def buildSeedPoints(image, mode='com'):
""" Successive set of filters to take a still image, isolate cell-like ROIs, and return a
list of points representing center points to pass into core.segmentation.pickCells.
Filters are, in order: thresholding, morphological closing, and then a connected pixel cutoff filter.
Often, the best thing to pass into this image as a high pass filtered version of your field of view.
:param image: a 2d numpy array to build points from
:param mode: an optional string, either: 'centriod' or 'com'
:returns: tuple, (seedPoints, seedPointImage) 2d and 3d numpy array, containing coordinates and an image of points, respectively
"""
# seedMask = ipg.binaryErode(ipg.connectedPixelFilter(pymorph.label(ipg.threshold(ipg.subGaussian(image))>0)))
# binarySeedMask = ipg.connectedPixelFilter(pymorph.label(pymorph.close(ipg.threshold(ipg.subGaussian(image))>0)))
binarySeedMask = ipg.connectedPixelFilter(pymorph.label(pymorph.close(ipg.threshold(image))))
seedMask = pymorph.label(binarySeedMask)
seedingRegionProps = regionProps(image, seedMask)
if mode is 'centroid':
seedPoints = [r['centroid'] for r in sorted(seedingRegionProps, key=lambda x: x['meanIntensity'],reverse=True)]
elif mode is 'com':
seedPoints = [r['com'] for r in sorted(seedingRegionProps, key=lambda x: x['meanIntensity'],reverse=True)]
# pdb.set_trace()
seedPoints = np.floor(np.array(seedPoints))
seedPointImage = np.zeros_like(seedMask)
for point in seedPoints:
seedPointImage[point] = 255
return seedPoints, seedPointImage
def extract2(self):
im=self.image
invimage=np.ones((np.size(im,0),np.size(im,1)))-im
bloblabels=pymorph.label(im)
holelabels=pymorph.label(invimage)
print ("Image is ", (np.size(im,0),np.size(im,1)))
self.blobs=[] # pikseli predmeta
self.holes=[] # pikseli rupa
for i in range(0,bloblabels.max()):
self.blobs.append([])
for i in range(0,holelabels.max()):
self.holes.append([])
for i in range(0,np.size(im,0)):
for j in range(0,np.size(im,1)):
if im[i][j]==1:
self.blobs[bloblabels[i][j]-1].append([i,j]) #
else: # Razdvajanje rupa i predmeta
self.holes[holelabels[i][j]-1].append([i,j]) #
def updateImage(self, image, mask=None, labels=False):
"""image is a 2d image, mask is a 2d RGBA image"""
if np.any(np.not_equal(self.mask, mask)):
labels_changed = True
else:
labels_changed = False
if len(self.labels) == 0:
labels_empty = True
else:
labels_empty = False
self.image = image
self.mask = mask
self.image_ax.set_data(image)
self.mask_ax.set_data(mask)
if labels is True and (labels_changed or labels_empty):
for item in self.labels:
item.remove()
self.labels = []
labeled_mask = pymorph.label((mask[:, :, 3] > 0).astype(int))
for cell in range(1, labeled_mask.max() + 1):
xx, yy = zip(*np.argwhere(labeled_mask == cell))
# NOTE INVERSION
y_loc = np.median(np.unique(xx))
x_loc = np.median(np.unique(yy))
self.labels.append(
self.axes.text(
x_loc,
y_loc,
str(cell),
verticalalignment="center",
horizontalalignment="center",
color="yellow",
size=9,
)
)
elif labels is False:
for item in self.labels:
item.remove()
self.labels = []
else:
pass
self.draw()
def bright_object_detection(image):
""" Perform bright object detection on an array image."""
# Store all intermediate steps in a dictionary. Useful for debugging.
steps = dict()
steps['input'] = image
# Reduce noise using a median filter.
med_filter_size = (MED_SIZE, MED_SIZE, MED_SIZE)
steps['median'] = ndimg.median_filter(steps['input'], med_filter_size)
# Convert median filtered image to grayscale.
steps['luminance'] = scikits.image.color.rgb2gray(steps['median']) * 255.
