fitscube 2.2.0__tar.gz → 2.3.1__tar.gz

{fitscube-2.2.0 → fitscube-2.3.1}/.github/workflows/cd.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -43,7 +43,7 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           name: Packages
           path: dist

{fitscube-2.2.0 → fitscube-2.3.1}/.github/workflows/ci.yml

@@ -21,7 +21,7 @@ jobs:
     name: Format
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v5
@@ -42,7 +42,7 @@ jobs:
         runs-on: [ubuntu-latest]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
@@ -62,6 +62,6 @@ jobs:
           --durations=20
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v5.4.3
+        uses: codecov/codecov-action@v5.5.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

{fitscube-2.2.0 → fitscube-2.3.1}/.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
   #       additional_dependencies: [black==24.*]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v5.0.0"
+    rev: "v6.0.0"
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -33,7 +33,7 @@ repos:
       - id: rst-inline-touching-normal
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.12.7"
+    rev: "v0.12.11"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
@@ -56,7 +56,7 @@ repos:
           - tomli
 
   - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: "v0.10.0.1"
+    rev: "v0.11.0.1"
     hooks:
       - id: shellcheck
 
@@ -75,7 +75,7 @@ repos:
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: "0.33.2"
+    rev: "0.33.3"
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

{fitscube-2.2.0 → fitscube-2.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fitscube
-Version: 2.2.0
+Version: 2.3.1
 Summary: A package to produce produce FITS cubes.
 Project-URL: Homepage, https://github.com/AlecThomson/fitscube
 Project-URL: Bug Tracker, https://github.com/AlecThomson/fitscube/issues
@@ -58,6 +58,7 @@ Requires-Dist: sphinx-autodoc-typehints; extra == 'docs'
 Requires-Dist: sphinx-copybutton; extra == 'docs'
 Requires-Dist: sphinx>=7.0; extra == 'docs'
 Provides-Extra: test
+Requires-Dist: pytest-asyncio; extra == 'test'
 Requires-Dist: pytest-cov>=3; extra == 'test'
 Requires-Dist: pytest>=6; extra == 'test'
 Provides-Extra: uvloop

fitscube-2.3.1/fitscube/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '2.3.1'
+__version_tuple__ = version_tuple = (2, 3, 1)
+
+__commit_id__ = commit_id = None

