oct-to-tiff 0.6.0__py3-none-any.whl → 0.6.1__py3-none-any.whl

oct_to_tiff/cli.py

@@ -52,12 +52,47 @@ def reshape_volume(
     return volume
 
 
+def volume_metadata(
+    pixel_size_x: float | None,
+    pixel_size_y: float | None,
+    pixel_size_z: float | None,
+) -> dict[str, Any]:
+    """Build a dictionary of metadata.
+
+    Parameters
+    ----------
+    pixel_size_x : float | None
+        The pixel (voxel) width in mm.
+    pixel_size_y : float | None
+        The pixel (voxel) height in mm.
+    pixel_size_z : float | None
+        The pixel (voxel) depth in mm.
+
+    Returns
+    -------
+    metadata : dict[str, Any]
+        A dictionary of metadata.
+
+    """
+    metadata: dict[str, Any] = {"axes": "ZYX"}
+    if pixel_size_x is not None:
+        metadata["PhysicalSizeX"] = pixel_size_x
+        metadata["PhysicalSizeXUnit"] = "mm"
+    if pixel_size_y is not None:
+        metadata["PhysicalSizeY"] = pixel_size_y
+        metadata["PhysicalSizeYUnit"] = "mm"
+    if pixel_size_z is not None:
+        metadata["PhysicalSizeZ"] = pixel_size_z
+        metadata["PhysicalSizeZUnit"] = "mm"
+    return metadata
+
+
 def write_volume(
     output_path: Path,
     volume: npt.NDArray[Any],
-    pixel_size_x: float,
-    pixel_size_y: float,
-    pixel_size_z: float,
+    pixel_size_x: float | None,
+    pixel_size_y: float | None,
+    pixel_size_z: float | None,
 ) -> None:
     """Write a 3-dimensional array to the output path as an OME-TIFF file, including voxel size in the metadata.
 
@@ -79,15 +114,7 @@ def write_volume(
         output_path,
         volume,
         photometric="minisblack",
-        metadata={
-            "axes": "ZYX",
-            "PhysicalSizeX": pixel_size_x,
-            "PhysicalSizeXUnit": "mm",
-            "PhysicalSizeY": pixel_size_y,
-            "PhysicalSizeYUnit": "mm",
-            "PhysicalSizeZ": pixel_size_z,
-            "PhysicalSizeZUnit": "mm",
-        },
+        metadata=volume_metadata(pixel_size_x, pixel_size_y, pixel_size_z),
     )
 
 
@@ -245,7 +272,7 @@ def main() -> None:
             xy_scan_length = int(len(volume) ** 0.5)
             pixel_size_x = args.size / oct_window_height
             pixel_size_y = args.size / xy_scan_length
-            pixel_size_z = 1
+            pixel_size_z = None
         elif args.seg_curve:
             volume = np.frombuffer(f.read(), dtype=np.single)
             if len(volume) == 1280000 or len(volume) == 1120000:
@@ -256,9 +283,9 @@ def main() -> None:
                 oct_window_height = 304
             total_data_groups = 1
             xy_scan_length = len(volume) // (frames_per_data_group * oct_window_height)
-            pixel_size_x = 1
-            pixel_size_y = 1
-            pixel_size_z = 1
+            pixel_size_x = None
+            pixel_size_y = None
+            pixel_size_z = None
         elif "3D Cornea" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 106
@@ -338,7 +365,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.002941
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Cornea Cross Line" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 2
@@ -347,7 +374,7 @@ def main() -> None:
             xy_scan_length = 941
             pixel_size_x = 0.008502
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Cornea Line" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 1
@@ -356,7 +383,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.007843
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Cross Line" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 2
@@ -365,7 +392,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.009804
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Enhanced HD Line" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 1
@@ -374,7 +401,7 @@ def main() -> None:
             xy_scan_length = 998
             pixel_size_x = 0.012024
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "GCC" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 16
@@ -383,7 +410,7 @@ def main() -> None:
             xy_scan_length = 933
             pixel_size_x = 0.007503
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Grid" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 10
@@ -392,7 +419,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.005882
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "HD Angio Disc" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 400
@@ -446,7 +473,7 @@ def main() -> None:
             xy_scan_length = 1024
             pixel_size_x = 0.009766
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Line" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 1
@@ -455,7 +482,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.008824
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "ONH" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single, count=2223360)
             frames_per_data_group = 3
@@ -464,7 +491,7 @@ def main() -> None:
             xy_scan_length = 965
             pixel_size_x = 0.015952
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "PachymetryWide" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 16
@@ -473,7 +500,7 @@ def main() -> None:
             xy_scan_length = 1536
             pixel_size_x = 0.005859
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Raster" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 21
@@ -482,7 +509,7 @@ def main() -> None:
             xy_scan_length = 1020
             pixel_size_x = 0.011765
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
         elif "Retina Map" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single, count=6680960)
             frames_per_data_group = 13
@@ -491,7 +518,7 @@ def main() -> None:
             xy_scan_length = 803
             pixel_size_x = 0.007472
             pixel_size_y = 0.003071
-            pixel_size_z = 1
+            pixel_size_z = None
 