# Compute local pixel average.
k_avg = np.ones((AVG_SIZE, AVG_SIZE)) / AVG_SIZE**2
steps['average'] = ndimg.convolve(steps['luminance'], k_avg)
# Compute local pixel variance.
steps['diff_mean'] = steps['luminance'] - steps['average']
steps['diff_mean_sq'] = steps['diff_mean'] * steps['diff_mean']
steps['variance'] = ndimg.convolve(steps['diff_mean_sq'], k_avg)
# Compute binary threshold image using mahalonobis distance. Use the sign
# of the difference between the pixel and its local mean to ignore dark
# pixels.
steps['maha_sq'] = (steps['diff_mean'] > 0) * steps['diff_mean_sq'] / \
steps['variance']
steps['thresh_maha'] = (steps['maha_sq'] > (NUM_STDDEV * NUM_STDDEV))
# Integrate global illumination effects by taking a top percentage of
# intensities from the detected light regions.
steps['masked_regions_lum'] = steps['thresh_maha'] * steps['luminance']
steps['masked_regions_hist'] = pymorph.histogram(steps['masked_regions_lum'])
steps['global_bright_thresh'] = int((len(steps['masked_regions_hist']) * \
(1.0 - GLOBAL_BRIGHT_PCT)) + 0.5)
steps['thresh_global'] = steps['masked_regions_lum'] >= \
steps['global_bright_thresh']
# Morphological operations on detected blobs.
steps['detect_erode'] = pymorph.erode(steps['thresh_global'])
steps['detect_dilate'] = pymorph.dilate(steps['detect_erode'])
# Count bright objects. Connected components and raw pixels.
steps['detect_labels'] = pymorph.label(steps['detect_dilate'])
steps['bright_blob_count'] = steps['detect_labels'].max()
steps['bright_pixel_count'] = sum(steps['masked_regions_hist']
[steps['global_bright_thresh']:])
return steps
def pickCellsMatlab(stack, seedPoints=None):
"""
This is a wrapper function for MATLAB code that allows for semi-automated picking
of cells via some MATLAB code from the Reid lab. Depends on a simple matlab
function which opens the hdf5 file and aligns the array, and writes it back out to
another part of the hdf5 file
Algorithm uses the average across time (axis=2) to form the image to pick cells with,
generally is the average of the green channel
Optional parameter seedPoints is a N x 2 np.array with coordinates of points to 'pre-click'
Generated by core.morphProcessing.buildSeedPoints, for example. Ideally sorted by brightest
to dimmest object.
Returns two 2d arrays- one is a binary array and one a labeled array
:param stack: 3d nparray to use for picking.
:param seedPoints: optional, N x 2 numpy array
:returns: (bwOut, mask): tuple of binary mask and labeled mask, both 2d numpy arrays
"""
fovimage = np.mean(np.atleast_3d(stack),axis=2)
temp_dir = tempfile.mkdtemp()
f = h5py.File(os.path.join(temp_dir, 'temp.hdf5'))
f.create_dataset('fovimage',data=fovimage)
if seedPoints is not None:
f.create_dataset('seedPoints',data=seedPoints)
# else:
# f.create_dataset('seedPoints',data=np.array([]))
f.close()
# call picking code (external matlab function, yuck)
print 'Launching MATLAB to pick cells...\n'
handle = subprocess.Popen('matlab -nodesktop -r \'imCellEditinteractiveExternal\'',stdin=open('/dev/null'), shell=True, executable="/bin/bash", cwd=temp_dir)
handle.wait()
# import the masks and delete temporary files
f = h5py.File(os.path.join(temp_dir, 'temp.hdf5'),'r')
bwOut = np.array(f.get('bwOut')[:])
# mask = np.array(f.get('mask')[:])
f.close()
os.system("rm -rf " + temp_dir)
return bwOut, pymorph.label(bwOut)
steps['thresh_global']))
###############################################################################
# Morpohological operations on detected blobs.
# <demo> stop
# <demo> auto
steps['detect_erode'] = pymorph.erode(steps['thresh_global'])
steps['detect_dilate'] = pymorph.dilate(steps['detect_erode'])
print "Morphed mask (erode, dilate):"
plab.imshow(pymorph.overlay(steps['luminance'].astype('uint8'),
steps['detect_dilate']))
# <demo> stop
# <demo> auto
# Count bright objects. Connected components and raw pixels.
steps['detect_labels'] = pymorph.label(steps['detect_dilate'])
steps['bright_blob_count'] = steps['detect_labels'].max()
print "Bright blob count:", steps['bright_blob_count']
steps['bright_pixel_count'] = sum(steps['masked_regions_hist']
[steps['global_bright_thresh']:])
print "Bright pixel count:", steps['bright_pixel_count']
print "Input image:"
plab.imshow(steps['input'])
# <demo> stop
def tracker(frames, event, thresh_amp, thresh_dis, blob_ext,
direction='forward', plots=False, verbose=False):
"""
Track the blob in a dynamic intervall forward or backward in time, as long
as its amplitude is over a given threshold and the peak has detected less
than a given threshold over consecutive frames.