fitscube-2.3.1/fitscube/bounding_box.py

@@ -0,0 +1,153 @@
+"""Some basic utilities to help with the creating of
+bounding boxes to use in fitscube"""
+
+from __future__ import annotations
+
+import asyncio
+from dataclasses import dataclass
+from pathlib import Path
+
+import numpy as np
+from astropy.io import fits
+
+from fitscube.logging import logger
+
+
+@dataclass(frozen=True)
+class BoundingBox:
+    """Simple container to represent a bounding box. Maximum values can be
+    used as is when slicing."""
+
+    xmin: int
+    """Minimum x pixel"""
+    xmax: int
+    """Maximum x pixel"""
+    ymin: int
+    """Minimum y pixel. Can be used as is in slice (e.g. is exclusive). """
+    ymax: int
+    """Maximum y pixel Can be used as is in slice (e.g. is exclusive)."""
+    original_shape: tuple[int, int]
+    """The original shape of the image. If constructed against a cube this is the shape of a single plane."""
+    y_span: int
+    """The span between ymax and ymin"""
+    x_span: int
+    """The span between xmax and xmin"""
+
+
+def create_bound_box_plane(image_data: np.ndarray) -> BoundingBox | None:
+    """Create a bounding box around pixels in a 2D image. If all
+    pixels are not valid, then ``None`` is returned.
+
+    Args:
+        image_data (np.ndarray): The 2D image to construct a bounding box around
+
+    Returns:
+        Optional[BoundingBox]: None if no valid pixels, a bounding box with the (xmin,xmax,ymin,ymax) of valid pixels
+    """
+    assert len(image_data.shape) == 2, (
+        f"Only two-dimensional arrays supported, received {image_data.shape}"
+    )
+
+    # First convert to a boolean array
+    image_valid = np.isfinite(image_data)
+
+    if not any(image_valid.reshape(-1)):
+        logger.info("No pixels to creating bounding box for")
+        return None
+
+    # Then make them 1D arrays
+    x_valid = np.any(image_valid, axis=1)
+    y_valid = np.any(image_valid, axis=0)
+
+    # Now get the first and last index
+    xmin, xmax = np.where(x_valid)[0][[0, -1]]
+    ymin, ymax = np.where(y_valid)[0][[0, -1]]
+
+    xmax += 1
+    ymax += 1
+
+    y_span = ymax - ymin
+    x_span = xmax - xmin
+
+    return BoundingBox(
+        xmin=xmin,
+        xmax=xmax,
+        ymin=ymin,
+        ymax=ymax,
+        y_span=y_span,
+        x_span=x_span,
+        original_shape=image_data.shape[-2:],
+    )
+
+
+def extract_common_bounding_box(
+    bounding_boxes: list[BoundingBox | None],
+) -> BoundingBox:
+    """Get the smallest bounding box that encompasses all bounding boxes
+
+    Args:
+        bounding_boxes (list[BoundingBox | None]): A list of bounding boxes. If None (returned for invalid images) skip it.
+
+    Raises:
+        ValueError: If all input bounding boxes are invalid
+        ValueError: If there is an `original_shape` mismatch
+
+    Returns:
+        BoundingBox: The smallest bounding box
+    """
+
+    # Step 1: filter out all Nones
+    valid_boxes: list[BoundingBox] = [bb for bb in bounding_boxes if bb is not None]
+
+    if len(valid_boxes) == 0:
+        msg = "No valid input boxes to consider"
+        raise ValueError(msg)
+
+    if not all(
+        valid_boxes[0].original_shape == bb.original_shape for bb in valid_boxes
+    ):
+        msg = "Different shapes, and not sure this is really supported or meaningful"
+        raise ValueError(msg)
+
+    xmin = int(np.min([bb.xmin for bb in valid_boxes]))
+    xmax = int(np.max([bb.xmax for bb in valid_boxes]))
+    ymin = int(np.min([bb.ymin for bb in valid_boxes]))
+    ymax = int(np.max([bb.ymax for bb in valid_boxes]))
+
+    y_span = ymax - ymin
+    x_span = xmax - xmin
+
+    return BoundingBox(
+        xmin=xmin,
+        xmax=xmax,
+        ymin=ymin,
+        ymax=ymax,
+        y_span=y_span,
+        x_span=x_span,
+        original_shape=valid_boxes[0].original_shape,
+    )
+
+
+async def get_bounding_box_for_fits_coro(
+    fits_path: Path, invalidate_zeros: bool = False
+) -> BoundingBox | None:
+    """Create a bounding box for an image contained in a FITS file.
+
+    The assumption is that the FITS file contains an image, not a cube.
+    If the cube can bot be reshapped to an image without losing data
+    the underlying bounding box creation will fail.
+
+    Args:
+        fits_path (Path): The fits image to call
+        invalidate_zeros (bool, optional): Mark pixels that are exactly 0.0 as invalid (NaN them). Defaults to False.
+
+    Returns:
+        BoundingBox | None: The bounding box that describes the bounds of valid data. If all data are invalid (and not bounding box possible) None is returned.
+    """
+    data = await asyncio.to_thread(fits.getdata, fits_path, memmap=False)
+    data = np.squeeze(data)
+
+    if invalidate_zeros:
+        data[data == 0.0] = np.nan
+
+    return await asyncio.to_thread(create_bound_box_plane, image_data=data)

{fitscube-2.2.0 → fitscube-2.3.1}/fitscube/combine_fits.py

@@ -16,10 +16,7 @@ import asyncio
 import warnings
 from io import BufferedRandom
 from pathlib import Path
-from typing import (
-    NamedTuple,
-    TypeVar,
-)
+from typing import Literal, NamedTuple, TypeVar
 
 import astropy.units as u
 import numpy as np
@@ -34,6 +31,11 @@ from radio_beam.beam import NoBeamException
 from tqdm.asyncio import tqdm
 
 from fitscube.asyncio import gather_with_limit, sync_wrapper
+from fitscube.bounding_box import (
+    BoundingBox,
+    extract_common_bounding_box,
+    get_bounding_box_for_fits_coro,
+)
 from fitscube.logging import TQDM_OUT, logger, set_verbosity
 
