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[easy] Rename tile_coordinates to tile_identifier #1401

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Jun 12, 2019
Merged

[easy] Rename tile_coordinates to tile_identifier #1401

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26 changes: 13 additions & 13 deletions starfish/core/experiment/builder/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ def _fov_path_generator(parent_toc_path: Path, toc_name: str) -> Path:


def build_irregular_image(
tile_coordinates: Iterable[TileIdentifier],
tile_identifiers: Iterable[TileIdentifier],
image_fetcher: TileFetcher,
default_shape: Optional[Mapping[Axes, int]] = None,
) -> Collection:
Expand All @@ -76,7 +76,7 @@ def build_irregular_image(

Parameters
----------
tile_coordinates : Iterable[TileIdentifier]
tile_identifiers : Iterable[TileIdentifier]
Iterable of all the TileCoordinates that are valid in the image.
image_fetcher : TileFetcher
Instance of TileFetcher that provides the data for the tile.
Expand All @@ -100,7 +100,7 @@ def reducer_to_sets(
initial_value: Sequence[MutableSet[int]] = tuple(set() for _ in range(4))

fovs, rounds, chs, zplanes = functools.reduce(
reducer_to_sets, tile_coordinates, initial_value)
reducer_to_sets, tile_identifiers, initial_value)

collection = Collection()
for expected_fov in fovs:
Expand All @@ -120,7 +120,7 @@ def reducer_to_sets(
ImageFormat.TIFF,
)

for tile_coordinate in tile_coordinates:
for tile_coordinate in tile_identifiers:
current_fov, current_round, current_ch, current_zplane = astuple(tile_coordinate)
# filter out the fovs that are not the one we are currently processing
if expected_fov != current_fov:
Expand Down Expand Up @@ -198,20 +198,20 @@ def build_image(
"""
axes_sizes = join_axes_labels(
axes_order, rounds=rounds, chs=chs, zplanes=zplanes)
tile_coordinates = [
tile_identifiers = [
TileIdentifier(fov_id, selector[Axes.ROUND], selector[Axes.CH], selector[Axes.ZPLANE])
for fov_id in fovs
for selector in ordered_iterator(axes_sizes)
]

return build_irregular_image(tile_coordinates, image_fetcher, default_shape)
return build_irregular_image(tile_identifiers, image_fetcher, default_shape)


def write_irregular_experiment_json(
path: str,
tile_format: ImageFormat,
*,
image_tile_coordinates: Mapping[str, Iterable[TileIdentifier]],
image_tile_identifiers: Mapping[str, Iterable[TileIdentifier]],
tile_fetchers: Mapping[str, TileFetcher],
postprocess_func: Optional[Callable[[dict], dict]]=None,
default_shape: Optional[Mapping[Axes, int]]=None,
Expand All @@ -227,7 +227,7 @@ def write_irregular_experiment_json(
Directory to write the files to.
tile_format : ImageFormat
File format to write the tiles as.
image_tile_coordinates : Mapping[str, Iterable[TileIdentifier]]
image_tile_identifiers : Mapping[str, Iterable[TileIdentifier]]
Dictionary mapping the image type to an iterable of TileCoordinates.
tile_fetchers : Mapping[str, TileFetcher]
Dictionary mapping the image type to a TileFetcher.
Expand All @@ -250,10 +250,10 @@ def write_irregular_experiment_json(
'images': {},
'extras': {},
}
for image_type, tile_coordinates in image_tile_coordinates.items():
for image_type, tile_identifiers in image_tile_identifiers.items():
tile_fetcher = tile_fetchers[image_type]

image = build_irregular_image(tile_coordinates, tile_fetcher, default_shape)
image = build_irregular_image(tile_identifiers, tile_fetcher, default_shape)

Writer.write_to_path(
image,
Expand Down Expand Up @@ -353,7 +353,7 @@ def write_experiment_json(
if primary_tile_fetcher is not None:
all_tile_fetcher[FieldOfView.PRIMARY_IMAGES] = primary_tile_fetcher

image_tile_coordinates: MutableMapping[str, Iterable[TileIdentifier]] = dict()
image_tile_identifiers: MutableMapping[str, Iterable[TileIdentifier]] = dict()
image_tile_fetchers: MutableMapping[str, TileFetcher] = dict()

dimension_cardinality_of_images = {FieldOfView.PRIMARY_IMAGES: primary_image_dimensions}
Expand All @@ -367,7 +367,7 @@ def write_experiment_json(
chs=range(dimension_cardinality_of_image[Axes.CH]),
zplanes=range(dimension_cardinality_of_image[Axes.ZPLANE]),
)
image_tile_coordinates[image_type] = [
image_tile_identifiers[image_type] = [
TileIdentifier(fov_id, selector[Axes.ROUND], selector[Axes.CH], selector[Axes.ZPLANE])
for fov_id in range(fov_count)
for selector in ordered_iterator(axes_sizes)
Expand All @@ -378,7 +378,7 @@ def write_experiment_json(

return write_irregular_experiment_json(
path, tile_format,
image_tile_coordinates=image_tile_coordinates,
image_tile_identifiers=image_tile_identifiers,
tile_fetchers=image_tile_fetchers,
postprocess_func=postprocess_func,
default_shape=default_shape,
Expand Down