def test_readroi(self):
lb = [9, 15, 15]
ub = [11, 99, 99]
img = pyklb.readroi(self.testread_filepath, lb, ub)
self.assertEqual(np.prod(img.shape), np.prod([ 1+ub[i]-lb[i] for i in range(len(lb)) ]))
self.assertEqual(round(np.mean(img)), 568)
with self.assertRaises(IndexError):
img = pyklb.readroi(self.testread_filepath, [9, 15, 15], [66, 99, 99])
img = pyklb.readroi(self.testread_filepath, [-1, 15, 15], [11, 99, 99])
def test_readroi(self):
lb = [9, 15, 15]
ub = [11, 99, 99]
img = pyklb.readroi(self.testread_filepath, lb, ub)
self.assertEqual(np.prod(img.shape),
np.prod([1 + ub[i] - lb[i] for i in range(len(lb))]))
self.assertEqual(round(np.mean(img)), 568)
with self.assertRaises(IndexError):
img = pyklb.readroi(self.testread_filepath, [9, 15, 15],
[66, 99, 99])
img = pyklb.readroi(self.testread_filepath, [-1, 15, 15],
[11, 99, 99])
def test_pyklb():
"""
This merely tests pyklb itself, to make sure it was compiled correctly.
"""
if not _klb_available:
raise nose.SkipTest
# Create some simple data. Should compress well.
shape = (1, 1, 30, 40, 50)
data_tczyx = np.indices(shape).sum(0).astype(np.uint8)
assert data_tczyx.shape == shape
# Write the data as KLB
#print "writing..."
filepath = '/tmp/test_data.klb'
pyklb.writefull(data_tczyx,
filepath,
blocksize_xyzct=np.array([10, 10, 10, 1, 1],
dtype=np.uint32))
# Read it back
#print "reading..."
#readback = pyklb.readfull(filepath)
readback = pyklb.readroi(filepath, (0, 0, 0, 0, 0), np.array(shape) - 1)
assert (readback == data_tczyx).all()
def execute(self, slot, subindex, roi, result):
if result.flags.c_contiguous:
pyklb.readroi_inplace(result,
self._filepath,
roi.start,
roi.stop - 1,
nochecks=False)
else:
result[:] = pyklb.readroi(self._filepath, roi.start, roi.stop - 1)
def sample(filename, n):
header = pyklb.readheader(filename)
size = header['imagesize_tczyx'][-3:]
points = []
print("Sampling points...")
while len(points) < n:
z = random.randint(0, size[0] - 1)
y = random.randint(0, size[1] - 1)
x = random.randint(0, size[2] - 1)
if pyklb.readroi(filename, (z, y, x), (z, y, x)) > foreground_threshold:
points.append((z, y, x))
print("Done.")
return points
def testBasic(self):
tmpdir = tempfile.mkdtemp()
try:
filepath = tmpdir + '/random_data.klb'
shape = (1,1,30,40,50)
data_tczyx = np.indices( shape ).sum(0).astype( np.uint8 )
pyklb.writefull( data_tczyx, filepath, blocksize_xyzct=np.array([10,10,10,1,1], dtype=np.uint32) )
readback = pyklb.readroi(filepath, (0,0,0,0,0), np.array(shape)-1)
op = OpKlbReader( graph=Graph() )
op.FilePath.setValue( filepath )
assert op.Output.meta.shape == shape
assert op.Output.meta.dtype == np.uint8
read_data = op.Output[:].wait()
assert ( read_data == data_tczyx ).all()
finally:
shutil.rmtree(tmpdir)
def test_pyklb():
"""
This merely tests pyklb itself, to make sure it was compiled correctly.
"""
if not _klb_available:
raise nose.SkipTest
# Create some simple data. Should compress well.
shape = (1,1,30,40,50)
data_tczyx = np.indices( shape ).sum(0).astype( np.uint8 )
assert data_tczyx.shape == shape
# Write the data as KLB
#print "writing..."
filepath = '/tmp/test_data.klb'
pyklb.writefull( data_tczyx, filepath, blocksize_xyzct=np.array([10,10,10,1,1], dtype=np.uint32) )
# Read it back
#print "reading..."
#readback = pyklb.readfull(filepath)
readback = pyklb.readroi(filepath, (0,0,0,0,0), np.array(shape)-1)
assert (readback == data_tczyx).all()
def testBasic(self):
tmpdir = tempfile.mkdtemp()
try:
filepath = tmpdir + '/random_data.klb'
shape = (1, 1, 30, 40, 50)
data_tczyx = np.indices(shape).sum(0).astype(np.uint8)
pyklb.writefull(data_tczyx,
filepath,
blocksize_xyzct=np.array([10, 10, 10, 1, 1],
dtype=np.uint32))
readback = pyklb.readroi(filepath, (0, 0, 0, 0, 0),
np.array(shape) - 1)
op = OpKlbReader(graph=Graph())
op.FilePath.setValue(filepath)
assert op.Output.meta.shape == shape
assert op.Output.meta.dtype == np.uint8
read_data = op.Output[:].wait()
assert (read_data == data_tczyx).all()
finally:
shutil.rmtree(tmpdir)
def execute(self, slot, subindex, roi, result):
if result.flags.c_contiguous:
pyklb.readroi_inplace(result, self._filepath, roi.start, roi.stop-1, nochecks=False)
else:
result[:] = pyklb.readroi(self._filepath, roi.start, roi.stop-1)