The maximum number of frames the blob is tracked for, is given by dim0 of
frames
Input:
tau: Maximum number of frames to track blob
event: ndarray, [I0, t0, R0, z0] Index of original feature to
track
direction: Traverse frames 'forward' or 'backward' in dimension 0
thresh_amp: Threshold for amplitude decay relative to frame0
thresh_dis: Threshold for blob movement relative to previous frame
blob_ext: Extend of the blob used for determining its average shape
Returns:
numframes: Number of frames the blob was tracked
xycom: COM position of the blob in each frame
amp: Amplitude at COM in each frame
fwhm_rad_idx: Indices that mark left and right FWHM of the blob
fwhm_pol_idx: Indices that mark the lower and upper FWHM of the blob
blob: Array that stores the blob extend
"""
if (verbose is True):
print 'Called tracker with '
print '\tevent = ', event
print '\tthresh_amp = ', thresh_amp
print '\tthresh_dis = ', thresh_dis
print '\tblob_ext = ', blob_ext
print '\tplots = ', plots
assert (direction in ['forward', 'backward'])
assert (blob_ext % 2 == 0)
# Maximum number of frames the blob is tracked for is given by
# dimension 0 of frames
# tau_max = np.shape(frames)[0]
tau_max = frames.shape[0]
I0, z0_last, R0_last = event[0], event[2], event[3]
# I0 is the threshold amplitude we use for detecting blobs
# i.e. for blob tracking, we identify later all connected regions that are larger than
# I0 * thresh_amp
if (direction is 'forward'):
f_idx = 0 # Index used to access frames
tau = 0 # Start with zero offset
elif (direction is 'backward'):
f_idx = -1 # Start at the second to last frame, 0 based indexing
tau = 1 # Start with one frame offset
if (verbose):
print 'Tracking blob %s, t_idx %d x = %d, y = %d, I0 = %f' %\
(direction, tau, R0_last, z0_last, I0)
print 'thresh_amp = %f, thresh_dis = %f' %\
(thresh_amp * I0, thresh_dis)
xycom = np.zeros([tau_max, 2]) # Return values: COM position of peak
xymax = np.zeros([tau_max, 2]) # Position of the blob peak
fwhm_pol_idx = np.zeros([tau_max, 2], dtype='int') # Poloidal FWHM
fwhm_rad_idx = np.zeros([tau_max, 2], dtype='int') # Radial FWHM
amp = np.zeros([tau_max]) # Amplitude at COM position
good_blob = True
while (good_blob and tau < tau_max):
if (verbose):
print 'f_idx %d, blob from x = %d, y = %d, I0 = %f' %\
(f_idx, R0_last, z0_last, frames[f_idx, z0_last, R0_last])
event_frame = frames[f_idx, :, :]
#plt.figure()
#plt.contourf(event_frame, 64)
#plt.title('direction: %s, fidx=%d' % (direction, f_idx))
#plt.colorbar()
# Label all contiguous regions with ore than 60% of the original intensity
labels = pm.label(event_frame > thresh_amp * I0)
# Get the area of all contiguous regions
blob_area = pm.blob(labels, 'area', output='data')
# Get the controid of all contiguous regions
blob_cent = pm.blob(labels, 'centroid', output='data')
if (verbose):
print 'Centroid analysis:'
print ' -> blob_cent = ', blob_cent
print ' -> shape = ', blob_cent.shape
if (blob_cent.size < 1):
# No peak here, quit tracking
good_blob = False
print 'Frame %d, %ss: lost track of blob' % (f_idx, direction)
