def createVisualizerList(self):
ids={}
if isinstance(self.dataContainer, DataContainer.SampleContainer):
data_type = pyphant.core.Connectors.TYPE_ARRAY
elif isinstance(self.dataContainer, DataContainer.FieldContainer):
data_type = pyphant.core.Connectors.TYPE_IMAGE
for visualizer in DataVisReg.getInstance().getVisualizers(data_type):
id=wx.NewId()
ids[id]=visualizer
#self.GetCanvas().Bind(wx.EVT_MENU, self.visualize, id=id)
return ids
def createVisualizerList(self):
ids = {}
if isinstance(self.dataContainer, DataContainer.SampleContainer):
data_type = pyphant.core.Connectors.TYPE_ARRAY
elif isinstance(self.dataContainer, DataContainer.FieldContainer):
data_type = pyphant.core.Connectors.TYPE_IMAGE
for visualizer in DataVisReg.getInstance().getVisualizers(data_type):
id = wx.NewId()
ids[id] = visualizer
#self.GetCanvas().Bind(wx.EVT_MENU, self.visualize, id=id)
return ids
# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
"""
__id__ = "$Id: ImageVisualizer.py 22 2006-11-28 14:31:46Z liehr $"
__author__ = "$Author: liehr $"
__version__ = "$Revision: 22 $"
# $Source$
import pylab
import pyphant.core.Connectors
from pyphant.wxgui2.DataVisReg import DataVisReg
import scipy
class PrimitiveVisualizer(object):
name='Primitive Visualizer'
def __init__(self, fieldContainer):
self.fieldContainer = fieldContainer
self.execute()
def execute(self):
print self.fieldContainer
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_INT, PrimitiveVisualizer)
class SurfaceVisualizer(object):
name = "Surface"
def __init__(self, fc, show=True):
assert len(fc.dimensions) == 2, "2D FC expected"
self.fc = fc
self.draw()
if show:
self.show()
def draw(self):
fig = pyplot.figure()
ax = fig.gca(projection='3d')
y, x = np.meshgrid(*[d.data for d in self.fc.dimensions])
z = self.fc.data
zrange = z.max() - z.min()
ax.plot_surface(
x, y, z, cmap=cm.coolwarm, linewidth=0, rstride=1, cstride=1
)
ax.set_zlim(z.min() - zrange, z.max() + zrange)
def show(self):
pyplot.show()
DataVisReg.getInstance().registerVisualizer(
TYPE_IMAGE, SurfaceVisualizer
)
wx.Frame.__init__(self, None, -1,
"Visualize " + dataContainer.longname)
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.plot_panel = OscPlotPanel(self, dataContainer)
self.configuration_panel = ConfigurationPanel(self, dataContainer,
self.plot_panel)
self.sizer.Add(self.configuration_panel, 0, wx.EXPAND)
self.sizer.Add(self.plot_panel, 1, wx.LEFT | wx.TOP | wx.GROW)
self.SetSizer(self.sizer)
self.Centre()
self.Show(True)
def createVisualizerList(self):
ids = {}
if isinstance(self.dataContainer, DataContainer.SampleContainer):
data_type = pyphant.core.Connectors.TYPE_ARRAY
elif isinstance(self.dataContainer, DataContainer.FieldContainer):
data_type = pyphant.core.Connectors.TYPE_IMAGE
for visualizer in DataVisReg.getInstance().getVisualizers(data_type):
id = wx.NewId()
ids[id] = visualizer
#self.GetCanvas().Bind(wx.EVT_MENU, self.visualize, id=id)
return ids
def OnExit(self, event):
self.Close()
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_ARRAY,
PlotFrame)
self.init_cvalues(dataContainer)
self.dclongname = dataContainer.longname
wx.Frame.__init__(self, None, -1, "Z-Stack " + dataContainer.longname)
self.sizer = wx.BoxSizer(wx.VERTICAL)
imgFC = dataContainer[0]
self.dataContainer = dataContainer
self.plotPanel = ZStackPlotPanel(self, imgFC)
self.configPanel = ZStackConfigPanel(self, self.plotPanel)
self.sizer.Add(self.configPanel, 0, wx.EXPAND)
self.sizer.Add(self.plotPanel, 1, wx.LEFT | wx.TOP | wx.GROW)
self.SetSizer(self.sizer)
self.Centre()
self.Show(True)
def init_zvalues(self, dataContainer):
zunit = dataContainer.dimensions[0].unit
self.zvalues = [str(zvalue * zunit) for zvalue \
in dataContainer.dimensions[0].data]
def init_cvalues(self, dataContainer):
self.cmaps = pylab.cm._cmapnames
self.cbads = ['red', 'green', 'blue', 'yellow', 'black', 'white']
self.cmaps.sort()
self.cbads.sort()
def OnExit(self, event):
self.Close()
DataVisReg.getInstance().registerVisualizer(TYPE_IMAGE, ZStackVisualizer)
if u"Smoothed Absorption" in data.longnames.keys():
setField(u"Smoothed Absorption")
elif u"Absorption" in data.longnames.keys():
setField(u"Absorption")
else:
self.xData = data[u"Wellenlänge[nm]"]
self.yData = data[u"ScopRaw[counts]"]
pylab.ylabel("Scop Raw / a.u.")
