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Simplifying to a single file, perf improvements, better user experience #7

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Simplifying to a single file, perf improvements, better user experience #7

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d45e46b
combine logic into a single fle
JesseBuesking Dec 3, 2022
8ead4f0
updating readme
JesseBuesking Dec 3, 2022
61dd6c1
more readme changes
JesseBuesking Dec 3, 2022
eca08d0
support for different frameWidth and frameHeight
JesseBuesking Dec 3, 2022
7f5bd00
performance improvements
JesseBuesking Dec 3, 2022
ab47a5a
update the graticule when modified
JesseBuesking Dec 3, 2022
25c3738
take the peak nearest to where the user clicked
JesseBuesking Dec 3, 2022
005248d
fixing bugs in mouse clicks and graticule
JesseBuesking Dec 3, 2022
7e21695
a bit of cleanup, and a few more perf improvements
JesseBuesking Dec 5, 2022
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149 changes: 84 additions & 65 deletions src/PySpectrometer2.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@
cap = None
if use_device or use_webcam:
if use_device:
cap = cv2.VideoCapture('/dev/video'+str(dev), cv2.CAP_V4L)
cap = cv2.VideoCapture("/dev/video{}".format(dev), cv2.CAP_V4L)
elif use_webcam:
cap = cv2.VideoCapture(0)
print("[info] W, H, FPS")
Expand Down Expand Up @@ -197,16 +197,6 @@ def handle_mouse(event,x,y,flags,param):
caldata = readcal(frameWidth)
wavelengthData = caldata[0]

def compute_wavelength_rgbs(wavelengthData):
result = []
for wld in wavelengthData:
# derive the color from the wavelenthData array
rgb = wavelength_to_rgb(round(wld))
result.append(rgb)
return result

wavelength_data_rgbs = compute_wavelength_rgbs(wavelengthData)

calmsg1 = caldata[1]
calmsg2 = caldata[2]
calmsg3 = caldata[3]
Expand All @@ -230,14 +220,18 @@ def compute_wavelength_rgbs(wavelengthData):
# center the background img in the newly sized background
banner_image_resized[:, xoff:xoff+w1,:] = banner_image
banner_image = banner_image_resized
# white border at the bottom
cv2.line(banner_image,(0,79),(frameWidth,79),(255,255,255),1)
messages = np.copy(banner_image)

spectrum_vertical = None
waterfall_vertical = None
textoffset = 12

def build_graph_base():
global textoffset
# blank image for Graph, filled white
result = np.full([320, frameWidth, 3], fill_value=255, dtype=np.uint8)
textoffset = 12

# vertial lines every whole 10nm
for position in tens:
Expand All @@ -246,7 +240,7 @@ def build_graph_base():
# vertical lines every whole 50nm
for positiondata in fifties:
cv2.line(result,(positiondata[0],15),(positiondata[0],320),(0,0,0),1)
cv2.putText(result,str(positiondata[1])+'nm',(positiondata[0]-textoffset,12),font,0.4,(0,0,0),1, cv2.LINE_AA)
cv2.putText(result,"{}nm".format(positiondata[1]),(positiondata[0]-textoffset,12),font,0.4,(0,0,0),1, cv2.LINE_AA)

# horizontal lines
for i in range (320):
Expand All @@ -258,6 +252,26 @@ def build_graph_base():
graph_base = build_graph_base()
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Build the background of the display once, this way we can use np.copy to just overwrite the display at the start of each loop which is much faster and uses less memory.

graph = np.copy(graph_base)

def compute_wavelength_rgbs(wavelengthData):
result = []
for wld in wavelengthData:
# derive the color from the wavelenthData array
rgb = wavelength_to_rgb(round(wld))
result.append(rgb)
return result

def compute_wavelength_rgbs_bg(array, graph):
result = np.full([320, frameWidth, 3], fill_value=255, dtype=np.uint8)
for index, wl in enumerate(array):
r, g, b = wavelength_data_rgbs[index]
result[:, index, :] = [b, g, r]
# overlay the graticule
result = cv2.bitwise_and(graph, result)
return result

wavelength_data_rgbs = compute_wavelength_rgbs(wavelengthData)
wavelength_data_rgbs_bg = compute_wavelength_rgbs_bg(wavelength_data_rgbs, graph_base)

def snapshot(savedata):
now = time.strftime("%Y%m%d--%H%M%S")
timenow = time.strftime("%H:%M:%S")
Expand All @@ -270,7 +284,7 @@ def snapshot(savedata):
f = open("Spectrum-"+now+'.csv','w')
f.write('Wavelength,Intensity\r\n')
for x in zip(graphdata[0],graphdata[1]):
f.write(str(x[0])+','+str(x[1])+'\r\n')
f.write("{},{}\r\n".format(*x))
f.close()
message = "Last Save: "+timenow
return(message)
Expand All @@ -282,14 +296,20 @@ def snapshot(savedata):

def runall():
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I turned this into a function so that I could more easily profile the logic.

