aprict 0.0.24__tar.gz → 0.0.24.dev1__tar.gz

{aprict-0.0.24/src/aprict.egg-info → aprict-0.0.24.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aprict
-Version: 0.0.24
+Version: 0.0.24.dev1
 Summary: Tools to simulate and reconstruct XCT transmission data.
 Author: Murdock Grewar
 Author-email: Murdock Grewar <murdock.grewar@anu.edu.au>
@@ -36,6 +36,10 @@ Requires-Dist: neuroglancer>=2.41.0; extra == "gui"
 Dynamic: author
 Dynamic: license-file
 
+[![Static Badge](https://img.shields.io/badge/ORCiD-0000--0002--0015--8284-green?logo=orcid)](https://orcid.org/0000-0002-0015-8284)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23632625.svg)](https://doi.org/10.5281/zenodo.23632625)
+![PyPI Version](https://img.shields.io/pypi/v/aprict)
+[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 <details open><summary><h1>About</h1></summary>
 
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{aprict-0.0.24 → aprict-0.0.24.dev1}/README.md

@@ -1,3 +1,7 @@
+[![Static Badge](https://img.shields.io/badge/ORCiD-0000--0002--0015--8284-green?logo=orcid)](https://orcid.org/0000-0002-0015-8284)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23632625.svg)](https://doi.org/10.5281/zenodo.23632625)
+![PyPI Version](https://img.shields.io/pypi/v/aprict)
+[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 <details open><summary><h1>About</h1></summary>
 
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{aprict-0.0.24 → aprict-0.0.24.dev1}/src/aprict/lib/ne_tools.py

@@ -162,12 +162,15 @@ def downbin(  # ruff: ignore[complex-structure]
     return xnew
 
 
-def save(path: pathlib.Path, arr: np.ndarray) -> None:
+def save(path: pathlib.Path, arr: np.ndarray, flush: bool = True) -> None:
     """Save an array to a path in a faster manner than np.save."""
     mm: np.memmap = np.lib.format.open_memmap(
         path, shape=arr.shape, dtype=arr.dtype, mode="w+"
     )
     ne.evaluate("x", out=mm, local_dict={"x": arr})
+    if flush:
+        # Write changes to disk now.
+        mm.flush()
 
 
 class NETHREADS(enum.Enum):

{aprict-0.0.24 → aprict-0.0.24.dev1}/src/aprict/scripts/recon_cbfp_cyl_fbp.py

@@ -872,7 +872,7 @@ def main_from_args(args: types.SimpleNamespace) -> None:  # ruff: ignore[complex
             if logger is not None:
                 msg = f"Saving full volume to '{savepath}'..."
                 logger.debug(msg)
-            lib.ne_tools.save(savepath, x)
+            lib.ne_tools.save(savepath, x, flush=True)
             if logger is not None:
                 msg = "Full volume now saved to disk."
                 logger.debug(msg)
@@ -1139,7 +1139,9 @@ def main_from_args(args: types.SimpleNamespace) -> None:  # ruff: ignore[complex
                 logger.debug(msg)
                 if vol is not None:
                     # Not efficient. Can't copy from CUDAArray directly to the chunk because it's not C-contiguous.
-                    vol.as_numpy(out=vol_np[..., sl_vol], allow_indirect_copy=True)
+                    vol.as_numpy(
+                        out=vol_np[..., sl_vol], allow_indirect_copy=True
+                    )
                     del vol
                     lib.gpu_tools.clear_cache()
             else:

{aprict-0.0.24 → aprict-0.0.24.dev1}/src/aprict/scripts/recon_cbfp_cyl_gbc.py

@@ -946,7 +946,11 @@ def main_from_args(args: types.SimpleNamespace) -> None:  # ruff: ignore[complex
 
