def to_z_slice_pngs(self,
class_colors: Sequence[Color]) -> Iterator[io.BytesIO]:
for z_slice in self.split(self.shape.updated(z=1)):
print(f"\nz_slice: {z_slice}")
rendered_rgb = Array5D.allocate(z_slice.shape.updated(c=3),
dtype=np.dtype("float32"),
value=0)
rendered_rgb_yxc = rendered_rgb.raw("yxc")
for prediction_channel, color in zip(
z_slice.split(z_slice.shape.updated(c=1)), class_colors):
print(f"\nprediction_channel: {prediction_channel}")
class_rgb = Array5D(np.ones(
prediction_channel.shape.updated(c=3).to_tuple("yxc")),
axiskeys="yxc")
class_rgb.raw("yxc")[...] *= np.asarray(
[color.r, color.g, color.b])
class_rgb.raw("cyx")[...] *= prediction_channel.raw("yx")
rendered_rgb_yxc += class_rgb.raw("yxc")
out_image = PIL.Image.fromarray(
rendered_rgb.raw("yxc").astype(np.uint8)) # type: ignore
out_file = io.BytesIO()
out_image.save(out_file, "png")
_ = out_file.seek(0)
yield out_file
class SimpleSegmenter(Operator[DataRoi, List[Array5D]]):
def __init__(
self,
*,
preprocessor: Operator[DataRoi, Array5D] = OpRetriever(),
) -> None:
super().__init__()
self.preprocessor = preprocessor
def __call__(self, /, roi: DataRoi) -> List[Array5D]:
data = self.preprocessor(roi)
winning_channel_indices = Array5D(
arr=np.argmax(data.raw(data.axiskeys), axis=data.axiskeys.index("c")),
axiskeys=data.axiskeys.replace("c", ""),
location=roi.start,
)
segmentations: List[Array5D] = []
for class_index in range(data.shape.c):
class_seg = Array5D.allocate(data.interval.updated(c=(0,3)), dtype=np.dtype("uint8"), value=0)
red_channel = class_seg.cut(c=0)
raw_segmentation = (winning_channel_indices.raw("tzyx") == class_index).astype(np.dtype("uint8")) * 255
red_channel.raw("tzyx")[...] = raw_segmentation
segmentations.append(class_seg)
return segmentations
def test_simple_segmenter():
segmenter = SimpleSegmenter()
input_data = ArrayDataSource(
data=Array5D(np.asarray([
[[ 0.1, 0.1, 0.0, 1.0],
[ 0.2, 0.2, 0.0, 0.0],
[ 0.3, 0.3, 0.1, 0.2],
[ 0.4, 0.4, 0.0, 0.0]],
[[ 0.4, 0.4, 0.0, 0.0],
[ 0.3, 0.3, 0.0, 0.0],
[ 0.2, 0.2, 0.4, 0.0],
[ 0.1, 0.1, 0.0, 0.0]]
]), axiskeys="cyx"),
)
expected_segmentation = [
Array5D(np.asarray([
[[ 0, 0, 255, 255],
[ 0, 0, 255, 255],
[255, 255, 0, 255],
[255, 255, 255, 255]],
[[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0]],
[[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0]],
]), axiskeys="cyx"),
Array5D(np.asarray([
[[255, 255, 0, 0],
[255, 255, 0, 0],
[ 0, 0, 255, 0],
[ 0, 0, 0, 0]],
[[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0]],
[[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0],
[ 0, 0, 0, 0]],
]), axiskeys="cyx")
]
segmentations = segmenter(input_data.roi)
for seg, expected_seg in zip(segmentations, expected_segmentation):
assert np.all(seg.raw("cyx") == expected_seg.raw("cyx"))
def test_retrieve_roi_smaller_than_tile():
# fmt: off
data = Array5D(np.asarray([
[[ 1, 2, 3, 4, 5],
[ 6, 7, 8, 9, 10],
[ 11, 12, 13, 14, 15],
[ 16, 17, 18, 19, 20]],
[[ 100, 200, 300, 400, 500],
[ 600, 700, 800, 900, 1000],
[1100, 1200, 1300, 1400, 1500],
[1600, 1700, 1800, 1900, 2000]],
]).astype(np.uint32), axiskeys="cyx")
expected_cyx = np.asarray([
[[ 100, 200, 300, 400],
[ 600, 700, 800, 900],
[1100, 1200, 1300, 1400],
[1600, 1700, 1800, 1900]]
])
# fmt: on
path = PurePosixPath(create_n5(data, chunk_size=Shape5D(c=2, y=4, x=4)))
ds = N5DataSource(path=path / "data", filesystem=OsFs("/"))
smaller_than_tile = ds.retrieve(c=1, y=(0, 4), x=(0, 4))