global graticuleData, tens, fifties, msg1, saveMsg, waterfall, wavelengthData, peak_intensities
global caldata, calmsg1, calmsg2, calmsg3, savpoly, mindist, thresh
global caldata, calmsg1, calmsg2, calmsg3, savpoly, mindist, thresh, messages, banner_image
global calibrate, clickArray, cursorX, cursorY, picamGain, spectrum_vertical, waterfall_vertical
global graph, graph_base, wavelength_data_rgbs, raw_intensity, picam2, cap
global graph, graph_base, wavelength_data_rgbs, raw_intensity, picam2, cap, wavelength_data_rgbs_bg
global textoffset

holdpeaks = False
measure = False # show cursor measurements
recPixels = False # measure pixels and record clicks

pts = np.zeros((frameWidth+2, 2), dtype=np.int)
pts[0] = [frameWidth, 319]
pts[1] = [0, 319]
pts[2:, 0] = np.arange(frameWidth)
mask = np.zeros(graph.shape[:2], np.uint8)
while (True if use_picamera else cap.isOpened()):
# Capture frame-by-frame
frame = None
Expand All @@ -315,7 +335,7 @@ def runall():
cv2.line(cropped,(0,halfway-2),(frameWidth,halfway-2),(255,255,255),1)
cv2.line(cropped,(0,halfway+2),(frameWidth,halfway+2),(255,255,255),1)

messages = banner_image
np.copyto(messages, banner_image)
# reset the graph to the base
np.copyto(graph, graph_base)

Expand All @@ -330,18 +350,20 @@ def runall():
else:
raw_intensity = current_intensities

np.clip(raw_intensity, 0, 255, out=raw_intensity)

if dispWaterfall:
#data is smoothed at this point!!!!!!
#create an empty array for the data
wdata = np.zeros([1,frameWidth,3],dtype=np.uint8)
for index, i in enumerate(raw_intensity):
rgb = wavelength_data_rgbs[index]
luminosity = i/255.0
rgb = wavelength_data_rgbs[index]
b = int(round(rgb[0]*luminosity))
g = int(round(rgb[1]*luminosity))
r = int(round(rgb[2]*luminosity))
#wdata[0,index]=(r,g,b) #fix me!!! how do we deal with this data??
wdata[0,index]=(r,g,b)
wdata[0,index] = (r,g,b)

if use_picamera:
contrast = 2.5
Expand All @@ -353,9 +375,6 @@ def runall():
waterfall[index] = waterfall[index-1]
waterfall[0] = wdata

#Draw the intensity data :-)
#first filter if not holding peaks!

intensity = None
if not holdpeaks:
intensity = savitzky_golay(raw_intensity,17,savpoly)
Expand All @@ -364,17 +383,21 @@ def runall():
else:
intensity = np.int32(raw_intensity)
holdmsg = "Holdpeaks ON"

#now draw the intensity data....
for index, i in enumerate(intensity):
rgb = wavelength_data_rgbs[index]
r, g, b = rgb
# origin is top left
cv2.line(graph, (index,320), (index,320-i), (b,g,r), 1)
cv2.line(graph, (index,319-i), (index,320-i), (0,0,0), 1, cv2.LINE_AA)

#find peaks and label them
textoffset = 12

np.clip(intensity, 0, 255, out=intensity)
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Using numpy to draw the intensity data using vector ops over python loops.


# draw instensity data
pts[2:, 1] = 319-intensity
# mask holds where we should draw the rainbow
mask.fill(0)
cv2.drawContours(mask, [pts], -1, 1, -1, cv2.LINE_AA)
mask3d = np.dstack([mask]*3)
# draw the rainbow using the mask onto graph
np.putmask(graph, mask3d, wavelength_data_rgbs_bg)
# draw the black line
graph[pts[2:, 1], pts[2:, 0]] = 0

# find peaks and label them
thresh = int(thresh) #make sure the data is int.
peak_intensities = peakIndexes(intensity, thres=thresh/max(intensity), min_dist=mindist)

