def extalg_plot(gi, imgkey=None):
gi.set_plotting_params(gi)
if imgkey and imgkey == 'rainrate':
colormapper = cm.ScalarMappable(norm=colors.NoNorm(), cmap=get_cmap('frozen_cmap'))
currimg = colormapper.to_rgba(normalize(gi.image['rainrate']['frozen']))
# imshow expects upside down arrays, but we should not store them upside down
# so flipud here
gi.basemap.imshow(np.flipud(gi.image['rainrate']['frozen']))
colormapper = cm.ScalarMappable(norm=colors.NoNorm(), cmap=get_cmap('liquid_cmap'))
currimg = colormapper.to_rgba(normalize(gi.image['rainrate']['liquid']))
# imshow expects upside down arrays, but we should not store them upside down
# so flipud here
gi.basemap.imshow(np.flipud(gi.image['rainrate']['liquid']))
##if 'float' in str(gi.image[imgkey].dtype):
## pass
##else:
## gi.image[imgkey].dtype = 'float64'
##gi.basemap.imshow(np.flipud(currimg), ax=gi.axes, interpolation='nearest')
if gi.is_final:
gi.finalize()
def extalg_plot(gi, imgkey=None):
gi.set_plotting_params(gi)
if imgkey and imgkey == 'rainrate':
colormapper = cm.ScalarMappable(norm=colors.NoNorm(),
cmap=get_cmap('frozen_cmap'))
currimg = colormapper.to_rgba(normalize(
gi.image['rainrate']['frozen']))
gi.basemap.imshow(gi.image['rainrate']['frozen'])
colormapper = cm.ScalarMappable(norm=colors.NoNorm(),
cmap=get_cmap('liquid_cmap'))
currimg = colormapper.to_rgba(normalize(
gi.image['rainrate']['liquid']))
gi.basemap.imshow(gi.image['rainrate']['liquid'])
##if 'float' in str(gi.image[imgkey].dtype):
## pass
##else:
## gi.image[imgkey].dtype = 'float64'
##gi.basemap.imshow(currimg, ax=gi.axes, interpolation='nearest')
if gi.is_final:
gi.finalize()
def showImage(inputImage, outputImage):
pyplot.subplot(1, 2, 1)
pyplot.imshow(inputImage, cmap='gray', norm=colors.NoNorm())
pyplot.title('Original')
pyplot.subplot(1, 2, 2)
pyplot.imshow(outputImage, cmap='gray', norm=colors.NoNorm())
pyplot.title('Modified')
pyplot.show()
def _process_colors(self):
"""
Color argument processing for contouring.
Note that we base the color mapping on the contour levels,
not on the actual range of the Z values. This means we
don't have to worry about bad values in Z, and we always have
the full dynamic range available for the selected levels.
The color is based on the midpoint of the layer, except for
an extended end layers.
"""
self.monochrome = self.cmap.monochrome
if self.colors is not None:
i0, i1 = 0, len(self.layers)
if self.extend in ('both', 'min'):
i0 = -1
if self.extend in ('both', 'max'):
i1 = i1 + 1
self.cvalues = range(i0, i1)
self.set_norm(colors.NoNorm())
else:
self.cvalues = self.layers
if not self.norm.scaled():
self.set_clim(self.vmin, self.vmax)
if self.extend in ('both', 'max', 'min'):
self.norm.clip = False
self.set_array(self.layers)
def confirm_slot(self):
cmap = plt.get_cmap(self.colormaps_combox.currentText())
vmin = float(self.min_lineedit.text()
) if self.min_lineedit.text() != '' else None
vmax = float(self.max_lineedit.text()
) if self.max_lineedit.text() != '' else None
clip = self.clip_checkbox.isChecked()
if self.collection:
vmax = self.collection.norm.vmax if vmax is None else vmax
vmin = self.collection.norm.vmin if vmin is None else vmin
if clip:
vmin, vmax = None, None
if self.norms_combox.currentText() == 'Normalize':
norm = mcolors.Normalize(vmin, vmax, clip)
if self.norms_combox.currentText() == 'LogNorm':
norm = mcolors.LogNorm(vmin, vmax, clip)
if self.norms_combox.currentText() == 'NoNorm':
norm = mcolors.NoNorm(vmin, vmax, clip)
# self.ax.set_autoscale_on(True)
if not self.colorbar:
self.collection = self.ax.collections[
self.collections_combox.currentIndex()]
self.collection.cmap = cmap
self.collection.norm = norm
self.colorbar = self.canvas.figure.colorbar(
self.ax.collections[self.collections_combox.currentIndex()],
ax=self.ax)
else:
self.collection.autoscale()
self.collection.cmap = cmap
self.collection.norm = norm
self.colorbar.update_normal(self.collection)
# self.colorbar.norm=norm
self.canvas.draw_idle()
def save_to_file(pred_mask, display_image, gt_mask, i, save_dir):
plt.switch_backend('agg')
plt.figure()
plt.subplot(131)
plt.imshow(display_image)
plt.axis('off')
plt.title('original image')
NUM_CLASSES = 11
cmap = discrete_cmap(NUM_CLASSES, 'Paired')
norm = colors.NoNorm(vmin=0, vmax=NUM_CLASSES)
plt.subplot(132)
plt.imshow(display_image)
plt.imshow(gt_mask, alpha=0.8, cmap=cmap, norm=norm)
plt.axis('off')
plt.title('real mask')
plt.subplot(133)
plt.imshow(display_image)
plt.imshow(pred_mask, alpha=0.8, cmap=cmap, norm=norm)
plt.axis('off')
plt.title('predicted mask')
plt.savefig(os.path.join(save_dir, str(i) + '.png'))
plt.clf()
def showHistogram(inputImage, outputImage, bins=[256, 256]):
pyplot.subplot(2, 2, 1)
pyplot.imshow(inputImage, cmap='gray', norm=colors.NoNorm())
pyplot.title('Original image')
pyplot.subplot(2, 2, 2)
pyplot.hist(inputImage.ravel(), bins[0], [0, bins[0]])
pyplot.title('Original hist')
pyplot.subplot(2, 2, 3)
pyplot.imshow(outputImage, cmap='gray', norm=colors.NoNorm())
pyplot.title('Modified')
pyplot.subplot(2, 2, 4)
pyplot.hist(outputImage.ravel(), 255, [0, bins[1]])
pyplot.title('Modified')
pyplot.show()
def plt_images(images, rows, cols):
fig = plt.figure(figsize=(cols,rows))
fig.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0.05, hspace=0.05)
for i, x in enumerate(images[:cols * rows]):
plt.subplot(rows, cols, i + 1)
plt.axis('off')
plt.imshow(x, cmap='gray', norm=colors.NoNorm())
return fig
def overlay(self, image):
self._overlay = image
if image is None:
self.ax.images.remove(self._overlay_plot)
self._overlay_plot = None
elif self._overlay_plot is None:
props = dict(cmap=self.cmap, alpha=self.alpha,
norm=mcolors.NoNorm(), animated=True)
self._overlay_plot = self.ax.imshow(image, **props)
else:
self._overlay_plot.set_data(image)
self.redraw()
def full_multi_viewer(img, seg_mask, prediction):
remove_keymap_conflicts({'j', 'k'})
fig, (ax_img, ax_seg, ax_pre) = plt.subplots(1, 3)
ax_img.volume = img
ax_seg.volume = seg_mask
ax_pre.volume = prediction
ax_img.index = ax_img.volume.shape[1] // 2
ax_seg.index = ax_seg.volume.shape[1] // 2
ax_pre.index = ax_pre.volume.shape[1] // 2
ax_img.imshow(ax_img.volume[:, ax_img.index, :], cmap='gray')
ax_img.set_title('MRI Scan')
ax_seg.imshow(ax_seg.volume[:, ax_seg.index, :],
cmap='gray',
norm=clr.NoNorm())
ax_seg.set_title('Ground Truth')
ax_pre.imshow(ax_pre.volume[:, ax_pre.index, :],
cmap='gray',
norm=clr.NoNorm())
ax_pre.set_title('Prediction')
fig.canvas.mpl_connect('key_press_event', process_key)
plt.show()
def set_colormap(color=None,
boundaries=[],
normalization='linear',
color_bad='w',
**kwargs):
if color is None or boundaries == []:
return {}
if isinstance(boundaries, np.ndarray):
boundaries = np.atleast_2d(boundaries)
ncolors = len(np.unique(boundaries, axis=0))
boundaries = np.linalg.norm(boundaries, axis=1)
else:
try:
ncolors = len(set(boundaries))
except TypeError:
ncolors = 1
if ncolors == 1 or normalization == 'none':
cmap = matplotlib.cm.get_cmap(color)
norm = colors.NoNorm(None, None)
elif normalization == 'linear':
cmap = matplotlib.cm.get_cmap(color)
norm = colors.Normalize(min(boundaries), max(boundaries))
elif normalization == 'discrete':
cmap = matplotlib.cm.get_cmap(color, ncolors)
norm = colors.BoundaryNorm(boundaries, ncolors)
elif normalization == "log":
cmap = matplotlib.cm.get_cmap(color)
norm = colors.LogNorm(max(min(boundaries), 1e-14), max(boundaries))
else:
cmap = matplotlib.cm.get_cmap(color)
norm = colors.NoNorm(None, None)
cmap.set_bad(color=color_bad)
return {'cmap': cmap, 'norm': norm}
def image(self):
if not hasattr(self, '_image'):
img_dts = {}
pname = self.product.name
sname = self.sector.name
img_dts['start_fullsingleimg' + sname + pname] = datetime.utcnow()
log.info('Creating basic image.')