assert np.all(smaller_than_tile.raw("cyx") == expected_cyx)
def __init__(
self,
*,
path: PurePosixPath,
location: Point5D = Point5D.zero(),
filesystem: JsonableFilesystem,
tile_shape: Optional[Shape5D] = None,
spatial_resolution: Optional[Tuple[int, int, int]] = None,
):
raw_data: "np.ndarray[Any, Any]" = skimage.io.imread(filesystem.openbin(path.as_posix())) # type: ignore
c_axiskeys_on_disk = "yxc"[: len(raw_data.shape)]
self._data = Array5D(raw_data, axiskeys=c_axiskeys_on_disk, location=location)
if tile_shape is None:
tile_shape = Shape5D.hypercube(256).to_interval5d().clamped(self._data.shape).shape
super().__init__(
c_axiskeys_on_disk=c_axiskeys_on_disk,
filesystem=filesystem,
path=path,
dtype=self._data.dtype,
interval=self._data.interval,
tile_shape=tile_shape,
spatial_resolution=spatial_resolution,
)
def interpolate_from_points(cls, voxels: Sequence[Point5D],
raw_data: DataSource):
start = Point5D.min_coords(voxels)
stop = Point5D.max_coords(
voxels
) + 1 # +1 because slice.stop is exclusive, but max_point isinclusive
scribbling_roi = Interval5D.create_from_start_stop(start=start,
stop=stop)
if scribbling_roi.shape.c != 1:
raise ValueError(
f"Annotations must not span multiple channels: {voxels}")
scribblings = Array5D.allocate(scribbling_roi,
dtype=np.dtype(bool),
value=False)
anchor = voxels[0]
for voxel in voxels:
for interp_voxel in anchor.interpolate_until(voxel):
scribblings.paint_point(point=interp_voxel, value=True)
anchor = voxel
return cls(scribblings._data,
axiskeys=scribblings.axiskeys,
raw_data=raw_data,
location=start)
def _do_predict(self, roi: DataRoi) -> Predictions:
feature_data = self.feature_extractor(roi)
linear_feature_data = feature_data.raw("tzyxc").reshape(
(feature_data.shape.t * feature_data.shape.volume,
feature_data.shape.c))
predictions = Array5D.allocate(
axiskeys="tzyxc",
interval=self.get_expected_roi(roi),
dtype=np.dtype('float32'),
value=0,
)
assert predictions.interval == self.get_expected_roi(roi)
raw_linear_predictions: "ndarray[Any, dtype[float32]]" = predictions.raw(
"tzyxc").reshape((predictions.shape.t * predictions.shape.volume,
predictions.shape.c))
executor = get_executor(hint="predicting")
f = partial(_compute_partial_predictions, linear_feature_data)
futures = [executor.submit(f, forest) for forest in self.forests]
for partial_predictions_future in futures:
raw_linear_predictions += partial_predictions_future.result()
raw_linear_predictions /= self.num_trees
predictions.setflags(write=False)
return Predictions(
arr=predictions.raw(predictions.axiskeys),
axiskeys=predictions.axiskeys,
location=predictions.location,
)
def test_h5_datasource():
data_2d = Array5D(np.arange(100).reshape(10, 10), axiskeys="yx")
h5_path = create_h5(data_2d, axiskeys_style="vigra", chunk_shape=Shape5D(x=3, y=3))
ds = H5DataSource(outer_path=h5_path, inner_path=PurePosixPath("/data"), filesystem=OsFs("/"))
assert ds.shape == data_2d.shape
assert ds.tile_shape == Shape5D(x=3, y=3)
slc = ds.interval.updated(x=(0, 3), y=(0, 2))
assert (ds.retrieve(slc).raw("yx") == data_2d.cut(slc).raw("yx")).all()
data_3d = Array5D(np.arange(10 * 10 * 10).reshape(10, 10, 10), axiskeys="zyx")
h5_path = create_h5(data_3d, axiskeys_style="vigra", chunk_shape=Shape5D(x=3, y=3))
ds = H5DataSource(outer_path=h5_path, inner_path=PurePosixPath("/data"), filesystem=OsFs("/"))
assert ds.shape == data_3d.shape
assert ds.tile_shape == Shape5D(x=3, y=3)
slc = ds.interval.updated(x=(0, 3), y=(0, 2), z=3)
