def setup_labels(self, size=None, color=None, shadow=None):
"""Sets up coordinates for labels wrt SVG file (2D flatmap)"""
# Recursive call for multiple layers
if self.layer == 'multi_layer':
label_layers = []
for L in self.layer_names:
label_layers.append(self.layers[L].setup_labels())
self.svg.getroot().insert(0, label_layers[-1])
return label_layers
if self.layer in config.sections():
dlayer = self.layer
else:
# Unknown display layer; default to values for ROIs
import warnings
warnings.warn('No defaults set for display layer %s; Using defaults for ROIs in options.cfg file'%self.layer)
dlayer = 'rois'
if size is None:
size = config.get(dlayer, "labelsize")
if color is None:
color = tuple(map(float, config.get(dlayer, "labelcolor").split(",")))
if shadow is None:
shadow = self.shadow
alpha = color[3]
color = "rgb(%d, %d, %d)"%(color[0]*255, color[1]*255, color[2]*255)
try:
layer = _find_layer(self.svg, "%s_labels"%self.layer)
except ValueError: # Changed in _find_layer below... AssertionError: # Why assertion error?
layer = _make_layer(self.svg.getroot(), "%s_labels"%self.layer)
labelpos, candidates = [], []
for roi in list(self.rois.values()):
for i, pos in enumerate(roi.get_labelpos()):
labelpos.append(pos)
candidates.append((roi, i))
w, h = self.svgshape
nolabels = set(candidates)
txtstyle = "font-family:sans;font-size:%s;font-weight:bold;font-style:italic;fill:%s;fill-opacity:%f;text-anchor:middle;"%(size, color, alpha)
for text in layer.findall(".//{%s}text"%svgns):
x = float(text.get('x'))
y = float(text.get('y'))
text.attrib['style'] = txtstyle
text.attrib['data-ptidx'] = str(self.kdt.query((x / w, 1-(y / h)))[1])
pts, cand = [], []
for p, c in zip(labelpos, candidates):
if c[0].name == text.text:
pts.append((p[0]*w, (1-p[1])*h))
cand.append(c)
d, idx = cKDTree(pts).query((x,y))
nolabels.remove(cand[idx])
for roi, i in nolabels:
x, y = roi.get_labelpos()[i]
text = etree.SubElement(layer, "{%s}text"%svgns)
text.text = roi.name
text.attrib["x"] = str(x*w)
text.attrib["y"] = str((1-y)*h)
if self.shadow > 0:
text.attrib['filter'] = "url(#dropshadow)"
text.attrib['style'] = txtstyle
text.attrib['data-ptidx'] = str(self.kdt.query((x, y))[1])
self.labels = layer
return layer
def __init__(self, tcoords, svgfile, callback=None, linewidth=None,
linecolor=None, roifill=None, shadow=None, labelsize=None,
labelcolor=None, dashtype='fromsvg', dashoffset='fromsvg',
layer='rois'):
"""Contains ROI data in SVG form
Stores [[display elements]] from one layer of an svg file.
Most commonly, these are ROIs. Each ROI (or other display element)
can contain multiple paths.
If those paths are closed (i.e., if these are all ROIs), then
you can use the method ROIpack.get_roi() to get an index of the
vertices associated with each roi.
Parameters
----------
Notes
-----
The name and the function of this class have begun to diverge. This class
almost entirely has to do with parsing and storing elements of svg files,
*SOME* of which are related to ROIs, and some of which are not. In the future,
this class may be renamed to something like DispPack, display_pack, disp_elements,
etc
"""
if isinstance(layer,(list,tuple)):
# More elegant would be to have ROIpack be a fundamentally multi-layer
# object, but for backward compatibility and for not breaking other
# other parts of the code (e.g. finding roi indices, etc) I have kept
# it this way ML 2014.08.12
self.svgfile = svgfile
self.callback = callback
self.kdt = cKDTree(tcoords)
self.layer = 'multi_layer'
self.layers = {}
self.rois = {}
self.layer_names = layer
layer1 = layer[0]
# Recursive call to create multiple layers
for iL,L in enumerate(layer):
self.layers[L] = ROIpack(tcoords, svgfile, callback, linewidth, linecolor,
roifill, shadow, labelsize, labelcolor, dashtype, dashoffset,
layer=L)
