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add auto-tiling and fix weighting after merging #7

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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 dtype keyword to Merger that specifies dtype of data buffer
  • Loading branch information
@the-lay
the-lay committed Dec 10, 2021
commit a6e56e4cfc6ca8c99a4a3f4fddc0d91547105717
16 changes: 12 additions & 4 deletions tiler/merger.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,7 @@ def __init__(
tiler: Tiler,
window: Union[None, str, np.ndarray] = None,
logits: int = 0,
dtype: np.dtype = np.float64,
atol: float = 1e-10,
):
"""Merger precomputes everything for merging together tiles created by given Tiler.
Expand All @@ -73,6 +74,9 @@ def __init__(
Default is None which creates a boxcar window (constant 1s).

logits (int): Specify whether to add logits dimensions in front of the data array. Default is `0`.

dtype (np.dtype): Specify dtype of buffer that holds added tiles. Default is `np.float64`.

"""

self.tiler = tiler
Expand All @@ -86,6 +90,7 @@ def __init__(
self.logits = int(logits)

# Generate data and normalization arrays
self.dtype = dtype
self.data = self.data_visits = self.weights_sum = None
self.reset()

Expand Down Expand Up @@ -187,15 +192,15 @@ def reset(self) -> None:

# Image holds sum of all processed tiles multiplied by the window
if self.logits:
self.data = np.zeros((self.logits, *padded_data_shape))
self.data = np.zeros((self.logits, *padded_data_shape), dtype=self.dtype)
else:
self.data = np.zeros(padded_data_shape)
self.data = np.zeros(padded_data_shape, dtype=self.dtype)

# Normalization array holds the number of times each element was visited
self.data_visits = np.zeros(padded_data_shape, dtype=np.uint32)

# Total data window (weight) coefficients
self.weights_sum = np.zeros(padded_data_shape)
self.weights_sum = np.zeros(padded_data_shape, dtype=np.float64)

def add(self, tile_id: int, data: np.ndarray) -> None:
"""Adds `tile_id`-th tile into Merger.
Expand Down Expand Up @@ -233,6 +238,10 @@ def add(self, tile_id: int, data: np.ndarray) -> None:
f"must be less or equal than tile shape ({expected_tile_shape})."
)

# Check for dtype mismatch
if self.dtype != data.dtype:
raise ValueError(f"Passed data dtype ({data.dtype}) must match Merger initialized dtype ({self.dtype}).")

# Select coordinates for data
shape_diff = expected_tile_shape - data_shape
a, b = self.tiler.get_tile_bbox_position(tile_id, with_channel_dim=True)
Expand All @@ -243,7 +252,6 @@ def add(self, tile_id: int, data: np.ndarray) -> None:
for diff in shape_diff
]

# TODO check for self.data and data dtypes mismatch?
if self.logits > 0:
self.data[tuple([slice(None, None, None)] + sl)] += (
data * self.window[tuple(win_sl[1:])]
Expand Down