def get_scanpos_given_circles(XY_roi, XY, Circs, stm_r_roi, stm_r,
ax=None, max_pipette_xovershoot=300.):
"""
Parameters
----------
XY_roi - center positions of circular regions of interest
XY -
Circs -
stm_r_roi - radius of circular regions of interest, in microns
stm_r - radius of light stimulus, in microns
ax - matplotlib axes object on which IM is plotted.
max_pipette_xovershoot - In microns. Max x distance to move to the right
of pipette tip. Go to far and the objective will
touch the pipette and destroy the patch.
Assumes that the pipette enters from the right.
In microns.
Returns
-------
"""
# If no axes was set, plot on the currently active.
if ax is None:
ax = plt.gca()
step_len = np.floor(sqrt(2*stm_r**2))
xlim, ylim = np.sort(ax.get_xlim()), np.sort(ax.get_ylim())
# Draw a grid with spacing 'step_len' covering the entire image
y, x = np.ogrid[ylim[0]:ylim[1]:step_len,xlim[0]:xlim[1]:step_len]
mask = np.zeros((y.shape[0],x.shape[1]))
for xcntr,ycntr in XY_roi:
mask = logical_or(mask,
((y - ycntr)**2 + (x - xcntr)**2) <= stm_r_roi**2)
labeled_mask, n_labels = label( mask )
mask_labels = np.unique( labeled_mask )[1:]
ix0 = XY.shape[0]
XY.resize(ix0+mask.sum(), refcheck=False)
for ix, ml in enumerate(mask_labels):
y_ix, x_ix = nonzero(labeled_mask == ml)
ix1 = x_ix.shape[0] + ix0
XY[ix0:ix1] = zip(x[0,x_ix],y[y_ix,0])
ix0 = ix1
# Remove positions outside of max_pipette_xovershoot
if max_pipette_xovershoot > 0:
XY = XY[XY['X'] <= max_pipette_xovershoot]
elif max_pipette_xovershoot < 0:
XY = XY[XY['X'] >= max_pipette_xovershoot]
for x,y in XY:
c = Circle((x,y), stm_r, ec=prestm_col, ls='dotted', fill=False)
Circs.append(ax.add_patch(c))
plt.title(ax.get_title()+r', $N_{'+str(int(round(stm_r*2)))+'}='+str(len(XY))+'$')
plt.show()
plt.draw()
sleep(1e-3)
return XY, Circs
def get_scanpos_given_4_sides(stm_r,
corners,
ax=None,
max_pipette_xovershoot=300.):
"""
"""
# If no axes was set, plot on the currently active.
if ax is None:
ax = plt.gca()
step_len = np.floor(np.sqrt(2*stm_r**2))
flk = step_len/2.0
lo_l, up_l = corners["lo_left"], corners["up_left"]
lo_r, up_r = corners["lo_right"], corners["up_right"]
