIS
testmod(optionflags=ELLIPSIS)
elif spec == Hdf5DataSpec:
index = kwargs.get('index', 0)
data = self.cache.get(index, None)
if data is None:
path = self.bundle.get_path_at(index)
if not (path is None):
try:
data = File(path, mode='r')
self.cache[index] = data
except IOError:
pass
return data
return None
register_pipeline_node(Hdf5BundleLoaderNode)
class Hdf5BundleLoaderInspector(InspectorPage):
"""Sequential hdf5 selector inspector.
"""
def __init__(self, *args, **kwargs):
"""Initializer.
"""
InspectorPage.__init__(self, *args, **kwargs)
glob_pattern_label = wx.StaticText(self, -1, 'Glob pattern')
glob_pattern = wx.TextCtrl(self, -1, "%s" % self.target.glob_pattern)
self.Bind(wx.EVT_TEXT, self.OnGlobPatternText, glob_pattern)
self.sizer.Add(glob_pattern_label, 0, wx.ALL | wx.EXPAND, 5)
self.sizer.Add(glob_pattern, 0, wx.ALL | wx.EXPAND, 5)
self.glob_pattern = glob_pattern
def selected_data(self):
if self.index_cursor in range(-self.n_data, self.n_data):
debug("retriving data at index=%s" % self.index_cursor)
return self.parent.request_data(Hdf5DataSpec,
index=self.index_cursor)
else:
warning('Index cursor is set to wrong value.')
return None
def request_data(self, spec, **kwargs):
if spec is Hdf5DataSpec:
return self.selected_data
return None
register_pipeline_node(SequentialHdf5SelectorNode)
class SequentialHdf5SelectorInspector(InspectorPage):
"""Sequential hdf5 selector inspector.
"""
def __init__(self, *args, **kwargs):
"""Initializer.
"""
InspectorPage.__init__(self, *args, **kwargs)
n_data_label = wx.StaticText(self, -1, 'Number of data')
n_data = wx.TextCtrl(self,
-1,
"%s" % self.target.n_data,
style=wx.TE_READONLY)
cursor_label = wx.StaticText(self, -1, 'Current Index')
return
debug('hdf5 data uri=%s' % uri)
try:
parsed = urlparse(uri)
fullpath = parsed.netloc+parsed.path
if os.path.exists(fullpath):
self._hdf5_data = File(fullpath)
except IOError, e:
warning('Failed to open %s: %s', fullpath, str(e))
pass
# self._hdf5_data is left None if something wrong in loading data.
return self._hdf5_data
@log_call
def request_data(self, spec, **kwargs):
"""Provides particle data.
"""
if spec==Hdf5DataSpec:
debug('Serving Hdf5DataSpec')
return self.hdf5_data # this may be None if datasource is not valid.
return None
register_pipeline_node(SimpleHdf5LoaderNode)
if __name__=='__main__':
# TBD
from doctest import testmod, ELLIPSIS
testmod(optionflags=ELLIPSIS)
except IOError, e:
warning('Failed to open %s: %s', fullpath, str(e))
pass
# self._particle_space is left None if something wrong in loading data.
return self._particle_space
@log_call
def request_data(self, spec, **kwargs):
"""Provides particle data.
"""
if spec == NumberOfItemsSpec:
debug('Serving NumberOfItemsSpec')
if self.fetch_particle_space(**kwargs) is None:
return 0
else:
return 1
elif spec == ParticleSpaceSpec:
debug('Serving ParticleSpaceSpec')
# this may be None if datasource is not valid.
return self.fetch_particle_space(**kwargs)
return None
register_pipeline_node(ParticleCSVLoaderNode)
if __name__ == '__main__':
# TBD
from doctest import testmod, ELLIPSIS
testmod(optionflags=ELLIPSIS)
pass
# self._particle_space is left None if something wrong in loading data.
return self._particle_space
@log_call
def request_data(self, spec, **kwargs):
"""Provides particle data.
"""
if spec == NumberOfItemsSpec:
debug('Serving NumberOfItemsSpec')
ps = self.fetch_particle_space(**kwargs)
if ps is None:
return 0
else:
return ps.getNumberOfItems()
elif spec == ParticleSpaceSpec:
debug('Serving ParticleSpaceSpec')
# this may be None if datasource is not valid.
ps = self.fetch_particle_space(**kwargs)
return ps
return None
register_pipeline_node(ParticleSpatiocyteLoaderNode)
if __name__ == '__main__':
# TBD
from doctest import testmod, ELLIPSIS
testmod(optionflags=ELLIPSIS)
warning("Invalid timestamp/particles")
species_section = chunk.get("/species")
if species_section == None:
warning("No species table for index=%d" % (i))
continue
# iterate for species...
for id, name, radius, dvalue in species_section:
# count number of particles
n_particles = sum(particles["species_id"] == id)
bin_ = populations.setdefault(name, [])
bin_.append((ts, n_particles))
print populations
return populations
register_pipeline_node(TimecourseVisualizerNode)
class TimecourseVisualizer(VisualizerPage):
"""Simple timecourse visualizer.
"""
def __init__(self, *args, **kwargs):
"""
"""
VisualizerPage.__init__(self, *args, **kwargs)
figure = Figure()
figure.add_subplot("111")
canvas = FigureCanvasWxAgg(self, -1, figure)
self.sizer.Add(canvas, 1, wx.ALL | wx.EXPAND, 5)
self.figure = figure
species_section = self.hdf5_data.get('/species', None)
if species_section is None:
return None
return dict(
(id, dict(name=name, radius=radius, D=D))
for id, name, radius, D in species_section.value)
@property
def world_size(self):
"""Property getter for world size.
