def __init__(self, parameters=None, sa_type=None, **kwds):
super(MPDataWriter, self).__init__(**kwds)
self.movie_info_set = False
self.offsets = []
# Figure out how many planes there are.
self.n_planes = len(mpUtil.getExtAttrs(parameters))
# Save frame offsets for each plane.
for offset in mpUtil.getOffsetAttrs(parameters):
self.offsets.append(parameters.getAttr(offset))
# Figure out where to start if the analysis file already exists.
if os.path.exists(self.filename):
print(
"Existing analysis file found. Restarting from last analyzed frame."
)
self.h5 = saH5Py.SAH5Py(filename=self.filename)
self.movie_info_set = True
# Find the last frame that we analyzed.
i = self.h5.getMovieLength()
while (i > 0):
if self.h5.isAnalyzed(i):
break
i -= 1
self.start_frame = i
# Otherwise start from the beginning.
else:
self.h5 = saH5Py.SAH5Py(filename=self.filename,
is_existing=False,
sa_type=sa_type)
# Save analysis parameters.
etree = parameters.toXMLElementTree(False)
if (sys.version_info > (3, 0)):
self.h5.addMetadata(ElementTree.tostring(etree, 'unicode'))
else:
self.h5.addMetadata(ElementTree.tostring(etree, 'ISO-8859-1'))
# Save pixel size.
self.h5.setPixelSize(parameters.getAttr("pixel_size"))
# Adjust starting frame based on channel 0 offset.
if (self.offsets[0] != 0):
assert (self.offsets[0] >
0), "Channel 0 offset cannot be negative."
self.start_frame = self.offsets[0]
print("Adjusted start frame to", self.start_frame,
"based on channel 0 offset.")
self.h5.setAnalysisFinished(False)
def __init__(self, parameters = None, sa_type = None, **kwds):
super(MPDataWriter, self).__init__(**kwds)
self.movie_info_set = False
self.offsets = []
# Figure out how many planes there are.
self.n_planes = len(mpUtil.getExtAttrs(parameters))
# Save frame offsets for each plane.
for offset in mpUtil.getOffsetAttrs(parameters):
self.offsets.append(parameters.getAttr(offset))
# Figure out where to start if the analysis file already exists.
if os.path.exists(self.filename):
self.h5 = saH5Py.SAH5Py(filename = self.filename)
self.movie_info_set = True
# Find the last frame that we analyzed.
i = self.h5.getMovieLength()
while (i > 0):
if self.h5.isAnalyzed(i):
break
i -= 1
self.start_frame = i
# Otherwise start from the beginning.
else:
self.h5 = saH5Py.SAH5Py(filename = self.filename,
is_existing = False,
sa_type = sa_type)
# Save analysis parameters.
etree = parameters.toXMLElementTree(False)
if (sys.version_info > (3, 0)):
self.h5.addMetadata(ElementTree.tostring(etree, 'unicode'))
else:
self.h5.addMetadata(ElementTree.tostring(etree, 'ISO-8859-1'))
# Save pixel size.
self.h5.setPixelSize(parameters.getAttr("pixel_size"))
# Adjust starting frame based on channel 0 offset.
if (self.offsets[0] != 0):
assert(self.offsets[0] > 0), "Channel 0 offset cannot be negative."
self.start_frame = self.offsets[0]
print("Adjusted start frame to", self.start_frame, "based on channel 0 offset.")
self.h5.setAnalysisFinished(False)
def __init__(self, base_name=None, parameters=None, **kwds):
super(MPMovieReader, self).__init__(**kwds)
self.backgrounds = []
self.bg_estimators = []
self.cur_frame = 0
self.frames = []
self.max_frame = 0
self.offsets = []
self.parameters = parameters
self.planes = []
#
# Load the movies and offsets for each plane/channel. At present
# multiplane expects the sCMOS camera calibration data.
#
calib_name = mpUtil.getCalibrationAttrs(parameters)
for i, ext in enumerate(mpUtil.getExtAttrs(parameters)):
movie_name = base_name + parameters.getAttr(ext)
self.planes.append(
analysisIO.FrameReaderSCMOS(
parameters=parameters,
movie_file=movie_name,
calibration_file=parameters.getAttr(calib_name[i])))
for offset in mpUtil.getOffsetAttrs(parameters):
self.offsets.append(parameters.getAttr(offset))
print("Found data for", len(self.planes), "planes.")