assert (ds.retrieve(slc).raw("yxz") == data_3d.cut(slc).raw("yxz")).all()
def decode(
self,
*,
roi: Interval5D,
dtype: "np.dtype[Any]", #FIXME
raw_chunk: bytes) -> Array5D:
# "The (...) data (...) chunk is stored directly in little-endian binary format in [x, y, z, channel] Fortran order"
raw_tile: np.ndarray[Any, Any] = np.frombuffer(
raw_chunk,
dtype=dtype.newbyteorder("<")).reshape(roi.shape.to_tuple("xyzc"),
order="F")
tile_5d = Array5D(raw_tile, axiskeys="xyzc", location=roi.start)
return tile_5d
def test_n5_datasource():
# fmt: off
data = Array5D(np.asarray([
[1, 2, 3, 4, 5 ],
[6, 7, 8, 9, 10],
[11, 12, 13, 14, 15],
[16, 17, 18, 19, 20]
]).astype(np.uint8), axiskeys="yx")
# fmt: on
path = PurePosixPath(create_n5(data, chunk_size=Shape5D(x=2, y=2)))
ds = N5DataSource(path=path / "data", filesystem=OsFs("/"))
assert ds.shape == data.shape
# fmt: off
expected_raw_piece = Array5D(np.asarray([
[1, 2, 3],
[6, 7, 8]
]).astype(np.uint8), axiskeys="yx")
# fmt: on
assert ds.retrieve(x=(0, 3), y=(0, 2)) == expected_raw_piece
ds2 = pickle.loads(pickle.dumps(ds))
assert ds2.retrieve(x=(0, 3), y=(0, 2)) == expected_raw_piece
class FeatureExtractorCollection(FeatureExtractor):
def __init__(self, extractors: Iterable[FeatureExtractor]):
self.extractors = tuple(extractors)
assert len(self.extractors) > 0
super().__init__()
def is_applicable_to(self, datasource: DataSource) -> bool:
return all(fx.is_applicable_to(datasource) for fx in self.extractors)
def __call__(self, /, roi: DataRoi) -> FeatureData:
assert roi.interval.c[0] == 0
feature_promises: Dict[int, Future[FeatureData]] = {}
executor = get_executor(hint="feature_extraction",
max_workers=len(self.extractors))
from webilastik.features.ilp_filter import IlpGaussianSmoothing
feature_promises = {
fx_index: executor.submit(fx, roi)
for fx_index, fx in enumerate(self.extractors)
if isinstance(fx, IlpGaussianSmoothing)
}
feature_promises.update({
fx_index: executor.submit(fx, roi)
for fx_index, fx in enumerate(self.extractors)
if not isinstance(fx, IlpGaussianSmoothing)
})
assert len(feature_promises) == len(self.extractors)
features = [
feature_promises[i].result() for i in range(len(self.extractors))
]
out = Array5D.allocate(
dtype=np.dtype("float32"),
interval=roi.shape.updated(c=sum(feat.shape.c
for feat in features)),
axiskeys="tzyxc",
).translated(roi.start)
channel_offset: int = 0
for feature in features:
out.set(feature.translated(Point5D.zero(c=channel_offset)))
channel_offset += feature.shape.c
return FeatureData(arr=out.raw(out.axiskeys),
axiskeys=out.axiskeys,
location=out.location)
def create_h5(array: Array5D, axiskeys_style: str, chunk_shape: Optional[Shape5D] = None, axiskeys: str = "xyztc"):
raw_chunk_shape = (chunk_shape or Shape5D() * 2).clamped(maximum=array.shape).to_tuple(axiskeys)
path = tempfile.mkstemp()[1] + ".h5"
f = h5py.File(path, "w")
ds = f.create_dataset("data", chunks=raw_chunk_shape, data=array.raw(axiskeys))
if axiskeys_style == "dims":
for key, dim in zip(axiskeys, ds.dims):
dim.label = key
elif axiskeys_style == "vigra":
type_flags = {"x": 2, "y": 2, "z": 2, "t": 2, "c": 1}
axistags = [{"key": key, "typeflags": type_flags[key], "resolution": 0, "description": ""} for key in axiskeys]
ds.attrs["axistags"] = json.dumps({"axes": axistags})
else:
raise Exception(f"Bad axiskeys_style: {axiskeys_style}")
return PurePosixPath(path)
def decode(
self,
*,
roi: Interval5D,
dtype: np.dtype, #type: ignore
raw_chunk: bytes
) -> Array5D:
