def plot_imgs(imgs, ratios=[1, 1]):
plt.gray()
gs = gridspec.GridSpec(1, len(imgs), width_ratios=ratios)
for i in range(len(imgs)):
plt.subplot(gs[i])
plt.imshow(imgs[i])
return gs
def __init__(self,panelName,outBaseDir):
print("""Keybindings:
x : restart current rectangle
n : start next rectangle
w : save results and move to next image
= : (twice) terminate the program (without saving)
""")
self.outBaseDir=outBaseDir
self.quit=False
self.panelName=panelName
tif = TIFF.open(panelName, mode='r')
panel = tif.read_image()
if (np.max(panel>255)):
dmax=65535.0
else:
dmax=255.0
self.panel=np.uint8(255*(panel/dmax)) #16-> 8 bits
self.crops=[]
self.curCrop=[]
self.rects=[]
self.curRect=[]
self.fig, self.ax = plt.subplots()
self.fig.canvas.mpl_connect('button_press_event', self.onclick)
self.fig.canvas.mpl_connect('key_press_event', self.press)
plt.gray()
plt.title(basename(panelName))
self.ax.imshow(self.panel)
plt.show()
def plot_imgs(imgs, ratios=[1, 1]):
plt.gray()
gs = gridspec.GridSpec(1, len(imgs), width_ratios=ratios)
for i in range(len(imgs)):
plt.subplot(gs[i])
plt.imshow(imgs[i])
return gs
def plot_from_xml(fn1=None, fnx=None, window=7):
"""Makes a dot-plot from xml and fasta sequence.
:param fn1: Fasta file.
:param fnx: XML file.
:param window: Threshold, for example (5)'
:return: None
"""
if fn1 is not None and fnx is not None:
with open(fn1, 'r') as fh, open(fnx, 'r') as fx:
window = int(window)
file1 = NCBIXML.read(fh)
filex = NCBIXML.read(fx)
seq_one = str(file1.seq).upper()
seq_two = str(filex.seq).upper()
data = [[(seq_one[i:i + window] != seq_two[j:j + 5]) for j in range(len(seq_one) - window)] for i
in range(len(seq_two) - window)]
pylab.gray()
pylab.imshow(data)
pylab.xlabel(
'{} (length {} bp)'.format(file1.seq, len(file1.seq)))
pylab.ylabel(
'{} (length {} bp)'.format(filex.seq, len(filex.seq)))
pylab.title('Dot plot using window size {}\n(allowing no mis-matches)'.format(window))
pylab.show()
def rec_test(file_name, sino_start, sino_end):
print "\n#### Processing " + file_name
sino_start = sino_start + 200
sino_end = sino_start + 2
print "Test reconstruction of slice [%d]" % sino_start
# Read HDF5 file.
prj, flat, dark = tomopy.io.exchange.read_aps_32id(file_name, sino=(sino_start, sino_end))
# Manage the missing angles:
theta = tomopy.angles(prj.shape[0])
prj = np.concatenate((prj[0 : miss_angles[0], :, :], prj[miss_angles[1] + 1 : -1, :, :]), axis=0)
theta = np.concatenate((theta[0 : miss_angles[0]], theta[miss_angles[1] + 1 : -1]))
# normalize the prj
prj = tomopy.normalize(prj, flat, dark)
# reconstruct
rec = tomopy.recon(prj, theta, center=best_center, algorithm="gridrec", emission=False)
# Write data as stack of TIFs.
tomopy.io.writer.write_tiff_stack(rec, fname=output_name)
print "Slice saved as [%s_00000.tiff]" % output_name
# show the reconstructed slice
pl.gray()
pl.axis("off")
pl.imshow(rec[0])
def __init__(self, ax, collection, mmc, img):
self.colornormalizer = Normalize(vmin=0, vmax=1, clip=False)
self.scat = plt.scatter(img[:, 0], img[:, 1], c=mmc.classvec)
plt.gray()
plt.setp(ax.get_yticklabels(), visible=False)
ax.yaxis.set_tick_params(size=0)
plt.setp(ax.get_xticklabels(), visible=False)
ax.xaxis.set_tick_params(size=0)
self.img = img
self.canvas = ax.figure.canvas
self.collection = collection
#self.alpha_other = alpha_other
self.mmc = mmc
self.prevnewclazz = None
self.xys = collection
self.Npts = len(self.xys)
self.lockedset = set([])
self.lasso = LassoSelector(ax, onselect=self.onselect)#, lineprops = {:'prism'})
self.lasso.disconnect_events()
self.lasso.connect_event('button_press_event', self.lasso.onpress)
self.lasso.connect_event('button_release_event', self.onrelease)
self.lasso.connect_event('motion_notify_event', self.lasso.onmove)
self.lasso.connect_event('draw_event', self.lasso.update_background)
self.lasso.connect_event('key_press_event', self.onkeypressed)
#self.lasso.connect_event('button_release_event', self.onrelease)
self.ind = []
self.slider_axis = plt.axes(slider_coords, visible = False)
self.slider_axis2 = plt.axes(obj_fun_display_coords, visible = False)
self.in_selection_slider = None
newws = list(set(range(len(self.collection))) - self.lockedset)
self.mmc.new_working_set(newws)
self.lasso.line.set_visible(False)
def show_map(map):
num = len(map)
pylab.figure()
pylab.gray()
for i in xrange(num):
pylab.subplot(1, num, i + 1)
pylab.imshow(squareStack(map[i]))
pylab.show()
def show_beta(beta):
size, channels = beta.shape
beta = beta.T.reshape((channels, int(np.sqrt(size)), int(np.sqrt(size))))
beta = squareStack(beta)
pylab.figure()
pylab.gray()
pylab.imshow(beta)
pylab.show()
def testFaceImg():
read_file=open(imgPath+'olivettifaces.pkl','rb')
faces=pickle.load(read_file)
read_file.close()
img1=faces[1].reshape(57,47)
pylab.imshow(img1)
pylab.gray()
pylab.show()
def plot_harris_points(image, filtered_coords):
#绘制Harris检测结果
pylab.figure()
pylab.gray()
pylab.imshow(image)
pylab.plot([p[1] for p in filtered_coords],
[p[0] for p in filtered_coords], '*')
pylab.axis('off')
pylab.show()
def contour(image):
"""
contour plot
"""
plt.figure()
image = image.convert('L')
plt.gray()
plt.contour(image, origin='image')
plt.axis('equal')
def plot_representation(n_subplot_vertical, n_suplot_horizontal, location, filename, label):
# let's use this inappropriatly named function
[n_inputs, n_neurons, weights] = weights_filename_to_array(filename)
representations = weights