# Clean out x and ys outside outer border of ROI.
lbord_m = (lo_l[1] - up_l[1]) / (lo_l[0] - up_l[0])
lbord_b = lo_l[1] - lbord_m*lo_l[0]
rbord_m = (lo_r[1] - up_r[1]) / (lo_r[0] - up_r[0])
rbord_b = lo_r[1] - rbord_m*lo_r[0]
upbord_m = (up_l[1] - up_r[1]) / (up_l[0] - up_r[0])
upbord_b = up_l[1] - upbord_m*up_l[0]
lobord_m = (lo_l[1] - lo_r[1]) / (lo_l[0] - lo_r[0])
lobord_b = lo_l[1] - lobord_m*lo_l[0]
lbord = lambda x, y: x > (y - lbord_b) / lbord_m - flk
rbord = lambda x, y: x < (y - rbord_b) / rbord_m + flk
lobord = lambda x, y: y > lobord_m*x + lobord_b - flk
upbord = lambda x, y: y < upbord_m*x + upbord_b + flk
X_tmp = np.arange(min(lo_l[0],up_l[0]),
max(lo_r[0]+100,up_r[0]+100),
step_len)
Y_tmp = np.arange(min(lo_l[1],lo_r[1]),
max(up_l[1]+100,up_r[1]+100),
step_len)
# Remove positions outside of max_pipette_xovershoot
if max_pipette_xovershoot > 0:
X_tmp = X_tmp[X_tmp <= max_pipette_xovershoot]
elif max_pipette_xovershoot < 0:
X_tmp = X_tmp[X_tmp >= max_pipette_xovershoot]
X,Y = [],[]
Circs = [];pos_num = 0
for x in X_tmp:
for y in Y_tmp:
if lbord(x,y) and rbord(x,y) and lobord(x,y) and upbord(x,y) :
c = Circle((x, y), stm_r,ec=prestm_col,
ls='dotted', fill=False)
Circs.append(ax.add_patch(c))
X.append(x)
Y.append(y)
plt.text(x, y, str(pos_num))
pos_num += 1
nstmloc = len(X)
title(r'Stm pos: $N_{'+str(int(round(stm_r*2)))+'}='+str(nstmloc)+'$')
plt.show()
plt.draw()
sleep(1e-3)
XY = np.recarray(len(X), dtype=[('X',float),('Y',float)])
XY['X'], XY['Y'] = X, Y
return XY, Circs
def get_ROI_4_sides(ax = None):
"""
Returns four sides of an Region Of Interest
"""
# Assumes scale bar length 500 microns
scalebar_len_um = 500. # microns
#prestm_col = [.3,.7,.3]
# If no axes was set, plot on the currently active.
if ax is None:
ax = plt.gca()
print 'Click on the top and the bottom of the scalebar.\n'
sclbar_xy_px = np.array(plt.ginput(n=2))
print 'Click on pipette tip/cell.\n'
cell_xy_px = np.array(plt.ginput(n=1, timeout=60))[0]
sclbar_len_px = abs(diff(sclbar_xy_px[:,1]))[0]
um_to_px = sclbar_len_px/scalebar_len_um
xlim_px, ylim_px = ax.get_xlim(), ax.get_ylim()
xlim_um = ((xlim_px[0]-cell_xy_px[0])/um_to_px,
(xlim_px[1]-cell_xy_px[0])/um_to_px)
ylim_um = ((ylim_px[0]-cell_xy_px[1])/um_to_px,
(ylim_px[1]-cell_xy_px[1])/um_to_px)
IM = ax.get_images()[0]
IM.set_extent((xlim_um[0], xlim_um[1], ylim_um[0], ylim_um[1]))
xlabel('micron')
ylabel('micron')
plt.draw()
sleep(1e-3)
# Get and plot the outer borders of the area to stimulate
print 'Click on 4 corners making up the border of region to stimulate.\n'
region_border_xy = np.array(ginput(n=4))
lol_bix = np.ones(4, dtype=bool)
up_ix = np.argsort(region_border_xy[:,1])[2:]
r_ix = np.argsort(region_border_xy[:,0])[2:]
lol_bix[up_ix] = False
lor_bix = lol_bix.copy()
lol_bix[r_ix] = False
lor_bix[lol_bix] = False
upl_bix = ~(lor_bix | lol_bix)
upl_bix[r_ix] = False
upr_bix = ~(lor_bix | lol_bix | upl_bix)
lo_left = region_border_xy[lol_bix, :].flatten()
up_right = region_border_xy[upr_bix, :].flatten()
lo_right = region_border_xy[lor_bix, :].flatten()
up_left = region_border_xy[upl_bix, :].flatten()
plt.plot([lo_left[0], up_left[0], up_right[0], lo_right[0], lo_left[0]],
[lo_left[1], up_left[1], up_right[1], lo_right[1], lo_left[1]],
c=prestm_col)
ax.set_xlim(xlim_um)
ax.set_ylim(ylim_um)
corners = {'lo_left':lo_left,
'up_left':up_left,
'up_right':up_right,
'lo_right':lo_right}
return corners