# "The width and height of the JPEG image may be arbitrary (...)"
# "the total number of pixels is equal to the product of the x, y, and z dimensions of the subvolume"
# "(...) the 1-D array obtained by concatenating the horizontal rows of the image corresponds to the
# flattened [x, y, z] Fortran-order (i,e. zyx C order) representation of the subvolume."
# FIXME: check if this works with any sort of funny JPEG shapes
# FIXME: Also, what to do if dtype is weird?
raw_jpg: np.ndarray = skimage.io.imread(io.BytesIO(raw_chunk)) # type: ignore
tile_5d = Array5D(raw_jpg.reshape(roi.shape.to_tuple("zyxc")), axiskeys="zyxc")
return tile_5d
def __call__(self, roi: DataRoi) -> FeatureData:
haloed_roi = roi.enlarged(self.halo)
source_data = self.preprocessor(haloed_roi)
step_shape: Shape5D = Shape5D(
c=1,
t=1,
x=1 if self.axis_2d == "x" else source_data.shape.x,
y=1 if self.axis_2d == "y" else source_data.shape.y,
z=1 if self.axis_2d == "z" else source_data.shape.z,
)
out = Array5D.allocate(
interval=roi.updated(c=(roi.c[0] * self.channel_multiplier,
roi.c[1] * self.channel_multiplier)),
dtype=numpy.dtype("float32"),
axiskeys=source_data.axiskeys.replace("c", "") +
"c" # fastfilters puts channel last
)
for data_slice in source_data.split(step_shape):
source_axes = "zyx"
if self.axis_2d:
source_axes = source_axes.replace(self.axis_2d, "")
raw_data: "ndarray[Any, dtype[float32]]" = data_slice.raw(
source_axes).astype(numpy.float32)
raw_feature_data: "ndarray[Any, dtype[float32]]" = self.filter_fn(
raw_data)
feature_data = FeatureData(
raw_feature_data,
axiskeys=source_axes +
"c" if len(raw_feature_data.shape) > len(source_axes) else
source_axes,
location=data_slice.location.updated(c=data_slice.location.c *
self.channel_multiplier))
out.set(feature_data, autocrop=True)
out.setflags(write=False)
return FeatureData(
out.raw(out.axiskeys),
axiskeys=out.axiskeys,
location=out.location,
)
def test_data_roi_get_tiles_can_clamp_to_datasource_tiles():
# fmt: off
data = Array5D(np.asarray([
[1, 2, 3, 4, 5],
[6, 7, 8, 9, 10],
[11, 12, 13, 14, 15],
[16, 17, 18, 19, 20],
]).astype(np.uint8), axiskeys="yx")
# fmt: on
ds = ArrayDataSource(data=data, tile_shape=Shape5D(x=2, y=2))
data_slice = DataRoi(datasource=ds, x=(1, 4), y=(0, 3))
# fmt: off
dataslice_expected_data = Array5D(np.asarray([
[2, 3, 4],
[7, 8, 9],
[12, 13, 14]
]).astype(np.uint8), axiskeys="yx", location=Point5D.zero(x=1))
# fmt: on
assert data_slice.retrieve() == dataslice_expected_data
# fmt: off
dataslice_expected_slices = [
Array5D(np.asarray([
[1, 2],
[6, 7]
]).astype(np.uint8), axiskeys="yx", location=Point5D.zero()),
Array5D(np.asarray([
[3, 4],
[8, 9],
]).astype(np.uint8), axiskeys="yx", location=Point5D.zero(x=2)),
Array5D(np.asarray([
[11, 12],
[16, 17],
]).astype(np.uint8), axiskeys="yx", location=Point5D.zero(y=2)),
Array5D(np.asarray([
[13, 14],
[18, 19],
]).astype(np.uint8), axiskeys="yx", location=Point5D.zero(x=2, y=2))
]
# fmt: on
expected_slice_dict = {a.interval: a for a in dataslice_expected_slices}
for piece in data_slice.get_datasource_tiles(clamp_to_datasource=True):
expected_data = expected_slice_dict.pop(piece.interval)
assert expected_data == piece.retrieve()
assert len(expected_slice_dict) == 0
def create_n5(
array: Array5D, *, axiskeys: Optional[str] = None, chunk_size: Shape5D, compression: N5Compressor = RawCompressor()
):
path = PurePosixPath(tempfile.mkstemp()[1] + ".n5")
sink = N5DatasetSink(
outer_path=path,
inner_path=PurePosixPath("/data"),
filesystem=OsFs("/"),
attributes=N5DatasetAttributes(
dimensions=array.shape,
blockSize=chunk_size,
c_axiskeys=axiskeys or array.axiskeys,
dataType=array.dtype,
compression=compression,
)
)
sink_writer = sink.create()
assert not isinstance(sink_writer, Exception)
for tile in array.split(chunk_size):
sink_writer.write(tile)
return path.as_posix()
def _process_tile(self, tile: Array5D) -> None:
tile = N5Block.fromArray5D(tile)
tile_path = self.get_tile_dataset_path(global_roi=tile.roi)
with self.filesystem.openbin(tile_path, "w") as f:
f.write(tile.to_n5_bytes(axiskeys=self.axiskeys, compression_type=self.compression_type))
def _allocate(self, interval: Union[Shape5D, Interval5D], fill_value: int, axiskeys_hint: str = "tzyxc") -> Array5D:
return Array5D.allocate(interval, dtype=self.dtype, value=fill_value, axiskeys=axiskeys_hint)
