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Showing 1 of 2 files from the diff.

93.21% 100.00% +0.04%

pathml/core/slide_backends.py changed.

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tests/core_tests/test_slide_backends.py has changed.

@@ -198,16 +198,19 @@

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        stride_i, stride_j = stride

        if pad:
            n_chunk_i = i // stride_i + 1
            n_chunk_j = j // stride_j + 1

        # calculate number of expected tiles
        # check for tile shape evenly dividing slide shape to fix https://github.com/Dana-Farber-AIOS/pathml/issues/305
        if pad and i % stride_i != 0:
            n_tiles_i = i // stride_i + 1
        else:
            n_tiles_i = (i - shape[0]) // stride_i + 1
        if pad and j % stride_j != 0:
            n_tiles_j = j // stride_j + 1
        else:
            n_chunk_i = (i - shape[0]) // stride_i + 1
            n_chunk_j = (j - shape[1]) // stride_j + 1
            n_tiles_j = (j - shape[1]) // stride_j + 1

        for ix_i in range(n_chunk_i):
            for ix_j in range(n_chunk_j):
        for ix_i in range(n_tiles_i):
            for ix_j in range(n_tiles_j):
                coords = (int(ix_i * stride_i), int(ix_j * stride_j))
                # get image for tile
                tile_im = self.extract_region(location=coords, size=shape, level=level)

@@ -549,16 +552,19 @@

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        stride_i, stride_j = stride

        if pad:
            n_chunk_i = i // stride_i + 1
            n_chunk_j = j // stride_j + 1

        # calculate number of expected tiles
        # check for tile shape evenly dividing slide shape to fix https://github.com/Dana-Farber-AIOS/pathml/issues/305
        if pad and i % stride_i != 0:
            n_tiles_i = i // stride_i + 1
        else:
            n_tiles_i = (i - shape[0]) // stride_i + 1
        if pad and j % stride_j != 0:
            n_tiles_j = j // stride_j + 1
        else:
            n_chunk_i = (i - shape[0]) // stride_i + 1
            n_chunk_j = (j - shape[1]) // stride_j + 1
            n_tiles_j = (j - shape[1]) // stride_j + 1

        for ix_i in range(n_chunk_i):
            for ix_j in range(n_chunk_j):
        for ix_i in range(n_tiles_i):
            for ix_j in range(n_tiles_j):
                coords = (int(ix_i * stride_i), int(ix_j * stride_j))
                if coords[0] + shape[0] < i and coords[1] + shape[1] < j:
                    # get image for tile

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86.88% 100.00% +0.01%

Merge pull request #306 from Dana-Farber-AIOS/fix-tiling-bug

jacobrosenthaldfci

278e4a0

CI Passed

86.88% 100.00% +0.01%

fix tiling logic when tile size evenly divides slide size

jacobrosenthaldfci

#306 6f17f97

CI Passed

Hiding 1 contexual commits

+2

86.87% 100.00% -0.06%

Merge pull request #301 from Dana-Farber-AIOS/update-quantifyMIF

jacobrosenthaldfci

1bcbbc2

CI Passed

Files		•	•	•	Coverage
pathml	+2	+2	ø	ø	^0.01% 86.88%
Project Totals (26 files)	2,447	2,126	0	321	86.88%

198	198
199	199		stride_i, stride_j = stride
200	200
201		-	if pad:
202		-	n_chunk_i = i // stride_i + 1
203		-	n_chunk_j = j // stride_j + 1
204		-
	201	+	# calculate number of expected tiles
	202	+	# check for tile shape evenly dividing slide shape to fix https://github.com/Dana-Farber-AIOS/pathml/issues/305
	203	+	if pad and i % stride_i != 0:
	204	+	n_tiles_i = i // stride_i + 1
	205	+	else:
	206	+	n_tiles_i = (i - shape[0]) // stride_i + 1
	207	+	if pad and j % stride_j != 0:
	208	+	n_tiles_j = j // stride_j + 1
205	209		else:
206		-	n_chunk_i = (i - shape[0]) // stride_i + 1
207		-	n_chunk_j = (j - shape[1]) // stride_j + 1
	210	+	n_tiles_j = (j - shape[1]) // stride_j + 1
208	211
209		-	for ix_i in range(n_chunk_i):
210		-	for ix_j in range(n_chunk_j):
	212	+	for ix_i in range(n_tiles_i):
	213	+	for ix_j in range(n_tiles_j):
211	214		coords = (int(ix_i * stride_i), int(ix_j * stride_j))
212	215		# get image for tile
213	216		tile_im = self.extract_region(location=coords, size=shape, level=level)

549	552
550	553		stride_i, stride_j = stride
551	554
552		-	if pad:
553		-	n_chunk_i = i // stride_i + 1
554		-	n_chunk_j = j // stride_j + 1
555		-
	555	+	# calculate number of expected tiles
	556	+	# check for tile shape evenly dividing slide shape to fix https://github.com/Dana-Farber-AIOS/pathml/issues/305
	557	+	if pad and i % stride_i != 0:
	558	+	n_tiles_i = i // stride_i + 1
	559	+	else:
	560	+	n_tiles_i = (i - shape[0]) // stride_i + 1
	561	+	if pad and j % stride_j != 0:
	562	+	n_tiles_j = j // stride_j + 1
556	563		else:
557		-	n_chunk_i = (i - shape[0]) // stride_i + 1
558		-	n_chunk_j = (j - shape[1]) // stride_j + 1
	564	+	n_tiles_j = (j - shape[1]) // stride_j + 1
559	565
560		-	for ix_i in range(n_chunk_i):
561		-	for ix_j in range(n_chunk_j):
	566	+	for ix_i in range(n_tiles_i):
	567	+	for ix_j in range(n_tiles_j):
562	568		coords = (int(ix_i * stride_i), int(ix_j * stride_j))
563	569		if coords[0] + shape[0] < i and coords[1] + shape[1] < j:
564	570		# get image for tile

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