Expand All @@ -384,30 +407,26 @@ def runall():
wavelength = round(wavelengthData[i],1)
cv2.rectangle(graph,((i-textoffset)-2,height),((i-textoffset)+60,height-15),(0,255,255),-1)
cv2.rectangle(graph,((i-textoffset)-2,height),((i-textoffset)+60,height-15),(0,0,0),1)
cv2.putText(graph,str(wavelength)+'nm',(i-textoffset,height-3),font,0.4,(0,0,0),1, cv2.LINE_AA)
#flagpoles
cv2.putText(graph,"{}nm".format(wavelength),(i-textoffset,height-3),font,0.4,(0,0,0),1, cv2.LINE_AA)
# flagpoles
cv2.line(graph,(i,height),(i,height+10),(0,0,0),1)

if measure:
#show the cursor!
# show the cursor!
cv2.line(graph,(cursorX,cursorY-140),(cursorX,cursorY-180),(0,0,0),1)
cv2.line(graph,(cursorX-20,cursorY-160),(cursorX+20,cursorY-160),(0,0,0),1)
cv2.putText(graph,str(round(wavelengthData[cursorX],2))+'nm',(cursorX+5,cursorY-165),font,0.4,(0,0,0),1, cv2.LINE_AA)
cv2.putText(graph,"{}nm".format(round(wavelengthData[cursorX],2)),(cursorX+5,cursorY-165),font,0.4,(0,0,0),1, cv2.LINE_AA)

if recPixels:
#display the points
# display the points
cv2.line(graph,(cursorX,cursorY-140),(cursorX,cursorY-180),(0,0,0),1)
cv2.line(graph,(cursorX-20,cursorY-160),(cursorX+20,cursorY-160),(0,0,0),1)
cv2.putText(graph,str(cursorX)+'px',(cursorX+5,cursorY-165),font,0.4,(0,0,0),1, cv2.LINE_AA)
else:
#also make sure the click array stays empty
clickArray = []

if clickArray:
for mouseX, mouseY, _, _ in clickArray:
cv2.circle(graph,(mouseX,mouseY),5,(0,0,0),-1)
#we can display text :-) so we can work out wavelength from x-pos and display it ultimately
cv2.putText(graph,str(mouseX),(mouseX+5,mouseY),cv2.FONT_HERSHEY_SIMPLEX,0.4,(0,0,0))
cv2.putText(graph,"{}px".format(cursorX),(cursorX+5,cursorY-165),font,0.4,(0,0,0),1, cv2.LINE_AA)

for mouseX, mouseY, _, _ in clickArray:
cv2.circle(graph,(mouseX,mouseY),5,(0,0,0),-1)
#we can display text :-) so we can work out wavelength from x-pos and display it ultimately
cv2.putText(graph,str(mouseX),(mouseX+5,mouseY),cv2.FONT_HERSHEY_SIMPLEX,0.4,(0,0,0))

# stack the images and display the spectrum (using concatenate instead of
# vstack to reuse the array and save memory allocations/time)
Expand All @@ -416,25 +435,22 @@ def runall():
else:
np.concatenate((messages, cropped, graph), out=spectrum_vertical, axis=0)

#dividing lines...
cv2.line(spectrum_vertical,(0,80),(frameWidth,80),(255,255,255),1)
cv2.line(spectrum_vertical,(0,160),(frameWidth,160),(255,255,255),1)
#print the messages
cv2.putText(spectrum_vertical,calmsg1,(message_loc1,15),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(spectrum_vertical,calmsg3,(message_loc1,33),font,0.4,(0,255,255),1, cv2.LINE_AA)

if use_picamera:
cv2.putText(spectrum_vertical,saveMsg,(message_loc1,51),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(spectrum_vertical,"Gain: "+str(picamGain),(message_loc1,69),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(spectrum_vertical,"Gain: {}".format(picamGain),(message_loc1,69),font,0.4,(0,255,255),1, cv2.LINE_AA)
else:
cv2.putText(spectrum_vertical,"Framerate: "+str(cfps),(message_loc1,51),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(spectrum_vertical,"Framerate: {}".format(cfps),(message_loc1,51),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(spectrum_vertical,saveMsg,(message_loc1,69),font,0.4,(0,255,255),1, cv2.LINE_AA)

#Second column
cv2.putText(spectrum_vertical,holdmsg,(message_loc2,15),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(spectrum_vertical,"Savgol Filter: "+str(savpoly),(message_loc2,33),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(spectrum_vertical,"Label Peak Width: "+str(mindist),(message_loc2,51),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(spectrum_vertical,"Label Threshold: "+str(thresh),(message_loc2,69),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(spectrum_vertical,"Savgol Filter: {}".format(savpoly),(message_loc2,33),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(spectrum_vertical,"Label Peak Width: {}".format(mindist),(message_loc2,51),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(spectrum_vertical,"Label Threshold: {}".format(thresh),(message_loc2,69),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.imshow(title1,spectrum_vertical)

if dispWaterfall:
Expand All @@ -449,23 +465,22 @@ def runall():
cv2.line(waterfall_vertical,(0,160),(frameWidth,160),(255,255,255),1)
#Draw this stuff over the top of the image!
#Display a graticule calibrated with cal data
textoffset = 12

