oct-to-tiff 0.5.0__py3-none-any.whl → 0.6.1__py3-none-any.whl

oct_to_tiff/cli.py

@@ -6,24 +6,25 @@ from typing import Any
 
 import defusedxml.ElementTree as DET
 import numpy as np
+import numpy.typing as npt
 import tifffile
-from numpy.typing import NDArray
+from roifile import ROI_TYPE, ImagejRoi, roiwrite
 
 logger = logging.getLogger(__name__)
 
 
 def reshape_volume(
-    volume: NDArray[Any],
+    volume: npt.NDArray[Any],
     frames_per_data_group: int,
     total_data_groups: int,
     oct_window_height: int,
     xy_scan_length: int,
-) -> NDArray[Any]:
+) -> npt.NDArray[Any]:
     """Reshape a 1-dimensional array to a 3-dimensional array.
 
     Parameters
     ----------
-    volume : NDArray[Any]
+    volume : npt.NDArray[Any]
         A 1-dimensional array.
     frames_per_data_group : int
         The number of frames per data group.
@@ -36,7 +37,7 @@ def reshape_volume(
 
     Returns
     -------
-    volume : NDArray[Any]
+    volume : npt.NDArray[Any]
         A 3-dimensional array.
 
     """
@@ -51,32 +52,47 @@ def reshape_volume(
     return volume
 
 
-def rotate_volume(
-    volume: NDArray[Any],
-) -> NDArray[Any]:
-    """Rotate a 3-dimensional array 90 degrees left (anti-clockwise) about the z-axis.
+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
     ----------
-    volume : NDArray[Any]
-        A 3-dimensional array.
+    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
     -------
-    volume : NDArray[Any]
-        A rotated version of the input volume.
+    metadata : dict[str, Any]
+        A dictionary of metadata.
 
     """
-    volume = np.rot90(volume, k=1, axes=(1, 2))
-    return volume
+    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: NDArray[Any],
-    pixel_size_x: float,
-    pixel_size_y: float,
-    pixel_size_z: float,
+    volume: npt.NDArray[Any],
+    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.
 
@@ -84,7 +100,7 @@ def write_volume(
     ----------
     output_path : Path
         The specified output path.
-    volume : NDArray[Any]
+    volume : npt.NDArray[Any]
         A 3-dimensional array.
     pixel_size_x : float
         The pixel (voxel) width in mm.
@@ -98,19 +114,11 @@ 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),
     )
 
 
-def extract_boundaries(input_path: str | Path) -> None:
+def boundaries_to_arrays(input_path: str | Path) -> list[npt.NDArray[np.int_]]:
     """Extract segmentation lines.
 
     Parameters
@@ -118,6 +126,10 @@ def extract_boundaries(input_path: str | Path) -> None:
     input_path : str | Path
         The specified input path.
 
+    Returns
+    -------
+    arrays : list[npt.NDArray[np.int_]]
+        A list of 2-dimensional arrays.
     """
     input_path = Path(input_path)
     tree = DET.parse(input_path)
@@ -128,14 +140,36 @@ def extract_boundaries(input_path: str | Path) -> None:
         int(point.text) if point.text else 0
         for point in root.findall("./Curve_Set/Image/Curve/D")
     ]
-    scan_length = np.arange(len(data_points))
-    num_files = len(data_points) // array_size
-    for i in range(num_files):
+    num_arrays = len(data_points) // array_size
+
+    arrays = []
+    for i in range(num_arrays):
         start = i * array_size
         end = start + array_size
-        table = np.column_stack([scan_length[start:end], data_points[start:end]])
-        table_path = f"{input_path.parent}/{input_path.stem}_{i+1}.txt"
-        np.savetxt(table_path, table, delimiter="\t", fmt="%d")
+        array = np.column_stack([np.arange(array_size), data_points[start:end]])
+        arrays.append(array)
+
+    return arrays
+
+
+def arrays_to_rois(arrays: list[npt.NDArray[np.int_]], output_path: Path) -> None:
+    """
+    Convert a list of 2-dimensional arrays to ImageJ ROIs (ZIP file).
+
+    Parameters
+    ----------
+    arrays : list[npt.NDArray[np.int_]]
+        A list of 2-dimensional arrays.
+    output_path : Path
+        The specified output path.
+    """
+    rois = []
+    for array in arrays:
+        roi = ImagejRoi.frompoints(array)
+        roi.roitype = ROI_TYPE(4)  # FREELINE
+        rois.append(roi)
+
+    roiwrite(output_path, rois, mode="w")
 
 
 def main() -> None:
@@ -202,18 +236,22 @@ def main() -> None:
     else:
         dir_name = input_path.parent
     file_name = input_path.stem
-    file_extension = ".ome.tif"
+    if args.boundaries:
+        file_extension = "_rois.zip"
+    else:
+        file_extension = ".ome.tif"
     output_path = dir_name / (file_name + file_extension)
 
     if Path.is_file(output_path):
         if args.overwrite:
-            pass
+            logger.warning(f"Overwriting {output_path}")
         else:
             logger.error(f"{output_path} already exists.")
             return
 
     if args.boundaries:
-        extract_boundaries(input_path)
+        arrays = boundaries_to_arrays(input_path)
+        arrays_to_rois(arrays, output_path)
         return
 