 T = TypeVar("T")
@@ -45,6 +47,8 @@ BIT_DICT = {
     16: 2,
     8: 1,
 }
+FLOAT_LENGTH = Literal[16, 32, 64]
+FLOAT_TYPE = {64: ">f8", 32: ">f4"}
 
 warnings.filterwarnings("ignore", category=UserWarning, module="astropy.io.fits")
 warnings.filterwarnings("ignore", category=VerifyWarning)
@@ -170,6 +174,7 @@ async def create_cube_from_scratch_coro(
     output_shape = output_wcs.array_shape
     msg = f"Creating a new FITS file with shape {output_shape}"
     logger.info(msg)
+
     # If the output shape is less than 1801, we can create a blank array
     # in memory and write it to disk
     if np.prod(output_shape) < 1801:
@@ -240,19 +245,27 @@ async def create_output_cube_coro(
     single_beam: bool = False,
     overwrite: bool = False,
     time_domain_mode: bool = False,
+    bounding_box: BoundingBox | None = None,
+    float_length: FLOAT_LENGTH | None = None,
 ) -> InitResult:
-    """Initialize the data cube.
+    """Generate the output header and write a dummy cube to disk based on properties of the
+    inpute data. The output cube written here has a correctly formed header and a pre-zerod
+    data cube written as output.
 
     Args:
-        old_name (str): Old FITS file name
-        n_chan (int): Number of channels
-
-    Raises:
-        KeyError: If 2D and REFFREQ is not in header
-        ValueError: If not 2D and FREQ is not in header
+        old_name (Path): The path to a representative image to draw the base fits header from
+        out_cube (Path): Path of the output cube to create
+        specs (u.Quantity): Specification of the unit that denotes the 'cube' axis
+        ignore_spec (bool, optional): Whether the provided `specs` axis should be ignored. If True dummy placeholder fields added. Defaults to False.
+        has_beams (bool, optional): Indicates whether a CASA Beam table will also be generated and added to the output cube. Defaults to False.
+        single_beam (bool, optional): Indicates whether a constant restoring beam has been used among all input images. If so only the beam fields are need. Defaults to False.
+        overwrite (bool, optional): If True the out the output cube will overwrite any existing file. Defaults to False.
+        time_domain_mode (bool, optional): Whether to join images via the DATE-OBS (e.g. time) axis. If False cube joined along frequency axis. Defaults to False.
+        bounding_box (BoundingBox | None, optional): Whether a trimming operation should be applied to input images. If a BoundingBox is supplied this will be used to update the reference pixel position and data shape indicators. Defaults to None.
+        float_length (Literal[16, 32, 64] | None, optional): The precision of the output data. If None drawn from input data. Otherwise values accepted are 16, 32 and 64. Defaults to None.
 
     Returns:
-        InitResult: header, spec_idx, spec_fits_idx, is_2d
+        InitResult: Details of the output cube, including the output header
     """
 
     # define units if in time or freq domain
@@ -358,6 +371,14 @@ async def create_output_cube_coro(
         )
         del new_header["BMAJ"], new_header["BMIN"], new_header["BPA"]
 
+    if bounding_box:
+        logger.info("Updating CRPIX1 and CRPIX2 header values to reflect bounding box")
+        new_header["CRPIX1"] -= bounding_box.ymin
+        new_header["CRPIX2"] -= bounding_box.xmin
+        logger.info("Updating NAXIS1 and NAXIS2 ro reflect bounding box")
+        new_header["NAXIS1"] = bounding_box.y_span
+        new_header["NAXIS2"] = bounding_box.x_span
+
     plane_shape = list(old_data.shape)
     cube_shape = plane_shape.copy()
     if is_2d:
@@ -365,6 +386,23 @@ async def create_output_cube_coro(
     else:
         cube_shape[idx] = n_chan
 