def colored(self, value: np.uint8) -> Array5D:
return Array5D(self._data * value,
axiskeys=self.axiskeys,
location=self.location)
def _get_tile(self, tile: Interval5D) -> Array5D:
slices = tile.translated(-self.location).to_slices(self.axiskeys)
raw = self._dataset[slices]
if not isinstance(raw, ndarray):
raise IOError("Expected ndarray at {slices}, found {raw}")
return Array5D(raw, axiskeys=self.axiskeys, location=tile.start)
from pathlib import PurePosixPath
import numpy as np
from ndstructs.point5D import Point5D, Shape5D
from ndstructs.array5D import Array5D
from webilastik.datasink.n5_dataset_sink import N5DatasetSink
from webilastik.datasink.precomputed_chunks_sink import PrecomputedChunksScaleSink
from webilastik.datasource import DataRoi
from webilastik.datasource.array_datasource import ArrayDataSource
from webilastik.datasource.n5_datasource import N5DataSource
from webilastik.datasource.precomputed_chunks_info import PrecomputedChunksScale, RawEncoder
from webilastik.datasource.n5_attributes import GzipCompressor, N5DatasetAttributes, RawCompressor
from webilastik.datasource.precomputed_chunks_datasource import PrecomputedChunksDataSource
data = Array5D(np.arange(20 * 10 * 7).reshape(20, 10, 7), axiskeys="xyz")
data.setflags(write=False)
datasource = ArrayDataSource(data=data, tile_shape=Shape5D(x=10, y=10))
def test_n5_attributes():
attributes = N5DatasetAttributes(
dimensions=Shape5D(x=100, y=200),
blockSize=Shape5D(x=10, y=20),
c_axiskeys="yx",
dataType=np.dtype("uint16").newbyteorder(">"),
compression=GzipCompressor(level=3))
reserialized_attributes = N5DatasetAttributes.from_json_data(
attributes.to_json_data())
def make_some_random_array(seed: int) -> Array5D:
return Array5D(np.random.rand(5, 5), axiskeys="yx")
def parse(cls, group: h5py.Group, raw_data_sources: Mapping[int, "FsDataSource | None"]) -> "IlpPixelClassificationGroup":
LabelColors = ensure_color_list(group, "LabelColors")
LabelNames = ensure_encoded_string_list(group, "LabelNames")
class_to_color: Mapping[np.uint8, Color] = {np.uint8(i): color for i, color in enumerate(LabelColors, start=1)}
label_classes: Dict[Color, Label] = {color: Label(name=name, color=color, annotations=[]) for name, color in zip(LabelNames, LabelColors)}
LabelSets = ensure_group(group, "LabelSets")
for lane_key in LabelSets.keys():
if not lane_key.startswith("labels"):
continue
lane_index = int(lane_key.replace("labels", ""))
lane_label_blocks = ensure_group(LabelSets, lane_key)
if len(lane_label_blocks.keys()) == 0:
continue
raw_data = raw_data_sources.get(lane_index)
if raw_data is None:
raise IlpParsingError(f"No datasource for lane {lane_index:03d}")
for block_name in lane_label_blocks.keys():
if not block_name.startswith("block"):
continue
block = ensure_dataset(lane_label_blocks, block_name)
block_data = block[()]
if not isinstance(block_data, np.ndarray):
raise IlpParsingError("Expected annotation block to contain a ndarray")
raw_axistags = block.attrs.get("axistags")
if not isinstance(raw_axistags, str):
raise IlpParsingError(f"Expected axistags to be a str, found {raw_axistags}")
axistags = AxisTags.fromJSON(raw_axistags)
axiskeys = "".join(axistags.keys())
if "blockSlice" not in block.attrs:
raise IlpParsingError(f"Expected 'blockSlice' in attrs from {block.name}")
blockSlice = block.attrs["blockSlice"]
if not isinstance(blockSlice, str):
raise IlpParsingError(f"Expected 'blockSlice'' to be a str, found {blockSlice}")
# import pydevd; pydevd.settrace()
blockSpans: Sequence[List[str]] = [span_str.split(":") for span_str in blockSlice[1:-1].split(",")]
blockInterval = Interval5D.zero(**{
key: (int(span[0]), int(span[1]))
for key, span in zip(axiskeys, blockSpans)
})
block_5d = Array5D(block_data, axiskeys=axiskeys)
for color_5d in block_5d.unique_colors().split(shape=Shape5D(x=1, c=block_5d.shape.c)):
color_index = np.uint8(color_5d.raw("c")[0])
if color_index == np.uint8(0): # background
continue
color = class_to_color.get(color_index)
if color is None:
raise IlpParsingError(f"Could not find a label color for index {color_index}")
annotation_data: "np.ndarray[Any, np.dtype[np.uint8]]" = block_5d.color_filtered(color=color_5d).raw(axiskeys)
annotation = Annotation(
annotation_data.astype(np.dtype(bool)),
location=blockInterval.start,
axiskeys=axiskeys, # FIXME: what if the user changed the axiskeys in the data source?
