def __init__(self, x, y, text, axes, **kwargs):
super(CurvedText, self).__init__(x[0], y[0], ' ', **kwargs)
axes.add_artist(self)
self.__x = x
self.__y = y
self.__zorder = self.get_zorder()
self.__characters = []
for c in text:
t = mtext.Text(0, 0, c, **kwargs)
t.set_ha('center')
t.set_rotation(0)
t.set_zorder(self.__zorder + 1)
self.__characters.append((c, t))
axes.add_artist(t)
def addText(ax, xPos, yPos, textString, normalFont):
if ('DISK' not in textString):
size = 18
else:
size = 25
if (normalFont == True):
weight = 'normal'
else:
weight = 'bold'
txt = text.Text(xPos,
yPos,
textString,
ha='left',
va='bottom',
fontweight=weight,
fontsize=size,
axes=ax)
ax.add_artist(txt)
def __init__(self, Q, X, Y, U, label, **kw):
martist.Artist.__init__(self)
self.Q = Q
self.X = X
self.Y = Y
self.U = U
self.coord = kw.pop('coordinates', 'axes')
self.color = kw.pop('color', None)
self.label = label
self._labelsep_inches = kw.pop('labelsep', 0.1)
self.labelsep = (self._labelsep_inches * Q.ax.figure.dpi)
# try to prevent closure over the real self
weak_self = weakref.ref(self)
def on_dpi_change(fig):
self_weakref = weak_self()
if self_weakref is not None:
self_weakref.labelsep = (self_weakref._labelsep_inches *
fig.dpi)
self_weakref._initialized = False # simple brute force update
# works because _init is
# called at the start of
# draw.
self._cid = Q.ax.figure.callbacks.connect('dpi_changed', on_dpi_change)
self.labelpos = kw.pop('labelpos', 'N')
self.labelcolor = kw.pop('labelcolor', None)
self.fontproperties = kw.pop('fontproperties', dict())
self.kw = kw
_fp = self.fontproperties
# boxprops = dict(facecolor='red')
self.text = mtext.Text(
text=label, # bbox=boxprops,
horizontalalignment=self.halign[self.labelpos],
verticalalignment=self.valign[self.labelpos],
fontproperties=font_manager.FontProperties(**_fp))
if self.labelcolor is not None:
self.text.set_color(self.labelcolor)
self._initialized = False
self.zorder = Q.zorder + 0.1
def create_artists(i, v):
x = (i + 0.5) * self._spacing
y = 0.5
r = scaled_radius(v)
c = patches.Ellipse((x, y),
r,
yscale * r,
transform=fig.transFigure,
figure=fig,
fill=False)
t = text.Text(x,
y,
str(v),
transform=fig.transFigure,
figure=fig,
verticalalignment='center',
horizontalalignment='center',
fontsize=300 * r)
return c, t
def legend_artist(self, legend, orig_handle, fontsize, handlebox):
letter, index = orig_handle
x0, y0 = handlebox.xdescent, handlebox.ydescent
width, height = handlebox.width, handlebox.height
x = x0 + width / 2.0
y = y0 + height / 2.0
normVal = norm(index)
colorRgb = cmap(normVal)
patch = matplotlib.patches.RegularPolygon(
(x, y),
6,
height,
orientation=math.pi / 2.0,
facecolor=colorRgb,
transform=handlebox.get_transform(),
)
handlebox.add_artist(patch)
txt = mpl_text.Text(x=x, y=y, text=letter, ha="center", va="center", size=7)
handlebox.add_artist(txt)
return (patch, txt)
def legend_artist(self, legend, orig_handle, fontsize, handlebox):
# print orig_handle
x0, y0 = handlebox.xdescent, handlebox.ydescent
width, height = handlebox.width, handlebox.height
myfont = fm.FontProperties(
fname="/usr/share/fonts/truetype/ttf-ancient-scripts/Symbola605.ttf"
)
patch = mpl_text.Text(x=0,
y=0,
text=orig_handle.my_text,
color=orig_handle.my_color,
verticalalignment=u'baseline',
horizontalalignment=u'left',
multialignment=None,
rotation=0,
linespacing=None,
rotation_mode=None,
fontproperties=myfont,
size=orig_handle.my_size)
handlebox.add_artist(patch)
return patch
def __init__(self, axes, text, x, y):
self.axes = axes
self.text = text
self.x = x
self.y = y
self.bbox = {
'boxstyle': 'square',
'facecolor': "#98b2d3",
'edgecolor': "None",
'alpha': 0
}
self.text_obj = text_obj.Text(x=x,
y=y,
text=text,
alpha=0.,
color='#013a4b',
fontsize=30,
verticalalignment='center',
horizontalalignment='center',
bbox=self.bbox)
self.axes.add_artist(self.text_obj)
def labels(self, inline):
levels = self.label_levels
fslist = self.fslist
trans = self.ax.transData
_colors = self.label_mappable.to_rgba(self.label_cvalues)
fmt = self.fmt
for icon, lev, color, cvalue, fsize in zip(self.label_indices,
self.label_levels,
_colors,
self.label_cvalues, fslist):
con = self.collections[icon]
lw = self.get_label_width(lev, fmt, fsize)
additions = []
for segNum, linecontour in enumerate(con._segments):
# for closed contours add one more point to
# avoid division by zero
if npy.all(linecontour[0] == linecontour[-1]):
linecontour = npy.concatenate((linecontour,
linecontour[1][npy.newaxis,:]))
#linecontour.append(linecontour[1])
# transfer all data points to screen coordinates
slc = trans.seq_xy_tups(linecontour)
if self.print_label(slc,lw):
x,y, rotation, ind = self.locate_label(slc, lw)
# transfer the location of the label back to
# data coordinates
dx,dy = trans.inverse_xy_tup((x,y))
t = text.Text(dx, dy, rotation = rotation,
horizontalalignment='center',
verticalalignment='center')
_text = self.get_text(lev,fmt)
self.set_label_props(t, _text, color)
self.cl.append(t)
self.cl_cvalues.append(cvalue)
if inline:
new = self.break_linecontour(linecontour, rotation,
lw, ind)
con._segments[segNum] = new[0]
additions.append(new[1])
con._segments.extend(additions)
def inspect(self, vmentry):
# the patches use axes transform on the y coordinate to
# set the height position of the label independently of
# the Y scale
# rect = patches.Rectangle((vmentry.start, 0),
# vmentry.end - vmentry.start, self.y_max)
rect = patches.Rectangle((vmentry.start, 0.01),
vmentry.end - vmentry.start, 0.98)
self.patches.append(rect)
self.patch_colors.append(self._colors[vmentry.perms])
# the label position is centered based on the axes transform
label_position = ((vmentry.start + vmentry.end) / 2, self.label_y)
vme_path = str(vmentry.path).split("/")[-1] if str(vmentry.path) else ""
if not vme_path and vmentry.grows_down:
vme_path = "stack"
vme_label = "%s %s" % (vmentry.perms, vme_path)
label = text.Text(text=vme_label, rotation="vertical",
position=label_position,
horizontalalignment="center",
verticalalignment="center",
transform=self.transform)
self.annotations.append(label)
def get_real_label_width(self, lev, fmt, fsize):
"""
This computes actual onscreen label width.
This uses some black magic to determine onscreen extent of non-drawn
label. This magic may not be very robust.