print_mem_usage(self.logtag + 'gimgbeforeregister', True)
#Register data to area definition
#Performing prior to color gun generation in order to allow
# for multiple data resolutions
gun = self.product.images['img']
img_dts['start_clrgunsingle' + sname + pname] = datetime.utcnow()
self._image = np.flipud(create_color_gun(self.registered_data,
gun))
img_dts['end_clrgunsingle' + sname + pname] = datetime.utcnow()
# add flexibility: if Boundary is added in the productfile.mxl
# the discrete colorbar is selected.
if len(self.product.colorbars
) > 0 and self.product.colorbars[0].norm == 'Boundary':
#ticks = [float(i) for i in self.product.colorbars[0].bounds.split(' ')]
#bounds = [ticks[0]-1] + ticks + [ticks[-1]+1]
colormapper = cm.ScalarMappable(norm=None,
cmap=get_cmap(
self.product.cmap))
else:
colormapper = cm.ScalarMappable(norm=colors.NoNorm(),
cmap=get_cmap(
self.product.cmap))
img_dts['start_torgbasingle' + sname + pname] = datetime.utcnow()
self._image = colormapper.to_rgba(self.image)
img_dts['end_torgbasingle' + sname + pname] = datetime.utcnow()
log.info(sname + pname + ' Done Creating single channel image.')
img_dts['end_fullsingleimg' + sname + pname] = datetime.utcnow()
for sttag in sorted(img_dts.keys()):
if 'start_' in sttag:
tag = sttag.replace('start_', '')
try:
log.info('process image time %-40s: ' % tag +
str(img_dts['end_' + tag] -
img_dts['start_' + tag]))
except:
log.info('WARNING! No end time for ' + sttag)
return self._image
def patch_viewer(patch):
remove_keymap_conflicts({'j', 'k'})
fig, (ax_img, ax_seg) = plt.subplots(1, 2)
ax_img.volume = patch[..., 0]
ax_seg.volume = patch[..., 1]
ax_img.index = ax_img.volume.shape[1] // 2
ax_seg.index = ax_seg.volume.shape[1] // 2
ax_img.imshow(ax_img.volume[:, ax_img.index, :], cmap='gray')
ax_img.set_title('MRI Scan')
ax_seg.imshow(ax_seg.volume[:, ax_seg.index, :],
cmap='gray',
norm=clr.NoNorm())
ax_seg.set_title('Ground Truth')
fig.canvas.mpl_connect('key_press_event', process_key)
plt.show()
def X_singlePlot(imIn, ax, label):
if (imIn.getTypeAsString() == "RGB"):
im3ch = sp.Image()
sp.splitChannels(imIn, im3ch)
imArr = im3ch.getNumArray()
imArr = np.rot90(imArr, -1)
imArr = np.fliplr(imArr)
ax.imshow(imArr)
else:
imInArr = imIn.getNumArray()
imInArr = np.rot90(imInArr, -1)
imInArr = np.fliplr(imInArr)
if not label:
ax.imshow(imInArr, cmap=cm.Greys_r, norm=cl.NoNorm())
else:
ax.imshow(imInArr, cmap=randcmap)
def imshow(Is, titles, savePath=None):
plt.figure(facecolor='w', figsize=(16, 16))
n = len(Is)
sq = int(np.ceil(n**0.5))
r, c = int(np.ceil(n / sq)), sq
for i in range(n):
plt.subplot(n, c, i + 1)
plt.imshow(Is[i], norm=colors.NoNorm(), cmap='gray')
plt.axis('off')
plt.title(titles[i])
if savePath:
cv2.imwrite(os.path.join(savePath, titles[i] + '.png'), Is[i])
# plt.imsave(os.path.join(savePath,titles[i]),Is[i],cmap='gray')
plt.tight_layout()
def display(self, img_id, do_de_normalize=False):
img, _, masks = self[img_id]
if do_de_normalize:
img = de_normalize(img)
display_image = np.transpose(img.numpy(), (1, 2, 0))
plt.figure()
plt.subplot(121)
plt.imshow(display_image)
plt.axis('off')
plt.title('original image')
plt.subplot(122)
plt.imshow(display_image)
cmap = discrete_cmap(self.numClasses, 'Paired')
norm = colors.NoNorm(vmin=0, vmax=self.numClasses)
plt.imshow(masks, alpha=0.8, cmap=cmap, norm=norm)
plt.axis('off')
plt.title('annotated image')
plt.show()
def visualize_mask(trainer, loader, number):
total = 0
to_return = []
for data, mask_gt, gt_visual in loader:
if total < number:
data = data.cuda()
batch_size = data.size()[0]
total += batch_size
mask_pred = convert_to_mask(trainer._gen(data))
for i in range(len(data)):
img = de_normalize(data[i].detach().cpu().numpy())
gt_mask = gt_visual[i].detach().cpu().numpy()
pred_mask = np.argmax(mask_pred[i].detach().cpu().numpy(),
axis=0)
to_return.append((img, gt_mask, pred_mask))
display_image = np.transpose(img, (1, 2, 0))
plt.figure()
plt.subplot(131)
plt.imshow(display_image)
plt.axis('off')
plt.title('original image')
cmap = discrete_cmap(NUM_CLASSES, 'Paired')
norm = colors.NoNorm(vmin=0, vmax=NUM_CLASSES)
plt.subplot(132)
plt.imshow(display_image)
plt.imshow(gt_mask, alpha=0.8, cmap=cmap, norm=norm)
plt.axis('off')
plt.title('real mask')
plt.subplot(133)
plt.imshow(display_image)
plt.imshow(pred_mask, alpha=0.8, cmap=cmap, norm=norm)
plt.axis('off')
plt.title('predicted mask')
plt.show()
else:
break
return to_return
def smilToNumpyPlotNoNorm(imIn, labelImage=False):
if (imIn.getTypeAsString() == "RGB"):
imIn3ch = sp.Image()
sp.splitChannels(imIn, imIn3ch)
imInArr = imIn3ch.getNumArray()
imInArr = np.rot90(imInArr, -1)
imInArr = np.fliplr(imInArr)
plt.figure()
plt.imshow(imInArr)
plt.show()
else:
imInArr = imIn.getNumArray()
imInArr = np.rot90(imInArr, -1)
imInArr = np.fliplr(imInArr)
if not labelImage:
plt.figure()
plt.imshow(imInArr, cmap="gray", norm=cl.NoNorm())
plt.show()
else:
plt.figure()
plt.imshow(imInArr, cmap=randcmap)
plt.show()
def image(self):
if not hasattr(self, '_image'):
img_dts = {}
pname = self.product.name
sname = self.sector.name
img_dts['start_fullsingleimg' + sname + pname] = datetime.utcnow()
log.info('Creating basic image.')
