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Handle NaN in display devices #17

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daba1f9
Fix compatibility with recent PyQt in display.fast_plot
philsmt Dec 10, 2024
f3a4a41
Fix compatibility with recent PyQt in display.image
philsmt Dec 10, 2024
cc7265d
Fix compatibility with recent PyQt in display.hist2d
philsmt Dec 16, 2024
e3638fc
Fix compatibility with recent PyQt in display.plot
philsmt Dec 16, 2024
6aef942
Fix compatibility with recent PyQt in util.simulate.scalar*
philsmt Dec 16, 2024
6202018
Handle NaN in fast_plot and waveform
D4vidH4mm3r Dec 18, 2024
b642530
Add noexcept, DRY data coord transformation
D4vidH4mm3r Mar 5, 2025
6d9fecd
Add line segment - box clipping
D4vidH4mm3r Mar 5, 2025
6628812
Uses nan_to_num, but scale y based on finite values only
D4vidH4mm3r Mar 5, 2025
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2 changes: 1 addition & 1 deletion src/metro/devices/abstract/single_plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@


import metro
from metro.external import pyqtgraph
import pyqtgraph


class Device(metro.WidgetDevice, metro.DisplayDevice):
Expand Down
95 changes: 71 additions & 24 deletions src/metro/devices/display/_fast_plot_native.pyx
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
# distutils: language=c++
# cython: boundscheck=False, wraparound=False, cdivision=True

# This Source Code Form is subject to the terms of the Mozilla Public
Expand Down Expand Up @@ -74,7 +75,12 @@ cdef struct surface:
double div_y


cdef inline void draw_pixel(surface* s, int x, int y, int c) nogil:
cdef inline void data_coord_to_image_space(surface* s, x_t x, y_t y, int& out_x, int& out_y) noexcept nogil:
out_x = <int>(((<double>x - s.start_x) * s.div_x) + s.offset_x)
out_y = <int>(((<double>y - s.start_y) * s.div_y) + s.offset_y)


cdef inline void draw_pixel(surface* s, int x, int y, int c) noexcept nogil:
# We currently do pixel-level culling since we lose so little
# performance here. Sorting the set beforehand will probably
# only scale for very high data sets.
Expand All @@ -83,7 +89,11 @@ cdef inline void draw_pixel(surface* s, int x, int y, int c) nogil:
s.ptr[(s.height_complement - y) * s.line_length + x] = c


cdef void draw_rect(surface* s, int x1, int y1, int w, int h, int c) nogil:
cdef inline void draw_pixel_unsafe(surface* s, int x, int y, int c) noexcept nogil:
s.ptr[(s.height_complement - y) * s.line_length + x] = c


cdef void draw_rect(surface* s, int x1, int y1, int w, int h, int c) noexcept nogil:
# Draw a rectangle with x1/y1 as its upper-left edge and size w/h in
# color c

Expand All @@ -99,7 +109,7 @@ cdef void draw_rect(surface* s, int x1, int y1, int w, int h, int c) nogil:
draw_pixel(s, x2, y, c)


cdef void fill_rect(surface* s, int x1, int y1, int w, int h, int c) nogil:
cdef void fill_rect(surface* s, int x1, int y1, int w, int h, int c) noexcept nogil:
# Draw a filled rectangle with x1/y1 as its upper-left edge and size w/h in
# color c

Expand All @@ -111,15 +121,59 @@ cdef void fill_rect(surface* s, int x1, int y1, int w, int h, int c) nogil:
draw_pixel(s, x, y, c)


cdef inline void draw_square(surface* s, int x, int y, int l, int c) nogil:
cdef inline void draw_square(surface* s, int x, int y, int l, int c) noexcept nogil:
# Draw a square centered around x/y with length l in color c

draw_rect(s, x - ((l - 1) >> 1), y - ((l - 1) >> 1), l, l, c)