else:
self.xData = self.dataContainer[0]
self.yData = self.dataContainer[1]
for i in xrange(len(self.xData.data)):
self.ordinates.append(self.yData.data[i])
self.abscissae.append(self.xData.data[i])
if u"Minima" in data.longnames.keys():
mins = data[u"Minima"]
for i in xrange(len(mins.data)):
self.mins.append(mins.data[i])
pylab.xlabel("Wavelength $\lambda$ / nm")
pylab.title(self.dataContainer.longname)
def draw(self):
for i in xrange(len(self.ordinates)):
pylab.plot(self.abscissae[i], self.ordinates[i])
for i in xrange(len(self.mins)):
pylab.axvline(self.mins[i])
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_ARRAY, AbsorptionVisualizer)
wx.Frame.__init__(self, None, -1, "Visualize "+dataContainer.longname)
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.plot_panel = OscPlotPanel(self, dataContainer)
self.configuration_panel = ConfigurationPanel(self, dataContainer,
self.plot_panel)
self.sizer.Add(self.configuration_panel, 0, wx.EXPAND)
self.sizer.Add(self.plot_panel, 1, wx.LEFT | wx.TOP | wx.GROW)
self.SetSizer(self.sizer)
self.Centre()
self.Show(True)
def createVisualizerList(self):
ids={}
if isinstance(self.dataContainer, DataContainer.SampleContainer):
data_type = pyphant.core.Connectors.TYPE_ARRAY
elif isinstance(self.dataContainer, DataContainer.FieldContainer):
data_type = pyphant.core.Connectors.TYPE_IMAGE
for visualizer in DataVisReg.getInstance().getVisualizers(data_type):
id=wx.NewId()
ids[id]=visualizer
#self.GetCanvas().Bind(wx.EVT_MENU, self.visualize, id=id)
return ids
def OnExit(self, event):
self.Close()
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_ARRAY, PlotFrame)
self.abscissae.append(self.xData.data[i])
if u'Minima' in data.longnames.keys():
mins = data[u'Minima']
for i in xrange(len(mins.data)):
self.mins.append(mins.data[i])
pylab.xlabel('Wavelength $\lambda$ / nm')
pylab.title(self.dataContainer.longname)
def draw(self):
for i in xrange(len(self.ordinates)):
pylab.plot(self.abscissae[i],self.ordinates[i])
for i in xrange(len(self.mins)):
pylab.axvline(self.mins[i])
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_ARRAY, AbsorptionVisualizer)
def saveSample(self, path):
outData = self.dataContainer.data
if path[-3:] == 'csv':
outFile = file(path,'wb')
csvWriter = csv.writer(outFile,dialect='excel')
#csvWriter.writerow([self.dataContainer.dimensions[0].label, self.dataContainer.label])
csvWriter.writerows(outData.tolist())
else:
outFile = file(path,'w')
#outFile.write(str([self.dataContainer.dimensions[0].label, self.dataContainer.label])+"\n")
write_array(outFile,outData.tolist())
outFile.close()
DataVisReg.getInstance().registerVisualizer(Connectors.TYPE_ARRAY, ExternalDAT)
str([
self.dataContainer.dimensions[0].label,
self.dataContainer.label
]) + "\n")
write_array(outFile, outData)
outFile.close()
def saveSample(self, path):
outData = self.dataContainer.data
if path[-3:] == 'csv':
outFile = file(path, 'wb')
csvWriter = csv.writer(outFile, dialect='excel')
#csvWriter.writerow(
# [self.dataContainer.dimensions[0].label,
# self.dataContainer.label]
# )
csvWriter.writerows(outData.tolist())
else:
outFile = file(path, 'w')
#outFile.write(
# str([
# self.dataContainer.dimensions[0].label,
# self.dataContainer.label]) + "\n"
# )
write_array(outFile, outData.tolist())
outFile.close()
DataVisReg.getInstance().registerVisualizer(Connectors.TYPE_ARRAY, ExternalDAT)
name = u"Line chart"
linestyle = '-'
def draw(self, abscissa, data, maskedData, error, **kwargs):
if error == None:
for ordinate in maskedData:
pylab.plot(abscissa, ordinate, self.linestyle)
else:
for i in xrange(data.shape[0]):
line = pylab.plot(abscissa, maskedData[i], self.linestyle)
color = [l._color for l in line]
for direction in [-1., 1.]:
ordinate = maskedData[i] + direction * error[i]
line = pylab.plot(abscissa, ordinate, linestyle=':')
for j in xrange(len(color)):
line[j]._color = color[j]
pylab.axis([self.xmin, self.xmax, self.ymin, self.ymax])
class ScatterPlot(LineChart):
name = u"Scatter Plot"
linestyle = 'o'