print_mem_usage(self.logtag + 'gimgbeforeregister', True)
#Register data to area definition
#Performing prior to color gun generation in order to allow
# for multiple data resolutions
gun = self.product.images['img']
img_dts['start_clrgunsingle' + sname + pname] = datetime.utcnow()
self._image = np.flipud(create_color_gun(self.registered_data,
gun))
img_dts['end_clrgunsingle' + sname + pname] = datetime.utcnow()
colormapper = cm.ScalarMappable(norm=colors.NoNorm(),
cmap=get_cmap(self.product.cmap))
img_dts['start_torgbasingle' + sname + pname] = datetime.utcnow()
self._image = colormapper.to_rgba(self.image)
img_dts['end_torgbasingle' + sname + pname] = datetime.utcnow()
log.info(sname + pname + ' Done Creating single channel image.')
img_dts['end_fullsingleimg' + sname + pname] = datetime.utcnow()
for sttag in sorted(img_dts.keys()):
if 'start_' in sttag:
tag = sttag.replace('start_', '')
try:
log.info('process image time %-40s: ' % tag +
str(img_dts['end_' + tag] -
img_dts['start_' + tag]) + ' ' +
socket.gethostname())
except:
log.info('WARNING! No end time for ' + sttag)
return self._image
cropax = axarr[1].imshow(x, cmap=plt.get_cmap('gray'))
axarr[1].set_title('Cropped Image')
dx = np.arange(-np.floor(dsize[1] / 2), np.floor(dsize[1] / 2) + 1, dtype=int)
dy = np.arange(-np.floor(dsize[0] / 2), np.floor(dsize[0] / 2) + 1, dtype=int)
[dpx, dpy] = np.meshgrid(dx, dy)
dpx = dpx.reshape(-1, 1)
dpy = dpy.reshape(-1, 1)
dp = np.hstack((dpx, dpy))
N = dpx.size
all_patches = np.ones((N * dsize[0], dsize[1]))
all_patchax = axarr[2].imshow(all_patches,
cmap=plt.get_cmap('gray'),
aspect='auto',
norm=colors.NoNorm())
axarr[2].set_title('Concatenation of Sub-Images (X)')
X = np.zeros((N, N))
Y = np.zeros((N, 1))
sigma = 5
def init():
return [cropax, patch, all_patchax]
def animate(i):
global X, Y, dp, gnd_p, sigma, all_patches, patch, cropax, all_patchax, N
def genplots(save=False, folder="images", **kwargs):
if save:
import os
folder = os.path.join(os.getcwd(), folder)
if not os.path.exists(folder):
os.mkdir(folder)
for key in ('price', 'size_class', 'ratings_avg', 'brand', 'refresh',
'is_3d', 'tv_type', 'resolution'):
data[key] = []
for a in attrs:
try:
if key in ('price', 'size_class', 'ratings_avg', 'refresh'):
if a[key]:
precision = 0
accuracy = 1
if key in ['price', 'refresh']:
precision = -1
elif key in ['size_class']:
accuracy = 2
elif key in ['ratings_avg']:
precision = 0
data[key].append(
round(float(a[key]) / accuracy, precision) *
accuracy)
else:
data[key].append(NaN)
else:
if hasattr(a[key], 'strip'):
data[key].append(a[key].strip(u'\x99'))
else:
data[key].append(a[key])
except KeyError:
print(
u"Couldn't find key: %s for product with attributes: %s" %
(key, a))
unique = sorted(list(set(data[key])))
data[key + "map"] = array([unique.index(item) for item in data[key]])
data[key] = array(data[key])
largelims = None
zoomlims = None
if 'price' in data and 'size_class' in data and not largelims and not zoomlims:
xbuf = 5
ybuf = 100
largelims = {
'xmax': max(data['size_class']) + xbuf,
'xmin': min(data['size_class']) - xbuf,
'ymax': max(data['price']) + ybuf,
'ymin': min(data['price']) - ybuf
}
xmed = median(data['size_class'])
xsd = std(data['size_class'][:, ~isnan(data['size_class'])])
ymed = median(data['price'])
ysd = std(data['price'][:, ~isnan(data['price'])])
zoomlims = {
'xmax': xmed + xsd / 2,
'xmin': xmed - xsd / 2,
'ymax': ymed + ysd / 2,
'ymin': ymed - ysd / 2
}
if key not in ('price', 'size_class') and largelims and zoomlims:
largename = key + "large"
pyplot.figure(largename, figsize=(20, 15))
pyplot.xlim(xmax=largelims['xmax'], xmin=largelims['xmin'])
pyplot.ylim(ymax=largelims['ymax'], ymin=largelims['ymin'])
pyplot.title(largename)
zoomname = key + "zoom"
pyplot.figure(zoomname, figsize=(20, 15))
pyplot.xlim(xmax=zoomlims['xmax'], xmin=zoomlims['xmin'])
pyplot.ylim(ymax=zoomlims['ymax'], ymin=zoomlims['ymin'])
pyplot.title(zoomname)
#TODO: better nan handling
if key in ['price', 'size_class', 'ratings_avg', 'refresh']:
values = data[key][:, ~isnan(data[key])]
prices = data['price'][:, ~isnan(data[key])]
sizes = data['size_class'][:, ~isnan(data[key])]
else:
values = data[key][:, ~equal(data[key], None)]
prices = data['price'][:, ~equal(data[key], None)]
sizes = data['size_class'][:, ~equal(data[key], None)]
for value in set(values):
if len(values[:, equal(values, value)]) > 2:
print "graphing with key: %s and value %s" % (
key, unicode(value))
pyplot.figure(largename)
color = (float(unique.index(value))) / (float(len(unique)))
edgecolor = color #max(0,color-.2)
if kwargs['cmap']:
edgecolor = kwargs['cmap'](int(
round(float(kwargs['cmap'].N) * float(edgecolor))))
color = kwargs['cmap'](int(
round(float(kwargs['cmap'].N) * color)))
else:
edgecolor = str(edgecolor)
color = str(color)
cursizes = sizes[:, values == value]
curprices = prices[:, values == value]
rectlarge = pyplot.Rectangle(
(min(cursizes) - 1, min(curprices) - 10),
max(cursizes) - min(cursizes) + 2,
max(curprices) - min(curprices) + 20,
edgecolor=edgecolor,
linewidth=10,
facecolor=color,
alpha=.1)
pyplot.scatter(cursizes,
curprices,
c=color,
label=unicode(value),
norm=colors.NoNorm(),
**kwargs) #c=data[key+'map'],,cmap=cm.gray)
pyplot.gca().add_patch(rectlarge)
pyplot.gca().text(
max(largelims['xmin'] + 1,
min(cursizes) + 2),
min(largelims['ymax'] - 100,
max(curprices) - 300), unicode(value))
pyplot.figure(zoomname)
rectzoom = pyplot.Rectangle(
(min(cursizes) - 1, min(curprices) - 10),
max(cursizes) - min(cursizes) + 2,
max(curprices) - min(curprices) + 20,
edgecolor=edgecolor,
linewidth=10,
facecolor=color,
alpha=.1)
pyplot.scatter(cursizes,
curprices,
c=color,
label=unicode(value),
**kwargs)
pyplot.gca().add_patch(rectzoom)
pyplot.gca().text(
min(cursizes) + 1,
min(zoomlims['ymax'] - 100, max(curprices)),
unicode(value))
else:
print "rejecting key: %s and value %s" % (key,
unicode(value))
pyplot.figure(largename)
pyplot.legend()
if save:
pyplot.savefig("%s/%s.png" % (folder, largename))
pyplot.figure(zoomname)
pyplot.legend()
if save:
pyplot.savefig("%s/%s.png" % (folder, zoomname))
def clabel(self, *args, **kwargs):
"""
call signature::
clabel(cs, **kwargs)
adds labels to line contours in *cs*, where *cs* is a
:class:`~matplotlib.contour.ContourSet` object returned by
contour.