pylab.subplot(n_subplot_vertical, n_suplot_horizontal, location)
pylab.imshow(representations, aspect="auto", interpolation="nearest")
pylab.xlabel(label)
pylab.gray()
def plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal, location, filename, do_transpose, label):
[n_inputs, n_neurons, weights] = weights_filename_to_array(filename)
if do_transpose:
weights = numpy.transpose(weights)
pylab.subplot(nsubplot_vertical, nsubplot_horizontal, location)
pylab.imshow(weights, aspect="auto", interpolation="nearest")
pylab.xlabel(label)
pylab.gray()
def plot_representation(n_subplot_vertical, n_suplot_horizontal, location,
filename, label):
# let's use this inappropriatly named function
[n_inputs, n_neurons, weights] = weights_filename_to_array(filename)
representations = weights
pylab.subplot(n_subplot_vertical, n_suplot_horizontal, location)
pylab.imshow(representations, aspect='auto', interpolation='nearest')
pylab.xlabel(label)
pylab.gray()
def plot_feature_maps(layer, num_features, filename):
plt.figure()
plt.gray()
layer_array = np.array(layer)
for i in range(num_features):
plt.subplot(num_features / 10, 10, i + 1)
plt.axis("off")
plt.imshow(layer_array[0, :, :, i])
plt.savefig("../Out/" + filename + ".png")
plt.close()
def plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal, location,
filename, do_transpose, label):
[n_inputs, n_neurons, weights] = weights_filename_to_array(filename)
if do_transpose:
weights = numpy.transpose(weights)
pylab.subplot(nsubplot_vertical, nsubplot_horizontal, location)
pylab.imshow(weights, aspect='auto', interpolation='nearest')
pylab.xlabel(label)
pylab.gray()
def gray(image):
"""
plot gray image
:param image: PIL.Image object
:return:
"""
plt.figure()
image = image.convert('L')
aimage = np.array(image)
print(aimage.shape, aimage.dtype)
plt.gray()
plt.imshow(np.array(aimage))
def save_energy_map(img):
im = rgb2gray(imageio.imread(img)) # RGB image to gray scale
plt.gray()
plt.figure(figsize=(20,10))
plt.subplot(221)
plt.imshow(im)
plt.title('original', size=10)
plt.subplot(222)
edges = filters.sobel(im)
plt.imshow(edges)
plt.title('sobel', size=10)
plt.savefig('../energy/energymap.png', dpi = 100, bbox_inches='tight')
def save_D_figs(self, patchsize, dirname='./image/'):
from utils.image_patch_utils import gen_patch_image
import matplotlib
matplotlib.use('Agg')
import matplotlib.pylab as plt
plt.gray()
for i in range(len(self._ancestor_history)):
D = self._gen_D(i)
patch_img = gen_patch_image(D, patchsize, emphasis=True)
plt.imshow(patch_img)
plt.axis('off')
plt.savefig(dirname + 'bases_' + str(i) + '.png', bbox_inches='tight')
def show_image(self):
n = 8 # how many digits we will display
plt.figure(figsize=(20, 4))
for i in range(n):
# display original
ax = plt.subplot(2, n, i + 1)
plt.imshow(self.images[i])
plt.gray()
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
ax.title.set_text(self.labels[i])
plt.show()
def im_hist_eq_2(image):
aimage = np.array(image.convert('L'))
ae_image, cdf = histeq(aimage)
plt.figure()
plt.gray()
plt.subplot(211)
plt.imshow(aimage)
plt.subplot(212)
plt.imshow(ae_image)
plt.axis('off')
def save_images(self, n_image, result):
pic = np.zeros((n_image * self.n_canvas, n_image * self.n_canvas))
images = np.squeeze(self.__call__(False, n_image))
images = images.reshape((-1, self.n_canvas, self.n_canvas))
for i in six.moves.range(n_image):
for j in six.moves.range(n_image):
pic[self.n_canvas * i:self.n_canvas * i + self.n_canvas,
self.n_canvas * j:self.n_canvas * j + self.n_canvas] = \
images[i * n_image + j]
plt.imshow(pic, vmin=-1, vmax=1, interpolation='none')
plt.gray()
plt.savefig('{}/image_{}.png'.format(result, self.n_saved))
self.n_saved += 1
def test_rect():
im = array(Image.open('face.bmp').convert('L'))
pts = array([[90, 260], [90, 530], [400, 530], [400, 260]])
i0, j0 = pts.min(axis=0)
i1, j1 = pts.max(axis=0)
plt.figure()
plt.subplot(1, 2, 1)
plt.gray()
plt.imshow(im)
add_rect(i0, j0, i1 - i0, j1 - j0)
plt.subplot(1, 2, 2)
box = im[i0:i1, j0:j1]
plt.imshow(box)
plt.show()
def test_rect():
im = array(Image.open('face.bmp').convert('L'))
pts = array([[90, 260], [90, 530], [400, 530], [400, 260]])
i0, j0 = pts.min(axis=0)
i1, j1 = pts.max(axis=0)
plt.figure()
plt.subplot(1, 2, 1)
plt.gray()
plt.imshow(im)
add_rect(i0, j0, i1 - i0, j1 - j0)
plt.subplot(1, 2, 2)
box = im[i0:i1, j0:j1]
plt.imshow(box)
plt.show()
def save_beta_lrf(beta, dir, name):
global img_count
save_path = os.path.join('/home', username, 'images', dir)
if not os.path.exists(save_path):
os.makedirs(save_path)
pic_path = os.path.join(save_path, str(img_count) + name + '.png')
img_count += 1
size, channels = beta.shape
beta = beta.T.reshape((channels, int(np.sqrt(size)), int(np.sqrt(size))))
pylab.figure()
pylab.gray()
pylab.imshow(squareStack(beta), interpolation=interpolation)
pylab.savefig(pic_path)
pylab.close()
def save_map_lrf(map, dir, name):
global img_count
save_path = os.path.join('/home', username, 'images', dir)
if not os.path.exists(save_path):
os.makedirs(save_path)
pic_path = os.path.join(save_path, str(img_count) + name + '.png')
img_count += 1
num = len(map)
pylab.figure()
pylab.gray()
for i in xrange(num):
pylab.subplot(1, num, i + 1)
pylab.imshow(squareStack(map[i]), interpolation=interpolation)
pylab.savefig(pic_path)
pylab.close()
def make_onechannel_movie( image_data_file, outfile_name, lower_threshold = 0 ):
###This function takes a .tif stack as input and makes an .mp4 movie.
