def calc_median_profile(self, roll_offset=0):
"""Calculate the median profile of the Line Pair region.
Parameters
----------
roll_offset : int, float
The offset to apply to the start of the profile, in radians.
E.g. if set to pi/2, profile extraction will begin at 12 o clock (90 degrees).
Returns
-------
median profile : core.profile.Profile
A 1D Profile of the Line Pair regions.
"""
# extract the profile for each ROI (5 adjacent profiles)
for roi in self.ROIs.values():
roi.get_profile(self.image.array, size=2*np.pi*1000, start=np.pi+roll_offset)
# average profiles together
prof = np.zeros(len(roi.y_values))
for idx, roi in enumerate(self.ROIs.values()):
prof += roi.y_values
prof /= len(self.ROIs)
new_prof = Profile(prof)
new_prof.filter(0.001)
# new_prof.ground()
return new_prof
def _construct_pickets(self, tolerance, action_tolerance):
"""Construct the Picket instances."""
if self.orientation == orientations['UD']:
leaf_prof = np.median(self._analysis_array, 0)
else:
leaf_prof = np.median(self._analysis_array, 1)
leaf_prof = Profile(leaf_prof)
_, peak_idxs = leaf_prof.find_peaks(min_peak_distance=0.01, min_peak_height=0.5)
for peak in range(len(peak_idxs)):
self.pickets.append(Picket(self.image, tolerance, self.orientation, action_tolerance))
def _threshold(self):
"""Threshold the image by subtracting the minimum value. Allows for more accurate image orientation determination.
"""
col_prof = np.median(self.image.array, 0)
col_prof = Profile(col_prof)
row_prof = np.median(self.image.array, 1)
row_prof = Profile(row_prof)
_, r_peak_idx = row_prof.find_peaks(min_peak_distance=0.01, exclude_lt_edge=0.05, exclude_rt_edge=0.05)
_, c_peak_idx = col_prof.find_peaks(min_peak_distance=0.01, exclude_lt_edge=0.05, exclude_rt_edge=0.05)
min_val = self.image.array[r_peak_idx[0]:r_peak_idx[-1], c_peak_idx[0]:c_peak_idx[-1]].min()
self._analysis_array = self.image.array.copy()
self._analysis_array[self._analysis_array < min_val] = min_val
self._analysis_array -= min_val
def _calc_mlc_positions(self, leaf_centers):
"""Calculate the positions of all the MLC pairs."""
diff = np.diff(leaf_centers)
sample_width = np.round(np.median(diff*2/5)/2).astype(int)
for mlc_num, mlc_peak_loc in enumerate(np.round(leaf_centers).astype(int)):
mlc_rows = np.arange(mlc_peak_loc-sample_width, mlc_peak_loc+sample_width+1)
if self.orientation == orientations['UD']:
pix_vals = np.median(self._analysis_array[mlc_rows, :], axis=0)
else:
pix_vals = np.median(self._analysis_array[:, mlc_rows], axis=1)
prof = Profile(pix_vals)
prof.find_FWXM_peaks(fwxm=80, min_peak_distance=0.01, min_peak_height=0.5, interpolate=True)
for idx, peak in enumerate(prof.peaks):
if self.orientation == orientations['UD']:
meas = MLC_Meas((peak.idx, mlc_rows[0]), (peak.idx, mlc_rows[-1]))
else:
meas = MLC_Meas((mlc_rows[0], peak.idx), (mlc_rows[-1], peak.idx))
self.pickets[idx].mlc_meas.append(meas)
def _find_leaf_centers(self, hdmlc):
"""Return the leaf centers perpendicular to the leaf motion."""
# generate some settings
sm_lf_wdth = 5 * self.image.dpmm
bg_lf_wdth = sm_lf_wdth * 2
if hdmlc:
sm_lf_wdth /= 2
bg_lf_wdth /= 2
self._sm_lf_meas_wdth = slmw = int(round(sm_lf_wdth*3/4))
self._bg_lf_meas_wdth = blmw = int(round(bg_lf_wdth*3/4))
bl_ex = int(bg_lf_wdth/4)
sm_ex = int(sm_lf_wdth/4)
# generate leaf profile
if self.orientation == orientations['UD']:
leaf_prof = np.mean(self._analysis_array, 1)
center = self.image.center.y
else:
leaf_prof = np.mean(self._analysis_array, 0)
center = self.image.center.x
leaf_prof = Profile(leaf_prof)
# ground profile to reasonable level
_, peak_idxs = leaf_prof.find_peaks(min_peak_distance=self._sm_lf_meas_wdth, exclude_lt_edge=sm_ex,
exclude_rt_edge=sm_ex)
min_val = leaf_prof.y_values[peak_idxs[0]:peak_idxs[-1]].min()
leaf_prof.y_values[leaf_prof.y_values < min_val] = min_val
# remove unevenness in signal
leaf_prof.y_values = signal.detrend(leaf_prof.y_values, bp=[int(len(leaf_prof.y_values)/3), int(len(leaf_prof.y_values)*2/3)])
_, peak_idxs = leaf_prof.find_peaks(min_peak_distance=self._sm_lf_meas_wdth, exclude_lt_edge=sm_ex, exclude_rt_edge=sm_ex)
leaf_range = (peak_idxs[-1] - peak_idxs[0]) / self.image.dpmm # mm
sm_lf_range = 220 # mm
# find leaf peaks
if leaf_range > sm_lf_range:
lt_biglittle_lf_bndry = int(round(center - 100 * self.image.dpmm))
rt_biglittle_lf_bndry = int(round(center + 100 * self.image.dpmm))
pp = leaf_prof.subdivide([lt_biglittle_lf_bndry, rt_biglittle_lf_bndry], slmw)
if len(pp) != 3:
raise ValueError("3 Profiles weren't found but should have been")
# Left Big MLC region
_, peak_idxs = pp[0].find_peaks(min_peak_distance=blmw, exclude_lt_edge=bl_ex)
peak_diff = np.diff(peak_idxs).mean()
lt_v_idx = np.array(peak_idxs[:-1]) + peak_diff/2
# Middle, small MLC region
_, peak_idxs = pp[1].find_peaks(min_peak_distance=slmw)
peak_diff = np.diff(peak_idxs).mean()
mid_v_idx = np.array(peak_idxs[:-1]) + peak_diff / 2
# Right Big MLC region
_, peak_idxs = pp[2].find_peaks(min_peak_distance=blmw,
exclude_rt_edge=bl_ex)
peak_diff = np.diff(peak_idxs).mean()
rt_v_idx = np.array(peak_idxs[:-1]) + peak_diff / 2
leaf_center_idxs = np.concatenate((lt_v_idx, mid_v_idx, rt_v_idx))
else:
_, peak_idxs = leaf_prof.find_peaks(min_peak_distance=slmw, exclude_lt_edge=sm_ex,
exclude_rt_edge=sm_ex)
_, peak_idxs = leaf_prof.find_FWXM_peaks(min_peak_distance=slmw, interpolate=True)
peak_diff = np.diff(peak_idxs).mean()
leaf_center_idxs = np.array(peak_idxs[:-1]) + peak_diff / 2
return leaf_center_idxs