def saveInstrumentRegFile(self, filename):
'''
Similar to saveInstrumentFile, but saves the positions of the
pixelPoints used for registration
'''
regBlobs = [blob.blob(p[0], p[1]) for p in self.pixelPoints]
self.saveInstrumentFile(filename, regBlobs)
def loadInstrumentFile(self, filename):
'''
Loads all the targets associated with a given instrument file.
filename: the ptn file to load. Actually gets information from a partner text file.
returns a list of blobs of the target locations
'''
result = []
if os.path.exists(filename[0:-4] + '.txt'):
reader = open(filename[0:-4] + '.txt', 'r')
for l in reader.readlines():
toks = l.split('\t')
if len(toks) == 3:
result.append(blob.blob(float(toks[0]), float(toks[1]), group = int(toks[2])))
else:
result.append(blob.blob(float(toks[0]), float(toks[1])))
else:
print('{} containing pixel positions not found!'.format(filename[0:-4] + '.txt'))
return result
def loadInstrumentFile(self, filename):
'''
Loads target locations from a target file
filename: the file to read
returns a list of blobs
'''
input = open(filename, 'r')
result = []
for l in input.readlines()[1:]:
toks = l.split(' ')
toks = toks[2].split('_')
if len(toks) == 3:
result.append(
blob(int(toks[1][1:]),
int(toks[2][1:]),
group=int(toks[0][1:])))
elif len(toks) == 2:
result.append(blob(int(toks[0][1:]), int(toks[1][1:])))
return result
def loadInstrumentFile(self, filename):
'''
Loads a zaberMapper instrument file and returns a list of blobs
with the target locations.
filename: the file to load
returns a list of blob objects
'''
result = []
reader = open(filename, 'r')
for l in reader.readlines():
toks = l.split('\t')
if len(toks) == 3:
#group is encoded
result.append(blob.blob(float(toks[0]), float(toks[1]), group = int(toks[2])))
else:
#no group
result.append(blob.blob(float(toks[0]), float(toks[1])))
return result
def loadInstrumentFile(self, filename):
'''
Loads a srsMapper instrument file and returns a list of blobs
with the target locations.
filename: the file to load
returns a list of blob objects
'''
result = []
reader = open(filename, 'r')
for l in reader.readlines()[2:]:#toss focus plane
toks = l.split('\t')
pos = toks[0].split('_')
#parse pixel position and group
x = int(pos[1][:-1])
y = int(pos[2])
if len(toks) == 4:
s = int(toks[3])
result.append(blob.blob(x = x, y = y, group = s))
else:
result.append(blob.blob(x = x, y = y))
return result
def _blbHelp(img,
sizes,
channel=2,
threshold=200,
circs=(0.7, None),
xShift=0,
yShift=0):
'''
helper function to perform blob finding on the image
returns a list of blobs
img: the image to blob find
sizes: (min, max) size to consider max == None means not max size
channel: r,g,b channel to threshold
threshold: minimum pixel intensity to count as blob
circs: (min, max) circularity to consider max == None means no max
xShift: amount to add to x coordinate to shift into global coordinate
yShift: amount to add to x coordinate to shift into global coordinate
'''
#blob find
lbl, num = blobFinder._blbThresh(img, channel, threshold)
slices = scipy.ndimage.find_objects(lbl)
result = []
#for each blob
for i in range(num):
#convert to boolean image
s = slices[i]
dx, dy = s[:2]
region = lbl[dx.start - 1:dx.stop + 1, dy.start - 1:dy.stop + 1]
region = region == i + 1
#area is total number of true pixels
area = np.sum(region)
#if passes size threshold
if area > sizes[0] and (sizes[1] is None or area < sizes[1]):
#calculate circularity = 4 pi area / perimeter^2
perim = skimage.measure.perimeter(region)
circ = 4 * np.pi * area / perim**2
#if passes circularity threshold
if circ > circs[0] and (circs[1] is None or circ < circs[1]):
#determine center of mass, ignoring intensity
(x, y) = scipy.ndimage.measurements.center_of_mass(region)
#calculate radius assuming circle
r = np.sqrt(area / np.pi)
#add to result, note x,y transpose!
result.append(
blob(y=x + dx.start - 1 + yShift,
x=y + dy.start - 1 + xShift,
radius=r,
circularity=circ))
return result
def blobRequest(self, globalPoint, radius):
'''
Tries to add the blob to the current blob list.