###Parameters:
###image_data: numpy array containing images; TxYxX
###outfile_name: output file to write to; should be .mp4
###lower_threshold: pixel values will be thresholded frame-by-frame at the percentile chosen as 'lower_threshold'. Default is 0.
import matplotlib
matplotlib.use("Agg")
import matplotlib.pylab as pt
import matplotlib.animation as manimation
import numpy
from skimage import io
image_data = io.imread( image_data_file )
ntsteps, nx, ny = image_data.shape
figdimx = int(nx/200)
figdimy = int(ny/200)
FFMpegWriter = manimation.writers['ffmpeg']
metadata = dict(title=outfile_name.strip('.mp4'), artist='Matplotlib', comment='Movie support!')
writer = FFMpegWriter(fps=15, metadata=metadata)
pt.gray()
fig = pt.figure(figsize=(figdimx,figdimy))
l = pt.imshow(image_data[0,:,:].T/numpy.max(image_data[0,:,:]))
ax = pt.gca()
with writer.saving(fig, outfile_name, dpi=400):
for t in range(ntsteps):
#drift_mask = numpy.nonzero(image_data[t, :, :]) ###
frame_min = numpy.percentile(image_data[t, :, :], lower_threshold)
frame_max = numpy.max(image_data[t, :, :])
l.set_data( (image_data[t,:,:].T - frame_min)/(frame_max - frame_min))
ax.set_yticks([])
ax.set_xticks([])
writer.grab_frame()
def save_beta_mch(beta, mch, dir, name):
global img_count
save_path = os.path.join('/home', username, 'images', dir)
if not os.path.exists(save_path):
os.makedirs(save_path)
pic_path = os.path.join(save_path, str(img_count) + name + '.png')
img_count += 1
size, channels = beta.shape
size /= mch
beta = np.split(beta.T, mch, axis=1)
beta = np.concatenate(beta, axis=0)
beta = beta.reshape((mch * channels, int(np.sqrt(size)), int(np.sqrt(size))))
pylab.figure()
pylab.gray()
pylab.imshow(squareStack(beta))
pylab.savefig(pic_path)
pylab.close()
def save_beta_fc(beta):
save_path = os.path.join('/home', username, 'images', time.asctime())
if not os.path.exists(save_path):
os.makedirs(save_path)
n_feature, n_hidden = beta.shape
num = int(np.ceil(n_hidden / 100.))
img_side = int(np.sqrt(n_feature))
img = beta.T.reshape((-1, img_side, img_side))
pylab.figure()
pylab.gray()
for i in xrange(num):
one_img = img[:100]
img = img[100:]
pylab.imshow(squareStack(one_img), interpolation=interpolation)
pic_path = os.path.join(save_path, str(i) + '.png')
pylab.savefig(pic_path)
pylab.close()
def draw_out_put_digit(data, n, ans, recog):
"""
学習済みのモデルが判定した画像を描画します.
@param data 画像データ
@param n 画像の通し番号
@param ans 正解ラベル
@param recog 推定した数字
"""
plt.subplot(10, 10, n)
Z = data.reshape(SIZE, SIZE)
Z = Z[::-1, :]
plt.xlim(0, 27)
plt.ylim(0, 27)
plt.pcolor(Z)
plt.title('ans=%d, recog=%d' % (ans, recog), size=8)
plt.gray()
plt.tick_params(labelbottom='off')
plt.tick_params(labelleft='off')
def restruct_picture(x_test, decoded_imgs, dim):
n = 10 # how many digits we will display
plt.figure(figsize=(20, 4))
for i in range(n):
# display original
ax = plt.subplot(2, n, i + 1)
plt.imshow(x_test[i].reshape(dim, dim))
plt.gray()
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# display reconstruction
ax = plt.subplot(2, n, i + 1 + n)
plt.imshow(decoded_imgs[i].reshape(dim, dim))
plt.gray()
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
plt.show()
def plot_matches(img1, img2, locs1, locs2, matchscores, show_below=True):
pylab.figure()
pylab.gray()
img3 = append_images(img1, img2)
if show_below:
img3 = np.vstack((img3, img3))
pylab.imshow(img3)
clos1 = img1.shape[1]
count = 0
for i, m in enumerate(matchscores):
if (m > 0):
pylab.plot([locs1[i][1], locs2[m][1] + clos1],
[locs1[i][0], locs2[m][0]], 'c')
if (count > 10):
break
count += 1
pylab.axis('off')
pylab.show()
def _update_image(self):
" redraw image "
if self.AxesImage is not None: self.AxesImage.remove();
self.AxesImage = self.axis.imshow(self.image.T,cmap=plt.gray(),\
origin='lower',aspect='equal',extent=self.imginfo['extent']);
self.axis.set_xlabel("x [%s]" % self.imginfo['xunits']);
self.axis.set_ylabel("y [%s]" % self.imginfo['yunits']);
self.axis.set_xlim(*self.imginfo['extent'][0:2]);
self.axis.set_ylim(*self.imginfo['extent'][2:4]);
self._update();
def array_manipulate(image):