+    logger.critical(f"{float_length=} {new_header['BITPIX']=}")
+    if float_length is not None:
+        # Per astropy docs
+        # bITPIX    numpy data type
+        # 8         numpy.uint8 (note it is UNsigned integer)
+        # 16        numpy.int16
+        # 32        numpy.int32
+        # 64        numpy.int64
+        # -32       numpy.float32
+        # -64       numpy.float64
+        assert float_length in list(BIT_DICT.keys()), (
+            f"{float_length=} not in {BIT_DICT=}"
+        )
+        bit_pix = int(float_length)
+        logger.info(f"Specified {float_length=}, corresponding to {bit_pix=}")
+        new_header["BITPIX"] = -abs(bit_pix)
+
     output_header = await create_cube_from_scratch_coro(
         output_file=out_cube, output_header=new_header, overwrite=overwrite
     )
@@ -619,6 +657,8 @@ async def process_channel(
     old_channel: int,
     is_missing: bool,
     file_list: list[Path],
+    bounding_box: BoundingBox | None = None,
+    invalidate_zeros: bool = False,
 ) -> None:
     msg = f"Processing channel {new_channel}"
     logger.info(msg)
@@ -631,6 +671,20 @@ async def process_channel(
             fits.getdata, file_list[old_channel], memmap=False
         )
 
+    if bounding_box is not None:
+        plane = plane[
+            ...,
+            bounding_box.xmin : bounding_box.xmax,
+            bounding_box.ymin : bounding_box.ymax,
+        ]
+    if invalidate_zeros:
+        plane[plane == 0.0] = np.nan
+
+    if "BITPIX" in new_header:
+        bit_pix = abs(new_header["BITPIX"])
+        float_type = FLOAT_TYPE[bit_pix]
+        plane = plane.astype(float_type)
+
     await write_channel_to_cube_coro(
         file_handle=file_handle,
         plane=plane,
@@ -650,6 +704,9 @@ async def combine_fits_coro(
     overwrite: bool = False,
     max_workers: int | None = None,
     time_domain_mode: bool = False,
+    bounding_box: bool = False,
+    invalidate_zeros: bool = False,
+    float_length: FLOAT_LENGTH | None = None,
 ) -> u.Quantity:
     """Combine FITS files into a cube.
     Can handle either frequency or time dimensions agnostically
@@ -660,6 +717,9 @@ async def combine_fits_coro(
         ignore_spec (bool, optional): Ignore frequency/time information. Defaults to False.
         create_blanks (bool, optional): Attempt to create even frequency spacing. Defaults to False.
         time_domain_mode (bool, optional): Work in time domain mode - make a time-cube. Default = False.
+        bounding_box (bool, optional): Clip invalid/padded pixels when crafting the fits cube. When True an extra read of the input daata is needed, but output cube is smaller. Defaults to False.
+        invalidate_zeros (bool, optionals): Set pixels whose values are exactly zero to NaNs. Defaults to False.
+        float_length (Literal[16, 32, 64] | None, optional): The floating point precision in bits to use when creating the output cube. If None the size of the input data are used. Defaults to None.
 
     Returns:
         tuple[fits.HDUList, u.Quantity]: The combined FITS cube and frequencies
@@ -704,6 +764,21 @@ async def combine_fits_coro(
     specs = specs[new_sort_idx]
     missing_chan_idx = missing_chan_idx[new_sort_idx]
 
+    # Get the bounding box, if requested
+    final_bounding_box = None
+    if bounding_box:
+        boxes_futures = [
+            get_bounding_box_for_fits_coro(
+                fits_path=fits_path, invalidate_zeros=invalidate_zeros
+            )
+            for fits_path in file_list
+        ]
+        boxes = await gather_with_limit(
+            max_workers, *boxes_futures, desc="Bounding boxes"
+        )
+        final_bounding_box = extract_common_bounding_box(bounding_boxes=boxes)
+        logger.info(f"The final bounding box is: {final_bounding_box=}")
+
     # Initialize the data cube
     new_header, _, _, _ = await create_output_cube_coro(
         old_name=file_list[0],
@@ -714,6 +789,8 @@ async def combine_fits_coro(
         single_beam=single_beam,
         overwrite=overwrite,
         time_domain_mode=time_domain_mode,
+        bounding_box=final_bounding_box,
+        float_length=float_length,
     )
 
     new_channels = np.arange(len(specs))
@@ -741,6 +818,8 @@ async def combine_fits_coro(
                 old_channel=old_channel,
                 is_missing=is_missing,
                 file_list=file_list,
+                bounding_box=final_bounding_box,
+                invalidate_zeros=invalidate_zeros,
             )
             coros.append(coro)
 