     with open(input_path, "rb") as f:
@@ -234,7 +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:
@@ -245,9 +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
@@ -257,6 +295,32 @@ def main() -> None:
             pixel_size_x = 0.007797
             pixel_size_y = 0.003071
             pixel_size_z = 0.040000
+
+            volume = reshape_volume(
+                volume,
+                frames_per_data_group,
+                total_data_groups,
+                oct_window_height,
+                xy_scan_length,
+            )
+            volume = np.rot90(volume, k=1, axes=(1, 2))
+            volume_main = volume[:101]
+            volume_align = volume[101:frames_per_data_group]
+            align_path = dir_name / (file_name + "_Align.ome.tif")
+            pixel_size_x_align = 0.003899
+            pixel_size_y_align = 0.003071
+            pixel_size_z_align = 0.040000
+            write_volume(
+                output_path, volume_main, pixel_size_x, pixel_size_y, pixel_size_z
+            )
+            write_volume(
+                align_path,
+                volume_align,
+                pixel_size_x_align,
+                pixel_size_y_align,
+                pixel_size_z_align,
+            )
+            return
         elif "3D Disc" in file_name:
             volume = np.frombuffer(f.read(), dtype=np.single)
             frames_per_data_group = 106
@@ -301,7 +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
@@ -310,7 +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
@@ -319,7 +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
@@ -328,7 +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
@@ -337,7 +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
@@ -346,7 +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
@@ -355,7 +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
@@ -409,7 +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
@@ -418,7 +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
@@ -427,7 +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
@@ -436,7 +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
@@ -445,7 +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
@@ -454,7 +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,
@@ -465,7 +529,7 @@ def main() -> None:
         )
 
         if not args.en_face and not args.seg_curve:
-            volume = rotate_volume(volume)
+            volume = np.rot90(volume, k=1, axes=(1, 2))
 
         write_volume(output_path, volume, pixel_size_x, pixel_size_y, pixel_size_z)
 

{oct_to_tiff-0.5.0.dist-info → oct_to_tiff-0.6.1.dist-info}/METADATA

@@ -1,63 +1,36 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: oct-to-tiff
-Version: 0.5.0
+Version: 0.6.1
 Summary: A command line tool for converting optical coherence tomography angiography (OCTA) data.
-Author-email: Cameron Lloyd <lloyd@med.unideb.hu>
-Maintainer-email: Cameron Lloyd <lloyd@med.unideb.hu>
-License: BSD 3-Clause License
-        
-        Copyright (c) 2021, Cameron Lloyd
-        All rights reserved.
-        
-        Redistribution and use in source and binary forms, with or without
-        modification, are permitted provided that the following conditions are met:
-        
-        1. Redistributions of source code must retain the above copyright notice, this
-           list of conditions and the following disclaimer.
-        
-        2. Redistributions in binary form must reproduce the above copyright notice,
-           this list of conditions and the following disclaimer in the documentation
-           and/or other materials provided with the distribution.
-        
-        3. Neither the name of the copyright holder nor the names of its
-           contributors may be used to endorse or promote products derived from
-           this software without specific prior written permission.
-        
-        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-        
-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
+Author: Cameron Lloyd
+Author-email: Cameron Lloyd <lloyd@med.unideb.hu>
+License-Expression: BSD-3-Clause
+License-File: LICENSE.txt
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-License-File: LICENSE.txt
+Classifier: Programming Language :: Python :: 3.14
 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"
+Description-Content-Type: text/markdown
 
 # oct-to-tiff
 
@@ -74,9 +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
@@ -214,4 +187,4 @@ This project uses [Ruff](https://github.com/astral-sh/ruff) for linting and form
 
 ## Requirements
 
-Requires Python 3.10 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-0.5.0.dist-info → oct_to_tiff-0.6.1.dist-info}/WHEEL

@@ -1,5 +1,4 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: uv 0.9.29
 Root-Is-Purelib: true
 Tag: py3-none-any
-

{oct_to_tiff-0.5.0.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-0.5.0.dist-info/RECORD

@@ -1,8 +0,0 @@
-oct_to_tiff/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-oct_to_tiff/cli.py,sha256=tHRUNBff0TTTtc0pnecF_t5mLWyoGG0kNKNVopyL4Sw,15934
-oct_to_tiff-0.5.0.dist-info/LICENSE.txt,sha256=8KO0dluzLStmIF0HM18BOP9T2miIcX8q-GOfMOw6Ngk,1521
-oct_to_tiff-0.5.0.dist-info/METADATA,sha256=8-nIJ6Pg_vvfxovcjIHgax-D1nMQaWYZ_9cJLT7lq2g,6649
-oct_to_tiff-0.5.0.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-oct_to_tiff-0.5.0.dist-info/entry_points.txt,sha256=mKWNdkTThZm2JKtLwp4PGMpXkvAWk-xnQDAOyRsCo9Y,53
-oct_to_tiff-0.5.0.dist-info/top_level.txt,sha256=_ovqm7f48yb_IAiVqWzB3VPnHXwzkkEqQQ_ZJz_McSY,12
-oct_to_tiff-0.5.0.dist-info/RECORD,,

oct_to_tiff-0.5.0.dist-info/top_level.txt

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