"""
# Find middle of axes
xx = np.mean(np.asarray(self.ax.axis()).reshape(2, 2), axis=1)
# Temporarily create text object
t = text.Text(xx[0], xx[1])
self.set_label_props(t, self.get_text(lev, fmt), 'k')
# Some black magic to get onscreen extent
# NOTE: This will only work for already drawn figures, as the canvas
# does not have a renderer otherwise. This is the reason this function
# can't be integrated into the rest of the code.
bbox = t.get_window_extent(renderer=self.ax.figure.canvas.renderer)
# difference in pixel extent of image
lw = np.diff(bbox.corners()[0::2, 0])[0]
return lw
def plot(self, ax, title):
'''
Plot data on given axis
Parameters
----------
ax: matplotlib.axes.Axes
axis on which data will be drawn
title:
title of graph
'''
if self.freq is None:
scale = 1
ax.get_xaxis().set_visible(False)
else:
scale = self.freq
self._plot(ax, scale)
height = ax.get_ylim()
if len(self.con) > 1:
for txt, cn in zip(self.text, self.con):
l = lines.Line2D([cn * scale] * 2,
height,
lw=1,
color='black',
axes=ax)
t = text.Text(cn * scale + 2,
height[1],
txt,
axes=ax,
horizontalalignment='left',
verticalalignment='top')
ax.add_line(l)
ax.add_artist(t)
ax.set_title(title)
def __init__(
self,
s,
textprops=None,
multilinebaseline=None,
minimumdescent=True,
):
"""
*s* : a string to be displayed.
*textprops* : property dictionary for the text
*multilinebaseline* : If True, baseline for multiline text is
adjusted so that it is (approximatedly)
center-aligned with singleline text.
*minimumdescent* : If True, the box has a minimum descent of "p".
"""
if textprops is None:
textprops = {}
if not textprops.has_key("va"):
textprops["va"] = "baseline"
self._text = mtext.Text(0, 0, s, **textprops)
OffsetBox.__init__(self)
self._children = [self._text]
self.offset_transform = mtransforms.Affine2D()
self.offset_transform.clear()
self.offset_transform.translate(0, 0)
self._baseline_transform = mtransforms.Affine2D()
self._text.set_transform(self.offset_transform +
self._baseline_transform)
self._multilinebaseline = multilinebaseline
self._minimumdescent = minimumdescent
def __init__(self, Q, X, Y, U, label, **kw):
artist.Artist.__init__(self)
self.Q = Q
self.X = X
self.Y = Y
self.U = U
self.coord = kw.pop('coordinates', 'axes')
self.color = kw.pop('color', None)
self.label = label
self.labelsep = (kw.pop('labelsep', 0.1) * Q.ax.figure.dpi)
self.labelpos = kw.pop('labelpos', 'N')
self.labelcolor = kw.pop('labelcolor', None)
self.fontproperties = kw.pop('fontproperties', dict())
self.kw = kw
_fp = self.fontproperties
self.text = text.Text(
text=label,
horizontalalignment=self.halign[self.labelpos],
verticalalignment=self.valign[self.labelpos],
fontproperties=font_manager.FontProperties(**_fp))
if self.labelcolor is not None:
self.text.set_color(self.labelcolor)
self._initialized = False
self.zorder = Q.zorder + 0.1
def __init__(self, Q, X, Y, U, label, **kw):
martist.Artist.__init__(self)
self.Q = Q
self.X = X
self.Y = Y
if type(U) in (tuple, list): self.U, self.V = U
else: self.U, self.V = U, 0
self.coord = kw.pop('coordinates', 'axes')
self.color = kw.pop('color', None)
self.label = label
self._labelsep_inches = kw.pop('labelsep', 0.1)
self.labelsep = (self._labelsep_inches * Q.ax.figure.dpi)
def on_dpi_change(fig):
self.labelsep = (self._labelsep_inches * fig.dpi)
self._initialized = False # simple brute force update
# works because _init is called
# at the start of draw.
Q.ax.figure.callbacks.connect('dpi_changed', on_dpi_change)
self.labelpos = kw.pop('labelpos', 'N')
self.labelcolor = kw.pop('labelcolor', None)
self.fontproperties = kw.pop('fontproperties', dict())
self.kw = kw
_fp = self.fontproperties
#boxprops = dict(facecolor='red')
self.text = mtext.Text(
text=label, # bbox=boxprops,
horizontalalignment=self.halign[self.labelpos],
verticalalignment=self.valign[self.labelpos],
fontproperties=font_manager.FontProperties(**_fp))
if self.labelcolor is not None:
self.text.set_color(self.labelcolor)
self._initialized = False
self.zorder = Q.zorder + 0.1
np.random.rand(2, random.randint(2, 15))))
lc = collections.LineCollection(verts, axes=ax)
ax.add_collection(lc)
# test a plain-ol-line
line = lines.Line2D([0 * cm, 1.5 * cm], [0 * cm, 2.5 * cm],
lw=2,
color='black',
axes=ax)
ax.add_line(line)
if 0:
# test a patch
# Not supported at present.
rect = patches.Rectangle((1 * cm, 1 * cm),
width=5 * cm,
height=2 * cm,
alpha=0.2,
axes=ax)
ax.add_patch(rect)
t = text.Text(3 * cm, 2.5 * cm, 'text label', ha='left', va='bottom', axes=ax)
ax.add_artist(t)
ax.set_xlim(-1 * cm, 10 * cm)
ax.set_ylim(-1 * cm, 10 * cm)
# ax.xaxis.set_units(inch)
ax.grid(True)
ax.set_title("Artists with units")
plt.show()
def legend_artist(self, legend, orig_handle, fontsize, handlebox):
patch = mpl_text.Text(x=0, y=0, text=orig_handle.my_text, color=orig_handle.my_color,
verticalalignment=u'baseline', horizontalalignment=u'left',
fontsize=fontsize_legnd)
handlebox.add_artist(patch)
return patch
def create_artists(self):
self.line_left = lines.Line2D([], [],
color=set_interval.lc,
lw=set_interval.lw,
visible=False)
self.line_right = lines.Line2D([], [],
color=set_interval.lc,
lw=set_interval.lw,
visible=False)
self.collection = colls.PolyCollection([self.verts],
facecolors=set_interval.fc,
edgecolors=set_interval.ec,
visible=False,
alpha=set_interval.alpha)
# Texts
self.bounds_textboxes = []
x = self.left
y = -1.8 * self.height * 1.7
text = str(round(self.left, 1))
self.bounds_textboxes += [
text_obj.Text(x=x,
y=y,
text=text,
visible=False,
color=set_text.fc,
alpha=1.,
fontsize=set_text.fs,
bbox=set_interval.bbox,
verticalalignment='center',
horizontalalignment='center')
]
x = self.right
text = str(round(self.right, 1))
self.bounds_textboxes += [
text_obj.Text(x=x,
y=y,
text=text,
visible=False,
color=set_text.fc,
alpha=1.,
fontsize=set_text.fs,
bbox=set_interval.bbox,
verticalalignment='center',
horizontalalignment='center')
]
x = (self.left + self.right) / 2.