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_IMAGE,
BarChart)
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_IMAGE,
LineChart)
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_IMAGE,
ScatterPlot)
self.dclongname = dataContainer.longname
wx.Frame.__init__(self, None, -1, "Z-Stack " + dataContainer.longname)
self.sizer = wx.BoxSizer(wx.VERTICAL)
imgFC = dataContainer[0]
self.dataContainer = dataContainer
self.plotPanel = ZStackPlotPanel(self, imgFC)
self.configPanel = ZStackConfigPanel(self, self.plotPanel)
self.sizer.Add(self.configPanel, 0, wx.EXPAND)
self.sizer.Add(self.plotPanel, 1, wx.LEFT | wx.TOP | wx.GROW)
self.SetSizer(self.sizer)
self.Centre()
self.Show(True)
def init_zvalues(self, dataContainer):
zunit = dataContainer.dimensions[0].unit
self.zvalues = [str(zvalue * zunit) for zvalue \
in dataContainer.dimensions[0].data]
def init_cvalues(self, dataContainer):
self.cmaps = pylab.cm._cmapnames
self.cbads = ['red', 'green', 'blue', 'yellow',
'black', 'white']
self.cmaps.sort()
self.cbads.sort()
def OnExit(self, event):
self.Close()
DataVisReg.getInstance().registerVisualizer(TYPE_IMAGE, ZStackVisualizer)
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""This module provides a visualizer that simply prints the input"""
import pyphant.core.Connectors
from pyphant.wxgui2.DataVisReg import DataVisReg
class PrimitiveVisualizer(object):
name = 'Primitive Visualizer'
def __init__(self, fieldContainer):
self.fieldContainer = fieldContainer
self.execute()
def execute(self):
print self.fieldContainer
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_INT,
PrimitiveVisualizer)
pylab.imshow(self.fieldContainer.maskedData,
aspect='auto',
interpolation='nearest',
vmin=vmin,
vmax=vmax,
origin='lower',
extent=(xmin, xmax, ymin, ymax))
pylab.colorbar(format=F(self.fieldContainer), ax=ax)
else:
im = NonUniformImage(ax, extent=(xmin,xmax,ymin,ymax))
if vmin is not None or vmax is not None:
im.set_clim(vmin, vmax)
im.set_data(x, y, self.fieldContainer.maskedData)
else:
im.set_data(x, y, self.fieldContainer.maskedData)
im.autoscale_None()
ax.images.append(im)
ax.set_xlim(xmin,xmax)
ax.set_ylim(ymin,ymax)
pylab.colorbar(im,format=F(self.fieldContainer), ax=ax)
pylab.xlabel(self.fieldContainer.dimensions[-1].shortlabel)
pylab.ylabel(self.fieldContainer.dimensions[-2].shortlabel)
pylab.title(self.fieldContainer.label)
#ax=pylab.gca()
if self.show:
pylab.ion()
pylab.show()
DataVisReg.getInstance().registerVisualizer(TYPE_IMAGE, ImageVisualizer)
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
u"""
"""
__id__ = "$Id$"
__author__ = "$Author$"
__version__ = "$Revision$"
# $Source$
from pyphant.core.Connectors import (TYPE_IMAGE, TYPE_ARRAY)
from pyphant.wxgui2.DataVisReg import DataVisReg
from pyphant.core.KnowledgeManager import KnowledgeManager
class KMVisualizer(object):
name='Register @ KnowledgeManager'
def __init__(self, DataContainer, show=True):
if show:
kmanager = KnowledgeManager.getInstance()
kmanager.registerDataContainer(DataContainer)
DataVisReg.getInstance().registerVisualizer(TYPE_IMAGE, KMVisualizer)
DataVisReg.getInstance().registerVisualizer(TYPE_ARRAY, KMVisualizer)
class LineChart(Chart):
name = u"Line chart"
linestyle = '-'
def draw(self, abscissa, data, maskedData, error, **kwargs):
if error == None:
for ordinate in maskedData:
pylab.plot(abscissa, ordinate, self.linestyle)
else:
for i in xrange(data.shape[0]):
line = pylab.plot(abscissa, maskedData[i], self.linestyle)
color = [l._color for l in line]
for direction in [-1.,1.]:
ordinate = maskedData[i] + direction*error[i]
line = pylab.plot(abscissa, ordinate, linestyle=':')
for j in xrange(len(color)):
line[j]._color = color[j]
pylab.axis([self.xmin, self.xmax, self.ymin, self.ymax])
class ScatterPlot(LineChart):
name = u"Scatter Plot"
linestyle = 'o'
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_IMAGE, BarChart)
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_IMAGE, LineChart)
DataVisReg.getInstance().registerVisualizer(pyphant.core.Connectors.TYPE_IMAGE, ScatterPlot)