::
clabel(cs, v, **kwargs)
only labels contours listed in *v*.
Optional keyword arguments:
*fontsize*:
See http://matplotlib.sf.net/fonts.html
*colors*:
- if *None*, the color of each label matches the color of
the corresponding contour
- if one string color, e.g. *colors* = 'r' or *colors* =
'red', all labels will be plotted in this color
- if a tuple of matplotlib color args (string, float, rgb, etc),
different labels will be plotted in different colors in the order
specified
*inline*:
controls whether the underlying contour is removed or
not. Default is *True*.
*inline_spacing*:
space in pixels to leave on each side of label when
placing inline. Defaults to 5. This spacing will be
exact for labels at locations where the contour is
straight, less so for labels on curved contours.
*fmt*:
a format string for the label. Default is '%1.3f'
Alternatively, this can be a dictionary matching contour
levels with arbitrary strings to use for each contour level
(i.e., fmt[level]=string)
*manual*:
if *True*, contour labels will be placed manually using
mouse clicks. Click the first button near a contour to
add a label, click the second button (or potentially both
mouse buttons at once) to finish adding labels. The third
button can be used to remove the last label added, but
only if labels are not inline. Alternatively, the keyboard
can be used to select label locations (enter to end label
placement, delete or backspace act like the third mouse button,
and any other key will select a label location).
*rightside_up*:
if *True* (default), label rotations will always be plus
or minus 90 degrees from level.
*use_clabeltext*:
if *True* (default is False), ClabelText class (instead of
matplotlib.Text) is used to create labels. ClabelText
recalculates rotation angles of texts during the drawing time,
therefore this can be used if aspect of the axes changes.
.. plot:: mpl_examples/pylab_examples/contour_demo.py
"""
"""
NOTES on how this all works:
clabel basically takes the input arguments and uses them to
add a list of "label specific" attributes to the ContourSet
object. These attributes are all of the form label* and names
should be fairly self explanatory.
Once these attributes are set, clabel passes control to the
labels method (case of automatic label placement) or
BlockingContourLabeler (case of manual label placement).
"""
fontsize = kwargs.get('fontsize', None)
inline = kwargs.get('inline', 1)
inline_spacing = kwargs.get('inline_spacing', 5)
self.labelFmt = kwargs.get('fmt', '%1.3f')
_colors = kwargs.get('colors', None)
self._use_clabeltext = kwargs.get('use_clabeltext', False)
# Detect if manual selection is desired and remove from argument list
self.labelManual = kwargs.get('manual', False)
self.rightside_up = kwargs.get('rightside_up', True)
if len(args) == 0:
levels = self.levels
indices = range(len(self.levels))
elif len(args) == 1:
levlabs = list(args[0])
indices, levels = [], []
for i, lev in enumerate(self.levels):
if lev in levlabs:
indices.append(i)
levels.append(lev)
if len(levels) < len(levlabs):
msg = "Specified levels " + str(levlabs)
msg += "\n don't match available levels "
msg += str(self.levels)
raise ValueError(msg)
else:
raise TypeError("Illegal arguments to clabel, see help(clabel)")
self.labelLevelList = levels
self.labelIndiceList = indices
self.labelFontProps = font_manager.FontProperties()
if fontsize == None:
font_size = int(self.labelFontProps.get_size_in_points())
else:
if type(fontsize) not in [int, float, str]:
raise TypeError("Font size must be an integer number.")
# Can't it be floating point, as indicated in line above?
else:
if type(fontsize) == str:
font_size = int(self.labelFontProps.get_size_in_points())
else:
self.labelFontProps.set_size(fontsize)
font_size = fontsize
self.labelFontSizeList = [font_size] * len(levels)
if _colors == None:
self.labelMappable = self
self.labelCValueList = np.take(self.cvalues, self.labelIndiceList)
else:
cmap = colors.ListedColormap(_colors, N=len(self.labelLevelList))
self.labelCValueList = range(len(self.labelLevelList))
self.labelMappable = cm.ScalarMappable(cmap=cmap,
norm=colors.NoNorm())
#self.labelTexts = [] # Initialized in ContourSet.__init__
#self.labelCValues = [] # same
self.labelXYs = []
if self.labelManual:
print 'Select label locations manually using first mouse button.'
print 'End manual selection with second mouse button.'
if not inline:
print 'Remove last label by clicking third mouse button.'
blocking_contour_labeler = BlockingContourLabeler(self)
blocking_contour_labeler(inline, inline_spacing)
else:
self.labels(inline, inline_spacing)
# Hold on to some old attribute names. These are depricated and will
# be removed in the near future (sometime after 2008-08-01), but keeping
# for now for backwards compatibility
self.cl = self.labelTexts
self.cl_xy = self.labelXYs
self.cl_cvalues = self.labelCValues
self.labelTextsList = cbook.silent_list('text.Text', self.labelTexts)
return self.labelTextsList
def _i_mtv(self, data, wcs, title, isMask):
"""Internal routine to display an Image or Mask on a DS9 display"""
title = str(title) if title else ""
dataArr = data.getArray()
if isMask:
maskPlanes = data.getMaskPlaneDict()
nMaskPlanes = max(maskPlanes.values()) + 1
planes = {} # build inverse dictionary
for key in maskPlanes:
planes[maskPlanes[key]] = key
planeList = range(nMaskPlanes)
maskArr = np.zeros_like(dataArr, dtype=np.int32)
colorNames = ['black']
colorGenerator = self.display.maskColorGenerator(omitBW=True)
for p in planeList:
color = self.display.getMaskPlaneColor(
planes[p]) if p in planes else None
if not color: # none was specified
color = next(colorGenerator)
elif color.lower() == afwDisplay.IGNORE:
color = 'black' # we'll set alpha = 0 anyway
colorNames.append(color)
#
# Set the maskArr image to be an index into our colour map (cmap; see below)
#
for i, p in enumerate(planeList):
color = colorNames[i]
maskArr[(dataArr & (1 << p)) !=
0] += i + 1 # + 1 as we set colorNames[0] to black
#
# Convert those colours to RGBA so we can have per-mask-plane transparency
# and build a colour map
#
colors = mpColors.to_rgba_array(colorNames)
colors[0][3] = 0.0 # it's black anyway
for i, p in enumerate(planeList):
if colorNames[i + 1] == 'black':
alpha = 0.0
else:
alpha = 1 - self._getMaskTransparency(planes[p] if p in
planes else None)
colors[i + 1][3] = alpha
dataArr = maskArr
cmap = mpColors.ListedColormap(colors)
norm = mpColors.NoNorm()
else:
cmap = pyplot.cm.gray
norm = self._normalize
ax = self._figure.gca()
bbox = data.getBBox()
mappable = ax.imshow(
dataArr,
origin='lower',
interpolation='nearest',
extent=(bbox.getBeginX() - 0.5, bbox.getEndX() - 0.5,
bbox.getBeginY() - 0.5, bbox.getEndY() - 0.5),
cmap=cmap,
norm=norm)
if not isMask:
self._mappable = mappable
self._figure.canvas.draw_idle()
def __init__(self,
labels=None,
seed=None,
alpha=150,
index_direct=True,
min_val=0,
max_val=255,
min_any=0,
background=None,
dup_for_neg=False,
symmetric_colors=False,
cmap_labels=None):
"""Generate discrete colormap for labels using
:func:``discrete_colormap``.