y = 1.8 * self.height * 1.7
p_left, p_center, p_right = self._bounds_to_p()
text = str(int(round(100. * p_center))) + '%'
self.bounds_textboxes += [
text_obj.Text(x=x,
y=y,
text=text,
visible=False,
color=set_text.fc,
alpha=1.,
fontsize=set_text.fs,
bbox=set_interval.bbox,
verticalalignment='center',
horizontalalignment='center')
]
self.line_left.set_zorder(10)
self.line_right.set_zorder(10)
self.collection.set_zorder(2)
self.artists = [self.line_left, self.line_right, self.collection]
self.artists += self.bounds_textboxes
def create_artists(self):
self.artists = []
# Pdf line
self.pdf_line = lines.Line2D([], [],
alpha=set_pdf_line.alpha,
color=set_pdf_line.lc,
lw=set_pdf_line.lw)
self.artists = [self.pdf_line]
# Mean line
self.mean_line = lines.Line2D([self.mean, self.mean], [0, self.y_mean],
color=set_mean_line.lc,
lw=set_mean_line.lw,
visible=False)
self.artists += [self.mean_line]
# Areas
self._update_area_verts()
self.area_collections = []
for i, k in enumerate(self.area_verts.keys()):
fc = set_area.fc[1]
ec = set_area.ec[1]
if self.area_status:
fc = set_area.fc[0]
ec = set_area.ec[0]
verts = self.area_verts[k]
collection = colls.PolyCollection([verts],
facecolors=fc,
edgecolors=ec,
visible=False,
alpha=1.)
self.area_collections += [collection]
self.artists += self.area_collections # 3 polygons for areas
# Texts
p_left, p_center, p_right = self._bounds_to_p()
self.textboxes = []
for k in self.texts.keys():
if k == 'center':
x = (self.left + self.right) / 2.
y = 0.9 * (self.area_verts['center'][1, 1] +
self.area_verts['center'][-2, 1]) / 2.
self.texts[k] = str(int(round(100 * p_center))) + '%'
if k == 'left':
x = self.left
y = 1.1 * (self.area_verts['center'][1, 1])
self.texts[k] = str(int(round(100. * p_left))) + '%'
if k == 'right':
x = self.right
y = 1.1 * (self.area_verts['center'][-2, 1])
self.texts[k] = str(int(round(100 * p_right))) + '%'
self.textboxes += [
text_obj.Text(x=x,
y=y,
text=self.texts[k],
visible=False,
color=set_text.fc,
alpha=1.,
fontsize=set_text.fs,
bbox=set_text.bbox,
verticalalignment='center',
horizontalalignment='center')
]
self.artists += self.textboxes
# correct z_orders
z0 = self.area_collections[0].get_zorder()
self.mean_line.set_zorder(z0 + 1)
self.pdf_line.set_zorder(z0 + 2)
for t in self.textboxes:
t.set_zorder(z0 + 3)
def _add_gridline_label(self, value, axis, upper_end):
"""
Create a Text artist on our axes for a gridline label.
Args:
* value
Coordinate value of this gridline. The text contains this
value, and is positioned centred at that point.
* axis
which axis the label is on: 'x' or 'y'.
* upper_end
If True, place at the maximum of the "other" coordinate (Axes
coordinate == 1.0). Else 'lower' end (Axes coord = 0.0).
"""
transform = self._crs_transform()
shift_dist_points = 5 # A margin from the map edge.
if upper_end is False:
shift_dist_points = -shift_dist_points
if axis == 'x':
x = value
y = 1.0 if upper_end else 0.0
h_align = 'center'
v_align = 'bottom' if upper_end else 'top'
tr_x = transform
tr_y = self.axes.transAxes + \
mtrans.ScaledTranslation(
0.0,
shift_dist_points * (1.0 / 72),
self.axes.figure.dpi_scale_trans)
str_value = self.xformatter(value)
user_label_style = self.xlabel_style
elif axis == 'y':
y = value
x = 1.0 if upper_end else 0.0
if matplotlib.__version__ > '2.0':
v_align = 'center_baseline'
else:
v_align = 'center'
h_align = 'left' if upper_end else 'right'
tr_y = transform
tr_x = self.axes.transAxes + \
mtrans.ScaledTranslation(
shift_dist_points * (1.0 / 72),
0.0,
self.axes.figure.dpi_scale_trans)
str_value = self.yformatter(value)
user_label_style = self.ylabel_style
else:
raise ValueError(
"Unknown axis, {!r}, must be either 'x' or 'y'".format(axis))
# Make a 'blended' transform for label text positioning.
# One coord is geographic, and the other a plain Axes
# coordinate with an appropriate offset.
label_transform = mtrans.blended_transform_factory(
x_transform=tr_x, y_transform=tr_y)
label_style = {'verticalalignment': v_align,
'horizontalalignment': h_align,
}
label_style.update(user_label_style)
# Create and add a Text artist with these properties
text_artist = mtext.Text(x, y, str_value,
clip_on=False,
transform=label_transform, **label_style)
if axis == 'x':
self.xlabel_artists.append(text_artist)
elif axis == 'y':
self.ylabel_artists.append(text_artist)
self.axes.add_artist(text_artist)
def legend_artist(self, legend, orig_handle, fontsize, handlebox):
x0, y0 = handlebox.xdescent, handlebox.ydescent
title = mtext.Text(x0, y0, orig_handle, **self.text_props)
handlebox.add_artist(title)
return title
def boxrlabel(box, s, **kargs):
if 'fontsize' not in kargs:
kargs['fontsize'] = 15
x, y = box.xmax, (box.ymin + box.ymax) / 2
return mtext.Text(x, y, s, va='center', ha='left', **kargs)
def __init__(self, Q, X, Y, U, label,
*, angle=0, coordinates='axes', color=None, labelsep=0.1,
labelpos='N', labelcolor=None, fontproperties=None,
**kw):
"""
Add a key to a quiver plot.
The positioning of the key depends on *X*, *Y*, *coordinates*, and
*labelpos*. If *labelpos* is 'N' or 'S', *X*, *Y* give the position of
the middle of the key arrow. If *labelpos* is 'E', *X*, *Y* positions
the head, and if *labelpos* is 'W', *X*, *Y* positions the tail; in
either of these two cases, *X*, *Y* is somewhere in the middle of the
arrow+label key object.
Parameters
----------
Q : `matplotlib.quiver.Quiver`
A `.Quiver` object as returned by a call to `~.Axes.quiver()`.
X, Y : float
The location of the key.
U : float
The length of the key.
label : str
The key label (e.g., length and units of the key).
angle : float, default: 0
The angle of the key arrow, in degrees anti-clockwise from the
x-axis.
coordinates : {'axes', 'figure', 'data', 'inches'}, default: 'axes'
Coordinate system and units for *X*, *Y*: 'axes' and 'figure' are
normalized coordinate systems with (0, 0) in the lower left and
(1, 1) in the upper right; 'data' are the axes data coordinates
(used for the locations of the vectors in the quiver plot itself);
'inches' is position in the figure in inches, with (0, 0) at the
lower left corner.
color : color
Overrides face and edge colors from *Q*.
labelpos : {'N', 'S', 'E', 'W'}
Position the label above, below, to the right, to the left of the
arrow, respectively.
labelsep : float, default: 0.1
Distance in inches between the arrow and the label.
labelcolor : color, default: :rc:`text.color`
Label color.
fontproperties : dict, optional
A dictionary with keyword arguments accepted by the
`~matplotlib.font_manager.FontProperties` initializer:
*family*, *style*, *variant*, *size*, *weight*.
**kwargs
Any additional keyword arguments are used to override vector
properties taken from *Q*.
