renaming: pixelsize to pixel_size

Author: quentinblampey

CHANGELOG.md

@@ -1,4 +1,7 @@
-## [0.1.x] - tbd
+## [0.1.6] - tbd
+
+### Breaking changes
+- `pixelsize` is now renamed `pixel_size`
 
 ## [0.1.5] - 2024-01-30
 

docs/cli.md

@@ -106,7 +106,7 @@ $ spatialdata_xenium_explorer write [OPTIONS] SDATA_PATH
 * `--shapes-key TEXT`: Name of the cell shapes (key of `sdata.shapes`). This argument doesn't need to be provided if there is only one shapes key or a table with only one region.
 * `--points-key TEXT`: Name of the transcripts (key of `sdata.points`). This argument doesn't need to be provided if there is only one points key.
 * `--gene-column TEXT`: Column name of the points dataframe containing the gene names
-* `--pixelsize FLOAT`: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.  [default: 0.2125]
+* `--pixel_size FLOAT`: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.  [default: 0.2125]
 * `--spot / --no-spot`: Whether the technology is based on spots  [default: no-spot]
 * `--layer TEXT`: Layer of `sdata.table` where the gene counts are saved. If `None`, uses `sdata.table.X`.
 * `--lazy / --no-lazy`: If `True`, will not load the full images in memory (except if the image memory is below `ram_threshold_gb`)  [default: lazy]

spatialdata_xenium_explorer/_constants.py

@@ -77,7 +77,7 @@ def group_attrs() -> dict:
     }
 
 
-def experiment_dict(run_name: str, region_name: str, num_cells: int, pixelsize: float) -> dict:
+def experiment_dict(run_name: str, region_name: str, num_cells: int, pixel_size: float) -> dict:
     return {
         "major_version": Versions.EXPERIMENT[0],
         "minor_version": Versions.EXPERIMENT[1],
@@ -97,7 +97,7 @@ def experiment_dict(run_name: str, region_name: str, num_cells: int, pixelsize:
         "panel_organism": "Human",
         "panel_num_targets_predesigned": 0,
         "panel_num_targets_custom": 0,
-        "pixel_size": pixelsize,
+        "pixel_size": pixel_size,
         "instrument_sn": "N/A",
         "instrument_sw_version": "N/A",
         "analysis_sw_version": "xenium-1.3.0.5",
@@ -122,12 +122,12 @@ def experiment_dict(run_name: str, region_name: str, num_cells: int, pixelsize:
     }
 
 
-def image_metadata(channel_names: list[str], pixelsize: float) -> dict:
+def image_metadata(channel_names: list[str], pixel_size: float) -> dict:
     return {
         "SignificantBits": 8,
-        "PhysicalSizeX": pixelsize,
+        "PhysicalSizeX": pixel_size,
         "PhysicalSizeXUnit": "µm",
-        "PhysicalSizeY": pixelsize,
+        "PhysicalSizeY": pixel_size,
         "PhysicalSizeYUnit": "µm",
         "Channel": {"Name": channel_names},
     }

spatialdata_xenium_explorer/cli/app.py

@@ -27,7 +27,7 @@ def write(
     gene_column: str = typer.Option(
         None, help="Column name of the points dataframe containing the gene names"
     ),
-    pixelsize: float = typer.Option(
+    pixel_size: float = typer.Option(
         0.2125,
         help="Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.",
     ),
@@ -68,7 +68,7 @@ def write(
         shapes_key=shapes_key,
         points_key=points_key,
         gene_column=gene_column,
-        pixelsize=pixelsize,
+        pixel_size=pixel_size,
         spot=spot,
         layer=layer,
         lazy=lazy,

spatialdata_xenium_explorer/converter.py

@@ -27,7 +27,7 @@ def write(
     shapes_key: str | None = None,
     points_key: str | None = None,
     gene_column: str | None = None,
-    pixelsize: float = 0.2125,
+    pixel_size: float = 0.2125,
     spot: bool = False,
     layer: str | None = None,
     polygon_max_vertices: int = 13,
@@ -64,7 +64,7 @@ def write(
         shapes_key: Name of the cell shapes (key of `sdata.shapes`). This argument doesn't need to be provided if there is only one shapes key or a table with only one region.
         points_key: Name of the transcripts (key of `sdata.points`). This argument doesn't need to be provided if there is only one points key.
         gene_column: Column name of the points dataframe containing the gene names.
-        pixelsize: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.
+        pixel_size: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.
         spot: Whether the technology is based on spots
         layer: Layer of `sdata.table` where the gene counts are saved. If `None`, uses `sdata.table.X`.
         polygon_max_vertices: Maximum number of vertices for the cell polygons. A higher value will display smoother cells.
@@ -106,7 +106,7 @@ def write(
 
         geo_df = utils._standardize_shapes(geo_df)
 
