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add auto-tiling and fix weighting after merging #7

Merged
merged 23 commits into from
Dec 14, 2021
Merged

add auto-tiling and fix weighting after merging #7

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5351226
add auto-tiling and fix weighting after merging
renerichter Sep 27, 2021
fdc38c8
add minimal overlap
renerichter Sep 29, 2021
6db742e
Merge remote-tracking branch 'origin/master' into renerichter-rl
the-lay Nov 8, 2021
c10c04c
Code linting
the-lay Nov 9, 2021
a14beea
Added ndarray types; Throw an exception in case of non-matching data.…
the-lay Nov 18, 2021
ab58cd3
Removing flattop window since it has negative values
the-lay Nov 18, 2021
46e948b
Code linting
the-lay Nov 19, 2021
a6e56e4
Added dtype keyword to Merger that specifies dtype of data buffer
the-lay Dec 10, 2021
4474666
Added apply_padding method; overlap now can be given as a numpy array
the-lay Dec 10, 2021
3640e2d
Small documentation fixes
the-lay Dec 10, 2021
ae79a80
Saving Merger data_visits is now optional
the-lay Dec 10, 2021
ebac20a
Fixed data visits check
the-lay Dec 10, 2021
51cc98c
Added an uncovered edge case test
the-lay Dec 11, 2021
5eee24b
Added test for Merger with disabled save_visits
the-lay Dec 11, 2021
aa86420
Refactored normalization by weights in merging
the-lay Dec 11, 2021
69ab5c9
Fixed explicit padding for odd data shapes
the-lay Dec 11, 2021
d0a559e
Hiding division by zero warning when normalizing by weight
the-lay Dec 11, 2021
f0b1f9b
Code linting
the-lay Dec 11, 2021
bd1cd9e
Updated documentation
the-lay Dec 11, 2021
f032b09
Fixing trying to submit coveralls on pull requests
the-lay Dec 11, 2021
054b5d7
Teaser image generated script now actually tiles and merges the image :)
the-lay Dec 11, 2021
a02c0c6
Merger buffer dtypes are now hardcoded, optional casting to specified…
the-lay Dec 11, 2021
c230be4
Refactored extra padding system and updated examples
the-lay Dec 12, 2021
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Added ndarray types; Throw an exception in case of non-matching data.… 
…shape and self.data_shape in get_tile
  • Loading branch information
@the-lay
the-lay committed Nov 18, 2021
commit a14beea4005e4e2cee25f5886da923242a46732b
2 changes: 2 additions & 0 deletions tests/test_tiler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -289,6 +289,8 @@ def test_get_tile(self):
tiler.get_tile(self.data, len(tiler))
with self.assertRaises(IndexError):
tiler.get_tile(self.data, -1)
with self.assertRaises(ValueError):
tiler.get_tile(np.zeros((self.n_elements + 1, )), 0)

# copy test
t = tiler.get_tile(self.data, 0, copy_data=True)
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14 changes: 10 additions & 4 deletions tiler/tiler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,8 @@ class Tiler:

def __init__(
self,
data_shape: Union[Tuple, List],
tile_shape: Union[Tuple, List],
data_shape: Union[Tuple, List, np.ndarray],
tile_shape: Union[Tuple, List, np.ndarray],
overlap: Union[int, float, Tuple, List] = 0,
channel_dimension: Optional[int] = None,
mode: str = "constant",
Expand All @@ -48,10 +48,10 @@ def __init__(
- allow other numpy padding modes (maximum, minimum, mean, median)

Args:
data_shape (tuple or list): Input data shape, e.g. (1920, 1080, 3) or [512, 512, 512].
data_shape (tuple, list or np.ndarray): Input data shape, e.g. (1920, 1080, 3), [512, 512, 512] or np.ndarray([3, 1024, 768]).
If there is a channel dimension, it should be included in the shape.

tile_shape (tuple or list): Shape of a tile, e.g. (256, 256, 3) or [64, 64, 64].
tile_shape (tuple, list or np.ndarray): Shape of a tile, e.g. (256, 256, 3), [64, 64, 64] or np.ndarray([3, 128, 128]).
Tile must have the same number of dimensions as data.

overlap (int, float, tuple or list): Specifies overlap between tiles.
Expand Down Expand Up @@ -363,6 +363,12 @@ def get_tile(
f"There are {len(self) - 1} tiles, starting from index 0."
)

if isinstance(data, np.ndarray) and np.not_equal(data.shape, self.data_shape).any():
raise ValueError(
f"Shape of provided data array ({data.shape}) does not match "
f"same as Tiler's data_shape ({tuple(self.data_shape)})."
)

# get tile data
tile_corner = self._tile_index[tile_id] * self._tile_step
# take the lesser of the tile shape and the distance to the edge
Expand Down