cdef void draw_line(surface* s, int x1, int y1, int x2, int y2, int c) nogil:
cdef char clip_line_segment(surface* s, int& x1, int& y1, int& x2, int& y2) noexcept nogil:
# Clips the line segment provided to bounding box of surface s
# Return value: 0 for line entirely segment outside bbox
if (x1 < s.min_x and x2 < s.min_x) or \
(x1 > s.max_x and x2 > s.max_x) or \
(y1 < s.min_y and y2 < s.min_y) or \
(y1 > s.max_y and y2 > s.max_y):
return 0
cdef double res_x[2]
cdef double res_y[2]
cdef double slope_y = (<double>y2 - <double>y1) / (<double>x2 - <double>x1)
cdef double slope_x = (<double>x2 - <double>x1) / (<double>y2 - <double>y1)
res_x[0] = x1
res_x[1] = x2
res_y[0] = y1
res_y[1] = y2
cdef int i
for i in range(2):
if res_x[i] < s.min_x:
res_x[i] = s.min_x
res_y[i] = (y1 + slope_y * <double>(s.min_x - x1))
elif res_x[i] > s.max_x:
res_x[i] = s.max_x
res_y[i] = (y1 + slope_y * <double>(s.max_x - x1))
if res_y[i] < s.min_y:
res_y[i] = s.min_y
res_x[i] = (x1 + slope_x * <double>(s.min_y - x1))
elif res_y[i] > s.max_y:
res_y[i] = s.max_y
res_x[i] = (x1 + slope_x * <double>(s.max_y - x1))
# check if shifting put us outside bounds
if (res_x[0] < s.min_x and res_x[1] < s.min_x) or \
(res_x[0] > s.max_x and res_x[1] > s.max_x):
return 0
x1 = <int>res_x[0]
x2 = <int>res_x[1]
y1 = <int>res_y[0]
y2 = <int>res_y[1]
return 1


cdef void draw_line(surface* s, int x1, int y1, int x2, int y2, int c) noexcept nogil:
cdef int x, y, dx, dy, ix, iy

if not clip_line_segment(s, x1, y1, x2, y2):
return

# Swap the coordinates in case x1/y1 is bigger than x2/y2.

if x2 >= x1:
Expand All @@ -146,7 +200,7 @@ cdef void draw_line(surface* s, int x1, int y1, int x2, int y2, int c) nogil:
y2 = x2

for y from y1 <= y <= y2 by 1:
draw_pixel(s, x1, y, c)
draw_pixel_unsafe(s, x1, y, c)

return
elif dy == 0:
Expand All @@ -156,7 +210,7 @@ cdef void draw_line(surface* s, int x1, int y1, int x2, int y2, int c) nogil:
x2 = y2

for x from x1 <= x <= x2 by 1:
draw_pixel(s, x, y1, c)
draw_pixel_unsafe(s, x, y1, c)

return

Expand All @@ -173,7 +227,7 @@ cdef void draw_line(surface* s, int x1, int y1, int x2, int y2, int c) nogil:
dx <<= 1

while x != x2:
draw_pixel(s, x, y, c)
draw_pixel_unsafe(s, x, y, c)

if error >= 0:
y += iy
Expand All @@ -182,14 +236,14 @@ cdef void draw_line(surface* s, int x1, int y1, int x2, int y2, int c) nogil:
x += ix
error += dy

draw_pixel(s, x, y, c)
draw_pixel_unsafe(s, x, y, c)
else:
dx <<= 1
error = dx - dy
dy <<= 1

while y != y2:
draw_pixel(s, x, y, c);
draw_pixel_unsafe(s, x, y, c);

if error >= 0:
x += ix
Expand All @@ -198,7 +252,7 @@ cdef void draw_line(surface* s, int x1, int y1, int x2, int y2, int c) nogil:
y += iy
error += dx

draw_pixel(s, x, y, c)
draw_pixel_unsafe(s, x, y, c)


def stack(numpy.ndarray[y_t, ndim=2, mode="c"] inp,
Expand Down Expand Up @@ -276,7 +330,7 @@ def plot(uintptr_t s_bits,
raise ValueError('len(x) != len(y)')

cdef surface* s = <surface*>s_bits
cdef int N = data_y.shape[0], i, cur_x, cur_y, last_x, last_y
cdef int N = data_y.shape[0], i, cur_x = 0, cur_y = 0, last_x = 0, last_y = 0

cdef int line_color = (color_idx + 1) * 10 + 1
cdef int symbol_color = line_color + 1
Expand All @@ -285,20 +339,16 @@ def plot(uintptr_t s_bits,
# is very misleading! Then we can also stop using s.x_max down there

with nogil:
last_x = <int>((<double>data_x[0] - s.start_x) * s.div_x) + s.offset_x
last_y = <int>((<double>data_y[0] - s.start_y) * s.div_y) + s.offset_y
data_coord_to_image_space(s, data_x[0], data_y[0], last_x, last_y)

if marker and last_x >= s.offset_x and last_x <= s.max_x:
draw_square(s, last_x, last_y, 5, symbol_color)