-        write_polygons(path, geo_df.geometry, polygon_max_vertices, pixelsize=pixelsize)
+        write_polygons(path, geo_df.geometry, polygon_max_vertices, pixel_size=pixel_size)
 
     ### Saving transcripts
     if spot and sdata.table is not None:
@@ -117,17 +117,19 @@ def write(
 
     if _should_save(mode, "t") and df is not None:
         if gene_column is not None:
-            write_transcripts(path, df, gene_column, pixelsize=pixelsize)
+            write_transcripts(path, df, gene_column, pixel_size=pixel_size)
         else:
             log.warn("The argument 'gene_column' has to be provided to save the transcripts")
 
     ### Saving image
     if _should_save(mode, "i"):
-        write_image(path, image, lazy=lazy, ram_threshold_gb=ram_threshold_gb, pixelsize=pixelsize)
+        write_image(
+            path, image, lazy=lazy, ram_threshold_gb=ram_threshold_gb, pixel_size=pixel_size
+        )
 
     ### Saving experiment.xenium file
     if _should_save(mode, "m"):
-        write_metadata(path, image_key, shapes_key, _get_n_obs(sdata, geo_df), pixelsize)
+        write_metadata(path, image_key, shapes_key, _get_n_obs(sdata, geo_df), pixel_size)
 
     log.info(f"Saved files in the following directory: {path}")
     log.info(f"You can open the experiment with 'open {path / FileNames.METADATA}'")
@@ -164,7 +166,7 @@ def write_metadata(
     shapes_key: str = "NA",
     n_obs: int = 0,
     is_dir: bool = True,
-    pixelsize: float = 0.2125,
+    pixel_size: float = 0.2125,
 ):
     """Create an `experiment.xenium` file that can be open by the Xenium Explorer.
 
@@ -177,10 +179,10 @@ def write_metadata(
         shapes_key: Key of `SpatialData` object containing the boundaries shown on the explorer.
         n_obs: Number of cells
         is_dir: If `False`, then `path` is a path to a single file, not to the Xenium Explorer directory.
-        pixelsize: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.
+        pixel_size: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.
     """
     path = utils.explorer_file_path(path, FileNames.METADATA, is_dir)
 
     with open(path, "w") as f:
-        metadata = experiment_dict(image_key, shapes_key, n_obs, pixelsize)
+        metadata = experiment_dict(image_key, shapes_key, n_obs, pixel_size)
         json.dump(metadata, f, indent=4)

spatialdata_xenium_explorer/core/images.py

@@ -29,15 +29,15 @@ class MultiscaleImageWriter:
     resolutionunit = "CENTIMETER"
     dtype = np.uint8
 
-    def __init__(self, image: MultiscaleSpatialImage, tile_width: int, pixelsize: float):
+    def __init__(self, image: MultiscaleSpatialImage, tile_width: int, pixel_size: float):
         self.image = image
         self.tile_width = tile_width
-        self.pixelsize = pixelsize
+        self.pixel_size = pixel_size
 
         self.scale_names = list(image.children)
         self.channel_names = list(map(str, image[self.scale_names[0]].c.values))
         self.channel_names = _set_colors(self.channel_names)
-        self.metadata = image_metadata(self.channel_names, pixelsize)
+        self.metadata = image_metadata(self.channel_names, pixel_size)
         self.data = None
 
         self.lazy = True
@@ -74,7 +74,7 @@ def _scale(self, array: np.ndarray):
 
     def _write_image_level(self, tif: tf.TiffWriter, scale_index: int, **kwargs):
         xarr: xr.DataArray = next(iter(self.image[self.scale_names[scale_index]].values()))
-        resolution = 1e4 * 2**scale_index / self.pixelsize
+        resolution = 1e4 * 2**scale_index / self.pixel_size
 
