def save_klb(
image: Any,
uri: str,
compress: bool = True,
partition: Optional[str] = None,
# Format-specific kwargs
block_shape: Tuple[int, ...] = None,
compression_type: str = "bzip2"):
if partition is None:
partition = "tczyx"
if not compress:
compression_type = "none"
if block_shape is not None:
block_shape = block_shape[::-1]
for img, _uri in partition_gen(image, partition, uri):
axes = get_axes(img)
shape = [
img.shape[axes.index(ax)] if ax in axes else 1 for ax in "tczyx"
]
spacing = [get_spacing(img, ax) or 1.0 for ax in "tczyx"]
# TODO: Convert spacing units to match convention.
klb.writefull(to_numpy(img).reshape(shape),
_uri,
pixelspacing_tczyx=spacing,
blocksize_xyzct=block_shape,
compression=compression_type)
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 _convert(fname):
print("converting {}".format(fname))
try:
with h5py.File('{}/{}'.format(dense_pred_dir, fname), 'r') as pred_file:
print("loading")
predictions = pred_file['predictions'][:].squeeze()[np.newaxis, np.newaxis, ...]
predictions = np.ascontiguousarray(predictions)
print("writing")
pyklb.writefull(predictions, '{}/{}.klb'.format(klb_pred_dir, fname[:-3]))
except:
print("Failed on {}".format(fname))
def test_writefull(self):
print("Testing KLB writing to %s" % self.testwrite_filepath)
if os.path.exists(self.testwrite_filepath):
print("Skipping writing tests because file %s exists.\n Please move or delete this file and re-run the tests." % self.testwrite_filepath)
return
img = pyklb.readfull(self.testread_filepath)
pyklb.writefull(img, self.testwrite_filepath, pixelspacing_tczyx=[0.5, 0.5, 5.0])
self.assertTrue(os.path.exists(self.testwrite_filepath))
img2 = pyklb.readfull(self.testwrite_filepath)
self.assertEqual(img.dtype, img2.dtype)
self.assertEqual(img.shape, img2.shape)
self.assertEqual(np.mean(img), np.mean(img2))
header = pyklb.readheader(self.testwrite_filepath)
self.assertTrue(np.all( header["pixelspacing_tczyx"] == [1, 1, 0.5, 0.5, 5.0] ))
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_writefull(self):
print("Testing KLB writing to %s" % self.testwrite_filepath)
if os.path.exists(self.testwrite_filepath):
print(
"Skipping writing tests because file %s exists.\n Please move or delete this file and re-run the tests."
% self.testwrite_filepath)
return
img = pyklb.readfull(self.testread_filepath)
pyklb.writefull(img,
self.testwrite_filepath,
pixelspacing_tczyx=[0.5, 0.5, 5.0])
self.assertTrue(os.path.exists(self.testwrite_filepath))
img2 = pyklb.readfull(self.testwrite_filepath)
self.assertEqual(img.dtype, img2.dtype)
self.assertEqual(img.shape, img2.shape)
self.assertEqual(np.mean(img), np.mean(img2))
header = pyklb.readheader(self.testwrite_filepath)
self.assertTrue(
np.all(header["pixelspacing_tczyx"] == [1, 1, 0.5, 0.5, 5.0]))
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 write_klb(filename, im):
if np.isfortran(im):
if len(im.shape) == 3:
writefull(im.transpose(2, 1, 0),
filename,
pixelspacing_tczyx=(1, 1) + tuple(im.resolution[::-1]))
else:
writefull(im.transpose(1, 0),
filename,
pixelspacing_tczyx=(1, 1) + tuple(im.resolution[::-1]))
else:
writefull(im, filename)
def _klb_writer(klb_path, image):
from pyklb import writefull
writefull(image, str(klb_path))
def klb_writer(data, klb_path):
from pyklb import writefull
writefull(data, klb_path)
import re
for root, dirs, files in os.walk("."):
for filename in files:
if re.search(
"\d\.h5", filename
): #( filename.endswith("00.h5") or filename.endswith("01.h5") ):
#print(filename)
#print "Please note that renaming rules are coded in this python script; please modify script to change rules for renaming if desired!"
file_to_modify = filename
print("Exporting KLBs from file", file_to_modify)
f = h5py.File(file_to_modify, "r")
group_names = f.keys()
last_group_name = list(group_names)[len(group_names) - 1]
print("Working on group:", last_group_name)
last_group = f["/" + last_group_name + "/"]
subgroup_names = last_group.keys()
#print "Subgroups: ", subgroup_names
for this_name in list(subgroup_names):
print(" subgroup:", this_name)
pyklb.writefull(
np.array(f["/" + last_group_name + "/" + this_name +
"/0/cells"]).astype("uint8"),
last_group_name + "_" + this_name + ".klb")
f.close()