@@ -823,6 +902,23 @@ def get_parser(
         default=None,
         help="Maximum number of workers to use for concurrent processing",
     )
+    parser.add_argument(
+        "--bounding-box",
+        action="store_true",
+        help="Attempt to consider padded images when creating the cube. Requires an extract read of the input data.",
+    )
+    parser.add_argument(
+        "--invalidate-zeros",
+        action="store_true",
+        help="Set pixels whose values are exactly zero to NaNs",
+    )
+    parser.add_argument(
+        "--floating",
+        type=int,
+        choices=(8, 16, 32, 64),
+        default=None,
+        help="The number of floating point bits to use in the out cube. If None the input data precision is used.",
+    )
 
     return parser
 
@@ -863,6 +959,9 @@ def cli(args: argparse.Namespace | None = None) -> None:
         overwrite=overwrite,
         max_workers=args.max_workers,
         time_domain_mode=time_domain_mode,
+        bounding_box=args.bounding_box,
+        invalidate_zeros=args.invalidate_zeros,
+        float_length=args.floating,
     )
 
     spequency = "times" if time_domain_mode else "frequencies"

{fitscube-2.2.0 → fitscube-2.3.1}/pyproject.toml

@@ -38,6 +38,7 @@ dependencies = [
 [project.optional-dependencies]
 test = [
   "pytest >=6",
+  "pytest-asyncio",
   "pytest-cov >=3",
 ]
 dev = [

{fitscube-2.2.0 → fitscube-2.3.1}/tests/conftest.py

@@ -4,6 +4,7 @@ from pathlib import Path
 from shutil import unpack_archive
 
 import pytest
+from astropy.io import fits
 
 EXAMPLE_HEADER = "SIMPLE  =                    T / conforms to FITS standard                      BITPIX  =                  -32 / array data type                                NAXIS   =                    4 / number of array dimensions                     NAXIS1  =                 6192                                                  NAXIS2  =                 6192                                                  NAXIS3  =                    1                                                  NAXIS4  =                   72                                                  EXTEND  =                    T                                                  BSCALE  =                  1.0                                                  BZERO   =                  0.0                                                  BUNIT   = 'JY/BEAM '                                                            BMAJ    =  0.00398184964207042                                                  BMIN    =  0.00332268385509243                                                  BPA     =     77.3858939868987                                                  EQUINOX =               2000.0                                                  LONPOLE =                180.0                                                  BTYPE   = 'Intensity'                                                           TELESCOP= 'ASKAP   '                                                            OBJECT  = 'EMU_1141-55'                                                         ORIGIN  = 'WSClean '                                                            CTYPE1  = 'RA---SIN'                                                            CRPIX1  =               3097.0                                                  CRVAL1  =     173.522555019647                                                  CDELT1  =            -0.000625                                                  CUNIT1  = 'deg     '                                                            CTYPE2  = 'DEC--SIN'                                                            CRPIX2  =               3097.0                                                  CRVAL2  =    -55.3190947400628                                                  CDELT2  =             0.000625                                                  CUNIT2  = 'deg     '                                                            CTYPE3  = 'STOKES  '                                                            CRPIX3  =                  1.0                                                  CRVAL3  =                  1.0                                                  CDELT3  =                  1.0                                                  CUNIT3  = ''                                                                    CTYPE4  = 'FREQ    '                                                            CRPIX4  =                    1                                                  CRVAL4  =     801490740.740741                                                  CDELT4  =            4000000.0                                                  CUNIT4  = 'Hz      '                                                            SPECSYS = 'TOPOCENT'                                                            DATE-OBS= '2023-01-08T15:36:40.9'                                               WSCDATAC= 'DATA    '                                                            WSCVDATE= '2022-10-21'                                                          WSCVERSI= '3.2     '                                                            WSCWEIGH= 'Briggs''(-0)'                                                        WSCENVIS=     1026544.24656423                                                  WSCFIELD=                  0.0                                                  WSCGAIN =                  0.1                                                  WSCGKRNL=                  7.0                                                  WSCIMGWG=     4052355.35920529                                                  WSCMAJOR=                  9.0                                                  WSCMGAIN=                  0.9                                                  WSCMINOR=              62860.0                                                  WSCNEGCM=                  1.0                                                  WSCNEGST=                  0.0                                                  WSCNITER=            5000000.0                                                  WSCNORMF=     4052355.35920529                                                  WSCNVIS =            7648518.0                                                  WSCNWLAY=                  1.0                                                  WSCTHRES=                  0.0                                                  WSCVWSUM=           30594072.0                                                  COMMENT   FITS (Flexible Image Transport System) format is defined in 'AstronomyCOMMENT   and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H HISTORY wsclean -abs-mem 200 -local-rms-window 20 -size 6192 6192 -local-rms -foHISTORY rce-mask-rounds 4 -auto-mask 8.0 -auto-threshold 3.0 -channels-out 72 -mHISTORY gain 0.9 -nmiter 10 -niter 5000000 -multiscale-scale-bias 0.8 -multiscalHISTORY e-scales 0,4,8,16,24,32,48,64,92,128,196,512,796,1025 -fit-spectral-pol HISTORY 4 -weight briggs -0 -data-column DATA -scale 2.25asec -gridder wgridder HISTORY -wgridder-accuracy 0.0001 -join-channels -minuv-l 50.0 -beam-fitting-sizHISTORY e 1.25 -deconvolution-channels 8 -parallel-gridding 18 -temp-dir /dev/shHISTORY m/gal16b.8974844 -pol i -save-source-list -name /dev/shm/gal16b.8974844/HISTORY SB47138.EMU_1141-55.beam19.i /scratch3/gal16b/emu_download/flint_jollytrHISTORY actor/47138/SB47138.EMU_1141-55.beam19.ms                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               END                                                                             "
 