Args:
labels: Labels of integers for which a distinct color should be
mapped to each unique label. Defults to None, in which case
no colormap will be generated.
seed: Seed for randomizer to allow consistent colormap between
runs; defaults to None.
alpha: Transparency leve; defaults to 150 for semi-transparent.
index_direct: True if the colormap will be indexed directly, which
assumes that the labels will serve as indexes to the colormap
and should span sequentially from 0, 1, 2, ...; defaults to
True. If False, a colormap will be generated for the full
range of integers between the lowest and highest label values,
inclusive, with a :obj:`colors.BoundaryNorm`, which may
incur performance cost.
min_val (int): Minimum value for random numbers; defaults to 0.
max_val (int): Maximum value for random numbers; defaults to 255.
min_any (int, float): Minimum value above which at least one value
must be in each set of RGB values; defaults to 0
background: Tuple of (backround_label, (R, G, B, A)), where
background_label is the label value specifying the background,
and RGBA value will replace the color corresponding to that
label. Defaults to None.
dup_for_neg: True to duplicate positive labels as negative
labels to recreate the same set of labels as for a
mirrored labels map. Defaults to False.
symmetric_colors (bool): True to make symmetric colors, assuming
symmetric labels centered on 0; defaults to False.
cmap_labels (List[str]): Sequence of colors as Matplotlib color
strings or RGB(A) hex (eg "#0fab24ff") strings.
"""
self.norm = None
self.cmap_labels = None
self.img_labels = None
self.symmetric_colors = symmetric_colors
if labels is None: return
labels_unique = np.unique(labels)
if dup_for_neg and np.sum(labels_unique < 0) == 0:
# for labels that are only >= 0, duplicate the pos portion
# as neg so that images with or without negs use the same colors
labels_unique = np.append(
-1 * labels_unique[labels_unique > 0][::-1], labels_unique)
num_colors = len(labels_unique)
labels_offset = 0
if index_direct:
# assume label vals increase by 1 from 0 until num_colors; store
# sorted labels sequence to translate labels based on index
self.norm = colors.NoNorm()
self.img_labels = labels_unique
else:
# use labels as bounds for each color, including wide bounds
# for large gaps between successive labels; offset bounds to
# encompass each label and avoid off-by-one errors that appear
# when viewing images with additional extreme labels; float32
# gives unsymmetric colors for large values in mirrored atlases
# despite remaining within range for unclear reasons, fixed by
# using float64 instead
labels_offset = 0.5
bounds = labels_unique.astype(np.float64)
bounds -= labels_offset
# number of boundaries should be one more than number of labels to
# avoid need for interpolation of boundary bin numbers and
# potential merging of 2 extreme labels
bounds = np.append(bounds, [bounds[-1] + 1])
# TODO: may have occasional colormap inaccuracies from this bug:
# https://github.com/matplotlib/matplotlib/issues/9937;
self.norm = colors.BoundaryNorm(bounds, num_colors)
if cmap_labels is None:
# auto-generate colors for the number of labels
self.cmap_labels = discrete_colormap(num_colors,
alpha,
False,
seed,
min_val,
max_val,
min_any,
symmetric_colors,
jitter=20,
mode=DiscreteModes.RANDOMN)
else:
# generate RGBA colors from supplied color strings
self.cmap_labels = colors.to_rgba_array(cmap_labels) * max_val
if background is not None:
# replace background label color with given color
bkgdi = np.where(labels_unique == background[0] - labels_offset)
if len(bkgdi) > 0 and bkgdi[0].size > 0:
self.cmap_labels[bkgdi[0][0]] = background[1]
#print(self.cmap_labels)
self.make_cmap()
axarr[0].set_title('Image')
cropax = axarr[1].imshow(x, cmap=plt.get_cmap('gray'))
axarr[1].set_title('Cropped Image')
dx = np.arange(-np.floor(dsize[1]/2), np.floor(dsize[1]/2)+1, dtype=int)
dy = np.arange(-np.floor(dsize[0]/2), np.floor(dsize[0]/2)+1, dtype=int)
[dpx, dpy] = np.meshgrid(dx, dy)
dpx = dpx.reshape(-1, 1)
dpy = dpy.reshape(-1, 1)
dp = np.hstack((dpx, dpy))
N = dpx.size
all_patches = np.ones((N*dsize[0], dsize[1]))
all_patchax = axarr[2].imshow(all_patches, cmap=plt.get_cmap('gray'),
aspect='auto', norm=colors.NoNorm())
axarr[2].set_title('Concatenation of Sub-Images (X)')
X = np.zeros((N, N))
Y = np.zeros((N, 1))
sigma = 5
def init():
return [cropax, patch, all_patchax]
def animate(i):
global X, Y, dp, gnd_p, sigma, all_patches, patch, cropax, all_patchax, N
def _i_mtv(self, data, wcs, title, isMask):
"""Internal routine to display an Image or Mask on a DS9 display"""
title = str(title) if title else ""
dataArr = data.getArray()
if isMask:
maskPlanes = data.getMaskPlaneDict()
nMaskPlanes = max(maskPlanes.values()) + 1
planes = {} # build inverse dictionary
for key in maskPlanes:
planes[maskPlanes[key]] = key
planeList = range(nMaskPlanes)
maskArr = np.zeros_like(dataArr, dtype=np.int32)
colorNames = ['black']
colorGenerator = self.display.maskColorGenerator(omitBW=True)
for p in planeList:
color = self.display.getMaskPlaneColor(
planes[p]) if p in planes else None
if not color: # none was specified
color = next(colorGenerator)
elif color.lower() == afwDisplay.IGNORE:
color = 'black' # we'll set alpha = 0 anyway
colorNames.append(color)
#
# Convert those colours to RGBA so we can have per-mask-plane
# transparency and build a colour map
#
# Pixels equal to 0 don't get set (as no bits are set), so leave
# them transparent and start our colours at [1] --
# hence "i + 1" below
#
colors = mpColors.to_rgba_array(colorNames)
alphaChannel = 3 # the alpha channel; the A in RGBA
colors[0][alphaChannel] = 0.0 # it's black anyway
for i, p in enumerate(planeList):
if colorNames[i + 1] == 'black':
alpha = 0.0
else:
alpha = 1 - self._getMaskTransparency(planes[p] if p in
planes else None)
colors[i + 1][alphaChannel] = alpha
cmap = mpColors.ListedColormap(colors)