if marker:
for i in range(1, N):
cur_x = <int>((<double>data_x[i] - s.start_x) * s.div_x) \
+ s.offset_x
cur_y = <int>((<double>data_y[i] - s.start_y) * s.div_y) \
+ s.offset_y
data_coord_to_image_space(s, data_x[i], data_y[i], cur_x, cur_y)

if not ((last_x < s.offset_x and cur_x < s.offset_x) or
if not ((last_x < s.min_x and cur_x < s.min_x) or \
(last_x > s.max_x and cur_x > s.max_x)):
draw_line(s, last_x, last_y, cur_x, cur_y, line_color)
draw_square(s, cur_x, cur_y, 5, symbol_color)
Expand All @@ -308,12 +358,9 @@ def plot(uintptr_t s_bits,

else:
for i in range(1, N):
cur_x = <int>((<double>data_x[i] - s.start_x) * s.div_x) \
+ s.offset_x
cur_y = <int>((<double>data_y[i] - s.start_y) * s.div_y) \
+ s.offset_y
data_coord_to_image_space(s, data_x[i], data_y[i], cur_x, cur_y)

if not ((last_x < s.offset_x and cur_x < s.offset_x) or
if not ((last_x < s.min_x and cur_x < s.min_x) or \
(last_x > s.max_x and cur_x > s.max_x)):
draw_line(s, last_x, last_y, cur_x, cur_y, line_color)

Expand Down
31 changes: 21 additions & 10 deletions src/metro/devices/display/fast_plot.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -542,7 +542,7 @@ def paintEvent(self, event):
# Vertical annotation lines.
if self.vlines is not None and self.show_annotations:
div = self.plot_transform[0]
y_end = -self.plot_geometry[3]
y_end = int(-self.plot_geometry[3])

p.save()
p.translate(
Expand All @@ -558,8 +558,8 @@ def paintEvent(self, event):

for x_data, text in vlines_it:
if self.plot_axes[0] < x_data < self.plot_axes[1]:
x_widget = x_data * div
p.drawLine(x_widget, 0.0, x_widget, y_end)
x_widget = int(x_data * div)
p.drawLine(x_widget, 0, x_widget, y_end)

if text is not None:
p.drawText(p.boundingRect(
Expand All @@ -571,7 +571,7 @@ def paintEvent(self, event):
# Horizontal annotation lines.
if self.hlines is not None and self.show_annotations:
div = self.plot_transform[1]
x_end = self.plot_geometry[2]
x_end = int(self.plot_geometry[2])

p.save()
p.translate(
Expand All @@ -587,8 +587,8 @@ def paintEvent(self, event):

for y_data, text in hlines_it:
if self.plot_axes[2] < y_data < self.plot_axes[3]:
y_widget = -y_data * div
p.drawLine(0.0, y_widget, x_end, y_widget)
y_widget = int(-y_data * div)
p.drawLine(0, y_widget, x_end, y_widget)

if text is not None:
p.drawText(p.boundingRect(
Expand Down Expand Up @@ -791,7 +791,7 @@ def on_render_completed(self):
def _buildAxisLabel(self, value, x, y, p, flags):
text = str(value)

r = p.boundingRect(x, y, 1, 1, flags, text)
r = p.boundingRect(int(x), int(y), 1, 1, flags, text)
r._flags = flags
r._str = text

Expand Down Expand Up @@ -1235,8 +1235,11 @@ def dataSet(self, d):
def dataAdded(self, d):
self.ch_data = d

nan_replacement = 0
if isinstance(self.ch_data, xr.DataArray):
self.idx_data = self.ch_data.data[self.index]
if "replace_nan" in self.ch_data.attrs:
nan_replacement = self.ch_data.attrs["replace_nan"]
Comment on lines +1238 to +1242
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@D4vidH4mm3r D4vidH4mm3r Dec 18, 2024

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One could also allow specifying and utilizing the various dropna / fillna etc. available for DataArray. They don't handle inf, though. Also, dropping is tricky.


if self.idx_data.ndim == 1:
self.idx_data = self.idx_data[None, :]
Expand All @@ -1261,13 +1264,20 @@ def dataAdded(self, d):
self.idx_data = self.idx_data[1:]
else:
self.x = np.arange(self.idx_data.shape[1])