aimage = np.array(image.convert('L'))
ai_image = 255 - aimage # f(x) = 255 - x
ac_image = (100.0 / 255) * aimage + 100 # f(x) = (100 / 255)* x + 100
aq_image = 255.0 * (aimage / 255.0)**2 # f(x) = 255 * (x/255)
plt.figure()
plt.gray()
plt.subplot(311)
plt.imshow(ai_image)
plt.axis('off')
plt.subplot(312)
plt.imshow(ac_image)
plt.axis('off')
plt.subplot(313)
plt.imshow(aq_image)
plt.axis('off')
def test_ff_on_image(test_image_name):
print test_image_name
test_image = double(asarray(PIL.Image.open(test_image_name)))
if len(test_image.shape) == 3:
test_image = mean(test_image, 2)
radial_ff = FastRadialFeatureFinder()
radial_ff.target_kpixels = 3.0
radial_ff.correct_downsampling = True
radial_ff.radius_steps = 20
radial_ff.min_radius_fraction = 1. / 200
radial_ff.max_radius_fraction = 1. / 5
starburst_ff = \
CLSubpixelStarburstFeatureFinder()
composite_ff = CompositeFeatureFinder(radial_ff, starburst_ff)
composite_ff.analyze_image(test_image, {'timestamp': 0})
features = composite_ff.get_result()
# do it twice to allow compilation
composite_ff.analyze_image(test_image)
features = composite_ff.get_result()
plt.figure()
plt.imshow(test_image, interpolation='nearest')
plt.gray()
plt.hold(True)
cr_position = features['cr_position']
pupil_position = features['pupil_position']
plt.plot([cr_position[1]], [cr_position[0]], 'g+')
plt.plot([pupil_position[1]], [pupil_position[0]], 'g+')
sb = features['starburst']
cr_bounds = sb['cr_boundary']
pupil_bounds = sb['pupil_boundary']
for b in cr_bounds:
plt.plot([b[1]], [b[0]], 'rx')
for b in pupil_bounds:
plt.plot([b[1]], [b[0]], 'gx')
def test_ff_on_image(test_image_name):
print test_image_name
test_image = double(asarray(PIL.Image.open(test_image_name)))
if len(test_image.shape) == 3:
test_image = mean(test_image, 2)
radial_ff = FastRadialFeatureFinder()
radial_ff.target_kpixels = 3.0
radial_ff.correct_downsampling = True
radial_ff.radius_steps = 20
radial_ff.min_radius_fraction = 1. / 200
radial_ff.max_radius_fraction = 1. / 5
starburst_ff = \
CLSubpixelStarburstEyeFeatureFinder()
composite_ff = CompositeEyeFeatureFinder(radial_ff, starburst_ff)
composite_ff.analyze_image(test_image, {'timestamp': 0})
features = composite_ff.get_result()
# do it twice to allow compilation
composite_ff.analyze_image(test_image)
features = composite_ff.get_result()
plt.figure()
plt.imshow(test_image, interpolation='nearest')
plt.gray()
plt.hold(True)
cr_position = features['cr_position']
pupil_position = features['pupil_position']
plt.plot([cr_position[1]], [cr_position[0]], 'g+')
plt.plot([pupil_position[1]], [pupil_position[0]], 'g+')
sb = features['starburst']
cr_bounds = sb['cr_boundary']
pupil_bounds = sb['pupil_boundary']
for b in cr_bounds:
plt.plot([b[1]], [b[0]], 'rx')
for b in pupil_bounds:
plt.plot([b[1]], [b[0]], 'gx')
def plot_hidden_space(x_test, encode_func, zoom=0.5):
encoded = encode_func(x_test)
fig, ax = plt.subplots(figsize=(11, 11))
imscatter(encoded[:, 0],
encoded[:, 1],
x_test.reshape((-1, 28, 28)),
zoom=zoom,
ax=ax)
ax.spines['left'].set_position('center')
ax.spines['bottom'].set_position('center')
ax.spines['right'].set_color('none')
ax.spines['top'].set_color('none')
ax.xaxis.set_ticks_position('bottom')
ax.yaxis.set_ticks_position('left')
plt.gray()
plt.show()
def show_images(imnames, titles=None, rows=1, figsize=(30, 8)):
images = [plt.imread(imname) for imname in flatten(imnames)]
n_images = len(images)
if titles is None: titles = ['Image (%d)' % i for i in range(n_images + 1)]
elif type(titles) == str:
titles = [titles + '(%d)' % i for i in range(n_images + 1)]
fig = plt.figure(figsize=figsize)
for n, (image, title) in enumerate(zip(images, titles)):
a = fig.add_subplot(rows, np.ceil(n_images / float(rows)), n + 1)
image = np.squeeze(image)
if image.ndim == 2:
plt.gray()
plt.imshow(image)
plt.axis('off')
a.set_title(title, fontsize=20)
# fig.set_size_inches(np.array(fig.get_size_inches()) * n_images)
plt.show()
def plot_from_fasta(fn1=None, fn2=None, window=7):
"""Makes a dot-plot two fasta files.
:param fn1: Fasta file.
:param fn2: Fasta file.