[self.movie_x, self.movie_y, self.movie_l] = self.planes[0].filmSize()
self.movie_l -= self.offsets[0]
# Check if the movies for the other channels (adjusted for their offsets)
# are shorter than the movie for channel 0.
#
for i in range(1, len(self.planes)):
[px, py, pl] = self.planes[1].filmSize()
pl -= self.offsets[i]
if (pl < self.movie_l):
self.movie_l = pl
# Assert that all the movies are the same size, at least in x,y.
for i in range(1, len(self.planes)):
assert (self.movie_x == self.planes[i].filmSize()[0])
assert (self.movie_y == self.planes[i].filmSize()[1])
def __init__(self, base_name = None, parameters = None, **kwds):
super(MPMovieReader, self).__init__(**kwds)
self.backgrounds = []
self.bg_estimators = []
self.cur_frame = 0
self.frames = []
self.max_frame = 0
self.offsets = []
self.parameters = parameters
self.planes = []
#
# Load the movies and offsets for each plane/channel. At present
# multiplane expects the sCMOS camera calibration data.
#
calib_name = mpUtil.getCalibrationAttrs(parameters)
for i, ext in enumerate(mpUtil.getExtAttrs(parameters)):
movie_name = base_name + parameters.getAttr(ext)
self.planes.append(analysisIO.FrameReaderSCMOS(parameters = parameters,
movie_file = movie_name,
calibration_file = parameters.getAttr(calib_name[i])))
for offset in mpUtil.getOffsetAttrs(parameters):
self.offsets.append(parameters.getAttr(offset))
print("Found data for", len(self.planes), "planes.")
[self.movie_x, self.movie_y, self.movie_l] = self.planes[0].filmSize()
self.movie_l -= self.offsets[0]
# Check if the movies for the other channels (adjusted for their offsets)
# are shorter than the movie for channel 0.
#
for i in range(1, len(self.planes)):
[px, py, pl] = self.planes[1].filmSize()
pl -= self.offsets[i]
if (pl < self.movie_l):
self.movie_l = pl
# Assert that all the movies are the same size, at least in x,y.
for i in range(1, len(self.planes)):
assert(self.movie_x == self.planes[i].filmSize()[0])
assert(self.movie_y == self.planes[i].filmSize()[1])
def findOffsets(base_name,
params_file,
background_scale=4.0,
foreground_scale=1.0):
"""
The 'main' function of this module.
base_name - The basename for the group of movies.
params_file - An analysis XML file containing the details for this experiment.
background_scale - Features in the background change on this scale (in pixels)
or more slowly.
foreground_scale - Features that change on this scale are likely foreground.
Notes:
1. This only checks a limited range of offsets between the two channels.
2. This assumes that the movies are longer than just a few frames.
"""
n_tests = 10
search_range = 5
# Load parameters.
parameters = params.ParametersMultiplane().initFromFile(params_file)
# Load the movies from each camera.
n_channels = 0
movies = []
for ext in mpUtil.getExtAttrs(parameters):
movie_name = base_name + parameters.getAttr(ext)
movies.append(datareader.inferReader(movie_name))
n_channels += 1
print("Found", n_channels, "movies.")
# Load sCMOS calibration data.
offsets = []
gains = []
for calib_name in mpUtil.getCalibrationAttrs(parameters):
[offset, variance, gain,
rqe] = analysisIO.loadCMOSCalibration(parameters.getAttr(calib_name))
offsets.append(offset)
gains.append(1.0 / gain)
assert (len(offsets) == n_channels)
# Load the plane to plane mapping data & create affine transform objects.
mappings = {}
with open(parameters.getAttr("mapping"), 'rb') as fp:
mappings = pickle.load(fp)
atrans = []
for i in range(n_channels - 1):
xt = mappings["0_" + str(i + 1) + "_x"]
yt = mappings["0_" + str(i + 1) + "_y"]
atrans.append(affineTransformC.AffineTransform(xt=xt, yt=yt))