@@ -65,3 +66,31 @@ def time_image_paths(tmpdir) -> list[Path]:
     image_paths.sort()
 
     return image_paths
+
+
+@pytest.fixture
+def time_image_paths_withzeroborder(tmpdir) -> list[Path]:
+    """Same as above but zero out border pixels in the data"""
+    tmp_dir = Path(tmpdir) / "time_images"
+    tmp_dir.mkdir(exist_ok=True, parents=True)
+    images_zip = Path(__file__).parent / "data" / "time_images.zip"
+
+    unpack_archive(images_zip, tmp_dir)
+    image_paths = list(tmp_dir.glob("*fits"))
+    image_paths.sort()
+
+    output_paths = []
+    for image in image_paths:
+        with fits.open(image, memmap=False, lazy_load_hdus=False) as a:
+            data = a[0].data
+            data[..., :5, :] = 0
+            data[..., -5:, :] = 0
+            data[..., :, :5] = 0
+            data[..., :, -5:] = 0
+
+            a[0].data = data
+            image_output = image.with_suffix(".zero.fits")
+            fits.writeto(image_output, data=data, header=a[0].header)
+            output_paths.append(image_output)
+
+    return output_paths

fitscube-2.3.1/tests/test_bb.py

@@ -0,0 +1,97 @@
+# Tests to ensure the bounding box functionality is working
+from __future__ import annotations
+
+import numpy as np
+import pytest
+from fitscube.bounding_box import (
+    BoundingBox,
+    create_bound_box_plane,
+    extract_common_bounding_box,
+)
+
+
+def test_bound_box_plane() -> None:
+    """See if we can make the bounding box correctly"""
+
+    image = np.zeros((100, 100))
+
+    bb = create_bound_box_plane(image_data=image)
+    assert isinstance(bb, BoundingBox)
+    assert bb.xmin == 0
+    assert bb.ymin == 0
+    assert bb.xmax == 100
+    assert bb.ymax == 100
+    assert bb.x_span == 100
+    assert bb.y_span == 100
+
+    image[:, :4] = np.nan
+    image[96:, :] = np.nan
+
+    bb = create_bound_box_plane(image_data=image)
+    assert isinstance(bb, BoundingBox)
+    assert bb.xmin == 0
+    assert bb.ymin == 4
+    assert bb.xmax == 96
+    assert bb.ymax == 100
+    assert bb.x_span == 96
+    assert bb.y_span == 96
+
+
+def test_extract_common_bounding_box() -> None:
+    """Construct a set of bounding boxes to ensure a largest fits all
+    one can be created"""
+
+    bbs = []
+    for i in range(2, 8, 1):
+        image = np.zeros((100, 100))
+
+        print(i)
+
+        image[:i, :] = np.nan
+        image[:, -i:] = np.nan
+        assert np.sum(np.isnan(image)) > 1
+        bbs.append(create_bound_box_plane(image_data=image))
+
+    assert len(bbs) == 6
+
+    bb = extract_common_bounding_box(bounding_boxes=bbs)
+    assert bb.xmin == 2
+    assert bb.ymin == 0
+    assert bb.xmax == 100
+    assert bb.ymax == 98
+
+
+def test_extract_common_bounding_box_error() -> None:
+    """See if the correct errors are raised"""
+
+    with pytest.raises(ValueError, match="No valid"):
+        extract_common_bounding_box(bounding_boxes=[None, None, None])
+
+    bbs = []
+    for i in range(2, 8, 1):
+        image = np.zeros((100 + i, 100))
+        bbs.append(create_bound_box_plane(image_data=image))
+
+    with pytest.raises(ValueError, match="Different shapes"):
+        extract_common_bounding_box(bounding_boxes=bbs)
+
+
+# @pytest.mark.asyncio
+# async def test_get_bounding_box_from_fits(time_image_paths) -> None:
+#     """!!! NOTE: Sometimes this test can raise the following error:
+
+#     > Exception ignored in: <socket.socket fd=-1, family=1, type=1, proto=0>
+
+#     Not sure why it is capable of such a thing.
+#     """
+#     futures = [
+#         await get_bounding_box_for_fits_coro(fits_path=fits_path)
+#         for fits_path in time_image_paths
+#     ]
+#     assert all(isinstance(bb, BoundingBox) for bb in futures)
+
+#     common_bb = extract_common_bounding_box(bounding_boxes=futures)
+#     assert common_bb.xmin == 0
+#     assert common_bb.ymin == 0
+#     assert common_bb.xmax == 100
+#     assert common_bb.ymax == 100