:param window: Threshold, for example (5)
:return: None
"""
if fn1 is not None and fn2 is not None:
with open(fn1, 'r') as fh1, open(fn2, 'r') as fh2:
window = int(window)
file1 = SeqIO.read(fh1, format='fasta')
file2 = SeqIO.read(fh2, format='fasta')
dict_one = {}
dict_two = {}
for (seq, section_dict) in [(str(file1.seq).upper(), dict_one),
(str(file2.seq).upper(), dict_two)]:
for i in range(len(seq) - window):
section = seq[i:i + window]
try:
section_dict[section].append(i)
except KeyError:
section_dict[section] = [i]
matches = set(dict_one).intersection(dict_two)
print('{} unique matches'.format(len(matches)))
x, y = [], []
for section in matches:
for i in dict_one[section]:
for j in dict_two[section]:
x.append(i)
y.append(j)
pylab.cla()
pylab.gray()
pylab.scatter(x, y)
pylab.xlim(0, len(file1) - window)
pylab.ylim(0, len(file2) - window)
pylab.xlabel('{} (length {} bp)'.format(file1.id, len(file1.seq)))
pylab.ylabel('{} (length {} bp)'.format(file2.id, len(file2.seq)))
pylab.title('Dot plot using window size {}\n(allowing no mis-matches)'.format(window))
pylab.show()
def main():
valve = utils.valve_io.read_valve(sys.argv[1])
image = valve["image"]
# extract the patch
patch_size = 30
seg, smooth = filters.segmentation.segment_by_valve_patch(
image, valve["i1"],
float(sys.argv[2]), (patch_size,patch_size))
# display the image
fig, (ax1,ax2,ax3) = plt.subplots(1,3)
plt.gray()
ax1.imshow(image)
ax2.imshow(smooth)
ax3.imshow(seg)
plt.show()
def _reset_image(self):
" redraw image "
self.vmin = np.min(self.image);
self.vmax = np.max(self.image);
self.vmean= np.mean(self.image);
self.cmap = plt.cm.gray;
if self.AxesImage is not None: self.AxesImage.remove();
self.AxesImage = self.axis.imshow(self.image,cmap=plt.gray(),\
extent=self.imginfo['extent'],**self.kwargs);
self.axis.set_xlabel("%s [%s]" % (self.imginfo['xlabel'], self.imginfo['xunits']));
self.axis.set_ylabel("%s [%s]" % (self.imginfo['ylabel'], self.imginfo['yunits']));
self.axis.set_xlim(*self.imginfo['extent'][0:2]);
self.axis.set_ylim(*self.imginfo['extent'][2:4]);
self.set_style(self.currentstyle);
#figsize = fig_bmp.size[0]/dpi, fig_bmp.size[1]/dpi
#figure(figsize=figsize)
#ax2.axis('scaled')
#ax2.get_xaxis().set_ticks([]);
#ax2.get_yaxis().set_ticks([]);
ax3.get_xaxis().set_ticks([]);
ax3.get_yaxis().set_ticks([]);
#im2 = ax2.imshow(fig_bmp, origin='lower')
#im2 = ax2.imshow(fig_bmp, origin='lower', cmap=pylab.gray())
#im2 = ax2.imshow(fig_bmp, cmap=pylab.gray())
im3 = ax3.imshow(fig_tv03, cmap=pylab.gray())
pylab.savefig(filename+'.png',fmt='png',transparent=False,bbox_inches='tight');
pylab.clf()
# Merging to make .avi
not_found_msg = """
The mencoder command was not found;
mencoder is used by this script to make an avi file from a set of pngs.
It is typically not installed by default on linux distros because of
legal restrictions, but it is widely available.
"""
#figsize = fig_bmp.size[0]/dpi, fig_bmp.size[1]/dpi
#figure(figsize=figsize)
#ax2.axis('scaled')
ax2.get_xaxis().set_ticks([]);
ax2.get_yaxis().set_ticks([]);
ax3.get_xaxis().set_ticks([]);
ax3.get_yaxis().set_ticks([]);
#im2 = ax2.imshow(fig_bmp, origin='lower')
#im2 = ax2.imshow(fig_bmp, origin='lower', cmap=pylab.gray())
im2 = ax2.imshow(fig_bmp, cmap=pylab.gray())
im3 = ax3.imshow(fig_tv03)
pylab.savefig(filename+'.png',fmt='png',transparent=False,bbox_inches='tight');
pylab.clf()
# Merging to make .avi
not_found_msg = """
The mencoder command was not found;
mencoder is used by this script to make an avi file from a set of pngs.
It is typically not installed by default on linux distros because of
legal restrictions, but it is widely available.
"""
def show(im, gray=True):
plt.figure()
if gray:
plt.gray()
plt.imshow(im)
plt.show()
#-----------------------------------------------------------------------
import astra
import numpy as np
vol_geom = astra.create_vol_geom(256, 256)
proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False))
# As before, create a sinogram from a phantom
import scipy.io
P = scipy.io.loadmat('phantom.mat')['phantom256']
proj_id = astra.create_projector('line',proj_geom,vol_geom)
sinogram_id, sinogram = astra.create_sino(P, proj_id, gpuIndex=0)
import matplotlib.pylab as pylab
pylab.gray()
pylab.figure(1)
pylab.imshow(P)
pylab.figure(2)
pylab.imshow(sinogram)
# Create a data object for the reconstruction
rec_id = astra.data2d.create('-vol', vol_geom)
# Set up the parameters for a reconstruction algorithm using the GPU
cfg = astra.astra_dict('SIRT_CUDA')
cfg['ReconstructionDataId'] = rec_id
cfg['ProjectionDataId'] = sinogram_id
# Available algorithms:
# SIRT_CUDA, SART_CUDA, EM_CUDA, FBP_CUDA (see the FBP sample)
import numpy
from matplotlib import pylab
from PIL import Image
from conv import f
img = Image.open(open('./3wolfmoon.jpg'))
img = numpy.asarray(img, dtype='float64')/256
img_ = img.swapaxes(0,2).swapaxes(1,2).reshape(1,3,584,487)
#img_ = img.swapaxes(0,2).swapaxes(1,2).reshape(1,3,128,128)
filtered_img = f(img_)
pylab.subplot(1, 3, 1); pylab.axis('off'); pylab.imshow(img)
pylab.gray();
pylab.subplot(1, 3, 2); pylab.axis('off'); pylab.imshow(filtered_img[0,0,:,:])
pylab.subplot(1, 3, 3); pylab.axis('off'); pylab.imshow(filtered_img[0,1,:,:])