# Necessary?
self.rois.update(self.layers[L].rois)
# # Create combined svg out of individual layer svgs
if iL == 0:
self.tcoords = self.layers[layer1].tcoords
svg_fin = copy.copy(self.layers[layer1].svg)
elif iL>0:
to_add = _find_layer(self.layers[L].svg, L)
svg_fin.getroot().insert(0, to_add)
# linewidth, etc not set - set in individual layers
self.svg = svg_fin
else:
# Normalize coordinates 0-1
if np.any(tcoords.max(0) > 1) or np.any(tcoords.min(0) < 0):
tcoords -= tcoords.min(0)
tcoords /= tcoords.max(0)
self.tcoords = tcoords
self.svgfile = svgfile
self.callback = callback
self.kdt = cKDTree(tcoords)
self.layer = layer
# Display parameters
if layer in config.sections():
dlayer = layer
else:
# Unknown display layer; default to values for ROIs
import warnings
warnings.warn('No defaults set for display layer %s; Using defaults for ROIs in options.cfg file'%layer)
dlayer = 'rois'
self.linewidth = float(config.get(dlayer, "line_width")) if linewidth is None else linewidth
self.linecolor = tuple(map(float, config.get(dlayer, "line_color").split(','))) if linecolor is None else linecolor
self.roifill = tuple(map(float, config.get(dlayer, "fill_color").split(','))) if roifill is None else roifill
self.shadow = float(config.get(dlayer, "shadow")) if shadow is None else shadow
# For dashed lines, default to WYSIWYG from rois.svg
self.dashtype = dashtype
self.dashoffset = dashoffset
self.reload(size=labelsize, color=labelcolor)
def __init__(self, tcoords, svgfile, callback=None, linewidth=None,
linecolor=None, roifill=None, shadow=None, labelsize=None,
labelcolor=None, dashtype='fromsvg', dashoffset='fromsvg',
layer='rois'):
"""Contains ROI data in SVG form
Stores [[display elements]] from one layer of an svg file.
Most commonly, these are ROIs. Each ROI (or other display element)
can contain multiple paths.
If those paths are closed (i.e., if these are all ROIs), then
you can use the method ROIpack.get_roi() to get an index of the
vertices associated with each roi.
Parameters
----------
Notes
-----
The name and the function of this class have begun to diverge. This class
almost entirely has to do with parsing and storing elements of svg files,
*SOME* of which are related to ROIs, and some of which are not. In the future,
this class may be renamed to something like DispPack, display_pack, disp_elements,
etc
"""
if isinstance(layer,(list,tuple)):
# More elegant would be to have ROIpack be a fundamentally multi-layer
# object, but for backward compatibility and for not breaking other
# other parts of the code (e.g. finding roi indices, etc) I have kept
# it this way ML 2014.08.12
self.svgfile = svgfile
self.callback = callback
self.kdt = cKDTree(tcoords)
self.layer = 'multi_layer'
self.layers = {}
self.rois = {}
self.layer_names = layer
layer1 = layer[0]
# Recursive call to create multiple layers
for iL,L in enumerate(layer):
self.layers[L] = ROIpack(tcoords, svgfile, callback, linewidth, linecolor,
roifill, shadow, labelsize, labelcolor, dashtype, dashoffset,
layer=L)
