def get_gate_patch(self):
'''Returns a matplotlib patch to be drawn on the canvas whose dimensions
have been computed from the current gate.
'''
x_min, x_max = self.subplot.get_xlim()
x_range = x_max - x_min
y_min, y_max = self.subplot.get_ylim()
y_range = y_max - y_min
for subgate in self.gate.get_subgates():
col = subgate.get_column()
if col == self.x_column:
x_min = subgate.get_min()
x_range = subgate.get_max() - subgate.get_min()
if col == self.y_column:
y_min = subgate.get_min()
y_range = subgate.get_max() - subgate.get_min()
if self.patch not in self.subplot.patches:
rect = Rectangle((x_min, y_min), x_range, y_range, animated=True)
rect.set_fill(False)
rect.set_linestyle('dashed')
self.patch = self.subplot.add_patch(rect)
else:
self.patch.set_bounds(x_min, y_min, x_range, y_range)
return self.patch
class ImageAreaSelect(object):
def __init__(self, img, out, fit=False):
self.img = img
self.out = out
self.fit = fit
plt.figure()
plt.title("Testing Image")
plt.xlabel(r'M')
plt.ylabel(r'N')
self.ax = plt.gca()
self.rect = Rectangle((0, 0), 1, 1, antialiased=True, color='b',
linestyle='solid', lw=1.2)
self.rect.set_fill(False)
self.x0 = None
self.y0 = None
self.x1 = None
self.y1 = None
self.draw_rect = False
self.ax.add_patch(self.rect)
self.ax.figure.canvas.mpl_connect('button_press_event', self.on_press)
self.ax.figure.canvas.mpl_connect('button_release_event', self.on_release)
self.ax.figure.canvas.mpl_connect('motion_notify_event', self.on_motion)
plt.imshow(self.img, cmap="gray")
plt.show()
def on_press(self, event):
self.draw_rect = True
self.x0 = int(event.xdata)
self.y0 = int(event.ydata)
def on_motion(self, event):
if self.draw_rect:
if self.x1 != int(event.xdata) or self.y1 != int(event.ydata):
self.x1 = int(event.xdata)
self.y1 = int(event.ydata)
self.rect.set_width(self.x1 - self.x0)
self.rect.set_height(self.y1 - self.y0)
self.rect.set_xy((self.x0, self.y0))
self.ax.figure.canvas.draw()
def on_release(self, event):
self.draw_rect = False
self.x1 = int(event.xdata)
self.y1 = int(event.ydata)
self.calc()
def calc(self):
if self.x1 == self.x0 or self.y1 == self.y0:
return
print('crop(x,y):', self.x0, self.x1, self.y0, self.y1)
img = self.img[self.y0:self.y1, self.x0:self.x1]
mtf_from_img(img, self.out + "/" + str(self.x0) + "_" + str(self.x1) + "_" + str(self.y0) + "_" + str(self.y1), True)
class MainApp(App):
def build(self):
"""
some initialization
Args:
rect: a dummy rectangle, whose width and height will be reset trigger by user event
x0, y0: mouse click location
x1, y1: mouse release location
canvas: FigureCanvasKivyAgg object. Note that I'm using this back end right now
as the FigureCanvas backend has bug with plt.show()
selectors: store user-drawn rectangle data
offsetx: translation of origin on x direction
offsety: translation of origin on y direction
"""
self.selectors = []
img = mpimg.imread(sys.argv[1])
self.fig, self.ax = plt.subplots(1)
plt.imshow(img)
width, height = self.fig.canvas.get_width_height()
pxorigin = self.ax.transData.transform([(0, 0)])
self.offsetx = pxorigin[0][0]
self.offsety = height - pxorigin[0][1]
print('offsetx, offsety', self.offsetx, self.offsety)
self.rect = Rectangle((0, 0), 1, 1)
self.rect.set_fill(False)
self.rect.set_edgecolor('b')
self.x0 = None
self.y0 = None
self.x1 = None
self.y1 = None
self.canvas = FigureCanvasKivyAgg(
plt.gcf()) # get the current reference of plt
box = BoxLayout()
self.ax.add_patch(self.rect) # attach our rectangle to axis
self.canvas.mpl_connect("button_press_event", self.on_press)
self.canvas.mpl_connect("button_release_event", self.on_release)
box.add_widget(self.canvas)
return box
def on_press(self, event):
"""
record user click location
"""
self.x0 = event.xdata
self.y0 = event.ydata
print('x0, y0', self.x0, self.y0)
def on_release(self, event):