# Create background and foreground variance filters.
#
# FIXME: Is this right for movies that are not square?
#
[y_size, x_size] = movies[0].filmSize()[:2]
psf = dg.drawGaussiansXY((x_size, y_size),
numpy.array([0.5 * x_size]),
numpy.array([0.5 * y_size]),
sigma=background_scale)
psf = psf / numpy.sum(psf)
bg_filter = matchedFilterC.MatchedFilter(psf)
psf = dg.drawGaussiansXY((x_size, y_size),
numpy.array([0.5 * x_size]),
numpy.array([0.5 * y_size]),
sigma=foreground_scale)
psf = psf / numpy.sum(psf)
fg_filter = matchedFilterC.MatchedFilter(psf)
var_filter = matchedFilterC.MatchedFilter(psf * psf)
# Check background estimation.
if False:
frame = loadImage(movies[0], 0, offsets[0], gain[0])
frame_bg = estimateBackground(frame, bg_filter, fg_filter, var_filter)
with tifffile.TiffWriter("bg_estimate.tif") as tif:
tif.save(frame.astype(numpy.float32))
tif.save(frame_bg.astype(numpy.float32))
tif.save((frame - frame_bg).astype(numpy.float32))
votes = numpy.zeros((n_channels - 1, 2 * search_range + 1))
for i in range(n_tests):
print("Test", i)
# Load reference frame.
ref_frame = loadImage(movies[0], search_range + i, offsets[0], gain[0])
ref_frame_bg = estimateBackground(ref_frame, bg_filter, fg_filter,
var_filter)
ref_frame -= ref_frame_bg
# Load test frames and measure correlation.
for j in range(n_channels - 1):
best_corr = 0.0
best_offset = 0
for k in range(-search_range, search_range + 1):
test_frame = loadImage(movies[j + 1],
search_range + i + k,
offsets[j + 1],
gain[j + 1],
transform=atrans[j])
test_frame_bg = estimateBackground(test_frame, bg_filter,
fg_filter, var_filter)
test_frame -= test_frame_bg
test_frame_corr = numpy.sum(
ref_frame * test_frame) / numpy.sum(test_frame)
if (test_frame_corr > best_corr):
best_corr = test_frame_corr
best_offset = k + search_range
votes[j, best_offset] += 1
# Print results.
print("Offset votes:")
print(votes)
frame_offsets = [0]
frame_offsets += list(numpy.argmax(votes, axis=1) - search_range)
print("Best offsets:")
for i in range(n_channels):
print(str(i) + ": " + str(frame_offsets[i]))
# Create stacks with optimal offsets.
print("Saving image stacks.")
for i in range(n_channels):
with tifffile.TiffWriter("find_offsets_ch" + str(i) + ".tif") as tif:
for j in range(5):
if (i == 0):
frame = loadImage(movies[i],
search_range + frame_offsets[i] + j,
offsets[i], gain[i])
else:
frame = loadImage(movies[i],
search_range + frame_offsets[i] + j,
offsets[i],
gain[i],
transform=atrans[i - 1])
frame_bg = estimateBackground(frame, bg_filter, fg_filter,
var_filter)
frame -= frame_bg
tif.save(frame.astype(numpy.float32))
def findOffsets(base_name, params_file, background_scale = 4.0, foreground_scale = 1.0, im_slice = None):
"""
The 'main' function of this module.
base_name - The basename for the group of movies.
params_file - An analysis XML file containing the details for this experiment.
background_scale - Features in the background change on this scale (in pixels)
or more slowly.
foreground_scale - Features that change on this scale are likely foreground.
im_slice - A slice object created for example with numpy.s_ to limit the analysis
to a smaller AOI.
Notes:
1. This only checks a limited range of offsets between the two channels.
2. This assumes that the movies are longer than just a few frames.
"""
n_tests = 10
search_range = 5
# Load parameters.
parameters = params.ParametersMultiplane().initFromFile(params_file)
# Load the movies from each camera.
n_channels = 0
movies = []
for ext in mpUtil.getExtAttrs(parameters):
movie_name = base_name + parameters.getAttr(ext)
movies.append(datareader.inferReader(movie_name))
n_channels += 1
print("Found", n_channels, "movies.")