#pylab.savefig('lena_conv.jpg')
#pylab.savefig('conv.jpg')
pylab.show('./3wolfmoon.jpg')
data2dsmoth = smooth_2d(data2d, n_times) mask2d = find_mask_2d(data2d, data2dsmoth, n_times) # end code that will become production code from matplotlib import pyplot as plt col_from = 0 col_to = 950 row_from = 0 row_to = 550 print "Plotting data2d" data2d = data2d.as_numpy_array() data2d = data2d[row_from:row_to,col_from:col_to] plt.imshow(data2d, interpolation = "nearest") plt.show() print "Plotting data2dsmoth" np_data2dsmoth = data2dsmoth.as_numpy_array() np_data2dsmoth = np_data2dsmoth[row_from:row_to,col_from:col_to] plt.imshow(np_data2dsmoth, interpolation = "nearest")#, cmap = pylab.gray()) plt.show() print "Plotting data2d mask" np_data2dmask = mask2d.as_numpy_array() np_data2dmask = np_data2dmask[row_from:row_to,col_from:col_to] plt.imshow(np_data2dmask, interpolation = "nearest", cmap = pylab.gray())#, cmap = pylab.gray()) plt.show()
def set_cmap(self,cmap=None): "Change the colormap" if cmap is None: self.cmap=plt.gray(); else: self.cmap=cmap;
#---------------------------------------------------------- # Programme #on passe en niveau de gris (marche seulement avec des .jpg) img0 = cv2.cvtColor(img0,cv2.COLOR_GRAY2BGR) #on passe à un seul channel img1 = mh.colors.rgb2grey(img0) #on supprime les composantes connexes de trop petite taille img12 = binary(img1,200) img1 = areaclose(img12,2000) plt.imshow(img1) plt.gray() plt.show() #on supprime tout ce qui n'est pas barre horizontal (à quelques degrés près) a = 7 img2 = close(img1,seline(a,90)) img3 = close(img1,seline(a,89)) img4 = close(img1,seline(a,88)) img5 = close(img1,seline(a,87)) img6 = close(img1,seline(a,91)) img7 = close(img1,seline(a,92)) img8 = close(img1,seline(a,93)) img9 = close(img1,seline(a,94)) img = union(img2,img3,img4,img5,img6,img7,img8,img9) plt.imshow(img)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from PhloxAR.descriptor import harris
from PIL import Image
from matplotlib.pylab import gray
from numpy import array
img = array(Image.open('../data/empire.jpg').convert('L'))
gray()
harrisimg = harris.compute_harris_response(img)
filtered_coords = harris.get_harris_points(harrisimg, 6)
harris.plot_harris_points(img, filtered_coords)
# line plot connecting the first two points
pl.plot(x[:2], y[:2])
# add title and show the plot
pl.title('Plotting: "empire.jpg"')
pl.axis('off')
# Image Contours and Histograms
gray_im = pl.array(Image.open(PATH_TO_IMAGES + 'empire.jpg').convert('L'))
# figure 2
pl.figure()
# don't use clors
pl.gray()
# show contours with origin upper left corner
pl.contour(gray_im, origin='image')
pl.axis('equal')
pl.axis('off')
# Histogram - figure 3
pl.figure()
pl.hist(im.flatten(), 128)
# Interactive notation
# figure 4
pl.figure()
def plot_predictions(self):
epoch, batch, data = self.get_next_batch(train=False) # get a test batch
num_classes = self.test_data_provider.get_num_classes()
NUM_ROWS = 2
NUM_COLS = 4
NUM_IMGS = NUM_ROWS * NUM_COLS if not self.save_preds else data[0].shape[1]
NUM_TOP_CLASSES = min(num_classes, 5) # show this many top labels
NUM_OUTPUTS = self.model_state["layers"][self.softmax_name]["outputs"]
PRED_IDX = 1
label_names = [lab.split(",")[0] for lab in self.test_data_provider.batch_meta["label_names"]]
if self.only_errors:
preds = n.zeros((data[0].shape[1], NUM_OUTPUTS), dtype=n.single)
else:
preds = n.zeros((NUM_IMGS, NUM_OUTPUTS), dtype=n.single)
# rand_idx = nr.permutation(n.r_[n.arange(1), n.where(data[1] == 552)[1], n.where(data[1] == 795)[1], n.where(data[1] == 449)[1], n.where(data[1] == 274)[1]])[:NUM_IMGS]
rand_idx = nr.randint(0, data[0].shape[1], NUM_IMGS)
if NUM_IMGS < data[0].shape[1]:
data = [n.require(d[:, rand_idx], requirements="C") for d in data]
# data += [preds]
# Run the model
print [d.shape for d in data], preds.shape
self.libmodel.startFeatureWriter(data, [preds], [self.softmax_name])
IGPUModel.finish_batch(self)
print preds
data[0] = self.test_data_provider.get_plottable_data(data[0])
if self.save_preds:
if not gfile.Exists(self.save_preds):
gfile.MakeDirs(self.save_preds)
preds_thresh = preds > 0.5 # Binarize predictions
data[0] = data[0] * 255.0
data[0][data[0] < 0] = 0
data[0][data[0] > 255] = 255
data[0] = n.require(data[0], dtype=n.uint8)
dir_name = "%s_predictions_batch_%d" % (os.path.basename(self.save_file), batch)
tar_name = os.path.join(self.save_preds, "%s.tar" % dir_name)
tfo = gfile.GFile(tar_name, "w")
tf = TarFile(fileobj=tfo, mode="w")
for img_idx in xrange(NUM_IMGS):
img = data[0][img_idx, :, :, :]
imsave = Image.fromarray(img)
prefix = (
"CORRECT"
if data[1][0, img_idx] == preds_thresh[img_idx, PRED_IDX]
else "FALSE_POS"
if preds_thresh[img_idx, PRED_IDX] == 1
else "FALSE_NEG"
)
file_name = "%s_%.2f_%d_%05d_%d.png" % (
prefix,
preds[img_idx, PRED_IDX],
batch,
img_idx,
data[1][0, img_idx],
)
# gf = gfile.GFile(file_name, "w")
file_string = StringIO()
imsave.save(file_string, "PNG")
tarinf = TarInfo(os.path.join(dir_name, file_name))
tarinf.size = file_string.tell()
file_string.seek(0)
tf.addfile(tarinf, file_string)
tf.close()
tfo.close()
# gf.close()
print "Wrote %d prediction PNGs to %s" % (preds.shape[0], tar_name)
else:
fig = pl.figure(3, figsize=(12, 9))