raw_data=raw_data,
)
label_classes[color].annotations.append(annotation)
ClassifierFactory = ensure_bytes(group, "ClassifierFactory")
if ClassifierFactory != VIGRA_ILP_CLASSIFIER_FACTORY:
raise IlpParsingError(f"Expecting ClassifierFactory to be pickled ParallelVigraRfLazyflowClassifierFactory, found {ClassifierFactory}")
if "ClassifierForests" in group:
ClassifierForests = ensure_group(group, "ClassifierForests")
forests: List[VigraRandomForest] = []
for forest_key in sorted(ClassifierForests.keys()):
if not forest_key.startswith("Forest"):
continue
forest = VigraRandomForest(group.file.filename, f"{ClassifierForests.name}/{forest_key}")
# forest_bytes = ensure_bytes(ClassifierForests, forest_key)
# forest = h5_bytes_to_vigra_forest(h5_bytes=VigraForestH5Bytes(forest_bytes))
forests.append(forest)
feature_names = ensure_encoded_string_list(ClassifierForests, "feature_names")
feature_extractors, expected_num_channels = cls.ilp_filters_and_expected_num_channels_from_names(feature_names)
classifier = VigraPixelClassifier(
feature_extractors=feature_extractors,
forest_h5_bytes=[vigra_forest_to_h5_bytes(forest) for forest in forests],
num_classes=len([label for label in label_classes.values() if not label.is_empty()]),
num_input_channels=expected_num_channels,
)
else:
classifier = None
return IlpPixelClassificationGroup(
classifier=classifier,
labels=list(label_classes.values()),
)
def test_sequence_datasource():
# fmt: off
img1_data = Array5D(np.asarray([
[[100, 101, 102, 103, 104],
[105, 106, 107, 108, 109],
[110, 111, 112, 113, 114],
[115, 116, 117, 118, 119]],
[[120, 121, 122, 123, 124],
[125, 126, 127, 128, 129],
[130, 131, 132, 133, 134],
[135, 136, 137, 138, 139]],
[[140, 141, 142, 143, 144],
[145, 146, 147, 148, 149],
[150, 151, 152, 153, 154],
[155, 156, 157, 158, 159]]
]), axiskeys="cyx")
img2_data = Array5D(np.asarray([
[[200, 201, 202, 203, 204],
[205, 206, 207, 208, 209],
[210, 211, 212, 213, 214],
[215, 216, 217, 218, 219]],
[[220, 221, 222, 223, 224],
[225, 226, 227, 228, 229],
[230, 231, 232, 233, 234],
[235, 236, 237, 238, 239]],
[[240, 241, 242, 243, 244],
[245, 246, 247, 248, 249],
[250, 251, 252, 253, 254],
[255, 256, 257, 258, 259]]
]), axiskeys="cyx")
img3_data = Array5D(np.asarray([
[[300, 301, 302, 303, 304],
[305, 306, 307, 308, 309],
[310, 311, 312, 313, 314],
[315, 316, 317, 318, 319]],
[[320, 321, 322, 323, 324],
[325, 326, 327, 328, 329],
[330, 331, 332, 333, 334],
[335, 336, 337, 338, 339]],
[[340, 341, 342, 343, 344],
[345, 346, 347, 348, 349],
[350, 351, 352, 353, 354],
[355, 356, 357, 358, 359]]
]), axiskeys="cyx")
expected_x_2_4__y_1_3 = Array5D(np.asarray([
[[[107, 108],
[112, 113]],
[[127, 128],
[132, 133]],
[[147, 148],
[152, 153]]],
[[[207, 208],
[212, 213]],
[[227, 228],
[232, 233]],
[[247, 248],
[252, 253]]],
[[[307, 308],
[312, 313]],
[[327, 328],
[332, 333]],
[[347, 348],
[352, 353]]],
]), axiskeys="zcyx")
# fmt: on
slice_x_2_4__y_1_3 = {"x": (2, 4), "y": (1, 3)}
h5_outer_paths = [
# create_n5(img1_data, axiskeys="cyx"),
create_h5(img1_data, axiskeys_style="dims", axiskeys="cyx"),
# create_n5(img2_data, axiskeys="cyx"),
create_h5(img2_data, axiskeys_style="dims", axiskeys="cyx"),
# create_n5(img3_data, axiskeys="cyx"),
create_h5(img3_data, axiskeys_style="dims", axiskeys="cyx"),
]
def stack_h5s(stack_axis: str) -> List[H5DataSource]:
offset = Point5D.zero()
stack: List[H5DataSource] = []
for outer_path in h5_outer_paths:
stack.append(H5DataSource(outer_path=outer_path, inner_path=PurePosixPath("/data"), filesystem=OsFs("/"), location=offset))
offset += Point5D.zero(**{stack_axis: stack[-1].shape[stack_axis]})
return stack
