def to_dataset(self, data):
"""Converts the data into an ImageJ dataset"""
if self._is_xarraylike(data):
return self._xarray_to_dataset(data)
if self._is_arraylike(data):
return self._numpy_to_dataset(data)
if scyjava.isjava(data):
return self._java_to_dataset(data)
raise TypeError(f'Type not supported: {type(data)}')
def from_java(self, data):
"""
Converts the data into a python equivalent
"""
if not isjava(data): return data
if self._ij.convert().supports(data, Dataset):
# HACK: Converter exists for ImagePlus -> Dataset, but not ImagePlus -> RAI.
data = self._ij.convert().convert(data, Dataset)
if (self._ij.convert().supports(data, RandomAccessibleInterval)):
rai = self._ij.convert().convert(data, RandomAccessibleInterval)
return self.rai_to_numpy(rai)
return to_python(data)
def dims(self, image):
"""
Return the dimensions of the equivalent numpy array for the image. Reverse dimension order from Java.
"""
if isinstance(image, numpy.ndarray):
return image.shape
if not isjava(image):
raise TypeError('Unsupported type: ' + str(type(image)))
if jclass('net.imglib2.Dimensions').isInstance(image):
return [image.dimension(d) for d in range(image.numDimensions() -1, -1, -1)]
if jclass('ij.ImagePlus').isInstance(image):
dims = image.getDimensions()
dims.reverse()
dims = [dim for dim in dims if dim > 1]
return dims
raise TypeError('Unsupported Java type: ' + str(jclass(image).getName()))
def from_java(self, data):
"""
Converts the data into a python equivalent
"""
# todo: convert a datset to xarray
if not isjava(data): return data
try:
if self._ij.convert().supports(data, Dataset):
# HACK: Converter exists for ImagePlus -> Dataset, but not ImagePlus -> RAI.
data = self._ij.convert().convert(data, Dataset)
return self._dataset_to_xarray(data)
if self._ij.convert().supports(data, RandomAccessibleInterval):
rai = self._ij.convert().convert(data,
RandomAccessibleInterval)
return self.rai_to_numpy(rai)
except Exception as exc:
_dump_exception(exc)
raise exc
return to_python(data)
def dtype(self, image_or_type):
"""
Return the dtype of the equivalent numpy array for the given image or type.
"""
if type(image_or_type) == numpy.dtype:
return image_or_type
if self._is_arraylike(image_or_type):
return image_or_type.dtype
if not isjava(image_or_type):
raise TypeError('Unsupported type: ' +
str(type(image_or_type)))
# -- ImgLib2 types --
if jclass('net.imglib2.type.Type').isInstance(image_or_type):
ij2_types = {
'net.imglib2.type.logic.BitType': 'bool',
'net.imglib2.type.numeric.integer.ByteType': 'int8',
'net.imglib2.type.numeric.integer.ShortType': 'int16',
'net.imglib2.type.numeric.integer.IntType': 'int32',
'net.imglib2.type.numeric.integer.LongType': 'int64',
'net.imglib2.type.numeric.integer.UnsignedByteType':
'uint8',
'net.imglib2.type.numeric.integer.UnsignedShortType':
'uint16',
'net.imglib2.type.numeric.integer.UnsignedIntType':
'uint32',
'net.imglib2.type.numeric.integer.UnsignedLongType':
'uint64',
'net.imglib2.type.numeric.real.FloatType': 'float32',
'net.imglib2.type.numeric.real.DoubleType': 'float64',
}
for c in ij2_types:
if jclass(c).isInstance(image_or_type):
return numpy.dtype(ij2_types[c])
raise TypeError(
'Unsupported ImgLib2 type: {}'.format(image_or_type))
# -- ImgLib2 images --
if jclass('net.imglib2.IterableInterval').isInstance(
image_or_type):
ij2_type = image_or_type.firstElement()
return self.dtype(ij2_type)
if jclass('net.imglib2.RandomAccessibleInterval').isInstance(
image_or_type):
Util = autoclass('net.imglib2.util.Util')
ij2_type = Util.getTypeFromInterval(image_or_type)
return self.dtype(ij2_type)
# -- ImageJ1 images --
if jclass('ij.ImagePlus').isInstance(image_or_type):
ij1_type = image_or_type.getType()
ImagePlus = autoclass('ij.ImagePlus')
ij1_types = {
ImagePlus.GRAY8: 'uint8',
ImagePlus.GRAY16: 'uint16',
ImagePlus.GRAY32:
'float32', # NB: ImageJ1's 32-bit type is float32, not uint32.
}
for t in ij1_types:
if ij1_type == t:
return numpy.dtype(ij1_types[t])
raise TypeError(
'Unsupported ImageJ1 type: {}'.format(ij1_type))
raise TypeError('Unsupported Java type: ' +
str(jclass(image_or_type).getName()))