         volume = reshape_volume(
             volume,

{oct_to_tiff-0.6.0.dist-info → oct_to_tiff-0.6.1.dist-info}/METADATA

@@ -1,14 +1,12 @@
 Metadata-Version: 2.4
 Name: oct-to-tiff
-Version: 0.6.0
+Version: 0.6.1
 Summary: A command line tool for converting optical coherence tomography angiography (OCTA) data.
+Keywords: angiography,cli,oct,octa
+Author: Cameron Lloyd
 Author-email: Cameron Lloyd <lloyd@med.unideb.hu>
-Maintainer-email: Cameron Lloyd <lloyd@med.unideb.hu>
 License-Expression: BSD-3-Clause
-Project-URL: Homepage, https://github.com/camlloyd/oct-to-tiff
-Project-URL: Bug Tracker, https://github.com/camlloyd/oct-to-tiff/issues
-Project-URL: Changelog, https://github.com/camlloyd/oct-to-tiff/blob/main/CHANGELOG.md
-Keywords: angiography,cli,oct,octa
+License-File: LICENSE.txt
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
 Classifier: Natural Language :: English
@@ -18,18 +16,21 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
-Requires-Python: >=3.11
-Description-Content-Type: text/markdown
-License-File: LICENSE.txt
 Requires-Dist: defusedxml
 Requires-Dist: numpy
 Requires-Dist: roifile
 Requires-Dist: tifffile
+Requires-Dist: mypy ; extra == 'dev'
+Requires-Dist: ruff ; extra == 'dev'
+Requires-Dist: types-defusedxml ; extra == 'dev'
+Maintainer: Cameron Lloyd
+Maintainer-email: Cameron Lloyd <lloyd@med.unideb.hu>
+Requires-Python: >=3.11
+Project-URL: Homepage, https://github.com/camlloyd/oct-to-tiff
+Project-URL: Bug Tracker, https://github.com/camlloyd/oct-to-tiff/issues
+Project-URL: Changelog, https://github.com/camlloyd/oct-to-tiff/blob/main/CHANGELOG.md
 Provides-Extra: dev
-Requires-Dist: mypy; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: types-defusedxml; extra == "dev"
-Dynamic: license-file
+Description-Content-Type: text/markdown
 
 # oct-to-tiff
 
@@ -46,9 +47,9 @@ via pip:
 
     pip install oct-to-tiff
 
-via mamba:
+via conda:
 
-    mamba install -c conda-forge oct-to-tiff
+    conda install conda-forge::oct-to-tiff
 
 ## Getting started
     oct-to-tiff /path/to/image.OCT
@@ -186,4 +187,4 @@ This project uses [Ruff](https://github.com/astral-sh/ruff) for linting and form
 
 ## Requirements
 
-Requires Python 3.11 or higher.
+Requires Python 3.11 or higher.

oct_to_tiff-0.6.1.dist-info/RECORD

@@ -0,0 +1,7 @@
+oct_to_tiff/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+oct_to_tiff/cli.py,sha256=zocMW8eg3CG1Xx_gLHac8Qxb1jY4TFlSaVMJFhFK1gU,18047
+oct_to_tiff-0.6.1.dist-info/licenses/LICENSE.txt,sha256=8KO0dluzLStmIF0HM18BOP9T2miIcX8q-GOfMOw6Ngk,1521
+oct_to_tiff-0.6.1.dist-info/WHEEL,sha256=5DEXXimM34_d4Gx1AuF9ysMr1_maoEtGKjaILM3s4w4,80
+oct_to_tiff-0.6.1.dist-info/entry_points.txt,sha256=7kgVLpDuqbX5H38msz7NjYjUXQzmk4PW0TXc_FRz2uA,54
+oct_to_tiff-0.6.1.dist-info/METADATA,sha256=9OtspNGKdjnlwP5Pe2CpYRbzqyS91y5gbT0CgcaeymU,4939
+oct_to_tiff-0.6.1.dist-info/RECORD,,

{oct_to_tiff-0.6.0.dist-info → oct_to_tiff-0.6.1.dist-info}/WHEEL

@@ -1,5 +1,4 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: uv 0.9.29
 Root-Is-Purelib: true
 Tag: py3-none-any
-

{oct_to_tiff-0.6.0.dist-info → oct_to_tiff-0.6.1.dist-info}/entry_points.txt

@@ -1,2 +1,3 @@
 [console_scripts]
 oct-to-tiff = oct_to_tiff.cli:main
+

oct_to_tiff-0.6.0.dist-info/RECORD

@@ -1,8 +0,0 @@
-oct_to_tiff/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-oct_to_tiff/cli.py,sha256=GmIMXLuNfAEZaijX2_93XB95V0Mdr1yb73Q_j8eBiEI,17232
-oct_to_tiff-0.6.0.dist-info/licenses/LICENSE.txt,sha256=8KO0dluzLStmIF0HM18BOP9T2miIcX8q-GOfMOw6Ngk,1521
-oct_to_tiff-0.6.0.dist-info/METADATA,sha256=7atS8U7OhVhVpU48NjbGzqMtbGhlA_l4Dh6jZUiu010,4913
-oct_to_tiff-0.6.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-oct_to_tiff-0.6.0.dist-info/entry_points.txt,sha256=mKWNdkTThZm2JKtLwp4PGMpXkvAWk-xnQDAOyRsCo9Y,53
-oct_to_tiff-0.6.0.dist-info/top_level.txt,sha256=_ovqm7f48yb_IAiVqWzB3VPnHXwzkkEqQQ_ZJz_McSY,12
-oct_to_tiff-0.6.0.dist-info/RECORD,,

oct_to_tiff-0.6.0.dist-info/top_level.txt

@@ -1 +0,0 @@
-oct_to_tiff