"""
martist.Artist.__init__(self)
self.Q = Q
self.X = X
self.Y = Y
self.U = U
self.angle = angle
self.coord = coordinates
self.color = color
self.label = label
self._labelsep_inches = labelsep
self.labelsep = (self._labelsep_inches * Q.axes.figure.dpi)
# try to prevent closure over the real self
weak_self = weakref.ref(self)
def on_dpi_change(fig):
self_weakref = weak_self()
if self_weakref is not None:
self_weakref.labelsep = self_weakref._labelsep_inches * fig.dpi
# simple brute force update works because _init is called at
# the start of draw.
self_weakref._initialized = False
self._cid = Q.axes.figure.callbacks.connect(
'dpi_changed', on_dpi_change)
self.labelpos = labelpos
self.labelcolor = labelcolor
self.fontproperties = fontproperties or dict()
self.kw = kw
_fp = self.fontproperties
# boxprops = dict(facecolor='red')
self.text = mtext.Text(
text=label, # bbox=boxprops,
horizontalalignment=self.halign[self.labelpos],
verticalalignment=self.valign[self.labelpos],
fontproperties=font_manager.FontProperties._from_any(_fp))
if self.labelcolor is not None:
self.text.set_color(self.labelcolor)
self._initialized = False
self.zorder = Q.zorder + 0.1
def plotGraphs(jointPosSeq, jointAnglesSeq, musLengthsSeq, musExcSeq, musActSeq, musForcesSeq, t1, t2, msecInterval, armAnimation, saveGraphs, saveName):
# graph parameters
toDegrees = 360/(2*pi)
toSamples = 1/msecInterval*1000
legFont = 11
linWidth = 3
color1 = "red"
color2 = "blue"
color3 = "green"
color4 = "purple"
line1 = "-"
line2 = ":"
gridOn = 1
# plot with 6 subplots for joint angles, trajectory and each of muscles
fig1 = figure()
# time variables
T = arange(t1, t2, msecInterval/1000.0);
t1Samples = t1*toSamples
t2Samples = t2*toSamples
if armAnimation:
speedFactor = 1 # speed of animation
#create figure and axes
figAnim = figure()
axAnim = figAnim.add_subplot(111)
axAnim.grid(gridOn);
# set axes size to fit arm
axAnim.set_xlim(-armLen[0]-armLen[1]-0.1, armLen[0]+armLen[1]+0.1)
axAnim.set_ylim(-armLen[0]-armLen[1]-0.1, armLen[0]+armLen[1]+0.1)
###########################
# 2D arm movement animation
armImages=[]
for t in arange(t1Samples,t2Samples):
# Update the arm position based on jointPosSeq
if useJointPos:
# use x = z (pnt file) ; y = x (pnt file)
shoulderPosx = jointPosSeq[1, t]
shoulderPosy = jointPosSeq[0, t]
elbowPosx = jointPosSeq[3, t]
elbowPosy = jointPosSeq[2, t]
wristPosx = jointPosSeq[5, t]
wristPosy = jointPosSeq[4, t]
# update jointAnglesSeq based on pos !!!
# Update the arm position based on jointAnglesSeq
else:
armAng = jointAnglesSeq[:,t]
shoulderPosx = 0
shoulderPosy = 0
elbowPosx = armLen[0] * cos(armAng[0]) # end of elbow
elbowPosy = armLen[0] * sin(armAng[0])
wristPosx = elbowPosx + armLen[1] * cos(+armAng[0]+armAng[1]) # wrist=arm position
wristPosy = elbowPosy + armLen[1] * sin(+armAng[0]+armAng[1])
# create
armLine1 = lines.Line2D([0, elbowPosx-shoulderPosx], [0, elbowPosy-shoulderPosy], color=color1, linestyle=line1, linewidth=linWidth)
armLine2 = lines.Line2D([elbowPosx-shoulderPosx, wristPosx-shoulderPosx], [elbowPosy-shoulderPosy, wristPosy-shoulderPosy], color=color2, linestyle=line1, linewidth=linWidth)
axAnim.add_line(armLine1)
axAnim.add_line(armLine2)
#label = plt.legend(armLine1, str(t/toSamples) )
label = text.Text(x=0, y=0.5, text="time = "+str(t/toSamples), weight='bold' )
axAnim.add_artist(label)
armImages.append([armLine1, armLine2, label])
# add blank frames
blankFrames = int(1*toSamples)
for t in range(blankFrames):
# Update the arm position
armLine1 = lines.Line2D([0, 0], [0, 0], color=color1, linestyle=line1, linewidth=linWidth)
armLine2 = lines.Line2D([0,0 ], [0,0], color=color2, linestyle=line1, linewidth=linWidth)
axAnim.add_line(armLine1)
axAnim.add_line(armLine2)
armImages.append([armLine1, armLine2])
# generate animation
armAnim = animation.ArtistAnimation(figAnim, armImages, interval=msecInterval/speedFactor, repeat_delay=500, blit=True)
###########################
# Plot joint angles vs time
ax = fig1.add_subplot(321)
#T = arange(0, secLength, msecInterval/1000.0);
T=T[:len(jointAnglesSeq[0,t1Samples:t2Samples])]
ax.plot(T,jointAnglesSeq[0,t1Samples:t2Samples]*toDegrees,color=color1,linestyle=line1, linewidth=linWidth, label="shoulder")
ax.plot(T,jointAnglesSeq[1,t1Samples:t2Samples]*toDegrees,color=color2,linestyle=line1, linewidth=linWidth, label="elbow")
ax.set_ylabel('angle (deg)', fontsize = legFont)
ax.set_xlabel('time (sec)', fontsize = legFont)
ax.set_title('Joint angles')
ax.legend(loc='upper center', bbox_to_anchor=(1.0, 1.0), borderaxespad=0., prop={'size':legFont})
#ax.set_xlim([t1, t2])
#ax.set_ylim(bmmYlims_sh)
ax.grid(gridOn)
############################
# Plot x-y pos vs time
ax = fig1.add_subplot(322)
# calculate x and y trajectories based on angles
if useJointPos:
xTraj = jointPosSeq[4, t1Samples:t2Samples]
yTraj = jointPosSeq[5, t1Samples:t2Samples]
else:
xTraj = armLen[0]*cos(jointAnglesSeq[0,t1Samples:t2Samples])+armLen[1]*cos(jointAnglesSeq[1,t1Samples:t2Samples])
yTraj = armLen[0]*sin(jointAnglesSeq[0,t1Samples:t2Samples])+armLen[0]*sin(jointAnglesSeq[1,t1Samples:t2Samples])
#ax.plot(xTraj, yTraj,color=color2,linestyle=line1, linewidth=linWidth)
ax.plot(T, xTraj,color=color1,linestyle=line1, linewidth=linWidth, label="x")
ax.plot(T, yTraj,color=color2,linestyle=line1, linewidth=linWidth, label="y")
ax.set_ylabel('position (m)', fontsize = legFont)
#ax.set_xlabel('x position (m)', fontsize = legFont)
ax.set_xlabel('time (sec)', fontsize = legFont)
ax.set_title('X-Y trajectory')
ax.legend(loc='upper center', bbox_to_anchor=(1.0, 1.0), borderaxespad=0., prop={'size':legFont})
#ax.set_xlim([t1, t2])
#ax.set_ylim(bmmYlims_sh)
ax.grid(gridOn)
############################
# Plot excitation, activation and force for each muscle
# calculate normalized force (activation and length already normalized)
#musActSeqNorm = musActSeq/musActSeq[:,t1Samples:t2Samples].max()
musForcesSeqNorm = musForcesSeq/musForcesSeq[:,t1Samples:t2Samples].max()
#musLengthsSeqNorm = musLengthsSeq/musLengthsSeq[:,t1Samples:t2Samples].max()
# Note arrangement of muscle branches in data arrays:
#DELT1(0) DELT2(1) DELT3(2) Infraspinatus(3) Latissimus_dorsi_1(4) Latissimus_dorsi_2(5) Latissimus_dorsi_3(6)
#Teres_minor(7) PECM1(8) PECM2(9) PECM3(10) Coracobrachialis(11) TRIlong(12) TRIlat(13) TRImed(14) BIClong(15) BICshort(16) BRA(17)
# is different from muscle groups:
# Sh ext = DELT3, Infraspinatus, Latissimus_dorsi_1-3, Teres_minor
# Sh flex = PECM1, PECM2, PECM3, DELT1, Coracobrachialis
# El ext = TRIlong, TRIlat, TRImed
# El flex = BIClong, BICshort, BRA
shext=[2,3,4,5,6,7]
shflex=[0,8,9,10,11]
elext=[12,13,14]
elflex=[15,16,17]
musList=[shext, shflex,elext,elflex]
for iMus in range(numMuscles):
ax = fig1.add_subplot(3,2,iMus+3)
# set number of muscle branches - assume each node has 3 branches (treat the Brachialis as a branch of Biceps=elbow flexor)
#iBranches = 3
### Excitation and Activation ####
# equivalent for all branches of same muscle group
offset = 2 # use offset 3 because only DELT3 is used (order of muscle branches doesn't correspond muscle groups!)