{fitscube-2.2.0 → fitscube-2.3.1}/tests/test_times.py

@@ -92,6 +92,14 @@ def test_even_combine(file_list: list[Path], even_specs: u.Quantity, output_file
 def test_uneven_combine(
     file_list: list[Path], even_specs: u.Quantity, output_file: Path
 ):
+    """!!!! NOTE: For some unknown reason thios test *SOMETIMES* raises the
+    following error:
+
+    > FAILED tests/test_times.py::test_uneven - ValueError: operands could not be broadcast together with shapes (5,) (6,)
+
+    Completely unclear to me why
+    """
+
     # uneven_specs = np.concatenate([even_specs[0:1], even_specs[3:]])
     file_array = np.array(file_list)
     uneven_files = np.concatenate([file_array[0:1], file_array[3:]]).tolist()
@@ -149,3 +157,113 @@ def test_wsclean_images_create_axis(time_image_paths, tmpdir) -> None:
         # The TIME axis will be appended as a new dimension
         cube_image_data = cube_data[i]
         assert np.allclose(image_data.squeeze(), cube_image_data.squeeze())
+
+
+@pytest.mark.filterwarnings("ignore:'datfix' made the change")
+def test_wsclean_images_create_axis_floating(time_image_paths, tmpdir) -> None:
+    """Ensure that the combined cube conforms to the input data"""
+
+    tmpdir = Path(tmpdir) / "time_cube_combine"
+    tmpdir.mkdir(parents=True, exist_ok=True)
+    out_cube = tmpdir / "time_cube_mate.fits"
+
+    for float_length, float_rep in ((32, ">f4"), (64, ">f8")):
+        combine_fits(
+            file_list=time_image_paths,
+            out_cube=out_cube,
+            overwrite=True,
+            time_domain_mode=True,
+            float_length=float_length,  # type: ignore [arg-type]
+        )
+
+        cube_data = fits.getdata(out_cube)
+        assert cube_data.dtype == float_rep
+        for i, time_image_path in enumerate(time_image_paths):
+            image_data = fits.getdata(time_image_path)
+            # The TIME axis will be appended as a new dimension
+            cube_image_data = cube_data[i]
+            assert np.allclose(image_data.squeeze(), cube_image_data.squeeze())
+
+
+@pytest.mark.filterwarnings("ignore:'datfix' made the change")
+def test_wsclean_images_create_axis_withbb(time_image_paths, tmpdir) -> None:
+    """Ensure that the combined cube conforms to the input data. This will use the
+    bounding box option. This should led to no change."""
+
+    tmpdir = Path(tmpdir) / "time_cube_combine"
+    tmpdir.mkdir(parents=True, exist_ok=True)
+    out_cube = tmpdir / "time_cube_mate.fits"
+
+    combine_fits(
+        file_list=time_image_paths,
+        out_cube=out_cube,
+        overwrite=True,
+        time_domain_mode=True,
+        bounding_box=True,
+    )
+
+    cube_data = fits.getdata(out_cube)
+    for i, time_image_path in enumerate(time_image_paths):
+        image_data = fits.getdata(time_image_path)
+        # The TIME axis will be appended as a new dimension