If overlap with current blob, remove that point
globalPoint: (x,y) tuple in the image coordinate space
radius: the radius of the new blob to be added
returns true if a blob was added, false if one was removed
'''
for i, b in enumerate(self.blobs):
if (globalPoint[0]-b.X)**2 + (globalPoint[1]-b.Y)**2 <= \
b.radius**2:
self.blobs.pop(i)
return False, i
self.blobs.append(blob.blob(globalPoint[0], globalPoint[1], radius))
return True, -1
def hexagonallyClosePackPoints(self,
spacing,
numLayers,
r=GUIConstants.DEFAULT_PATTERN_RADIUS,
c=1,
dynamicLayering=False):
'''
Expands each blob into a grid of points, with hexagonal close packed spacing
blobs: list of blob objects to expand
spacing: spacing between new blobs
numLayers: number of layers around each blob. 1 generates a grid of 7 with the
initial blob in the center. This can be adjusted for radius
r: radius to set new blobs to
c: circularity of new blobs
dynamicLayering: set to True to account for blob size in making pattern positions
'''
#this may save some computation time to precompute
sqrt3ov2 = np.sqrt(3) / 2
#list of directions to march along to generate a layer
marcher = np.array([[-0.5, sqrt3ov2], [-1., 0.], [-0.5, -sqrt3ov2],
[0.5, -sqrt3ov2], [1., 0.], [0.5, sqrt3ov2]])
#use one mask each time
if dynamicLayering == False:
#start at center
mask = np.array([[0, 0]])
for n in range(numLayers):
current = np.array([[n + 1., 0]])
for i in range(6):
direction = marcher[i, :]
for j in range(n + 1):
current += direction
mask = np.append(mask, current, axis=0)
mask *= spacing
#strip off radius
result = []
ind = 0
for blb in self.blobs:
#use new mask each blob, with number of layers being size dependent
if dynamicLayering == True:
mask = np.array([[0, 0]])
#change number of layers by blb radius
for n in range(numLayers + int(np.ceil(blb.radius / spacing))):
current = np.array([[n + 1., 0]])
for i in range(6):
direction = marcher[i, :]
for j in range(n + 1):
current += direction
mask = np.append(mask, current, axis=0)
mask *= spacing
#expand blb into points based on mask
for b in map(
lambda x: blob.blob(
x=x[0], y=x[1], radius=r, circularity=c, group=ind),
list(mask + (blb.X, blb.Y))):
result.append(b)
ind += 1
result = self.partialDeepCopy(result)
result.generateGroupLabels()
return result
def rectangularlyPackPoints(self,
spacing,
numLayers,
r=GUIConstants.DEFAULT_PATTERN_RADIUS,
c=1,
dynamicLayering=False):
'''
Expands each blob into a grid of points, with regular rectangular spacing
blobs: list of blob objects to expand
spacing: spacing between new blobs
numLayers: number of layers around each blob. 1 generates a grid of 3x3 with the
initial blob in the center. This can be adjusted for radius
r: radius to set new blobs to
c: circularity of new blobs
dynamicLayering: set to True to account for blob size in making pattern positions
'''
#marcher is a list of directions to move to for generating the spacing
#this starts at the right, moves down, left, up, right, down, to spiral around the blob
#additional layers are generated by applying the marcher multiple times
marcher = np.array([[0, 1], [-1., 0.], [-1., 0.], [0., -1.], [0., -1.],
[1., 0.], [1., 0.], [0, 1]])
#use one mask each time
if dynamicLayering == False:
#start at center
mask = np.array([[0, 0]])
for n in range(numLayers):
#move to the right by n spaces
current = np.array([[n + 1., 0]])
for i in range(8):
#add the marcher n times
direction = marcher[i, :]
for j in range(n + 1):
current += direction
mask = np.append(mask, current, axis=0)
#scale unit mask by spacing
mask *= spacing
result = []
ind = 0
for blb in self.blobs:
#use new mask each blob, with number of layers being size dependent
if dynamicLayering == True:
mask = np.array([[0, 0]])
#only change from above is the blb.radius/spacing
for n in range(numLayers + int(np.ceil(blb.radius / spacing))):
current = np.array([[n + 1., 0]])
for i in range(8):
direction = marcher[i, :]
for j in range(n + 1):
current += direction
mask = np.append(mask, current, axis=0)
mask *= spacing
#expand blb by mask
for b in map(
lambda x: blob.blob(
x=x[0], y=x[1], radius=r, circularity=c, group=ind),
list(mask + (blb.X, blb.Y))):
#add each point to result
result.append(b)
ind += 1
result = self.partialDeepCopy(result)
result.generateGroupLabels()
return result
def circularPackPoints(self,
spacing,
maxSpots,
offset,
minSpots=4,
r=GUIConstants.DEFAULT_PATTERN_RADIUS,
c=1):
'''
Expands each blob into several points surrounding the blob.
blobs: list of blobs to expand
spacing: minimum spacing between points
maxSpots: max number of spots to expand for each blob
offset: offset of circumference to space blobs
minSpots: minimum number of spots for each blob. Ignores spacing with min spots
r: radius of new blobs
c: circumference of new blobs
returns a list of blobs of the expanded positions
'''
#check maxspots to ensure less than min
maxSpots = minSpots if maxSpots < minSpots else maxSpots
#calculate min and max r:
maxR = maxSpots * spacing / (2 * np.pi) - offset
#angles and unit vectors of max spots
thetas = np.linspace(0, 2 * np.pi, maxSpots, False)
maxUnits = np.vstack((np.cos(thetas), np.sin(thetas)))
minR = minSpots * spacing / (2 * np.pi) - offset
#angles and unit vectors at min number of spots
thetas = np.linspace(0, 2 * np.pi, minSpots, False)
minUnits = np.vstack((np.cos(thetas), np.sin(thetas)))
result = []
ind = 0
for blb in self.blobs:
#check radius for min, max or between
if (blb.radius > maxR):
unitvec = maxUnits
elif (blb.radius < minR):
unitvec = minUnits
#between min and max, use most spots as possible while retaining the spacing
else:
spots = np.floor(2 * np.pi * (blb.radius + offset) / spacing)
thetas = np.linspace(0, 2 * np.pi, spots, False)
unitvec = np.vstack((np.cos(thetas), np.sin(thetas)))
#expand each blob into a new x,y positions
targetSpots = unitvec*(blb.radius + offset) + \
np.matlib.repmat(np.array((blb.X, blb.Y))
,unitvec.shape[1],1).T
#add targets to result
for e in targetSpots.T:
result.append(
blob.blob(x=e[0],
y=e[1],
radius=r,
circularity=c,
group=ind))
#increment group number for next blob
ind += 1
result = self.partialDeepCopy(result)
result.generateGroupLabels()
return result