# Load sCMOS calibration data.
offsets = []
gains = []
for calib_name in mpUtil.getCalibrationAttrs(parameters):
[offset, variance, gain, rqe] = analysisIO.loadCMOSCalibration(parameters.getAttr(calib_name))
offsets.append(offset)
gains.append(1.0/gain)
assert(len(offsets) == n_channels)
# Load the plane to plane mapping data & create affine transform objects.
mappings = {}
with open(parameters.getAttr("mapping"), 'rb') as fp:
mappings = pickle.load(fp)
atrans = []
for i in range(n_channels-1):
xt = mappings["0_" + str(i+1) + "_x"]
yt = mappings["0_" + str(i+1) + "_y"]
atrans.append(affineTransformC.AffineTransform(xt = xt, yt = yt))
# Create background and foreground variance filters.
#
# FIXME: Is this right for movies that are not square?
#
[y_size, x_size] = movies[0].filmSize()[:2]
if im_slice is not None:
y_size = im_slice[0].stop - im_slice[0].start
x_size = im_slice[1].stop - im_slice[1].start
psf = dg.drawGaussiansXY((x_size, y_size),
numpy.array([0.5*x_size]),
numpy.array([0.5*y_size]),
sigma = background_scale)
psf = psf/numpy.sum(psf)
bg_filter = matchedFilterC.MatchedFilter(psf)
psf = dg.drawGaussiansXY((x_size, y_size),
numpy.array([0.5*x_size]),
numpy.array([0.5*y_size]),
sigma = foreground_scale)
psf = psf/numpy.sum(psf)
fg_filter = matchedFilterC.MatchedFilter(psf)
var_filter = matchedFilterC.MatchedFilter(psf*psf)
# Check background estimation.
if False:
frame = loadImage(movies[0], 0, offsets[0], gain[0])
frame_bg = estimateBackground(frame, bg_filter, fg_filter, var_filter)
with tifffile.TiffWriter("bg_estimate.tif") as tif:
tif.save(frame.astype(numpy.float32))
tif.save(frame_bg.astype(numpy.float32))
tif.save((frame - frame_bg).astype(numpy.float32))
votes = numpy.zeros((n_channels - 1, 2*search_range+1))
for i in range(n_tests):
print("Test", i)
# Load reference frame.
ref_frame = loadImage(movies[0], search_range + i, offsets[0], gain[0])
if im_slice is not None:
ref_frame = ref_frame[im_slice]
ref_frame_bg = estimateBackground(ref_frame, bg_filter, fg_filter, var_filter)
ref_frame -= ref_frame_bg
# Load test frames and measure correlation.
for j in range(n_channels - 1):
best_corr = 0.0
best_offset = 0
for k in range(-search_range, search_range + 1):
test_frame = loadImage(movies[j+1], search_range + i + k, offsets[j+1], gain[j+1], transform = atrans[j])
if im_slice is not None:
test_frame = test_frame[im_slice]
test_frame_bg = estimateBackground(test_frame, bg_filter, fg_filter, var_filter)
test_frame -= test_frame_bg
test_frame_corr = numpy.sum(ref_frame*test_frame)/numpy.sum(test_frame)
if (test_frame_corr > best_corr):
best_corr = test_frame_corr
best_offset = k + search_range
votes[j, best_offset] += 1
# Print results.
print("Offset votes:")
print(votes)
frame_offsets = [0]
frame_offsets += list(numpy.argmax(votes, axis = 1) - search_range)
print("Best offsets:")
for i in range(n_channels):
print(str(i) + ": " + str(frame_offsets[i]))
# Create stacks with optimal offsets.
print("Saving image stacks.")
for i in range(n_channels):
with tifffile.TiffWriter(base_name + "_offsets_ch" + str(i) + ".tif") as tif:
for j in range(5):
if (i == 0):
frame = loadImage(movies[i],
search_range + frame_offsets[i] + j,
offsets[i],
gain[i])
else:
frame = loadImage(movies[i],
search_range + frame_offsets[i] + j,
offsets[i],
gain[i],
transform = atrans[i-1])
if im_slice is not None:
frame = frame[im_slice]
frame_bg = estimateBackground(frame, bg_filter, fg_filter, var_filter)
frame -= frame_bg
tif.save(frame.astype(numpy.float32))
return frame_offsets