break
# We now have a bunch of contiguous regions.
# Loop over the regions that are at least 10% of the largest region
# and find the one, whose centroid is closest to the last known position
# of the blob
loop_area = np.where(blob_area > 0.1 * blob_area.max())[0]
min_idx = -1 #
min_dist_frame = np.sqrt(event_frame.shape[0] * event_frame.shape[1]) # Maximal distance on a 64x64 grid
for d_idx, i in enumerate(loop_area):
dist = np.sqrt((blob_cent[i, 1] - R0_last) ** 2 +
(blob_cent[i, 0] - z0_last) ** 2)
if (verbose):
print 'Region %d, distance to last peak: %f' % (d_idx, dist)
if (dist < min_dist_frame and dist < thresh_dis):
min_dist_frame = dist
min_idx = i
if (verbose):
print 'Accepted'
# If min_dist_frame is still sqrt(8192), no area was selected and the
# blob could not be tracked successfully
if (min_dist_frame is np.sqrt(event_frame.shape[0] * event_frame.shape[1])):
print 'No peak satisfying criteria.'
print '\tFound: dist = %f, Stopping %s tracking after %d frames' %\
(min_dist_frame, direction, tau)
break
if (min_idx is -1):
print 'This should not happen'
raise ValueError
# Compute the x and y COM coordinates of the blob, store
blob_mask = labels != (min_idx + 1)
event_masked = np.ma.MaskedArray(event_frame,
mask=blob_mask,
fill_value=0)
# When used to index frames[:,:,:]:
# xymax[tau,:] = [index for axis 2, index for axis 1]
# Maximum in the blob mask
xymax[tau, :] = np.unravel_index(event_masked.argmax(),
np.shape(labels))
# When used to index frames[:,:,:]:
# xycom[tau,:] = [index for axis 1, index for axis 2]
# To be consistent with indexing from xymax, flip this array
# COM returns com along second dimension at index 0
xycom[tau, ::-1] = com(event_masked)
ycom_off, xcom_off = xycom[tau, :].round().astype('int')
if (verbose):
print 'Peak at (%d,%d), COM at (%d,%d)' %\
(xymax[tau, 0], xymax[tau, 1],
xycom[tau, 0], xycom[tau, 1])
amp[tau] = event_frame[z0_last, R0_last]
# Follow the peak
z0_last, R0_last = xymax[tau, :].astype('int')
if (plots):
plt.figure()
plt.title('%s, frame %d' % (direction, f_idx))
plt.contour(event_frame, 16, colors='k', linewidth=0.5)
plt.contourf(event_frame, 16, cmap=plt.cm.hot)
plt.plot(xycom[tau, 1], xycom[tau, 0], 'wo')
plt.plot(xymax[tau, 1], xymax[tau, 0], 'w^')
plt.colorbar()
plt.xlabel('x / px')
plt.ylabel('y / px')
if (direction is 'forward'):
tau += 1 # Frame accepted, advance indices
f_idx += 1
elif (direction is 'backward'):
# We started at tau=1, subtract one to return correct number of frame
# tracked in one direction, ignoring the starting frame
# Ignore this for forward frame as we count the original frame here
tau -= 1
f_idx -= 1
if (plots):
plt.show()
return tau, amp, xycom, xymax, fwhm_rad_idx, fwhm_pol_idx
list_mask = glob.glob('data_papers/*_m.*')
count = 0
for file_mask in list_mask:
file_image = glob.glob(file_mask[:-6] + '.*')[0]
print "currently processing " + file_image
dummy, filename = os.path.split(file_image)
mask = cv2.imread(file_mask)
mask = cv2.resize(
mask,
(mask.shape[1] / resizing_factor, mask.shape[0] / resizing_factor))
height, width, c = mask.shape
ground_truth_ = np.zeros((height, width))
# get text bounding boxes
ground_truth_text = ground_truth_ + np.where(
np.linalg.norm(mask - [255, 0, 0], axis=2) < 10, 1, 0)
label_text = label(ground_truth_text)
bbox_text = blob(label_text, measurement='boundingbox', output="data")
if bbox_text.size > 0:
anno_text_x1 = bbox_text[:, 0].tolist()
anno_text_y1 = bbox_text[:, 1].tolist()
anno_text_x2 = bbox_text[:, 2].tolist()
anno_text_y2 = bbox_text[:, 3].tolist()
anno_text_label = list('t' * len(anno_text_x1))
else:
anno_text_x1 = []
anno_text_y1 = []
anno_text_x2 = []
anno_text_y2 = []
anno_text_label = []
# get illustration bounding boxes
ground_truth_illu = ground_truth_ + np.where(
def find_closest_region(frame, thresh_amp, x0, max_dist=2.0, verbose=False):
"""
Returns the contiguous area above a threshold in a frame, whose centroid coordinates
are closest to x0
Input:
frame : Input frame
thresh_amp : Threshold for area separation
x0 : Distance to centroid
max_dist : Maximal distance to centroid
Output:
Binary image with contiguous area marked with 1
"""
# Label all contiguous regions with ore than 60% of the original intensity
labels = pm.label(frame > thresh_amp)
# Get the area of all contiguous regions
blob_area = pm.blob(labels, 'area', output='data')
# Get the controid of all contiguous regions
blob_cent = pm.blob(labels, 'centroid', output='data')
if (verbose):
print 'x0 = (%f, %f)' % (x0[0], x0[1])
print 'Labelling found %d regions: ' % labels.max()
for i in np.arange(labels.max()):
print 'Region: %d, centroid at %d, %d, area: %d' % (i, blob_cent[i, 1], blob_cent[i, 0], blob_area[i])
if (blob_cent.size < 1):