"""
record user mouse release location
"""
self.x1 = event.xdata
self.y1 = event.ydata
self.rect.set_width(self.x1 - self.x0)
self.rect.set_height(self.y1 - self.y0)
self.rect.set_xy((self.x0, self.y0))
xy_pixels = self.ax.transData.transform(
np.vstack([self.x0, self.y0]).T)
px, py = xy_pixels.T
width, height = self.fig.canvas.get_width_height()
# transform from origin on lower left to orgin on upper right
py = height - py
# account for translation factor
px -= self.offsetx
py -= self.offsety
self.selectors.append(
[px, py, abs(self.x1 - self.x0),
abs(self.y1 - self.y0)])
print('your rectangle', px, py, abs(self.x1 - self.x0),
abs(self.y1 - self.y0))
self.canvas.draw()
class IMaGE(object):
def __init__(self, fit=False):
self.ax = plt.gca()
self.rect = Rectangle((0, 0),
1,
1,
antialiased=True,
color='b',
linestyle='solid',
lw=1.2)
self.rect.set_fill(False)
self.x0 = None
self.y0 = None
self.x1 = None
self.y1 = None
self.fit = fit
self.key = False
self.count = 0
self.ax.add_patch(self.rect)
self.ax.figure.canvas.mpl_connect('button_press_event', self.on_press)
self.ax.figure.canvas.mpl_connect('motion_notify_event',
self.on_motion)
def on_press(self, event):
self.count += 1
self.key = True if self.key % 2 == 0 else False
if self.key % 2 == 0:
self.x = range(int(self.x0), int(self.x1))
self.cut(im, x0=self.x0, y0=self.y0, x1=self.x1, y1=self.y1)
self.ESF()
self.LSF()
self.MTF()
self.x0 = event.xdata
self.y0 = event.ydata
def on_motion(self, event):
if self.key:
self.x1 = event.xdata
self.y1 = event.ydata
self.rect.set_width(self.x1 - self.x0)
self.rect.set_height(self.y1 - self.y0)
self.rect.set_xy((self.x0, self.y0))
self.ax.figure.canvas.draw()
def cut(self, image, **args):
for i in args.keys():
print "{} : {}".format(i, args[i])
M = image[int(args["y0"]):int(args["y1"]),
int(args["x0"]):int(args["x1"])]
self.M_out = 0.299 * M[:, :, 0] + 0.589 * M[:, :, 1] + 0.114 * M[:, :,
2]
# plt.figure()
# plt.title("operator box-area")
# plt.imshow(self.M_out)
# name = "box_selection_{}.png".format(self.count)
# imag = Image.fromarray(np.asarray(self.M_out),mode = "RGB")
# imag.save("prueba.png")
# plt.show()
def ESF(self):
"""
Edge Spread Function calculation
"""
self.X = self.M_out[100, :]
mu = np.sum(self.X) / self.X.shape[0]
tmp = (self.X[:] - mu)**2
sigma = np.sqrt(np.sum(tmp) / self.X.shape[0])
self.edge_function = (self.X[:] - mu) / sigma
self.edge_function = self.edge_function[::3]
x = range(0, self.edge_function.shape[0])
plt.figure()
plt.title(r'ESF')
plt.plot(x, self.edge_function, '-ob')
plt.show()
def LSF(self):
"""
Line Spread Function calculation
"""
self.lsf = self.edge_function[:-2] - self.edge_function[2:]
x = range(0, self.lsf.shape[0])
# plt.figure()
# plt.title("LSF")
# plt.xlabel(r'pixel') ; plt.ylabel('intensidad')
# plt.plot(x,self.lsf,'-or')
# plt.show()
def MTF(self):
"""
Modulation Transfer Function calculation
"""
self.mtf = abs(np.fft.fft(self.lsf))
self.mtf = self.mtf[:] / np.max(self.mtf)
self.mtf = self.mtf[:len(self.mtf) // 2]
ix = np.arange(self.mtf.shape[0]) / (self.mtf.shape[0])
mtf_poly = np.polyfit(ix, self.mtf, 6)
poly = np.poly1d(mtf_poly)
plt.figure()
plt.title("MTF")
plt.xlabel(r'Frecuency $[cycles/pixel]$')
plt.ylabel('mtf')
p, = plt.plot(ix, self.mtf, '-or')
ll, = plt.plot(ix, poly(ix))
plt.legend([p, ll], ["MTF values", "polynomial fit"])
plt.grid()
plt.show()
def draw_chiprep2(dm, cx, axi=0, fsel=None, in_image_bit=False, axi_color=0,
bbox_bit=None,
ell_alpha=None,
ell_bit=None,
xy_bit=None,
color=None,
qcm=None,
**kwargs):
'''
Draws a chip representation over an already drawn chip
cx - the chiprep to draw. Managed by the chip manager
axi - the axis index to draw it in
#TODO: in_image_bit becomes data_coordinates
in_image_bit - are the data coordinates image or rotated chip?
