def pltImAndCoords(h5file, frame, coordFiles, printerFriendly=True):
'''read image coordinates, plot them together with the raw data
save output as .png or .tiff or display with matplotlib'''
# read input data
rawData = h5.readHDF5Frame(h5file, frame)
coordDat = [(coord2im.readCoordsFile(f)) for f in coordFiles]
if printerFriendly:
rawData = -rawData
plt.imshow(rawData, interpolation='nearest')
plt.colorbar()
plt.gray()
axx = plt.axis()
markers = ['r+', 'bx', 'go', 'k,', 'co', 'yo']
for i in range(len(coordFiles)):
c, w, h = coordDat[i]
cc = np.array(c)
idxs = (cc[:,2] == frame)
cc = cc[idxs]
ll = coordFiles[i][coordFiles[i].rfind('/')+1:]
plt.plot(cc[:,0], cc[:,1], markers[i], label=ll)
plt.legend()
plt.axis(axx) # dont change axis by plotting coordinates
plt.show()
path = r'/net/gorgonzola/storage/jschleic/Documents/log/vigra-storm-cpp/'
files = [ #'20a_MT_Atto520-coords.txt',
'20a_MT_Atto520-coords-nofilter-thr800.txt',
'20a_MT_Atto520-coords-wiener-thr800.txt',
'20a_MT_Atto520-coords-invansc-thr800.txt',
'20a_MT_Atto520-coords-luisier_analyze75-thr800.txt',
'20a_MT_Atto520-coords-wiener-thr800-CatmullRom.txt',
'20a_MT_Atto520-coords-rapidstorm.txt', 'tmp.txt',
'20a_MT_Atto520-coords-wiener-thr800-CMR-Ortsraumfilter.txt'
]
# Overview plot (whole image)
plt.figure(1)
overviewfile = files[1]
coords = coordsToImage.readCoordsFile(path + overviewfile)
plt.title("Storm image: " + overviewfile)
roi = [77, 91, 72, 82]
#~ 89,105,44,62
#~ roi = [91,105,14,33 ]
# roi rectangle
mybox = np.array([[roi[0], roi[0], roi[1], roi[1], roi[0]],
[roi[2], roi[3], roi[3], roi[2], roi[2]]])
if 0:
coordsToImage.plot_coords(coords)
# plot roi as rectangle
plt.plot(mybox[0, ...], mybox[1, ...], '0.3')
else:
x, y, intensity = p
nearestIdx = 0 #initial guess
nearestDist = 32768 #large number
for i in range(len(beads)):
if not x - maxDist <= beads[i][0][0] <= x + maxDist:
continue
if not y - maxDist <= beads[i][0][1] <= y + maxDist:
continue
#check nearest neighbor
if dist(beads[i][0], p) < nearestDist:
nearestIdx = i
nearestDist = dist(beads[i][0], p)
return nearestDist, nearestIdx
cc, a, b = coord2im.readCoordsFile(filename)
beads = []
ign = 0
# sort beads in 'bins'
for x, y, frame, intensity, z in cc:
if frame == 0: #define bins
nearestDist, nearestIdx = nearestNeighbor((x, y, intensity), beads,
maxDist)
if nearestDist > maxDist:
beads.append([(x, y, intensity)])
else:
print "removing beads too close together: ", (
x, y, intensity), beads[nearestIdx]
beads.remove(beads[nearestIdx])
else:
def nearestNeighbor(p, beads, maxDist): x,y,intensity = p nearestIdx = 0 #initial guess nearestDist = 32768 #large number for i in range(len(beads)): if not x-maxDist <= beads[i][0][0] <= x+maxDist: continue if not y-maxDist <= beads[i][0][1] <= y+maxDist: continue #check nearest neighbor if dist(beads[i][0], p)<nearestDist: nearestIdx = i nearestDist = dist(beads[i][0], p) return nearestDist, nearestIdx cc, a, b = coord2im.readCoordsFile(filename) beads = [] ign=0 # sort beads in 'bins' for x, y, frame, intensity, z in cc: if frame==0: #define bins nearestDist, nearestIdx = nearestNeighbor((x,y,intensity), beads, maxDist) if nearestDist > maxDist: beads.append([(x,y,intensity)]) else: print "removing beads too close together: ", (x,y,intensity), beads[nearestIdx] beads.remove(beads[nearestIdx]) else: nearestDist, nearestIdx = nearestNeighbor((x,y,intensity), beads, maxDist) if nearestDist>maxDist: # no bin found