norm = mpColors.NoNorm()
else:
cmap = self._image_colormap
norm = self._normalize
ax = self._figure.gca()
bbox = data.getBBox()
extent = (bbox.getBeginX() - 0.5, bbox.getEndX() - 0.5,
bbox.getBeginY() - 0.5, bbox.getEndY() - 0.5)
with pyplot.rc_context(dict(interactive=False)):
if isMask:
for i, p in reversed(list(enumerate(planeList))):
if colors[i +
1][alphaChannel] == 0: # colors[0] is reserved
continue
bitIsSet = (dataArr & (1 << p)) != 0
if bitIsSet.sum() == 0:
continue
maskArr[
bitIsSet] = i + 1 # + 1 as we set colorNames[0] to black
if not self._fastMaskDisplay: # we draw each bitplane separately
ax.imshow(maskArr,
origin='lower',
interpolation='nearest',
extent=extent,
cmap=cmap,
norm=norm)
maskArr[:] = 0
if self._fastMaskDisplay: # we only draw the lowest bitplane
ax.imshow(maskArr,
origin='lower',
interpolation='nearest',
extent=extent,
cmap=cmap,
norm=norm)
else:
mappable = ax.imshow(dataArr,
origin='lower',
interpolation='nearest',
extent=extent,
cmap=cmap,
norm=norm)
self._mappable = mappable
self._figure.canvas.draw_idle()
def main_kohonen(args):
"""testing the map from extero to proprio sensor subspaces
it is general in that if the map is underdetermined (dim_e < dim_p),
the map can cope with multiple solutions and samples from the joint density
in-situ Hebbian linked SOMs (Miikkulainen) using lmjohns3's kohonen python lib"""
from kohonen.kohonen import Map, Parameters, ExponentialTimeseries, ConstantTimeseries
from kohonen.kohonen import Gas, GrowingGas, GrowingGasParameters, Filter
import matplotlib.colors as mcolors
from mpl_toolkits.mplot3d import Axes3D
# extract datadir from datfile
datadir = "/".join(args.datafile.split("/")[:-1])
# load offline data from active inference experiment
# EP = np.load("EP_1000.npy") # [:200]
# EP = np.load("EP.npy") # [:500]
# EP = np.load("EP.npy")[500:600]
EP = np.load(args.datafile)
som_e_save = datadir + "/" + "som_filter_e.pkl"
som_p_save = datadir + "/" + "som_filter_p.pkl"
som_e2p_link_save = datadir + "/" + "som_e2p_link.npy"
# learning rate proxy
ET = ExponentialTimeseries
# som argument dict
def kwargs(shape=(10, 10), z=0.001, dimension=2, lr_init = 1.0, neighborhood_size = 1):
return dict(dimension=dimension,
shape=shape,
neighborhood_size = neighborhood_size,
learning_rate=ET(-1e-4, lr_init, 0.01),
noise_variance=z)
mapsize = 4
# FIXME: make neighborhood_size decrease with time
# SOM exteroceptive stimuli 2D input
kw_e = kwargs(shape = (mapsize, mapsize), dimension = dim_e, lr_init = 0.5, neighborhood_size = 0.6)
som_e = Map(Parameters(**kw_e))
# SOM proprioceptive stimuli 3D input
kw_p = kwargs(shape = (int(mapsize * 1.5), int(mapsize * 1.5)), dimension = dim_p, lr_init = 0.5, neighborhood_size = 0.7)
som_p = Map(Parameters(**kw_p))
# kw = kwargs((64, ))
# som_e = Gas(Parameters(**kw))
# kw = kwargs((64, ))
# kw['growth_interval'] = 7
# kw['max_connection_age'] = 17
# som_e = GrowingGas(GrowingGasParameters(**kw))
# kw_f_e = kwargs(shape = (mapsize, mapsize), dimension = 2, neighborhood_size = 0.75, lr_init = 1.0)
# filter_e = Filter(Map(Parameters(**kw_f_e)))
# create "filter" using existing SOM_e, filter computes activation on distance
filter_e = Filter(som_e, history=lambda: 0.0)
filter_e.reset()
# kw_f_p = kwargs(shape = (mapsize * 3, mapsize * 3), dimension = 3, neighborhood_size = 0.5, lr_init = 0.1)
# filter_p = Filter(Map(Parameters(**kw_f_p)), history=lambda: 0.01)
# create "filter" using existing SOM_p, filter computes activation on distance
filter_p = Filter(som_p, history=lambda: 0.0)
filter_p.reset()
# Hebbian links
# hebblink_som = np.random.uniform(-1e-4, 1e-4, (np.prod(som_e._shape), np.prod(som_p._shape)))
# hebblink_filter = np.random.uniform(-1e-4, 1e-4, (np.prod(filter_e.map._shape), np.prod(filter_p.map._shape)))
hebblink_som = np.zeros((np.prod(som_e._shape), np.prod(som_p._shape)))
hebblink_filter = np.zeros((np.prod(filter_e.map._shape), np.prod(filter_p.map._shape)))
# # plot initial weights as images
# pl.subplot(211)
# pl.imshow(hebblink_som + 0.5, interpolation="none", norm=mcolors.NoNorm())
# pl.colorbar()
# pl.subplot(212)
# pl.imshow(hebblink_filter + 0.5, interpolation="none", norm=mcolors.NoNorm())
# pl.colorbar()
# pl.show()
fig = pl.figure()
numepisodes_som = 10 # 30
numepisodes_hebb = 10 # 30
numsteps = EP.shape[0]
################################################################################
# check for trained SOM
if not os.path.exists(som_e_save) and \
not os.path.exists(som_p_save):
################################################################################
# train the SOMs on the input
# som_e_barbase = np.linspace(-2, 2, np.prod(filter_e.map._shape))
# som_p_barbase = np.linspace(-2, 2, np.prod(filter_p.map._shape))
pl.ion()
# pl.figure()
# pl.show()
for j in range(numepisodes_som):
for i in range(numsteps):
e = EP[i,:dim_e]
p = EP[i,dim_e:]
# don't learn twice
# som_e.learn(e)
# som_p.learn(p)
filter_e.learn(e)
filter_p.learn(p)
# print np.argmin(som_e.distances(e)) # , som_e.distances(e)
# on plot interval, update plot :)
if i % 50 == 0:
ax = fig.add_subplot(121)
# pl.subplot(121)
ax.cla()
ax.plot(filter_e.map.neurons[:,:,0], filter_e.map.neurons[:,:,1], "ko", alpha=0.5, ms=10)
# data
ax.plot(e[0], e[1], "bx", alpha=0.7, ms=12)
# winner
# ax.plot(som_e.neurons[w_e[0],w_e[1],0], som_e.neurons[w_e[0],w_e[1],1], "ro", alpha=0.7, ms=12)
# ax.bar(som_e_barbase, filter_e.distances(e).flatten(), width=0.01, bottom = -2, alpha=0.1)
# ax.stem(filter_e.distances(e), "k", alpha=0.1)
ax.set_xlim((-2, 2))
ax.set_ylim((-2, 2))
ax.set_aspect(1)
ax.text(-1.0, 1.2, "%d / %d, eta = %f" % ((j * numsteps) + i, numepisodes_som * numsteps, som_e._learning_rate()))
ax = fig.add_subplot(122) #, projection='3d')
# pl.subplot(122)
ax.cla()
ax.plot(filter_p.map.neurons[:,:,0], filter_p.map.neurons[:,:,1], "ko", alpha=0.5, ms=10)
# ax.bar(som_p_barbase, filter_p.distances(p).flatten(), width=0.01, bottom = -2, alpha=0.1)
ax.set_xlim((-2, 2))