#vertical lines every whole 50nm
for positiondata in fifties:
for i in range(162,480):
if i%20 == 0:
cv2.line(waterfall_vertical,(positiondata[0],i),(positiondata[0],i+1),(0,0,0),2)
cv2.line(waterfall_vertical,(positiondata[0],i),(positiondata[0],i+1),(255,255,255),1)
cv2.putText(waterfall_vertical,str(positiondata[1])+'nm',(positiondata[0]-textoffset,475),font,0.4,(0,0,0),2, cv2.LINE_AA)
cv2.putText(waterfall_vertical,str(positiondata[1])+'nm',(positiondata[0]-textoffset,475),font,0.4,(255,255,255),1, cv2.LINE_AA)
cv2.putText(waterfall_vertical,"{}nm".format(positiondata[1]),(positiondata[0]-textoffset,475),font,0.4,(0,0,0),2, cv2.LINE_AA)
cv2.putText(waterfall_vertical,"{}nm".format(positiondata[1]),(positiondata[0]-textoffset,475),font,0.4,(255,255,255),1, cv2.LINE_AA)

cv2.putText(waterfall_vertical,calmsg1,(message_loc1,15),font,0.4,(0,255,255),1, cv2.LINE_AA)

if use_picamera:
cv2.putText(waterfall_vertical,calmsg3,(message_loc1,33),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(waterfall_vertical,saveMsg,(message_loc1,51),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(waterfall_vertical,"Gain: "+str(picamGain),(message_loc1,69),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(waterfall_vertical,"Gain: {}".format(picamGain),(message_loc1,69),font,0.4,(0,255,255),1, cv2.LINE_AA)
else:
cv2.putText(waterfall_vertical,calmsg2,(message_loc1,33),font,0.4,(0,255,255),1, cv2.LINE_AA)
cv2.putText(waterfall_vertical,calmsg3,(message_loc1,51),font,0.4,(0,255,255),1, cv2.LINE_AA)
Expand Down Expand Up @@ -503,8 +518,6 @@ def runall():
#overwrite wavelength data
#Go grab the computed calibration data
caldata = readcal(frameWidth)
wavelengthData = caldata[0]
wavelength_data_rgbs = compute_wavelength_rgbs(wavelengthData)
calmsg1 = caldata[1]
calmsg2 = caldata[2]
calmsg3 = caldata[3]
Expand All @@ -513,14 +526,20 @@ def runall():
tens = (graticuleData[0])
fifties = (graticuleData[1])
graph_base = build_graph_base()
wavelengthData = caldata[0]
wavelength_data_rgbs = compute_wavelength_rgbs(wavelengthData)
wavelength_data_rgbs_bg = compute_wavelength_rgbs_bg(wavelength_data_rgbs, graph_base)
elif keyPress == ord("x"):
clickArray = []
elif keyPress == ord("m"):
recPixels = False #turn off recpixels!
measure = not measure
recPixels = False # turn off recpixels!
clickArray = []
elif keyPress == ord("p"):
measure = False #turn off measure!
recPixels = not recPixels
if not recPixels:
clickArray = []
elif keyPress == ord("o"):#sav up
savpoly+=1
if savpoly >=15:
Expand Down Expand Up @@ -550,13 +569,13 @@ def runall():
if picamGain >=50:
picamGain = 50.0
picam2.set_controls({"AnalogueGain": picamGain})
print("Camera Gain: "+str(picamGain))
print("Camera Gain: {}".format(picamGain))
elif use_picamera and keyPress == ord("g"):#Gain down
picamGain -= 1
if picamGain <=0:
picamGain = 0.0
picam2.set_controls({"AnalogueGain": picamGain})
print("Camera Gain: "+str(picamGain))
print("Camera Gain: {}".format(picamGain))

runall()

Expand Down
16 changes: 11 additions & 5 deletions src/specFunctions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -208,11 +208,17 @@ def peakIndexes(y, thres=0.3, min_dist=1, thres_abs=False):

# for each chain of zero indexes
for plateau in zero_plateaus:
median = np.median(plateau)
# set leftmost values to leftmost non zero values
dy[plateau[plateau < median]] = dy[plateau[0] - 1]
# set rightmost and middle values to rightmost non zero values
dy[plateau[plateau >= median]] = dy[plateau[-1] + 1]
lplat = plateau.shape[0]
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I noticed that the data in plateau is always in sorted order, so we can skip finding medians and know that the middle element is the median.

left = dy[plateau[0] - 1]
right = dy[plateau[lplat-1] + 1]
middle = lplat // 2
# always in sorted order
median = plateau[middle]
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It's actually faster to just loop over the plateau elements once and do something with each element than to do the vectorized ops they were performing before. The changes in this function result in a roughly 4+x speedup which is awesome because the peak finding logic is a big cause of slowness when running the loop.

for p in plateau:
if p < median:
dy[p] = left
else:
dy[p] = right

# find the peaks by using the first order difference
peaks = np.where(
Expand Down