     # Convert the progress display ta more intuitive set of units using the progratio.
     # The displayed progress will correspond to bytes in the padded backprojection.
-    progratio: float = (math.prod(padded_volshape) * np.dtype(vol_dtype).itemsize / bytes_cumsum[-1])
+    progratio: float = (
+        math.prod(padded_volshape)
+        * np.dtype(vol_dtype).itemsize
+        / bytes_cumsum[-1]
+    )
     curr_slice: slice | None = None
     logger.info("Beginning reconstruction...")
     with logtools.ProgressBar(
@@ -1066,7 +1070,8 @@ def main_from_args(args: types.SimpleNamespace) -> None:  # ruff: ignore[complex
                         prog_evs_bytes.append(
                             (
                                 ev,
-                                progratio * (
+                                progratio
+                                * (
                                     (
                                         (sl.stop - sl.start)
                                         / tot_num_nonskipped_projs
@@ -1292,7 +1297,7 @@ def main_from_args(args: types.SimpleNamespace) -> None:  # ruff: ignore[complex
             x = vol_filtered
             # Save the volume as a .npy file
             tomo_path = path_output.joinpath("recon.npy")
-            lib.ne_tools.save(tomo_path, x)
+            lib.ne_tools.save(tomo_path, x, flush=True)
             msg = "Full volume now saved to disk."
             logger.debug(msg)
             # Now get rid of the temporary files, if applicable

{aprict-0.0.24 → aprict-0.0.24.dev1}/src/aprict/scripts/recon_cbfp_landweber.py

@@ -521,7 +521,7 @@ def main() -> None:
             save_path.joinpath("tomograms") if is_intermediate else save_path
         )
         tomo_path.mkdir(exist_ok=True)
-        lib.ne_tools.save(tomo_path.joinpath(id_str + ".npy"), x)
+        lib.ne_tools.save(tomo_path.joinpath(id_str + ".npy"), x, flush=True)
 
         # Save midslices from volume as .png files
         # The method used here can be a bit slow, because I get a full numpy array and process that.

{aprict-0.0.24 → aprict-0.0.24.dev1}/src/aprict/version.py

@@ -16,4 +16,4 @@
 # This file is read from by 'setup.py', from '__init__.py', and also by a git hook which increments the dev number each time a commit is made on the 'dev' branch. There should only be one line in the file which begins with "version".
 """File which stores the current version number of this module."""
 
-version = "0.0.24"
+version = "0.0.24.dev1"

{aprict-0.0.24 → aprict-0.0.24.dev1}/src/aprict/volume.py

@@ -193,7 +193,9 @@ class Volume[
             self._texture, vol._texture, tout=self._texture, eps=eps
         )
 
-    def as_numpy(self, out: np.ndarray | None = None, allow_indirect_copy: bool = False) -> np.ndarray:
+    def as_numpy(
+        self, out: np.ndarray | None = None, allow_indirect_copy: bool = False
+    ) -> np.ndarray:
         """Copy this volume's data into a numpy array."""
         # Note: the option 'allow_indirect_copy' allows a fast-but-not-fastest copy when the output array is not C-contiguous.
         if out is not None and not out.flags["C_CONTIGUOUS"]:
@@ -220,7 +222,7 @@ class Volume[
     def save(self, path: pathlib.Path) -> None:
         """Save this volume into a numpy array on disk."""
         x = self.as_numpy()
-        ne_tools.save(path, x)
+        ne_tools.save(path, x, flush=True)
 
     def as_cupy(self, out: cp.ndarray | None = None) -> cp.ndarray:
         """Copy this volume's data into a cupy array."""

{aprict-0.0.24 → aprict-0.0.24.dev1/src/aprict.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aprict
-Version: 0.0.24
+Version: 0.0.24.dev1
 Summary: Tools to simulate and reconstruct XCT transmission data.
 Author: Murdock Grewar
 Author-email: Murdock Grewar <murdock.grewar@anu.edu.au>
@@ -36,6 +36,10 @@ Requires-Dist: neuroglancer>=2.41.0; extra == "gui"
 Dynamic: author
 Dynamic: license-file
 
+[![Static Badge](https://img.shields.io/badge/ORCiD-0000--0002--0015--8284-green?logo=orcid)](https://orcid.org/0000-0002-0015-8284)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.23632625.svg)](https://doi.org/10.5281/zenodo.23632625)
+![PyPI Version](https://img.shields.io/pypi/v/aprict)
+[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 <details open><summary><h1>About</h1></summary>
 
 Description