+        cube_image_data = cube_data[i]
+        assert np.allclose(image_data.squeeze(), cube_image_data.squeeze())
+
+
+@pytest.mark.filterwarnings("ignore:'datfix' made the change")
+def test_wsclean_images_create_axis_withbb_noinvalidate0(
+    time_image_paths_withzeroborder, tmpdir
+) -> None:
+    """Ensure that the combined cube conforms to the input data. This will use the
+    bounding box option. This should led to no change."""
+
+    tmpdir = Path(tmpdir) / "time_cube_combine_zeros"
+    tmpdir.mkdir(parents=True, exist_ok=True)
+    out_cube = tmpdir / "time_cube_mate.fits"
+
+    combine_fits(
+        file_list=time_image_paths_withzeroborder,
+        out_cube=out_cube,
+        overwrite=True,
+        time_domain_mode=True,
+        bounding_box=True,
+        invalidate_zeros=False,
+    )
+
+    cube_data = fits.getdata(out_cube)
+    assert cube_data.squeeze().shape[-2:] == (100, 100)
+    for i, time_image_path in enumerate(time_image_paths_withzeroborder):
+        image_data = fits.getdata(time_image_path)
+        # The TIME axis will be appended as a new dimension
+        cube_image_data = cube_data[i]
+        assert np.allclose(image_data.squeeze(), cube_image_data.squeeze())
+
+
+@pytest.mark.filterwarnings("ignore:'datfix' made the change")
+def test_wsclean_images_create_axis_withbb_invalidatezeros(
+    time_image_paths_withzeroborder, tmpdir
+) -> None:
+    """Ensure that the combined cube conforms to the input data. This will use the
+    bounding box option. This should led to no change. Here we also get fitscube to
+    mark pixels that are exactly 0 to be nans"""
+
+    tmpdir = Path(tmpdir) / "time_cube_combine_zeros"
+    tmpdir.mkdir(parents=True, exist_ok=True)
+    out_cube = tmpdir / "time_cube_mate.fits"
+
+    combine_fits(
+        file_list=time_image_paths_withzeroborder,
+        out_cube=out_cube,
+        overwrite=True,
+        time_domain_mode=True,
+        bounding_box=True,
+        invalidate_zeros=True,
+    )
+
+    cube_data = fits.getdata(out_cube)
+    assert cube_data.squeeze().shape[-2:] == (90, 90)
+    for i, time_image_path in enumerate(time_image_paths_withzeroborder):
+        image_data = fits.getdata(time_image_path)
+        # The TIME axis will be appended as a new dimension
+        cube_image_data = cube_data[i]
+        assert np.allclose(image_data.squeeze()[5:-5, 5:-5], cube_image_data.squeeze())

fitscube-2.2.0/fitscube/_version.py

@@ -1,21 +0,0 @@
-# file generated by setuptools-scm
-# don't change, don't track in version control
-
-__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
-
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple
-    from typing import Union
-
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-else:
-    VERSION_TUPLE = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-
-__version__ = version = '2.2.0'
-__version_tuple__ = version_tuple = (2, 2, 0)