"""
if self.data_section is None:
return None
attrs = self.data_section.attrs
if bool(attrs)==False:
return None
return attrs.get('world_size', None)
def request_data(spec, **kwargs):
"""Provides data for children.
"""
if spec is ParticlesSpec:
return self.particles
elif spec is SpeciesTableSpec:
return self.species_table
elif spec is WorldSizeSpec:
return self.world_size
register_pipeline_node(ParticleConstructorNode)
# self._particle_space is left None if something wrong in loading data.
return self._particle_space
@log_call
def request_data(self, spec, **kwargs):
"""Provides particle data.
"""
if spec == NumberOfItemsSpec:
debug('Serving NumberOfItemsSpec')
ps = self.fetch_particle_space(**kwargs)
if ps is None:
return 0
else:
return ps.getNumberOfItems()
elif spec == ParticleSpaceSpec:
debug('Serving ParticleSpaceSpec')
# this may be None if datasource is not valid.
ps = self.fetch_particle_space(**kwargs)
return ps
return None
register_pipeline_node(ParticleSpatiocyteLoaderNode)
if __name__=='__main__':
# TBD
from doctest import testmod, ELLIPSIS
testmod(optionflags = ELLIPSIS)
"""
# examine cache
if self._particle_data:
pass
else: # self._particle_data is None
uri = self.parent.request_data(UriSpec)
if isinstance(uri, str):
parsed = urlparse(uri)
fullpath = parsed.netloc + parsed.path
if os.path.exists(fullpath):
pass #TBDDDDDDD
# self._particle_data is left None if something wrong in loading data.
return self._particle_data
def request_data(self, spec, **params):
"""Provides particle data.
"""
if spec is ParticleDataSpec:
return self.particle_data # this may be None if datasource is not valid.
return None
# Finally, register node to registry.
register_pipeline_node(SimpleParticleLoaderNode)
# You may write doctests, which runs on executing this module.
if __name__ == '__main__':
# TBD
from doctest import testmod, ELLIPSIS
testmod(optionflags=ELLIPSIS)
return ps
@log_call
def update_list(self, **kwargs):
ps = self.parent.request_data(ParticleSpaceSpec, **kwargs)
if ps is None:
return
if self.sid_color_map is None:
self.sid_color_map = {}
for sp in ps.species:
if sp not in self.sid_color_map.keys():
self.sid_color_map[sp] = get_new_color(len(self.sid_color_map))
register_pipeline_node(ParticleSpaceVisualizerNode)
class ParticleSpaceVisualizer(Vtk3dVisualizerPage):
@log_call
def update(self):
self.render()
register_visualizer_page('ParticleSpaceVisualizerNode', ParticleSpaceVisualizer)
class ParticleSpaceVisualizerInspector(InspectorPage):
"""Inspector page for ParticleSpaceVisualizer.
"""
def __init__(self, *args, **kwargs):
"""Initializer.
"""
self.sid_list = particle_space.species
@log_call
def request_data(self, spec, **kwargs):
"""Provides particle data.
"""
if spec == NumberOfItemsSpec:
debug('Serving NumberOfItemsSpec')
return self.parent.request_data(NumberOfItemsSpec, **kwargs)
elif spec == ParticleSpaceSpec:
debug('Serving ParticleSpaceSpec')
return self.fetch_particle_space(**kwargs)
return None
register_pipeline_node(ParticleSpaceFilterNode)
class ParticleSpaceFilterInspector(InspectorPage):
"""Inspector page for ParticleSpaceFilter.
"""
# PROP_NAMES = ['filename', 'mode', 'driver', 'libver', 'userblock_size',
# 'name', 'id', 'ref', 'attrs']
def __init__(self, *args, **kwargs):
"""Initializer.
"""
InspectorPage.__init__(self, *args, **kwargs)
widgets = []
self.renderer.GetActiveCamera().ParallelProjectionOn()
self.particles_visual = ParticlesVisual(renderer=self.renderer,
name='particles')
@log_call
def internal_update(self):
"""Reset cached particles
"""
self.particles_visual.update(
dict(world_size=self.parent.world_size,
species_table=self.parent.species_table,
particles=self.parent.particles))
self.particles_visual.enable()
register_pipeline_node(ParticleVisualizerNode)
class ParticleVisualizer(Vtk3dVisualizerPage):
"""Visualizer.
"""
@log_call
def update(self):
"""Updates content of the rendering window.
TODO: this method call should be handled in superclass...
"""
self.render()
register_visualizer_page('ParticleVisualizerNode', ParticleVisualizer)
elif spec==Hdf5DataSpec:
index = kwargs.get('index', 0)
data = self.cache.get(index, None)
if data is None:
path = self.bundle.get_path_at(index)
if not(path is None):
try:
data = File(path, mode='r')
self.cache[index] = data
except IOError:
pass
return data
return None
register_pipeline_node(Hdf5BundleLoaderNode)
class Hdf5BundleLoaderInspector(InspectorPage):
"""Sequential hdf5 selector inspector.
"""
def __init__(self, *args, **kwargs):
"""Initializer.
"""
InspectorPage.__init__(self, *args, **kwargs)
glob_pattern_label = wx.StaticText(self, -1, 'Glob pattern')
glob_pattern = wx.TextCtrl(self, -1, "%s" %self.target.glob_pattern)
self.Bind(wx.EVT_TEXT, self.OnGlobPatternText, glob_pattern)
self.sizer.Add(glob_pattern_label, 0, wx.ALL|wx.EXPAND, 5)
self.sizer.Add(glob_pattern, 0, wx.ALL|wx.EXPAND, 5)
self.glob_pattern = glob_pattern