seq_ds = SequenceDataSource(datasources=stack_h5s("z"), stack_axis="z")
assert seq_ds.shape == Shape5D(x=5, y=4, c=3, z=3)
data = seq_ds.retrieve(**slice_x_2_4__y_1_3)
assert (expected_x_2_4__y_1_3.raw("xyzc") == data.raw("xyzc")).all()
seq_ds = SequenceDataSource(datasources=stack_h5s("z"), stack_axis="z")
data = seq_ds.retrieve(**slice_x_2_4__y_1_3)
assert (expected_x_2_4__y_1_3.raw("xyzc") == data.raw("xyzc")).all()
def test_neighboring_tiles():
# fmt: off
arr = Array5D(np.asarray([
[10, 11, 12, 20, 21, 22, 30],
[13, 14, 15, 23, 24, 25, 33],
[16, 17, 18, 26, 27, 28, 36],
[40, 41, 42, 50, 51, 52, 60],
[43, 44, 45, 53, 54, 55, 63],
[46, 47, 48, 56, 57, 58, 66],
[70, 71, 72, 80, 81, 82, 90],
[73, 74, 75, 83, 84, 85, 93],
[76, 77, 78, 86, 87, 88, 96],
[0, 1, 2, 3, 4, 5, 6]], dtype=np.uint8), axiskeys="yx")
ds = SkimageDataSource(path=create_png(arr), filesystem=OsFs("/"))
fifties_slice = DataRoi(ds, x=(3, 6), y=(3, 6))
expected_fifties_slice = Array5D(np.asarray([
[50, 51, 52],
[53, 54, 55],
[56, 57, 58]
]), axiskeys="yx")
# fmt: on
top_slice = DataRoi(ds, x=(3, 6), y=(0, 3))
bottom_slice = DataRoi(ds, x=(3, 6), y=(6, 9))
right_slice = DataRoi(ds, x=(6, 7), y=(3, 6))
left_slice = DataRoi(ds, x=(0, 3), y=(3, 6))
# fmt: off
fifties_neighbor_data = {
top_slice: Array5D(np.asarray([
[20, 21, 22],
[23, 24, 25],
[26, 27, 28]
]), axiskeys="yx"),
right_slice: Array5D(np.asarray([
[60],
[63],
[66]
]), axiskeys="yx"),
bottom_slice: Array5D(np.asarray([
[80, 81, 82],
[83, 84, 85],
[86, 87, 88]
]), axiskeys="yx"),
left_slice: Array5D(np.asarray([
[40, 41, 42],
[43, 44, 45],
[46, 47, 48]
]), axiskeys="yx"),
}
# fmt: on
assert (fifties_slice.retrieve().raw("yx") == expected_fifties_slice.raw("yx")).all()
for neighbor in fifties_slice.get_neighboring_tiles(tile_shape=Shape5D(x=3, y=3)):
try:
expected_slice = fifties_neighbor_data.pop(neighbor)
assert (expected_slice.raw("yx") == neighbor.retrieve().raw("yx")).all()
except KeyError:
print(f"\nWas searching for ", neighbor, "\n")
for k in fifties_neighbor_data.keys():
print("--->>> ", k)
assert len(fifties_neighbor_data) == 0
def encode(self, data: Array5D) -> bytes:
return data.raw("xyzc").tobytes("F")
f = h5py.File(path, "w")
ds = f.create_dataset("data", chunks=raw_chunk_shape, data=array.raw(axiskeys))
if axiskeys_style == "dims":
for key, dim in zip(axiskeys, ds.dims):
dim.label = key
elif axiskeys_style == "vigra":
type_flags = {"x": 2, "y": 2, "z": 2, "t": 2, "c": 1}
axistags = [{"key": key, "typeflags": type_flags[key], "resolution": 0, "description": ""} for key in axiskeys]
ds.attrs["axistags"] = json.dumps({"axes": axistags})
else:
raise Exception(f"Bad axiskeys_style: {axiskeys_style}")
return PurePosixPath(path)
png_image: PurePosixPath = create_png(Array5D(raw, axiskeys="yx"))
def tile_equals(tile: DataSource, axiskeys: str, raw: "np.ndarray[Any, Any]") -> bool:
return (tile.retrieve().raw(axiskeys) == raw).all()
def test_retrieve_roi_smaller_than_tile():
# fmt: off
data = Array5D(np.asarray([
[[ 1, 2, 3, 4, 5],
[ 6, 7, 8, 9, 10],
[ 11, 12, 13, 14, 15],
[ 16, 17, 18, 19, 20]],
[[ 100, 200, 300, 400, 500],
[ 600, 700, 800, 900, 1000],
def populate_group(self, group: h5py.Group):
LabelColors: "ndarray[Any, dtype[int64]]" = np.asarray([label.color.rgba for label in self.labels], dtype=int64)
# expected group keys to look like this:
# ['Bookmarks', 'ClassifierFactory', 'LabelColors', 'LabelNames', 'PmapColors', 'StorageVersion', 'LabelSets', 'ClassifierForests']>
bookmark = group.create_group("Bookmarks").create_dataset("0000", data=np.void(pickle.dumps([], 0))) # empty value is [], serialized with SerialPickleableSlot
bookmark.attrs["version"] = 1