fig.text(0.4, 0.95, "%s test samples" % ("Mistaken" if self.only_errors else "Random"))
if self.only_errors:
# what the net got wrong
if NUM_OUTPUTS > 1:
err_idx = [i for i, p in enumerate(preds.argmax(axis=1)) if p not in n.where(data[2][:, i] > 0)[0]]
else:
err_idx = n.where(data[1][0, :] != preds[:, 0].T)[0]
print err_idx
err_idx = r.sample(err_idx, min(len(err_idx), NUM_IMGS))
data[0], data[1], preds = data[0][:, err_idx], data[1][:, err_idx], preds[err_idx, :]
import matplotlib.gridspec as gridspec
import matplotlib.colors as colors
cconv = colors.ColorConverter()
gs = gridspec.GridSpec(NUM_ROWS * 2, NUM_COLS, width_ratios=[1] * NUM_COLS, height_ratios=[2, 1] * NUM_ROWS)
# print data[1]
for row in xrange(NUM_ROWS):
for col in xrange(NUM_COLS):
img_idx = row * NUM_COLS + col
if data[0].shape[0] <= img_idx:
break
pl.subplot(gs[(row * 2) * NUM_COLS + col])
# pl.subplot(NUM_ROWS*2, NUM_COLS, row * 2 * NUM_COLS + col + 1)
pl.xticks([])
pl.yticks([])
img = data[0][img_idx, :, :, :]
img = img.squeeze()
if len(img.shape) > 2: # more than 2 dimensions
if img.shape[2] is 2: # if two channels
# copy 2nd to 3rd channel for visualization
a1 = img
a2 = img[:, :, 1]
a2 = a2[:, :, n.newaxis]
img = n.concatenate((a1, a2), axis=2)
pl.imshow(img, interpolation="lanczos")
else:
pl.imshow(img, interpolation="lanczos", cmap=pl.gray())
show_title = data[1].shape[0] == 1
true_label = [int(data[1][0, img_idx])] if show_title else n.where(data[1][:, img_idx] == 1)[0]
# print true_label
# print preds[img_idx,:].shape
# print preds[img_idx,:].max()
true_label_names = [label_names[i] for i in true_label]
img_labels = sorted(zip(preds[img_idx, :], label_names), key=lambda x: x[0])[-NUM_TOP_CLASSES:]
# print img_labels
axes = pl.subplot(gs[(row * 2 + 1) * NUM_COLS + col])
height = 0.5
ylocs = n.array(range(NUM_TOP_CLASSES)) * height
pl.barh(
ylocs,
[l[0] for l in img_labels],
height=height,
color=["#ffaaaa" if l[1] in true_label_names else "#aaaaff" for l in img_labels],
)
# pl.title(", ".join(true_labels))
if show_title:
pl.title(", ".join(true_label_names), fontsize=15, fontweight="bold")
else:
print true_label_names
pl.yticks(
ylocs + height / 2,
[l[1] for l in img_labels],
x=1,
backgroundcolor=cconv.to_rgba("0.65", alpha=0.5),
weight="bold",
)
for line in enumerate(axes.get_yticklines()):
line[1].set_visible(False)
# pl.xticks([width], [''])
# pl.yticks([])
pl.xticks([])
pl.ylim(0, ylocs[-1] + height)
pl.xlim(0, 1)
n_times = 1 data2dsmoth_tmp = smooth_2d(flex.int(data2d), n_times).as_numpy_array() data2dsmoth = numpy.float64(data2dsmoth_tmp) n_times = 5 data2dsmoth_2t_tmp = smooth_2d(flex.int(data2d), n_times).as_numpy_array() data2dsmoth_2t = numpy.float64(data2dsmoth_2t_tmp) #n = write_2d(flex.double(data2dsmoth)) print "Plotting data2dsmoth" plt.imshow(data2dsmoth, interpolation = "nearest", cmap = pylab.gray()) plt.show() line = numpy.copy(data2d[230, :]) pylab.subplot2grid((3, 3), (0, 0), colspan = 3) pylab.plot(line) line1 = numpy.copy(data2dsmoth[230, :]) pylab.subplot2grid((3, 3), (1, 0), colspan = 3) pylab.plot(line1) line2 = numpy.copy(data2dsmoth_2t[230, :]) pylab.subplot2grid((3, 3), (2, 0), colspan = 3) pylab.plot(line2)
def C99(masksize=3, startind=1, show_plot=False, sdscale=1.2):
logger.debug("C99")
if self.vecs == None:
logger.error("No vector input")
raise SystemExit(1)
# nsents = numpy.unique(self.vecs.indices).shape[0]
nsents = self.nsents # numpy.unique(self.vecs.indices).shape[0]
logger.debug("nsents: %d %d" % (nsents, self.nsents))
## Similarity matrix: sentence id 1 -> vdist[0,]
logger.debug("get pairwise cosine distances")
logger.debug(self.vecs.shape)
vdist_cond = pdist(self.vecs.toarray()[startind:], "cosine") ## in condensed format
vdist = csc_matrix(squareform(vdist_cond))
logger.debug(vdist.shape)
## Ranking: An elements rank is the number of neighbours
## with lower similarity scores in the similarity matrix
rankmat = numpy.zeros(vdist.shape)
# logger.debug(rankmat)
csize = int((masksize - 1) / 2)
logger.debug("csize: %d ", csize)
logger.debug("nfeats: %d ", self.nfeats)
logger.debug("masksize: %d ", masksize)
rankmat = generic_filter(
numpy.nan_to_num(vdist.toarray()),
self.maskrank,
footprint=numpy.ones((masksize, masksize)),
mode="constant",
cval=-1.0,
extra_keywords={"masksize": masksize, "csize": csize},
)
# logger.debug(rankmat)
# logger.debug(vdist.shape)
# logger.debug(rankmat.shape)
if show_plot:
plt.subplot(2, 1, 1)
plt.imshow(1 - vdist.toarray(), cmap=plt.gray())
plt.subplot(2, 1, 2)
plt.imshow(rankmat, cmap=plt.gray())
plt.show()
## Clustering as described in Choi's paper
smat = numpy.zeros(rankmat.shape)
# logger.debug(smat.shape[0])
n = smat.shape[0]
for i in range(n):
smat[i, i] = rankmat[i, i]
for i in range(n - 1):
smat[i + 1, i] = 2 * rankmat[i + 1, i] + smat[i, i] + smat[i + 1, i + 1]
smat[i, i + 1] = smat[i + 1, i]
for j in range(2, n - 1):
for i in range(n - j):
smat[i + j, i] = 2 * rankmat[i + j, i] + smat[i + j - 1, i] + smat[i + j, i + 1] - smat[i + j - 1, i + 1]
smat[i, i + j] = smat[i + j, i]
## Start doing splits
currsplits = [(0, n - 1)]
prev_D = smat[0, n - 1] / get_area((0, n - 1))
Ds = []
diff_Ds = []
splits = {}
prev_D = smat[i, n - 1] / get_area((i, n - 1))