         if not self._should_load_memory(xarr.shape, xarr.dtype):
             n_tiles = xarr.shape[0] * self._n_tiles_axis(xarr, 1) * self._n_tiles_axis(xarr, 2)
@@ -172,7 +172,7 @@ def write_image(
     lazy: bool = True,
     tile_width: int = 1024,
     n_subscales: int = 5,
-    pixelsize: float = 0.2125,
+    pixel_size: float = 0.2125,
     ram_threshold_gb: int | None = 4,
     is_dir: bool = True,
 ):
@@ -184,7 +184,7 @@ def write_image(
         lazy: If `False`, the image will not be read in-memory (except if the image size is below `ram_threshold_gb`). If `True`, all the images levels are always loaded in-memory.
         tile_width: Xenium tile width (do not update).
         n_subscales: Number of sub-scales in the pyramidal image.
-        pixelsize: Xenium pixel size (do not update).
+        pixel_size: Xenium pixel size (do not update).
         ram_threshold_gb: If an image (of any level of the pyramid) is below this threshold, it will be loaded in-memory.
         is_dir: If `False`, then `path` is a path to a single file, not to the Xenium Explorer directory.
     """
@@ -197,7 +197,7 @@ def write_image(
 
     image: MultiscaleSpatialImage = to_multiscale(image, [2] * n_subscales)
 
-    image_writer = MultiscaleImageWriter(image, pixelsize=pixelsize, tile_width=tile_width)
+    image_writer = MultiscaleImageWriter(image, pixel_size=pixel_size, tile_width=tile_width)
     image_writer.write(path, lazy=lazy, ram_threshold_gb=ram_threshold_gb)
 
 

spatialdata_xenium_explorer/core/points.py

@@ -23,7 +23,7 @@ def write_transcripts(
     gene: str = "gene",
     max_levels: int = 15,
     is_dir: bool = True,
-    pixelsize: float = 0.2125,
+    pixel_size: float = 0.2125,
 ):
     """Write a `transcripts.zarr.zip` file containing pyramidal transcript locations
 
@@ -33,19 +33,19 @@ def write_transcripts(
         gene: Column of `df` containing the genes names.
         max_levels: Maximum number of levels in the pyramid.
         is_dir: If `False`, then `path` is a path to a single file, not to the Xenium Explorer directory.
-        pixelsize: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.
+        pixel_size: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.
     """
     path = explorer_file_path(path, FileNames.POINTS, is_dir)
 
     # TODO: make everything using dask instead of pandas
     df = df.compute()
 
     num_transcripts = len(df)
-    grid_size = ExplorerConstants.GRID_SIZE / ExplorerConstants.PIXELS_TO_MICRONS * pixelsize
+    grid_size = ExplorerConstants.GRID_SIZE / ExplorerConstants.PIXELS_TO_MICRONS * pixel_size
     df[gene] = df[gene].astype("category")
 
     location = df[["x", "y"]]
-    location *= pixelsize
+    location *= pixel_size
     location = np.concatenate([location, np.zeros((num_transcripts, 1))], axis=1)
 
     if location.min() < 0:

spatialdata_xenium_explorer/core/shapes.py

@@ -49,7 +49,7 @@ def write_polygons(
     polygons: Iterable[Polygon],
     max_vertices: int,
     is_dir: bool = True,
-    pixelsize: float = 0.2125,
+    pixel_size: float = 0.2125,
 ) -> None:
     """Write a `cells.zarr.zip` file containing the cell polygonal boundaries
 
@@ -58,13 +58,13 @@ def write_polygons(
         polygons: A list of `shapely` polygons to be written
         max_vertices: The number of vertices per polygon (they will be transformed to have the right number of vertices)
         is_dir: If `False`, then `path` is a path to a single file, not to the Xenium Explorer directory.
-        pixelsize: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.
+        pixel_size: Number of microns in a pixel. Invalid value can lead to inconsistent scales in the Explorer.
     """
     path = explorer_file_path(path, FileNames.SHAPES, is_dir)
 
     log.info(f"Writing {len(polygons)} cell polygons")
     coordinates = np.stack([pad_polygon(p, max_vertices) for p in polygons])
-    coordinates *= pixelsize
+    coordinates *= pixel_size
 
     num_cells = len(coordinates)
     cells_fourth = ceil(num_cells / 4)