ax.plot(T, musExcSeq[musList[iMus][offset],t1Samples:t2Samples],color=color1,linestyle=line1, linewidth=linWidth, label="excitation")
ax.plot(T, musActSeq[musList[iMus][offset],t1Samples:t2Samples],color=color2,linestyle=line1, linewidth=linWidth, label="activation")
# for show branches plot individual branches and mean value for force and length
if showBranches:
### Force and Length ###
for iBranch in range(len(musList[iMus])):
ax.plot(T, musForcesSeqNorm[musList[iMus][iBranch],t1Samples:t2Samples],color=color3,linestyle=line2, linewidth=linWidth-1)
ax.plot(T, musLengthsSeq[musList[iMus][iBranch],t1Samples:t2Samples],color=color4,linestyle=line2, linewidth=linWidth-1)
ax.plot(T, musForcesSeqNorm[musList[iMus],t1Samples:t2Samples].mean(axis=0),color=color3,linestyle=line1, linewidth=linWidth, label="force (mean)")
ax.plot(T, musLengthsSeq[musList[iMus],t1Samples:t2Samples].mean(axis=0),color=color4,linestyle=line1, linewidth=linWidth, label="length (mean)")
# for NOT show branches show mean value for force and single value for length
else:
### Force ###
# For shoulder extensor group show only posterior Deltoid, branch 3 (DELT3) or Infraspinatus (INFSP)
# branch 2 (DELT2 = lateral deltoid) also available but currently not included in shoulder extensor group
if iMus == 0:
offset = 2 # DELT3
#offset = 12 # INFSP
ax.plot(T, musForcesSeqNorm[musList[iMus][offset],t1Samples:t2Samples],color=color3,linestyle=line1, linewidth=linWidth, label="force")
# For rest of muscles use mean value of all branches
else:
offset=0
ax.plot(T, musForcesSeqNorm[musList[iMus],t1Samples:t2Samples].mean(axis=0),color=color3,linestyle=line1, linewidth=linWidth, label="force")
### Length ####
# show length only of one muscle indicated by the index 'offset' - DELT3, PECM1, BIClong, TRIlong
maxLength = 0.20
ax.plot(T, musLengthsSeq[musList[iMus][offset],t1Samples:t2Samples]/maxLength,color=color4,linestyle=line1, linewidth=linWidth, label="length")
# show branche label
if (showBranches):
ax.plot(-1, -1,color=color3,linestyle=line2, linewidth=linWidth, label="force (branches)")
ax.plot(-1, -1,color=color4,linestyle=line2, linewidth=linWidth, label="length (branches)")
# axis properties
ax.set_ylabel('normalized value', fontsize = legFont)
ax.set_ylim([0,1])
ax.set_xlim([t1,t2])
ax.set_xlabel('time (sec)', fontsize = legFont)
ax.set_title(muscleNames[iMus])
if iMus==3:
ax.legend(loc='upper center', bbox_to_anchor=(-0.2, 1.8), borderaxespad=0., prop={'size':legFont})
ax.grid(gridOn)
# show graphs
fig1.tight_layout()
show()
# save graphs using startPos and pattern in filename
if saveGraphs:
saveFolder = 'gif/'
fig1.savefig(saveFolder+saveName, bbox_inches=0)
def plotHtsTrajHM(hchem_id,
exp_id,
add_t0=False,
use_resp='fc',
fgsz=(18, 4),
vmin=-3,
vmax=3,
fs=0.9,
xyoff=[2, -6],
ctrl=False,
iconc=3,
FT=FT1,
FTLB=FTLB1,
LCi=None,
draw_chem=False,
CM=cm.RdYlBu_r,
suffix=1,
save=None,
loc=None,
cb=False,
sub_title=None):
# Get the conc-resp data
X_CR = getChemConcResp(hchem_id,
exp_id=exp_id,
ret='df',
add_t0=add_t0,
prows=[
'chem_id', 'hchem_id', 'chem_name',
'chem_casrn', 'timeh', 'lconc'
],
pcols=['assay_id'])
if X_CR.shape[0] == 0: return
resp_col = None
leg_txt = None
if use_resp == 'zs':
resp_col = 'pzsc'
leg_txt = 'Z'
elif use_resp == 'fc':
resp_col = 'slfc',
leg_txt = r'$log_2(FC)$'
elif use_resp == 'pct':
resp_col = 'ppct'
leg_txt = 'Prcnt'
else:
resp_col = 'slfc'
leg_txt = r'$log_2(FC)$'
X_FC = X_CR.ix[:, resp_col]
# Get LEC
LEC = None
EFF = None
#X_AR = getChemAssayResults(hchem_id,exp_id=exp_id,ret='df')
#if X_AR.shape[0]==0: return
#try:
# LEC = X_AR['llec']
# EFF = X_AR['lfc_eff']
#except:
# print "No LEC data"
fig = pl.figure(figsize=fgsz)
FT0 = set([i for i in X_FC.columns])
TM0 = sorted(set([i[-2] for i in X_FC.index]))
LC0 = list(sorted(set([i[-1] for i in X_FC.index])))
if LCi:
LC0 = [LC0[i] for i in LCi]
#gs1 = gridspec.GridSpec(2,6,width_ratios=[1,1,1,1,1,1])
#if ctrl:
# gs1 = gridspec.GridSpec(1,8,width_ratios=[1,1,1,1,1,1,1,1])
#else:
gs1 = None
if len(LC0) > 5:
gs1 = gridspec.GridSpec(2, 8, width_ratios=[1, 1, 1, 1, 1, 1, 1, 0.3])
ax = pl.subplot(gs1[0:1, 0:1])
else:
gs1 = gridspec.GridSpec(1, 7, width_ratios=[1.2, 1, 1, 1, 1, 1, 0.3])
ax = pl.subplot(gs1[0, 0])
# Chemical name casrn
# ['chem_id', 'hchem_id', 'chem_name', 'chem_casrn', 'lconc']
chem = X_FC.index[0][2]
casrn = X_FC.index[0][3]
sid = X_FC.index[0][1]
cid = X_FC.index[0][0]
nm = None
if len(LC0) > 5:
nm = '\n'.join(wrap(chem, 30)) + '\n' + casrn + '\n' + sid
if sub_title: nm += '\n' + sub_title
else:
nm = '\n'.join(wrap(chem, 25))
txt = text.Text(50,
50,
nm,
ha='center',
va='center',
color='#111111',
fontproperties=fm.FontProperties(size=10))
ax.add_artist(txt)
ax.set_axis_off()
ax.set_xlim(0, 100)
ax.set_ylim(0, 100)
k = 0
iconc = -1
for lc in LC0:
uM = np.round(10**(lc + 6), decimals=2)
X = X_FC[FT].select(lambda xx: xx[iconc] == lc, axis=0)
#print lc,X_FC.shape,X.shape
TM = ['%dh' % tm for tm in TM0]
i = k % 5 + 1
if k < 5:
j = 0
else:
j = 1