raw the chip by itself or in its original image
axi_color - use the color associated with axis index
(used for ploting queries)
---
Others are preference overloads
bbox_bit -
ell_alpha
ell_bit
xy_bit
ell_color
'''
# Allows display of cross database queries
cm = dm.hs.cm if qcm is None else qcm
# Grab Preferences
xy_bit = dm.draw_prefs.points_bit if xy_bit is None else xy_bit
ell_bit = dm.draw_prefs.ellipse_bit if ell_bit is None else ell_bit
bbox_bit = dm.draw_prefs.bbox_bit if bbox_bit is None else bbox_bit
ell_alpha = dm.draw_prefs.ellipse_alpha if ell_alpha is None else ell_alpha
# Make sure alpha in range [0,1]
if ell_alpha > 1: ell_alpha = 1.0
if ell_alpha < 0: ell_alpha = 0.0
# Get color from colormap or overloaded parameter
if color is None:
color = plt.get_cmap('hsv')(float(axi_color)/len(dm.ax_list))[0:3]
if axi_color == 0:
color = [color[0], color[1]+.5, color[2]]
# Axis We are drawing to.
ax = dm.ax_list[axi]
T_data = ax.transData # data coordinates -> display coordinates
# Data coordinates are chip coords
if xy_bit or ell_bit or fsel != None:
T_fpts = T_data if not in_image_bit else\
Affine2D(cm.cx2_T_chip2img(cx) ) + T_data
fpts = cm.get_fpts(cx)
if fsel is None: fsel = range(len(fpts))
# ---DEVHACK---
# Randomly sample the keypoints. (Except be sneaky)
elif fsel == 'rand':
# Get Relative Position
minxy = fpts.min(0)[0:2]
maxxy = fpts.max(0)[0:2]
rel_pos = (fpts[:,0]-minxy[0])/(maxxy[0]-minxy[0])
to_zero = 1 - np.abs(rel_pos - .5)/.5
pdf = (to_zero / to_zero.sum())
# Transform Relative Position to Probabilities
# making it more likely to pick a centerpoint
fsel = np.random.choice(xrange(len(fpts)), size=88, replace=False, p=pdf)
# ---/DEVHACK---
# Plot ellipses
if ell_bit and len(fpts) > 0 and len(fsel) > 0:
ells = dm._get_fpt_ell_collection(fpts[fsel,:],
T_fpts,
ell_alpha,
color)
ax.add_collection(ells)
# Plot xy points
if xy_bit and len(fpts) > 0 and len(fsel) > 0:
ax.plot(fpts[fsel,0], fpts[fsel,1], 'o',\
markeredgecolor=color,\
markerfacecolor=color,\
transform=T_fpts,\
markersize=2)
# ===
if bbox_bit:
# Draw Bounding Rectangle in Image Coords
[rx,ry,rw,rh] = cm.cx2_roi[cx]
rxy = (rx,ry)
# Convert to Chip Coords if needbe
T_bbox = T_data if in_image_bit else\
Affine2D( np.linalg.inv(cm.cx2_T_chip2img(cx)) ) + T_data
bbox = Rectangle(rxy,rw,rh,transform=T_bbox)
# Visual Properties
bbox.set_fill(False)
bbox.set_edgecolor(color)
ax.add_patch(bbox)
# Draw Text Annotation
cid = cm.cx2_cid[cx]
name = cm.cx2_name(cx)
# Lower the value to .2 for the background color and set alpha=.7
rgb_textFG = [1,1,1]
hsv_textBG = colorsys.rgb_to_hsv(*color)[0:2]+(.2,)
rgb_textBG = colorsys.hsv_to_rgb(*hsv_textBG)+(.7,)
# Draw Orientation Backwards
degrees = 0 if not in_image_bit else -cm.cx2_theta[cx]*180/np.pi
txy = (0,rh) if not in_image_bit else (rx, ry+rh)
chip_text = 'name='+name+'\n'+'cid='+str(cid)
ax.text(txy[0]+1, txy[1]+1, chip_text,
horizontalalignment ='left',
verticalalignment ='top',
transform =T_data,
rotation =degrees,
color =rgb_textFG,
backgroundcolor =rgb_textBG)
return fsel
class IMaGE(object):