# logger.debug("prev D: %f", prev_D)
for i in range(n):
curr_D, currsplits = self.c99_add_boundary(smat=smat, splits=currsplits)
Ds.append(curr_D)
diff_D = curr_D - prev_D
diff_Ds.append(diff_D)
prev_D = curr_D
splits[i] = currsplits
if show_plot:
plt.plot(Ds)
plt.show()
diff_Ds = numpy.array(diff_Ds)
Ds = numpy.array(Ds)
mean_diffD = numpy.mean(diff_Ds)
sd_diffD = numpy.std(diff_Ds)
logger.debug("D: mean %f, sd %f" % (mean_diffD, sd_diffD))
threshhold = mean_diffD + (sdscale * sd_diffD)
logger.debug("threshhold %f" % threshhold)
pass_thresh = numpy.where(diff_Ds > threshhold)[0]
if len(pass_thresh) == 0: # or splits[pass_thresh[-1]] == []:
logger.debug("-----> Nothing passes the threshold? Returning")
return ([], [], vdist)
else:
logger.debug("splits")
logger.debug(splits[pass_thresh[-1]])
end_inds = [b + 1 for a, b in splits[pass_thresh[-1]]]
start_ids = [a + 1 for a, b in splits[pass_thresh[-1]]]
logger.debug("start_ids:")
logger.debug(start_ids)
logger.debug("end_ids:")
logger.debug(end_inds)
logger.debug("vdist")
logger.debug(vdist)
logger.debug("C99 returning normally")
return end_inds, start_ids, vdist
#-*- coding:utf-8 -*-
'''
Created on 2012-6-18
@author: liaoyuhua
'''
from PCV import tools as tls
from PIL import Image
import numpy as np
from matplotlib import pylab as ply
if __name__ == '__main__':
imlist= tls.imtools.get_imlist(r"D:\Python_Computer_Vision\data\fontimages\a_thumbs")
im = np.array(Image.open(imlist[0]))
m,n = im.shape[0:2]
imnbr = len(imlist)
immatrix=np.array([np.array(Image.open(im)).flatten() for im in imlist],'f')
V,S,immean=tls.pca.pca(immatrix)
ply.figure()
ply.gray()
ply.subplot(2,4,1)
ply.imshow(immean.reshape(m,n))
for i in range(7):
ply.subplot(2,4,i+2)
ply.imshow(V[i].reshape(m,n))
ply.show()
def main(argv):
#if len(argv) < 4:
# print """Usage:
# """
# sys.exit(1)
#nlayers = int(argv[1])
# get number of layers
f = open(FLAGS.dir+"weights/nlayers.txt")
nlayers = int(f.readlines()[0])
f.close()
print str(nlayers) + " layer(s) detected."
pylab.figure(figsize=(32, 24), dpi=320, facecolor='w', edgecolor='k')
# Make a picture with the filters
[n_inputs, n_neurons, weights] = visualizing.weights_filename_to_array(FLAGS.dir+"weights/W0.txt")
image_side_length = int(pylab.sqrt(n_inputs))
nsubplot = pylab.ceil(pylab.sqrt(n_neurons))
for i in range(n_neurons):
filter = pylab.resize(weights[i], [image_side_length, image_side_length])
pylab.subplot(nsubplot, nsubplot, i+1)
pylab.imshow(filter, interpolation='nearest')
pylab.gray()
pylab.savefig(FLAGS.dir + "filters" + ".png")
pylab.clf()
# Make a picture with the all weights
nsubplot_vertical = nlayers+1
nsubplot_horizontal = 4
for i in range(nlayers):
# V
location = 1+(nlayers-i)*nsubplot_horizontal+0
filename = FLAGS.dir+"weights/V" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal, location,
filename, True, "V"+str(i))
# W
location = 1+(nlayers-i)*nsubplot_horizontal+1
filename = FLAGS.dir+"weights/W" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, False, "W"+str(i))
# F
location = 1+(nlayers-i)*nsubplot_horizontal+2
filename = FLAGS.dir+"weights/F" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, False, "F"+str(i))
# G
location = 1+(nlayers-i)*nsubplot_horizontal+3
filename = FLAGS.dir+"weights/G" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, True, "G"+str(i))
# Last layer
location = 1+1
filename = FLAGS.dir+"weights/W" + str(nlayers) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, False, "W"+str(nlayers))
pylab.savefig(FLAGS.dir + "weights" + ".png")
# Make pictures with examples and representations
visualizing.visualize_representations(FLAGS.dir, nlayers)
def plot(input_path,file_name,output_path):
#data = np.fromfile('t3/reconstruction_sarlo.rec',dtype='float32',sep='') # modify this to read the file
data = np.fromfile(input_path+'/'+file_name,dtype='float32',sep='')
data = data.reshape([array_size_z,array_size_y,array_size_x])
# apply a sobel file
data = nd.generic_gradient_magnitude(data, nd.sobel) # apply a 3-D sobel filter
# plot 1 and title
fig1 = plt.figure()
fig1.suptitle(file_name)
# turn into gray figure
plt.gray()
subfig1 = fig1.add_subplot(2,2,1)
subfig1.imshow(data[:,:,100])
subfig2 = fig1.add_subplot(2,2,2)
subfig2.imshow(data[:,:,300])
subfig3 = fig1.add_subplot(2,2,3)
subfig3.imshow(data[:,:,500])
subfig4 = fig1.add_subplot(2,2,4)
subfig4.imshow(data[:,:,700])
# save image to the output
plt.savefig(output_path+'/'+'sobel_X_'+file_name+'.png', bbox_inches=0)
# plot 3 and title
fig3 = plt.figure()
fig3.suptitle(file_name)
subfig7 = fig3.add_subplot(3,1,1)
subfig7.imshow(data[100,:,:])
subfig8 = fig3.add_subplot(3,1,2)
subfig8.imshow(data[200,:,:])
subfig9 = fig3.add_subplot(3,1,3)
subfig9.imshow(data[300,:,:])
# save image to the output
plt.savefig(output_path+'/'+'sobel_Z_'+file_name+'.png', bbox_inches=0)
# plot 2 and title
fig2 = plt.figure()
fig2.suptitle(file_name)
subfig5 = fig2.add_subplot(2,1,1)
subfig5.imshow(data[:,100,:])
#subfig5.set_title('100')
subfig6 = fig2.add_subplot(2,1,2)
subfig6.imshow(data[:,200,:])
# subfig6.set_title('200')
# save image to the output
plt.savefig(output_path+'/'+'sobel_Y_'+file_name+'.png', bbox_inches=0)
# show the fig2 for reference
fig2.show()