ax = pl.subplot(gs1[j, i])
x = ax.pcolor(X.as_matrix(),
cmap=CM,
edgecolors='white',
lw=1,
vmin=vmin,
vmax=vmax)
ax.set_title(r'%5.2f$\mu$M' % uM)
if len(LC0) <= 5 or j == 1:
ax.xaxis.tick_bottom()
ax.set_xticks(np.arange(len(FT0)) + 0.5, minor=False)
ax.set_xticklabels([FTLB[ft] for ft in X.columns], rotation=90)
for tick in ax.get_xticklines():
tick.set_visible(True)
for tick in ax.get_xticklabels():
tick.set_fontsize(9)
else:
for tick in ax.get_xticklines():
tick.set_visible(True)
for lab in ax.get_xticklabels():
lab.set_visible(False)
if (len(LC0) > 5 and i == 2) or i == 1:
ax.yaxis.tick_left()
ax.set_ylim(top=len(TM))
ax.set_yticks(np.arange(len(TM)) + 0.5, minor=False)
ax.set_yticklabels(TM)
for tick in ax.get_yticklines():
tick.set_visible(True)
for tick in ax.get_yticklabels():
tick.set_fontsize(10)
else:
for tick in ax.get_yticklines():
tick.set_visible(False)
for lab in ax.get_yticklabels():
lab.set_visible(False)
k += 1
if len(LC0) > 5:
ax = pl.subplot(gs1[:, 7])
else:
ax = pl.subplot(gs1[:, 6])
ax.set_axis_off()
if cb:
cbr = pl.colorbar(x, ax=ax, shrink=0.9, ticks=range(-vmax, vmax + 1))
cbr.ax.set_xlabel(leg_txt, fontsize=10)
pl.subplots_adjust(wspace=0.3, hspace=0.3, top=1, bottom=0)
if save and loc:
fig.savefig(loc + "traj-hm-%s-%s-%s-%s-%d.svg" %
(resp_col, exp_id.lower(), hchem_id.lower(),
chem.lower().replace(' ', '-'), suffix))
fig.savefig(loc + "traj-hm-%s-%s-%s-%s-%d.png" %
(resp_col, exp_id.lower(), hchem_id.lower(),
chem.lower().replace(' ', '-'), suffix))
def plotHtsConcRespHM(hchem_id,
exp_id,
add_t0=False,
use_resp='fc',
fgsz=(20, 4),
vmin=-3,
vmax=3,
fs=0.9,
xyoff=[2, -6],
ctrl=False,
iconc=3,
FT=FT1,
FTLB=FTLB1,
lec=False,
CM=cm.RdYlBu_r,
draw_chem=False,
save=None,
loc=None,
cb=False,
sub_title=None):
# Get the conc-resp data
X_CR = getChemConcResp(hchem_id, exp_id=exp_id, ret='df', add_t0=add_t0)
if X_CR.shape[0] == 0: return
# Get the fold change
resp_col = None
leg_txt = None
if use_resp == 'zs':
resp_col = 'pzsc'
leg_txt = 'Z'
elif use_resp == 'fc':
resp_col = 'slfc',
leg_txt = r'$log_2(FC)$'
elif use_resp == 'pct':
resp_col = 'ppct'
leg_txt = 'Prcnt'
else:
resp_col = 'slfc'
leg_txt = r'$log_2(FC)$'
X_FC = X_CR[resp_col]
# Get LEC
LEC = None
EFF = None
X_AR = getChemAssayResults(hchem_id, exp_id=exp_id, ret='df')
if X_AR.shape[0] == 0: return
try:
LEC = X_AR['llec']
EFF = X_AR['lfc_eff']
except:
print "No LEC data"
if not lec: LEC = None
fig = pl.figure(figsize=fgsz)
FT0 = set([i[1] for i in X_FC.columns])
TM0 = sorted(set([i[0] for i in X_FC.columns]))
#gs1 = gridspec.GridSpec(2,6,width_ratios=[1,1,1,1,1,1])
#if ctrl:
# gs1 = gridspec.GridSpec(1,8,width_ratios=[1,1,1,1,1,1,1,1])
#else:
gs1 = gridspec.GridSpec(2, 8, width_ratios=[1, 1, 1, 1, 1, 1, 1, 0.3])
# Chemical name casrn
# ['chem_id', 'hchem_id', 'chem_name', 'chem_casrn', 'lconc']
ax = pl.subplot(gs1[0:2, 0:2])
chem = X_FC.index[0][2]
casrn = X_FC.index[0][3]
sid = X_FC.index[0][1]
cid = X_FC.index[0][0]
nm = '\n'.join(wrap(chem, 30)) + '\n' + casrn + '\n' + sid
if sub_title: nm += '\n' + sub_title
txt = text.Text(60,
100,
nm,
ha='center',
va='center',
color='#111111',
fontproperties=fm.FontProperties(size=10))
ax.add_artist(txt)
ax.set_axis_off()
ax.set_xlim(right=120)
ax.set_ylim(top=120)
k = 0
iconc = -1
for ft in FT:
if ft not in FT0: continue
X = X_FC[[(tm, ft) for tm in TM0]]
TM = ['%dh' % tm for tm in TM0]
i = k % 5 + 2
if k < 5:
j = 0
else:
j = 1
ax = pl.subplot(gs1[j, i])
x = ax.pcolor(X.T,
cmap=CM,
edgecolors='white',
lw=1,
vmin=vmin,
vmax=vmax)
ax.set_title(FTLB[ft])
# Calc conc
LC = [ii[iconc] for ii in X.index]
uM_log = np.array(LC)
uM = np.round(10**np.array(uM_log + 6, dtype=np.float), decimals=2)
try:
LLC = [v[iconc] for v in X_FC.index]
LLCx = np.arange(len(LLC)) + 0.5
for it, tm in enumerate(TM0):
if tm == 0: continue
lec_ft = LEC[(tm, ft)]
if lec_ft == 0 or np.isnan(lec_ft): continue
lec_fc = EFF[(tm, ft)]
col = ifthen(lec_fc < 0, 'red', 'blue')
ilc = np.interp(lec_ft, LLC, LLCx)
ax.text(ilc,
it + 0.5,
r'$\bullet$',
ha='center',
va='center',
color=col,
fontproperties=fm.FontProperties(size=20))
except:
pass
#print i
#if i == 0:
#print i,j,ft
if j == 1 or ctrl:
ax.xaxis.tick_bottom()
ax.set_xticks(np.arange(len(uM)) + 0.5, minor=False)
ax.set_xticklabels(uM, rotation=90)
for tick in ax.get_xticklines():
tick.set_visible(True)
for tick in ax.get_xticklabels():
tick.set_fontsize(9)
else:
for tick in ax.get_xticklines():
tick.set_visible(True)
for lab in ax.get_xticklabels():
lab.set_visible(False)
if i == 2:
ax.yaxis.tick_left()
ax.set_ylim(top=len(TM))
ax.set_yticks(np.arange(len(TM)) + 0.5, minor=False)
ax.set_yticklabels(TM)
for tick in ax.get_yticklines():
tick.set_visible(True)
for tick in ax.get_yticklabels():
tick.set_fontsize(10)
else:
for tick in ax.get_yticklines():
tick.set_visible(False)
for lab in ax.get_yticklabels():
lab.set_visible(False)
k += 1
ax = pl.subplot(gs1[:, 7])
ax.set_axis_off()
if cb:
cbr = pl.colorbar(x, ax=ax, shrink=0.9, ticks=range(-vmax, vmax + 1))