def __init__(self,fit = False):
self.ax = plt.gca()
self.rect = Rectangle((0,0), 1, 1,antialiased = True,color = 'b',
linestyle = 'solid', lw = 1.2)
self.rect.set_fill(False)
self.x0 = None
self.y0 = None
self.x1 = None
self.y1 = None
self.fit = fit
self.key = False
self.count = 0
self.ax.add_patch(self.rect)
self.ax.figure.canvas.mpl_connect('button_press_event', self.on_press)
self.ax.figure.canvas.mpl_connect('motion_notify_event', self.on_motion)
def on_press(self, event):
self.count += 1
self.key = True if self.key % 2 == 0 else False
if self.key % 2 == 0:
self.x = range(int(self.x0),int(self.x1))
self.cut(im,x0 = self.x0,y0 = self.y0,x1 = self.x1,y1 = self.y1)
self.ESF()
self.LSF()
self.MTF()
self.x0 = event.xdata
self.y0 = event.ydata
def on_motion(self,event):
if self.key:
self.x1 = event.xdata
self.y1 = event.ydata
self.rect.set_width(self.x1 - self.x0)
self.rect.set_height(self.y1 - self.y0)
self.rect.set_xy((self.x0, self.y0))
self.ax.figure.canvas.draw()
def cut(self,image,**args):
for i in args.keys():
print "{} : {}".format(i,args[i])
M = image[int(args["y0"]):int(args["y1"]),int(args["x0"]):int(args["x1"])]
self.M_out = 0.299*M[:,:,0] + 0.589*M[:,:,1]+0.114*M[:,:,2]
# plt.figure()
# plt.title("operator box-area")
# plt.imshow(self.M_out)
# name = "box_selection_{}.png".format(self.count)
# imag = Image.fromarray(np.asarray(self.M_out),mode = "RGB")
# imag.save("prueba.png")
# plt.show()
def ESF(self):
"""
Edge Spread Function calculation
"""
self.X = self.M_out[100,:]
mu = np.sum(self.X)/self.X.shape[0]
tmp = (self.X[:] - mu)**2
sigma = np.sqrt(np.sum(tmp)/self.X.shape[0])
self.edge_function = (self.X[:] - mu)/sigma
self.edge_function = self.edge_function[::3]
x = range(0,self.edge_function.shape[0])
plt.figure()
plt.title(r'ESF')
plt.plot(x,self.edge_function,'-ob')
plt.show()
def LSF(self):
"""
Line Spread Function calculation
"""
self.lsf = self.edge_function[:-2] - self.edge_function[2:]
x = range(0,self.lsf.shape[0])
# plt.figure()
# plt.title("LSF")
# plt.xlabel(r'pixel') ; plt.ylabel('intensidad')
# plt.plot(x,self.lsf,'-or')
# plt.show()
def MTF(self):
"""
Modulation Transfer Function calculation
"""
self.mtf = abs(np.fft.fft(self.lsf))
self.mtf = self.mtf[:]/np.max(self.mtf)
self.mtf = self.mtf[:len(self.mtf)//2]
ix = np.arange(self.mtf.shape[0]) / (self.mtf.shape[0])
mtf_poly = np.polyfit(ix, self.mtf, 6)
poly = np.poly1d(mtf_poly)
plt.figure()
plt.title("MTF")
plt.xlabel(r'Frecuency $[cycles/pixel]$') ; plt.ylabel('mtf')
p, = plt.plot(ix,self.mtf,'-or')
ll, = plt.plot(ix,poly(ix))
plt.legend([p,ll],["MTF values","polynomial fit"])
plt.grid()
plt.show()
def draw_chiprep2(
dm,
cx,
axi=0,
fsel=None,
in_image_bit=False,
axi_color=0,
bbox_bit=None,
ell_alpha=None,
ell_bit=None,
xy_bit=None,
color=None,
qcm=None,
**kwargs
):
"""
Draws a chip representation over an already drawn chip
cx - the chiprep to draw. Managed by the chip manager
axi - the axis index to draw it in
#TODO: in_image_bit becomes data_coordinates
in_image_bit - are the data coordinates image or rotated chip?