group["ClassifierFactory"] = VIGRA_ILP_CLASSIFIER_FACTORY
group["LabelColors"] = LabelColors
group["LabelColors"].attrs["isEmpty"] = False
group["LabelNames"] = [label.name.encode("utf8") for label in self.labels]
group["LabelNames"].attrs["isEmpty"] = False
group["PmapColors"] = LabelColors
group["PmapColors"].attrs["isEmpty"] = False
group["StorageVersion"] = "0.1".encode("utf8")
merged_annotation_tiles: Dict[DataSource, Dict[Interval5D, Array5D]] = {}
for label_class, label in enumerate(self.labels, start=1):
for annotation in label.annotations:
datasource = annotation.raw_data
merged_tiles = merged_annotation_tiles.setdefault(datasource, {})
for interval in annotation.interval.get_tiles(
tile_shape=datasource.tile_shape.updated(c=1), tiles_origin=datasource.interval.start.updated(c=0)
):
annotation_tile = annotation.cut(interval.clamped(annotation.interval))
tile = merged_tiles.setdefault(interval, Array5D.allocate(interval=interval, value=0, dtype=np.dtype("uint8")))
tile.set(annotation_tile.colored(np.uint8(label_class)), mask_value=0)
LabelSets = group.create_group("LabelSets")
for lane_index, (lane_datasource, blocks) in enumerate(merged_annotation_tiles.items()):
assert isinstance(lane_datasource, FsDataSource) #FIXME? how do autocontext annotations work? They wouldn't be on FsDataSource
axiskeys = lane_datasource.c_axiskeys_on_disk
label_set = LabelSets.create_group(f"labels{lane_index:03}")
for block_index, block in enumerate(blocks.values()):
labels_dataset = label_set.create_dataset(f"block{block_index:04d}", data=block.raw(axiskeys))
labels_dataset.attrs["blockSlice"] = "[" + ",".join(f"{slc.start}:{slc.stop}" for slc in block.interval.updated(c=0).to_slices(axiskeys)) + "]"
labels_dataset.attrs["axistags"] = vigra.defaultAxistags(axiskeys).toJSON()
if len(LabelSets.keys()) == 0:
_ = LabelSets.create_group("labels000") # empty labels still produce this in classic ilastik
if self.classifier:
# ['Forest0000', ..., 'Forest000N', 'feature_names', 'known_labels', 'pickled_type']
ClassifierForests = group.create_group("ClassifierForests")
feature_names: List[bytes] = []
get_feature_extractor_order: Callable[[IlpFilter], int] = lambda ex: self.feature_classes.index(ex.__class__)
for fe in sorted(self.classifier.feature_extractors, key=get_feature_extractor_order):
for c in range(self.classifier.num_input_channels * fe.channel_multiplier):
feature_names.append(self.make_feature_ilp_name(fe, channel_index=c).encode("utf8"))
for forest_index, forest_bytes in enumerate(self.classifier.forest_h5_bytes):
forests_h5_path = dump_to_temp_file(forest_bytes)
with h5py.File(forests_h5_path, "r") as f:
forest_group = f["/"]
assert isinstance(forest_group, h5py.Group)
ClassifierForests.copy(forest_group, f"Forest{forest_index:04}") # 'Forest0000', ..., 'Forest000N'
ClassifierForests["feature_names"] = feature_names
ClassifierForests["known_labels"] = np.asarray(self.classifier.classes).astype(np.uint32)
ClassifierForests["pickled_type"] = b"clazyflow.classifiers.parallelVigraRfLazyflowClassifier\nParallelVigraRfLazyflowClassifier\np0\n."
def enlarged(self, radius: Point5D, limits: Interval5D) -> "ConnectedComponents":
"""Enlarges the array by 'radius', and fills this halo with zero"""
haloed_roi = self.interval.enlarged(radius).clamped(limits)
haloed_data = Array5D.allocate(haloed_roi, value=0, dtype=self.dtype)
haloed_data.set(self)
return ConnectedComponents.from_array5d(haloed_data, labels=self.labels)
def create_png(array: Array5D) -> PurePosixPath:
png_path = tempfile.mkstemp()[1] + ".png"
skimage.io.imsave(png_path, array.raw("yxc"))
return PurePosixPath(png_path)