cbr.ax.set_xlabel(leg_txt, fontsize=10)
if save and loc:
fig.savefig(loc + "cr-%s-%s-%s-%s.svg" %
(resp_col, exp_id.lower(), hchem_id.lower(),
chem.lower().replace(' ', '-')))
pl.subplots_adjust(wspace=0.1, hspace=0.3, top=0.9, bottom=0.1)
def __init__(self, *args, **kwargs):
# we'll update the position when the line data is set
self.text = mtext.Text(0, 0, '')
LINES.Line2D.__init__(self, *args, **kwargs)
self.text.set_text(kwargs["label"])
def create_artists(self, legend, orig_handle, x0, y0, width, height,
fontsize, trans):
if orig_handle == 'CloudTopPressure':
l1 = plt.Line2D([0.5 * width], [0.5 * height],
marker='s',
ms=2.5,
color='xkcd:magenta')
l2 = plt.Line2D([
x0 + 0.5 * width - 0.4 * height,
x0 + 0.5 * width + 0.4 * height
], [0.5 * height, 0.5 * height],
linestyle='-',
color='xkcd:magenta',
lw=1)
l3 = plt.Line2D([0.5 * width, 0.5 * width],
[0.1 * height, 0.9 * height],
linestyle='-',
color='xkcd:magenta',
lw=1)
return [l1, l2, l3]
if orig_handle == 'SurfacePressure':
l1 = plt.Line2D([0.5 * width], [0.5 * height],
marker='o',
ms=2.5,
color='xkcd:red')
l2 = plt.Line2D([
x0 + 0.5 * width - 0.4 * height,
x0 + 0.5 * width + 0.4 * height
], [0.5 * height, 0.5 * height],
linestyle='-',
color='xkcd:red',
lw=1)
l3 = plt.Line2D([0.5 * width, 0.5 * width],
[0.1 * height, 0.9 * height],
linestyle='-',
color='xkcd:red',
lw=1)
return [l1, l2, l3]
if orig_handle == 'ErrorBar':
l1 = plt.Line2D([width / 2], [0.5 * height],
marker='o',
ms=10,
color='w',
markeredgecolor='k',
alpha=0.2)
l2 = plt.Line2D([x0, x0], [0.2 * height, 0.8 * height],
linestyle='-',
color='k',
lw=2)
l3 = plt.Line2D([y0 + width, y0 + width],
[0.2 * height, 0.8 * height],
linestyle='-',
color='k',
lw=2)
l4 = plt.Line2D([x0, y0 + width], [0.5 * height, 0.5 * height],
color='k',
lw=2)
return [l1, l2, l3, l4]
elif orig_handle == 'Limit':
l1 = plt.Line2D([2 * width / 3], [0.5 * height],
marker='o',
ms=10,
color='w',
markeredgecolor='k',
alpha=0.2)
l2 = plt.Line2D([x0 + width / 3, x0 + width / 3],
[0.2 * height, 0.8 * height],
linestyle='-',
color='k',
lw=2)
l3 = plt.Line2D([y0 + width, y0 + width],
[0.2 * height, 0.8 * height],
linestyle='-',
color='k',
lw=2)
l4 = plt.Line2D([x0 + width / 3, y0 + width],
[0.5 * height, 0.5 * height],
color='k',
lw=2)
l5 = plt.Line2D([x0, y0 + width / 3], [0.5 * height, 0.5 * height],
color='k',
ls=':',
lw=2)
l6 = plt.Line2D([x0 + 3 * 0.2 * height, x0, x0 + 3 * 0.2 * height],
[0.2 * height, 0.5 * height, 0.8 * height],
color='k',
ls='-',
lw=2)
return [l1, l2, l3, l4, l5, l6]
elif orig_handle == 'UpperLimit':
#l1 = plt.Line2D([width/2], [0.5*height], marker = 'o', ms=10,color='w',markeredgecolor='k',alpha=0.2)
l2 = plt.Line2D([x0 + width, x0 + width],
[0.2 * height, 0.8 * height],
linestyle='-',
color='k',
lw=2)
l3 = plt.Line2D([x0, y0 + width], [0.5 * height, 0.5 * height],
color='k',
lw=2)
l4 = plt.Line2D([x0 + 3 * 0.2 * height, x0, x0 + 3 * 0.2 * height],
[0.2 * height, 0.5 * height, 0.8 * height],
color='k',
ls='-',
lw=2)
return [l1, l2, l3, l4]
elif orig_handle == 'LowerLimit':
l1 = plt.Line2D([width / 2], [0.5 * height],
marker='o',
ms=10,
color='w',
markeredgecolor='k',
alpha=0.2)
l2 = plt.Line2D([x0 + width, x0 + width],
[0.2 * height, 0.8 * height],
linestyle='-',
color='k',
lw=2)
l3 = plt.Line2D([x0, y0 + width], [0.5 * height, 0.5 * height],
color='k',
lw=2)
l4 = plt.Line2D([x0 + 3 * 0.2 * height, x0, x0 + 3 * 0.2 * height],
[0.2 * height, 0.5 * height, 0.8 * height],
color='k',
ls='-',
lw=2)
return [l1, l2, l3, l4]
elif orig_handle == 'Unconstrained':
l1 = plt.Line2D([width / 2], [0.5 * height],
marker='o',
ms=10,
color='w',
markeredgecolor='k',
alpha=0.2)
l2 = plt.Line2D([
x0 + width - 3 * 0.2 * height, x0 + width,
x0 + width - 3 * 0.2 * height
], [0.2 * height, 0.5 * height, 0.8 * height],
linestyle='-',
color='k',
lw=2)
l3 = plt.Line2D([x0, y0 + width], [0.5 * height, 0.5 * height],
color='k',
lw=2,
ls=':')
l4 = plt.Line2D([x0 + 3 * 0.2 * height, x0, x0 + 3 * 0.2 * height],
[0.2 * height, 0.5 * height, 0.8 * height],
color='k',
ls='-',
lw=2)
return [l1, l2, l3, l4]
elif orig_handle == 'SNR5':
l1 = plt.Line2D([x0, x0 + width], [0.5 * height, 0.5 * height],
lw=2,
color='k',
ls='-',
alpha=0.2)
l2 = plt.Line2D([width / 2], [0.5 * height],
marker='o',
ms=10,
color='w',
markeredgecolor='k')
return [l1, l2]
elif orig_handle == 'SNR10':
l1 = plt.Line2D([x0, x0 + width], [0.5 * height, 0.5 * height],
lw=2,
color='k',
ls='-',
alpha=0.2)
l2 = plt.Line2D([width / 2], [0.5 * height],
marker='s',
ms=10,
color='w',
markeredgecolor='k')
return [l1, l2]
elif orig_handle == 'SNR15':
l1 = plt.Line2D([x0, x0 + width], [0.5 * height, 0.5 * height],
lw=2,
color='k',
ls='-',
alpha=0.2)
l2 = plt.Line2D([width / 2], [0.5 * height],
marker='D',
ms=10,
color='w',
markeredgecolor='k')
return [l1, l2]
elif orig_handle == 'SNR20':
l1 = plt.Line2D([x0, x0 + width], [0.5 * height, 0.5 * height],
lw=2,
color='k',
ls='-',
alpha=0.2)
l2 = plt.Line2D([width / 2], [0.5 * height],
marker='v',
ms=10,
color='w',
markeredgecolor='k')
return [l1, l2]