raise TrackingError
# We now have a bunch of contiguous regions.
# Loop over the regions that are at least 10% of the largest region
# and find the one, whose centroid is closest to the last known position
# of the blob
min_idx = -1
min_dist_frame = np.sqrt(frame.shape[0] * frame.shape[1]) # Maximal distance on a 64x64 grid
for d_idx, i in enumerate(blob_area):
# Compute distance of current areas centroid to the last centroids position
dist = np.sqrt((blob_cent[d_idx, 1] - x0[1]) ** 2 +
(blob_cent[d_idx, 0] - x0[0]) ** 2)
if (verbose):
print 'Region %d, center: x=%d, y=%d, A=%f, distance to last centroid: %f' %\
(d_idx, blob_cent[d_idx, 0], blob_cent[d_idx, 1], i, dist)
# Skip areas who are less than 10% of the original
if (i < 0.1 * blob_area.max()):
if(verbose):
print 'passing blob with area %f, d_idx = %d' % (i, d_idx)
continue
if (dist < min(max_dist, min_dist_frame)):
min_dist_frame = dist
min_idx = d_idx
if (verbose):
print 'Accepted'
# If min_dist_frame is still sqrt(8192), no area was selected and the
# blob could not be tracked successfully
if (min_idx is -1):
print 'No peak satisfying criteria.'
raise TrackingError
x_centroid = blob_cent[min_idx]
# Compute the x and y COM coordinates of the blob, store
blob_mask = labels != (min_idx + 1)
event_masked = np.ma.MaskedArray(frame,
mask=blob_mask,
fill_value=0)
# plt.figure()
# plt.subplot(131)
# plt.contourf(labels)
# plt.colorbar()
#
# plt.subplot(132)
# plt.contourf(frame, 64)
# plt.colorbar()
#
# plt.subplot(133)
# plt.contourf(event_masked)
# plt.colorbar()
#
# plt.show()
return (x_centroid, event_masked)
import pymorph as m
import mahotas
from numpy import where, reshape
image = mahotas.imread('B.png') # Load image
b1 = image[:,:,0] < 100 # Make a binary image from the thresholded red channel
b2 = m.erode(b1, m.sedisk(4)) # Erode to enhance contrast of the bridge
b3 = m.open(b2,m.sedisk(4)) # Remove the bridge
b4 = b2-b3 # Bridge plus small noise
b5 = m.areaopen(b4,1000) # Remove small areas leaving only a thinned bridge
b6 = m.dilate(b3)*b5 # Extend the non-bridge area slightly and get intersection with the bridge.
#b6 is image of end of bridge, now find single points
b7 = m.thin(b6, m.endpoints('homotopic')) # Narrow regions to single points.
labelled = m.label(b7) # Label endpoints.
x1, y1 = reshape(where(labelled == 1),(1,2))[0]
x2, y2 = reshape(where(labelled == 2),(1,2))[0]
outputimage = m.overlay(b1, m.dilate(b7,m.sedisk(5)))
mahotas.imsave('output.png', outputimage)
def test_label():
assert (h,w) == pymorph.label(pieces > 0).shape
def test_randomcolor():
assert (h,w,3) == pymorph.randomcolor(pymorph.label(pieces > 0)).shape