# Necessary?
self.rois.update(self.layers[L].rois)
# # Create combined svg out of individual layer svgs
if iL == 0:
self.tcoords = self.layers[layer1].tcoords
svg_fin = copy.copy(self.layers[layer1].svg)
elif iL>0:
to_add = _find_layer(self.layers[L].svg, L)
svg_fin.getroot().insert(0, to_add)
# linewidth, etc not set - set in individual layers
self.svg = svg_fin
else:
# Normalize coordinates 0-1
if np.any(tcoords.max(0) > 1) or np.any(tcoords.min(0) < 0):
tcoords -= tcoords.min(0)
tcoords /= tcoords.max(0)
self.tcoords = tcoords
self.svgfile = svgfile
self.callback = callback
self.kdt = cKDTree(tcoords)
self.layer = layer
# Display parameters
if layer in config.sections():
dlayer = layer
else:
# Unknown display layer; default to values for ROIs
import warnings
warnings.warn('No defaults set for display layer %s; Using defaults for ROIs in options.cfg file'%layer)
dlayer = 'rois'
self.linewidth = float(config.get(dlayer, "line_width")) if linewidth is None else linewidth
self.linecolor = tuple(map(float, config.get(dlayer, "line_color").split(','))) if linecolor is None else linecolor
self.roifill = tuple(map(float, config.get(dlayer, "fill_color").split(','))) if roifill is None else roifill
self.shadow = float(config.get(dlayer, "shadow")) if shadow is None else shadow
# For dashed lines, default to WYSIWYG from rois.svg
self.dashtype = dashtype
self.dashoffset = dashoffset
self.reload(size=labelsize, color=labelcolor)
def setup_labels(self, size=None, color=None, shadow=None):
"""Sets up coordinates for labels wrt SVG file (2D flatmap)"""
# Recursive call for multiple layers
if self.layer == 'multi_layer':
label_layers = []
for L in self.layer_names:
label_layers.append(self.layers[L].setup_labels())
self.svg.getroot().insert(0, label_layers[-1])
return label_layers
if self.layer in config.sections():
dlayer = self.layer
else:
# Unknown display layer; default to values for ROIs
import warnings
warnings.warn('No defaults set for display layer %s; Using defaults for ROIs in options.cfg file'%self.layer)
dlayer = 'rois'
if size is None:
size = config.get(dlayer, "labelsize")
if color is None:
color = tuple(map(float, config.get(dlayer, "labelcolor").split(",")))
if shadow is None:
shadow = self.shadow
alpha = color[3]
color = "rgb(%d, %d, %d)"%(color[0]*255, color[1]*255, color[2]*255)
try:
layer = _find_layer(self.svg, "%s_labels"%self.layer)
except ValueError: # Changed in _find_layer below... AssertionError: # Why assertion error?
layer = _make_layer(self.svg.getroot(), "%s_labels"%self.layer)
labelpos, candidates = [], []
for roi in list(self.rois.values()):
for i, pos in enumerate(roi.get_labelpos()):
labelpos.append(pos)
candidates.append((roi, i))
w, h = self.svgshape
nolabels = set(candidates)
txtstyle = "font-family:sans;font-size:%s;font-weight:bold;font-style:italic;fill:%s;fill-opacity:%f;text-anchor:middle;"%(size, color, alpha)
for text in layer.findall(".//{%s}text"%svgns):
x = float(text.get('x'))
y = float(text.get('y'))
text.attrib['style'] = txtstyle
text.attrib['data-ptidx'] = str(self.kdt.query((x / w, 1-(y / h)))[1])
pts, cand = [], []
for p, c in zip(labelpos, candidates):
if c[0].name == text.text:
pts.append((p[0]*w, (1-p[1])*h))
cand.append(c)
d, idx = cKDTree(pts).query((x,y))
nolabels.remove(cand[idx])
for roi, i in nolabels:
x, y = roi.get_labelpos()[i]
text = etree.SubElement(layer, "{%s}text"%svgns)
text.text = roi.name
text.attrib["x"] = str(x*w)
text.attrib["y"] = str((1-y)*h)
if self.shadow > 0:
text.attrib['filter'] = "url(#dropshadow)"
text.attrib['style'] = txtstyle
text.attrib['data-ptidx'] = str(self.kdt.query((x, y))[1])
self.labels = layer
return layer
This comes in useful when things don't work because the config file is not set correctly.
"""
from __future__ import print_function
import cortex
from cortex.options import config
##########################################################
# Finding where your config file is.
print(cortex.options.usercfg)
##########################################################
# Finding where the current filestore is.
# Useful for when your subjects don't show up in cortex.db, and all you have is S1.
print(config.get('basic', 'filestore'))
##########################################################
# Finding where pycortex is looking for colormaps.
# Useful for when you get color map not found messages.
print(config.get('webgl', 'colormaps'))
##########################################################
# To look at your config file, it is recommended that you open it with a text editor.
# However, you *can* still look at options from within pycortex.
# sections gets the upper-level sections in the config file
sections = config.sections()
print(sections)
# items gets the option items within a section as a list of key-value pairs.
basic_config = config.items('paths_default')
print(basic_config)