ax.set_ylim((-2, 2))
pl.gca().set_aspect(1)
pl.pause(0.01)
pl.draw()
# print som_e.neurons
################################################################################
# save SOMs
# print "filter.map shapes", filter_e.map._shape, filter_p.map._shape
cPickle.dump(filter_e.map, open(som_e_save, "wb"))
cPickle.dump(filter_p.map, open(som_p_save, "wb"))
else:
print "loading existing SOMs"
filter_e.map = cPickle.load(open(som_e_save, "rb"))
filter_p.map = cPickle.load(open(som_p_save, "rb"))
# filter_e.reset()
# filter_p.reset()
# print "filter.map shapes", filter_e.map._shape, filter_p.map._shape
j = numepisodes_som - 1
i = numsteps - 1
# sys.exit()
################################################################################
# plot final SOM configurations
pl.ioff()
# pl.subplot(121)
ax = fig.add_subplot(121)
ax.cla()
ax.plot(filter_e.map.neurons[:,:,0], filter_e.map.neurons[:,:,1], "ko", alpha=0.5, ms=10)
ax.plot(EP[:,0], EP[:,1], "r.", alpha=0.3, label="data_e")
ax.set_xlim((-2, 2))
ax.set_ylim((-2, 2))
ax.set_aspect(1)
ax.text(-0.8, 0.7, "%d, eta = %f" % ((j * EP.shape[0]) + i, som_e._learning_rate()))
ax.legend()
# pl.subplot(224)
ax = fig.add_subplot(122, projection='3d')
ax.scatter(filter_p.map.neurons[:,:,0], filter_p.map.neurons[:,:,1], filter_p.map.neurons[:,:,2], "ko", alpha=0.5)#, ms=10)
ax.plot(EP[:,2], EP[:,3], EP[:,4], "r.", alpha=0.3, ms=5)
#ax.set_xlim((-2, 2))
#ax.set_ylim((-2, 2))
#ax.set_zlim((-2, 2))
pl.gca().set_aspect(1)
pl.show()
################################################################################
# fix the SOMs with learning rate constant 0
CT = ConstantTimeseries
filter_e.map.learning_rate = CT(0.0)
filter_p.map.learning_rate = CT(0.0)
################################################################################
# now train Hebbian associations on fixed SOM
use_activity = True
# Hebbian learning rate
if use_activity:
et = ExponentialTimeseries(-1e-4, 0.8, 0.001)
# et = ConstantTimeseries(0.5)
else:
et = ConstantTimeseries(1e-5)
e_shape = (np.prod(filter_e.map._shape), 1)
p_shape = (np.prod(filter_p.map._shape), 1)
z_err_coef = 0.99
z_err_norm_ = 1
Z_err_norm = np.zeros((numepisodes_hebb*numsteps,1))
Z_err_norm_ = np.zeros((numepisodes_hebb*numsteps,1))
W_norm = np.zeros((numepisodes_hebb*numsteps,1))
if not os.path.exists(som_e2p_link_save):
for j in range(numepisodes_hebb):
# while
for i in range(numsteps):
e = EP[i,:dim_e]
p = EP[i,dim_e:]
# just activate
filter_e.learn(e)
filter_p.learn(p)
# fetch data induced activity
if use_activity:
p_ = filter_p.activity.reshape(p_shape)
else:
p_ = filter_p.distances(p).flatten().reshape(p_shape)
# # get winner coord and flattened index
# w_e_idx = som_e.winner(e)
# # w_p_idx = som_p.winner(p)
# w_e = som_e.flat_to_coords(w_e_idx)
# # w_p = som_p.flat_to_coords(w_p_idx)
# # get winner coord and flattened index
# w_f_e_idx = filter_e.winner(e)
# # w_f_p_idx = filter_p.winner(p)
# w_f_e = filter_e.flat_to_coords(w_f_e_idx)
# # w_f_p = filter_p.flat_to_coords(w_f_p_idx)
# print som_e.neuron(w_e), som_p.neuron(w_p)
#
# hebblink_som[w_e_idx,w_p_idx] += 0.01
# hebblink_filter[w_f_e_idx,w_f_p_idx] += 0.01
# print "filter_e.activity", filter_e.activity
# print "filter_p.activity", filter_p.activity
# print "np.outer(filter_e.activity.flatten(), filter_p.activity.flatten())", np.outer(filter_e.activity.flatten(), filter_p.activity.flatten()).shape
# compute prediction for p using e activation and hebbian weights
if use_activity:
p_bar = np.dot(hebblink_filter.T, filter_e.activity.reshape(e_shape))
else:
p_bar = np.dot(hebblink_filter.T, filter_e.distances(e).flatten().reshape(e_shape))
# inject activity prediction
p_bar_sum = p_bar.sum()
if p_bar_sum > 0:
p_bar_normed = p_bar / p_bar_sum
else:
p_bar_normed = np.zeros(p_bar.shape)
# print np.linalg.norm(p_), np.linalg.norm(p_bar)
# clip p_bar positive
# p_bar = np.clip(p_bar, 0, np.inf)
# compute prediction error: data induced activity - prediction
z_err = p_ - p_bar
# z_err = p_bar - p_
z_err_norm = np.linalg.norm(z_err, 2)
if j == 0 and i == 0:
z_err_norm_ = z_err_norm
else:
z_err_norm_ = z_err_coef * z_err_norm_ + (1 - z_err_coef) * z_err_norm
w_norm = np.linalg.norm(hebblink_filter)
logidx = (j*numsteps) + i
Z_err_norm [logidx] = z_err_norm
Z_err_norm_[logidx] = z_err_norm_
W_norm [logidx] = w_norm
# z_err = p_bar - filter_p.activity.reshape(p_bar.shape)
# print "p_bar.shape", p_bar.shape
# print "filter_p.activity.flatten().shape", filter_p.activity.flatten().shape
if i % 100 == 0:
print "iter %d/%d: z_err.shape = %s, |z_err| = %f, |W| = %f, |p_bar_normed| = %f" % (logidx, (numepisodes_hebb*numsteps), z_err.shape, z_err_norm_, w_norm, np.linalg.norm(p_bar_normed))
# print
# d_hebblink_filter = et() * np.outer(filter_e.activity.flatten(), filter_p.activity.flatten())
if use_activity:
d_hebblink_filter = et() * np.outer(filter_e.activity.flatten(), z_err)
else:
d_hebblink_filter = et() * np.outer(filter_e.distances(e), z_err)
hebblink_filter += d_hebblink_filter
np.save(som_e2p_link_save, hebblink_filter)
################################################################################
# show final Hebbian weights
pl.subplot(411)
pl.imshow(hebblink_som + 0.5, interpolation="none", norm=mcolors.NoNorm())
pl.colorbar()
pl.subplot(412)
# pl.imshow(hebblink_filter + 0.5, interpolation="none", norm=mcolors.NoNorm())
pl.imshow(hebblink_filter, interpolation="none")
pl.colorbar()
pl.subplot(413)
pl.plot(Z_err_norm, linewidth=0.5)
pl.plot(Z_err_norm_)
pl.gca().set_yscale("log")
pl.subplot(414)
pl.plot(W_norm)
pl.show()
else:
print "Loading existing Hebbian link"
hebblink_filter = np.load(som_e2p_link_save)
# do prediction using activation propagation from extero map to proprio map via hebbian links
from explauto import Environment
environment = Environment.from_configuration('simple_arm', 'low_dimensional')
environment.noise = 0.
