def test_crop_metadata(self, small_cont_1c: ImageContainer, dy: int):
crop = small_cont_1c.crop_corner(dy, 0, 50, mask_circle=True)
assert small_cont_1c.data.attrs[Key.img.coords] is _NULL_COORDS
assert crop.data.attrs[Key.img.coords] == CropCoords(0, 0, 50, 50 + dy)
assert crop.data.attrs[Key.img.padding] == CropPadding(x_pre=0,
y_pre=abs(dy),
x_post=0,
y_post=0)
assert crop.data.attrs[Key.img.mask_circle]
def transform_metadata(data: xr.Dataset) -> xr.Dataset:
data.attrs[Key.img.coords] = CropCoords.from_tuple(
data.attrs.get(Key.img.coords, _NULL_COORDS.to_tuple()))
data.attrs[Key.img.padding] = CropPadding.from_tuple(
data.attrs.get(Key.img.padding, _NULL_PADDING.to_tuple()))
if Key.img.mask_circle not in data.attrs:
data.attrs[Key.img.mask_circle] = False
if Key.img.scale not in data.attrs:
data.attrs[Key.img.scale] = 1
return data
def convert_to_full_image_coordinates(x: np.ndarray,
y: np.ndarray) -> np.ndarray:
if not len(y):
return np.array([[]], dtype=np.float64)
if self.data.attrs.get("mask_circle", False):
if self.data.dims["y"] != self.data.dims["x"]:
raise ValueError(
f"Crop is not a square: `{self.data.dims}`.")
c = self.data.dims["x"] // 2 # center
mask = (x - c)**2 + (y - c)**2 <= c**2
y = y[mask]
x = x[mask]
if not len(y):
return np.array(
[[]],
dtype=np.float64) # because of masking, should not happen
coord = self.data.attrs.get(
Key.img.coords,
CropCoords(x0=0,
y0=0,
x1=self.data.dims["x"],
y1=self.data.dims["y"]
)) # fall back to default (i.e no crop) coordinates
padding = self.data.attrs.get(
Key.img.padding, _NULL_PADDING) # fallback to no padding
y_slc, x_slc = coord.to_image_coordinates(padding).slice
# relative coordinates
y = (y - np.min(y)) / (np.max(y) - np.min(y))
x = (x - np.min(x)) / (np.max(x) - np.min(x))
# coordinates in the uncropped image
y = coord.slice[0].start + (y_slc.stop - y_slc.start) * y
x = coord.slice[1].start + (x_slc.stop - x_slc.start) * x
return np.c_[x, y] # type: ignore[no-any-return]
def crop_corner(
self,
y: FoI_t,
x: FoI_t,
size: Optional[Union[FoI_t, Tuple[FoI_t, FoI_t]]] = None,
scale: float = 1.0,
cval: Union[int, float] = 0,
mask_circle: bool = False,
preserve_dtypes: bool = True,
) -> "ImageContainer":
"""
Extract a crop from the upper-left corner.
Parameters
----------
%(yx)s
%(size)s
scale
Rescale the crop using :func:`skimage.transform.rescale`.
cval
Fill value to use if ``mask_circle = True`` or if crop goes out of the image boundary.
mask_circle
Whether to mask out values that are not within a circle defined by this crop.
Only available if ``size`` defines a square.
preserve_dtypes
Whether to preserver the data types of underlying :class:`xarray.DataArray`, even if ``cval``
is of different type.
Returns
-------
The cropped image of size ``size * scale``.
Raises
------
ValueError
If the crop would completely lie outside of the image or if ``mask_circle = True`` and
``size`` does not define a square.
Notes
-----
If ``preserve_dtypes = True`` but ``cval`` cannot be safely cast, ``cval`` will be set to 0.
"""
self._assert_not_empty()
y, x = self._convert_to_pixel_space((y, x))
size = self._get_size(size)
size = self._convert_to_pixel_space(size)
ys, xs = size
_assert_positive(ys, name="height")
_assert_positive(xs, name="width")
_assert_positive(scale, name="scale")
orig = CropCoords(x0=x, y0=y, x1=x + xs, y1=y + ys)
ymin, xmin = self.shape
coords = CropCoords(x0=min(max(x, 0), xmin),
y0=min(max(y, 0), ymin),
x1=min(x + xs, xmin),
y1=min(y + ys, ymin))
if not coords.dy:
raise ValueError("Height of the crop is empty.")
if not coords.dx:
raise ValueError("Width of the crop is empty.")
crop = self.data.isel(x=slice(coords.x0, coords.x1),
y=slice(coords.y0, coords.y1)).copy(deep=False)
crop.attrs[Key.img.coords] = coords
if orig != coords:
padding = orig - coords
# because padding does not change dtype by itself
for key, arr in crop.items():
if preserve_dtypes:
if not np.can_cast(cval, arr.dtype, casting="safe"):
cval = 0
else:
crop[key] = crop[key].astype(np.dtype(type(cval)),
copy=False)
crop = crop.pad(
y=(padding.y_pre, padding.y_post),
x=(padding.x_pre, padding.x_post),
mode="constant",
constant_values=cval,
)
crop.attrs["padding"] = padding
else:
crop.attrs["padding"] = _NULL_PADDING
return self._from_dataset(
self._post_process(data=crop,
scale=scale,
cval=cval,
mask_circle=mask_circle,
preserve_dtypes=preserve_dtypes))