elif orig_handle == 'R20':
l1 = plt.Line2D([width / 2], [0.5 * height],
marker='o',
ms=10,
color='w',
markeredgecolor='k',
alpha=0.2)
l2 = plt.Line2D([x0, x0 + width], [0.5 * height, 0.5 * height],
lw=2,
color='C3',
ls='-')
return [l1, l2]
elif orig_handle == 'R35':
l1 = plt.Line2D([width / 2], [0.5 * height],
marker='o',
ms=10,
color='w',
markeredgecolor='k',
alpha=0.2)
l2 = plt.Line2D([x0, x0 + width], [0.5 * height, 0.5 * height],
lw=2,
color='C2',
ls='-')
return [l1, l2]
elif orig_handle == 'R50':
l1 = plt.Line2D([width / 2], [0.5 * height],
marker='o',
ms=10,
color='w',
markeredgecolor='k',
alpha=0.2)
l2 = plt.Line2D([x0, x0 + width], [0.5 * height, 0.5 * height],
lw=2,
color='C0',
ls='-')
return [l1, l2]
elif orig_handle == 'R100':
l1 = plt.Line2D([width / 2], [0.5 * height],
marker='o',
ms=10,
color='w',
markeredgecolor='k',
alpha=0.2)
l2 = plt.Line2D([x0, x0 + width], [0.5 * height, 0.5 * height],
lw=2,
color='C1',
ls='-')
return [l1, l2]
elif orig_handle == 'Prior':
l1 = plt.Line2D([width / 2], [0.5 * height],
marker='o',
ms=10,
color='w',
markeredgecolor='k',
alpha=0.2)
l2 = plt.Line2D([x0, x0 + width], [0.5 * height, 0.5 * height],
lw=2,
color='Black',
ls='-')
return [l1, l2]
else:
title = mtext.Text(x0,
y0,
orig_handle + '',
weight='bold',
usetex=False,
**self.text_props,
fontsize=18)
return [title]
def main(argv=sys.argv):
parser = argparse.ArgumentParser(
description=(
"Stitch a multi-tile image using the nominal stage positions and"
" display the resulting image."
)
)
parser.add_argument(
"input", help="Path to image (BioFormats supported formats only)"
)
parser.add_argument(
"-n", "--numbers", action="store_true", help="Display tile numbers"
)
parser.add_argument(
"-b", "--bounds", action="store_true", help="Display tile bounds"
)
parser.add_argument(
"-c", "--channel", type=int, default=0,
help="Channel number to display; default: 0",
)
parser.add_argument(
"-l", "--log", action="store_true", help="Log-transform pixel intensities"
)
args = parser.parse_args()
reader = reg.BioformatsReader(args.input)
metadata = reader.metadata
positions = metadata.positions - metadata.origin
mshape = ((positions + metadata.size).max(axis=0) + 1).astype(int)
mosaic = np.zeros(mshape, dtype=np.uint16)
total = reader.metadata.num_images
for i in range(total):
sys.stdout.write("\rLoading %d/%d" % (i + 1, total))
sys.stdout.flush()
img = reader.read(c=args.channel, series=i)
img = skimage.util.img_as_uint(img)
if args.log:
scale = 65535 / np.log(65535)
img = (np.log(np.maximum(img, 1)) * scale).astype(np.uint16)
# Round position so paste will skip the expensive subpixel shift.
pos = np.round(positions[i])
utils.paste(mosaic, img, pos, np.maximum)
print()
ax = plt.gca()
plt.imshow(X=mosaic, axes=ax)
h, w = metadata.size
for i, (x, y) in enumerate(np.fliplr(positions)):
if args.bounds:
rect = mpatches.Rectangle((x, y), w, h, color='black', fill=False)
ax.add_patch(rect)
if args.numbers:
xc = x + w / 2
yc = y + h / 2
circle = mpatches.Circle((xc, yc), w / 5, color='salmon', alpha=0.5)
text = mtext.Text(
xc, yc, str(i), color='k', size=10, ha='center', va='center'
)
ax.add_patch(circle)
ax.add_artist(text)
plt.show()
def __init__(self, fig, sort_func, data):
# Create the animation objects
# Artists are scaled according to aspect ratio. We'll need to undo
# this to draw circles.
xsize, ysize = fig.get_size_inches()
yscale = xsize / ysize
# This magic invisible line makes the figure show up
fig.lines.append(
lines.Line2D([0, 0], [0, 1],
transform=fig.transFigure,
figure=fig,
color='white'))
self._spacing = 1.0 / (len(data) + 1)
self._radius = 0.8 * self._spacing
smallest = min(*data)
largest = max(*data)
def scaled_radius(value):
interp = (value - smallest) / (largest - smallest)
return self._radius * (0.6 + interp * 0.4)
def create_artists(i, v):
x = (i + 0.5) * self._spacing
y = 0.5
r = scaled_radius(v)
c = patches.Ellipse((x, y),
r,
yscale * r,
transform=fig.transFigure,
figure=fig,
fill=False)
t = text.Text(x,
y,
str(v),
transform=fig.transFigure,
figure=fig,
verticalalignment='center',
horizontalalignment='center',
fontsize=300 * r)
return c, t
def create_arrow():
return patches.Polygon(self._arrow_points(),
closed=True,
transform=fig.transFigure,
figure=fig,
visible=False)
self._circles, self._texts = map(
list, zip(*[create_artists(i, v) for i, v in enumerate(data)]))
self._arrows = [create_arrow(), create_arrow()]
fig.patches.extend(self._circles)
fig.patches.extend(self._arrows)
fig.texts.extend(self._texts)
self._label = text.Text(0,
0.9,
transform=fig.transFigure,
figure=fig,
verticalalignment='top',
horizontalalignment='left',
fontsize=200 * self._spacing)
fig.texts.append(self._label)
# Collect effects and generate animation frames
effects = []
sort.run(sort_func, data, lambda *e: effects.append(e))
self._generate_frames(effects)
self._focused = []
def __init__(self, *args, **kwargs):
self.text = mtext.Text(0, 0, '')
lines.Line2D.__init__(self, *args, **kwargs)
self.text.set_text(self.get_label())