sampling_search_num = 100
P_ = np.zeros((EP.shape[0], dim_p))
E_ = np.zeros((EP.shape[0], dim_e))
# e2p_w_p_weights = filter_p.neuron(filter_p.flat_to_coords(filter_p.sample(1)[0]))
for i in range(EP.shape[0]):
e = EP[i,:dim_e]
p = EP[i,dim_e:]
# print np.argmin(som_e.distances(e)), som_e.distances(e)
filter_e.learn(e)
# print "filter_e.winner(e)", filter_e.winner(e)
# filter_p.learn(p)
# print "filter_e.activity.shape", filter_e.activity.shape
# import pdb; pdb.set_trace()
if use_activity:
e2p_activation = np.dot(hebblink_filter.T, filter_e.activity.reshape((np.prod(filter_e.map._shape), 1)))
filter_p.activity = np.clip((e2p_activation / np.sum(e2p_activation)).reshape(filter_p.map._shape), 0, np.inf)
else:
e2p_activation = np.dot(hebblink_filter.T, filter_e.distances(e).flatten().reshape(e_shape))
# print "e2p_activation.shape, np.sum(e2p_activation)", e2p_activation.shape, np.sum(e2p_activation)
# print "filter_p.activity.shape", filter_p.activity.shape
# print "np.sum(filter_p.activity)", np.sum(filter_p.activity), (filter_p.activity >= 0).all()
# filter_p.learn(p)
emode = 0 # 1, 2
if i % 1 == 0:
if emode == 0:
e2p_w_p_weights_ = []
for k in range(sampling_search_num):
e2p_w_p_weights = filter_p.neuron(filter_p.flat_to_coords(filter_p.sample(1)[0]))
e2p_w_p_weights_.append(e2p_w_p_weights)
pred = np.array(e2p_w_p_weights_)
# print "pred", pred
pred_err = np.linalg.norm(pred - p, 2, axis=1)
# print "np.linalg.norm(e2p_w_p_weights - p, 2)", np.linalg.norm(e2p_w_p_weights - p, 2)
e2p_w_p = np.argmin(pred_err)
print "pred_err", e2p_w_p, pred_err[e2p_w_p]
e2p_w_p_weights = e2p_w_p_weights_[e2p_w_p]
elif emode == 1:
if use_activity:
e2p_w_p = np.argmax(e2p_activation)
else:
e2p_w_p = np.argmin(e2p_activation)
e2p_w_p_weights = filter_p.neuron(filter_p.flat_to_coords(e2p_w_p))
elif emode == 2:
e2p_w_p = filter_p.winner(p)
e2p_w_p_weights = filter_p.neuron(filter_p.flat_to_coords(e2p_w_p))
P_[i] = e2p_w_p_weights
E_[i] = environment.compute_sensori_effect(P_[i])
# print "e * hebb", e2p_w_p, e2p_w_p_weights
pl.ioff()
err_extero = EP[:,:dim_e] - E_
print "final error MSE", np.mean(np.square(err_extero))
pl.subplot(211)
pl.title("Extero measured and predicted by E2P with P prediction reexecuted through system")
pl.plot(EP[:,:dim_e])
pl.plot(E_)
pl.subplot(212)
pl.title("Proprio measured and predicted by E2P")
pl.plot(EP[:,dim_e:])
pl.plot(P_)
# pl.subplot(412)
# pl.title("Proprio dim 1")
# pl.plot(EP[:,2])
# pl.plot(P_[:,0])
# pl.subplot(413)
# pl.title("Proprio dim 2")
# pl.plot(EP[:,3])
# pl.plot(P_[:,1])
# pl.subplot(414)
# pl.title("Proprio dim 3")
# pl.plot(EP[:,4])
# pl.plot(P_[:,2])
pl.show()
def _i_mtv(self, data, wcs, title, isMask):
"""Internal routine to display an Image or Mask on a DS9 display"""
title = str(title) if title else ""
dataArr = data.getArray()
if isMask:
maskPlanes = data.getMaskPlaneDict()
nMaskPlanes = max(maskPlanes.values()) + 1
planes = {} # build inverse dictionary
for key in maskPlanes:
planes[maskPlanes[key]] = key
planeList = range(nMaskPlanes)
maskArr = np.zeros_like(dataArr, dtype=np.int32)
colors = ['black']
colorGenerator = self.display.maskColorGenerator(omitBW=True)
for p in planeList:
color = self.display.getMaskPlaneColor(planes[p]) if p in planes else None
if not color: # none was specified
color = next(colorGenerator)
colors.append(color)
#
# Set the maskArr image to be an index into our colour map (cmap; see below)
#
for i, p in enumerate(planeList):
color = colors[i]
if color.lower() == "ignore":
continue
maskArr[(dataArr & (1 << p)) != 0] += i + 1 # + 1 as we set colors[0] to black
#
# Convert those colours to RGBA so we can have per-mask-plane transparency
# and build a colour map
#
colors = mpColors.to_rgba_array(colors)
colors[0][3] = 0.0 # it's black anyway
for i, p in enumerate(planeList):
colors[i + 1][3] = 1 - self._getMaskTransparency(planes[p] if p in planes else None)
dataArr = maskArr
cmap = mpColors.ListedColormap(colors)
norm = mpColors.NoNorm()
else:
cmap = pyplot.cm.gray
norm = self._normalize
ax = self._figure.gca()
bbox = data.getBBox()
ax.imshow(dataArr, origin='lower', interpolation='nearest',
extent=(bbox.getBeginX() - 0.5, bbox.getEndX() - 0.5,
bbox.getBeginY() - 0.5, bbox.getEndY() - 0.5),
cmap=cmap, norm=norm)
if False:
if evData:
axes = self._figure.get_axes()[0]
myText = axes.text(0.05, 1.05, 'Press "return" to show intensity here',
transform=axes.transAxes, va='top')
global eventHandlers
eventHandlers[self._figure] = EventHandler((evData, myText), self._figure)
self._figure.canvas.draw_idle()
lim = axes.get_xlim() + axes.get_ylim()
for bar in bars:
bar.set_zorder(1)
bar.set_facecolor("none")
x, y = bar.get_xy()
w, h = bar.get_width(), bar.get_height()
a_min = 0.4
inverse = 1 - a_min
maximum = a_min + (inverse * w / max(y_val))
z = create_gradient_array(color, alpha_min=a_min, alpha_max=maximum)
z = np.rot90(z)
payload = dict(extent=[x, x + w, y, y + h],
aspect="auto",
zorder=0,
norm=mcolors.NoNorm(vmin=0, vmax=1))
axes.imshow(z, **payload)
axes.axis(lim)
return save_matplotlib(fig, axes)
def save_matplotlib(fig, axes):
fig.delaxes(axes)
fig.add_axes(axes)
buffer = io.BytesIO()
fig.savefig(buffer, transparent=True, bbox_inches="tight")
axes.clear()
fig.clf()
plt.close(fig)
return buffer
def clabel(self, *args, **kwargs):
"""
clabel(CS, **kwargs) - add labels to line contours in CS,
where CS is a ContourSet object returned by contour.
clabel(CS, V, **kwargs) - only label contours listed in V
keyword arguments:
* fontsize = None: as described in http://matplotlib.sf.net/fonts.html
* colors = None:
- a tuple of matplotlib color args (string, float, rgb, etc),
different labels will be plotted in different colors in the order
specified
- one string color, e.g. colors = 'r' or colors = 'red', all labels
will be plotted in this color
- if colors == None, the color of each label matches the color
of the corresponding contour
* inline = True: controls whether the underlying contour is removed
(inline = True) or not (False)
* fmt = '%1.3f': a format string for the label
"""
fontsize = kwargs.get('fontsize', None)
inline = kwargs.get('inline', 1)
self.fmt = kwargs.get('fmt', '%1.3f')
_colors = kwargs.get('colors', None)
if len(args) == 0:
levels = self.levels
indices = range(len(self.levels))
elif len(args) == 1:
levlabs = list(args[0])
indices, levels = [], []
for i, lev in enumerate(self.levels):
if lev in levlabs:
indices.append(i)
levels.append(lev)
if len(levels) < len(levlabs):
msg = "Specified levels " + str(levlabs)
msg += "\n don't match available levels "
msg += str(self.levels)
raise ValueError(msg)
else:
raise TypeError("Illegal arguments to clabel, see help(clabel)")
self.label_levels = levels
self.label_indices = indices
self.fp = font_manager.FontProperties()
if fontsize == None:
font_size = int(self.fp.get_size_in_points())
else:
if type(fontsize) not in [int, float, str]:
raise TypeError("Font size must be an integer number.")
# Can't it be floating point, as indicated in line above?
else:
if type(fontsize) == str:
font_size = int(self.fp.get_size_in_points())
else:
self.fp.set_size(fontsize)
font_size = fontsize
self.fslist = [font_size] * len(levels)
if _colors == None:
self.label_mappable = self
self.label_cvalues = npy.take(self.cvalues, self.label_indices)
else:
cmap = colors.ListedColormap(_colors, N=len(self.label_levels))
self.label_cvalues = range(len(self.label_levels))
self.label_mappable = cm.ScalarMappable(cmap = cmap,
norm = colors.NoNorm())
#self.cl = [] # Initialized in ContourSet.__init__
#self.cl_cvalues = [] # same
self.cl_xy = []
self.labels(inline)
for label in self.cl:
self.ax.add_artist(label)
self.label_list = cbook.silent_list('text.Text', self.cl)
return self.label_list