raw the chip by itself or in its original image
axi_color - use the color associated with axis index
(used for ploting queries)
---
Others are preference overloads
bbox_bit -
ell_alpha
ell_bit
xy_bit
ell_color
"""
# Allows display of cross database queries
cm = dm.hs.cm if qcm is None else qcm
# Grab Preferences
xy_bit = dm.draw_prefs.points_bit if xy_bit is None else xy_bit
ell_bit = dm.draw_prefs.ellipse_bit if ell_bit is None else ell_bit
bbox_bit = dm.draw_prefs.bbox_bit if bbox_bit is None else bbox_bit
ell_alpha = dm.draw_prefs.ellipse_alpha if ell_alpha is None else ell_alpha
# Make sure alpha in range [0,1]
if ell_alpha > 1:
ell_alpha = 1.0
if ell_alpha < 0:
ell_alpha = 0.0
# Get color from colormap or overloaded parameter
if color is None:
color = plt.get_cmap("hsv")(float(axi_color) / len(dm.ax_list))[0:3]
if axi_color == 0:
color = [color[0], color[1] + 0.5, color[2]]
# Axis We are drawing to.
ax = dm.ax_list[axi]
T_data = ax.transData # data coordinates -> display coordinates
# Data coordinates are chip coords
if xy_bit or ell_bit or fsel != None:
T_fpts = T_data if not in_image_bit else Affine2D(cm.cx2_T_chip2img(cx)) + T_data
fpts = cm.get_fpts(cx)
if fsel is None:
fsel = range(len(fpts))
# ---DEVHACK---
# Randomly sample the keypoints. (Except be sneaky)
elif fsel == "rand":
# Get Relative Position
minxy = fpts.min(0)[0:2]
maxxy = fpts.max(0)[0:2]
rel_pos = (fpts[:, 0] - minxy[0]) / (maxxy[0] - minxy[0])
to_zero = 1 - np.abs(rel_pos - 0.5) / 0.5
pdf = to_zero / to_zero.sum()
# Transform Relative Position to Probabilities
# making it more likely to pick a centerpoint
fsel = np.random.choice(xrange(len(fpts)), size=88, replace=False, p=pdf)
# ---/DEVHACK---
# Plot ellipses
if ell_bit and len(fpts) > 0 and len(fsel) > 0:
ells = dm._get_fpt_ell_collection(fpts[fsel, :], T_fpts, ell_alpha, color)
ax.add_collection(ells)
# Plot xy points
if xy_bit and len(fpts) > 0 and len(fsel) > 0:
ax.plot(
fpts[fsel, 0],
fpts[fsel, 1],
"o",
markeredgecolor=color,
markerfacecolor=color,
transform=T_fpts,
markersize=2,
)
# ===
if bbox_bit:
# Draw Bounding Rectangle in Image Coords
[rx, ry, rw, rh] = cm.cx2_roi[cx]
rxy = (rx, ry)
# Convert to Chip Coords if needbe
T_bbox = T_data if in_image_bit else Affine2D(np.linalg.inv(cm.cx2_T_chip2img(cx))) + T_data
bbox = Rectangle(rxy, rw, rh, transform=T_bbox)
# Visual Properties
bbox.set_fill(False)
bbox.set_edgecolor(color)
ax.add_patch(bbox)
# Draw Text Annotation
cid = cm.cx2_cid[cx]
name = cm.cx2_name(cx)
# Lower the value to .2 for the background color and set alpha=.7
rgb_textFG = [1, 1, 1]
hsv_textBG = colorsys.rgb_to_hsv(*color)[0:2] + (0.2,)
rgb_textBG = colorsys.hsv_to_rgb(*hsv_textBG) + (0.7,)
# Draw Orientation Backwards
degrees = 0 if not in_image_bit else -cm.cx2_theta[cx] * 180 / np.pi
txy = (0, rh) if not in_image_bit else (rx, ry + rh)
chip_text = "name=" + name + "\n" + "cid=" + str(cid)
ax.text(
txy[0] + 1,
txy[1] + 1,
chip_text,
horizontalalignment="left",
verticalalignment="top",
transform=T_data,
rotation=degrees,
color=rgb_textFG,
backgroundcolor=rgb_textBG,
)
return fsel