# TODO: option to drop instead of replace
self.x_label = self.y_label = self.legend_entries = \
self.vlines = self.hlines = None

if self.idx_data.shape[1] == 0:
return

# infinity replaced with very positive / negative values
finite_mask = np.isfinite(self.idx_data)
self.idx_data = np.nan_to_num(self.idx_data, copy=True,
nan=nan_replacement,
posinf=1e10,
neginf=-1e10)

self._notifyFittingCallbacks(self.x, self.idx_data[0])

if self.stacking > 0.0:
Expand Down Expand Up @@ -1297,8 +1307,9 @@ def dataAdded(self, d):
self.plot_axes[1] = x_max + x_pad

if self.autoscale_y:
y_min = self.idx_data.min()
y_max = self.idx_data.max()
data_for_scale = self.idx_data[finite_mask]
y_min = data_for_scale.min()
y_max = data_for_scale.max()

y_pad = (y_max - y_min) * 0.02

Expand Down
32 changes: 16 additions & 16 deletions src/metro/devices/display/hist2d.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -271,8 +271,9 @@ def paintEvent(self, event):

polygon = self.x_spectrum_polygon
for i in range(0, n_points):
polygon.setPoint(i, i / x_scale,
145 - int(x_spectrum[x_min+i] / y_scale))
polygon.setPoint(
i, int(i / x_scale),
145 - int(x_spectrum[x_min+i] / y_scale))

qp.drawPolyline(polygon)

Expand All @@ -291,14 +292,14 @@ def paintEvent(self, event):
x_scale = y_spectrum_max / 85
y_scale = n_points / self.data_img_dest.height()

x_offset = 5 + self.data_img_dest.right()
x_offset = 5 + int(self.data_img_dest.right())

polygon = self.y_spectrum_polygon
for i in range(0, n_points):
polygon.setPoint(
i, x_offset + int(y_spectrum[y_min+i] / x_scale),
150 + self.data_img_dest.height() - i / y_scale
)
i,
x_offset + int(y_spectrum[y_min+i] / x_scale),
150 + int(self.data_img_dest.height() - i / y_scale))

qp.drawPolyline(polygon)

Expand Down Expand Up @@ -347,12 +348,12 @@ def paintEvent(self, event):

for label, line in zip(self.axes_tick_x_labels,
self.axes_tick_x_lines):
qp.drawText(line.x1()-40, line.y1()-20, 80, 20,
qp.drawText(int(line.x1()) - 40, int(line.y1()) - 20, 80, 20,
QtCore.Qt.AlignCenter, str(label))

for label, line in zip(self.axes_tick_y_labels,
self.axes_tick_y_lines):
qp.drawText(line.x1()+10, line.y1()-10, 80, 20,
qp.drawText(int(line.x1()) + 10, int(line.y1()) - 10, 80, 20,
QtCore.Qt.AlignLeft | QtCore.Qt.AlignVCenter,
str(label))

Expand Down Expand Up @@ -524,8 +525,8 @@ def _rebuildStaticObjects(self, qp):

coords = roi['coords']

roi_x = s_x * (coords[0] - self.axes['x_min'])
roi_y = s_y * (self.axes['y_max'] - coords[3])
roi_x = int(s_x * (coords[0] - self.axes['x_min']))
roi_y = int(s_y * (self.axes['y_max'] - coords[3]))

top_visible = bottom_visible = left_visible = right_visible = True

Expand All @@ -543,8 +544,8 @@ def _rebuildStaticObjects(self, qp):
top_visible = False
roi_y = img_height

roi_width = s_x * (coords[2] - coords[0])
roi_height = s_y * (coords[3] - coords[1])
roi_width = int(s_x * (coords[2] - coords[0]))
roi_height = int(s_y * (coords[3] - coords[1]))

if (roi_x + roi_width) > img_width:
right_visible = False
Expand Down Expand Up @@ -1343,8 +1344,8 @@ def _buildColorPalette(self):
mx_60 = max_value * 0.6 + z_min
mx_80 = max_value * 0.8 + z_min

color_table = [QtGui.qRgb(255.0, 255.0, 255.0)] * 256
color_table[0] = QtGui.qRgb(0.0, 0.0, 0.0)
color_table = [QtGui.qRgb(255, 255, 255)] * 256
color_table[0] = QtGui.qRgb(0, 0, 0)

grad = QtGui.QLinearGradient()
grad.setStart(0, 0)
Expand Down Expand Up @@ -1382,8 +1383,7 @@ def _buildColorPalette(self):
blue = (i - mx_80) / (max_value - mx_80) # rising

color_table[i] = QtGui.qRgb(
red * 255.0, green * 255.0, blue * 255.0
)
int(red * 255.0), int(green * 255.0), int(blue * 255.0))
grad.setColorAt(1.0 - (i / max_value),
QtGui.QColor.fromRgb(color_table[i]))

Expand Down
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