oct-to-tiff 0.4.0__py3-none-any.whl → 0.6.0__py3-none-any.whl

oct_to_tiff/cli.py

@@ -1,25 +1,30 @@
 import argparse
 import logging
-import xml.etree.ElementTree as ET
+from importlib.metadata import version
 from pathlib import Path
+from typing import Any
 
+import defusedxml.ElementTree as DET
 import numpy as np
+import numpy.typing as npt
 import tifffile
+from roifile import ROI_TYPE, ImagejRoi, roiwrite
 
-logging.basicConfig(
-    format="%(asctime)s %(name)s:%(funcName)s %(levelname)s - %(message)s"
-)
 logger = logging.getLogger(__name__)
 
 
 def reshape_volume(
-    volume, frames_per_data_group, total_data_groups, oct_window_height, xy_scan_length
-):
+    volume: npt.NDArray[Any],
+    frames_per_data_group: int,
+    total_data_groups: int,
+    oct_window_height: int,
+    xy_scan_length: int,
+) -> npt.NDArray[Any]:
     """Reshape a 1-dimensional array to a 3-dimensional array.
 
     Parameters
     ----------
-    volume : ndarray
+    volume : npt.NDArray[Any]
         A 1-dimensional array.
     frames_per_data_group : int
         The number of frames per data group.
@@ -32,7 +37,7 @@ def reshape_volume(
 
     Returns
     -------
-    volume : ndarray
+    volume : npt.NDArray[Any]
         A 3-dimensional array.
 
     """
@@ -47,32 +52,20 @@ def reshape_volume(
     return volume
 
 
-def rotate_volume(volume):
-    """Rotate a 3-dimensional array 90 degrees left (anti-clockwise) about the z-axis.
-
-    Parameters
-    ----------
-    volume : ndarray
-        A 3-dimensional array.
-
-    Returns
-    -------
-    volume : ndarray
-        A rotated version of the input volume.
-
-    """
-    volume = np.rot90(volume, k=1, axes=(1, 2))
-    return volume
-
-
-def write_volume(output_path, volume, pixel_size_x, pixel_size_y, pixel_size_z):
+def write_volume(
+    output_path: Path,
+    volume: npt.NDArray[Any],
+    pixel_size_x: float,
+    pixel_size_y: float,
+    pixel_size_z: float,
+) -> None:
     """Write a 3-dimensional array to the output path as an OME-TIFF file, including voxel size in the metadata.
 
     Parameters
     ----------
     output_path : Path
         The specified output path.
-    volume : ndarray
+    volume : npt.NDArray[Any]
         A 3-dimensional array.
     pixel_size_x : float
         The pixel (voxel) width in mm.
@@ -98,33 +91,61 @@ def write_volume(output_path, volume, pixel_size_x, pixel_size_y, pixel_size_z):
     )
 
 
-def extract_boundaries(input_path):
+def boundaries_to_arrays(input_path: str | Path) -> list[npt.NDArray[np.int_]]:
     """Extract segmentation lines.
 
     Parameters
     ----------
-    input_path : Path
+    input_path : str | Path
         The specified input path.
 
+    Returns
+    -------
+    arrays : list[npt.NDArray[np.int_]]
+        A list of 2-dimensional arrays.
     """
-    tree = ET.parse(input_path)
+    input_path = Path(input_path)
+    tree = DET.parse(input_path)
     root = tree.getroot()
 
-    array_size = int(root.findtext("./Curve_Set/Image/Curve/ARRAY"))
+    array_size = int(root.findtext("./Curve_Set/Image/Curve/ARRAY", 0))
     data_points = [
-        int(point.text) for point in root.findall("./Curve_Set/Image/Curve/D")
+        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():
+
+def main() -> None:
     parser = argparse.ArgumentParser(
         description="Convert optical coherence tomography angiography (OCTA) data."
     )
@@ -162,9 +183,25 @@ def main():
         action="store_true",
         help="extract segmentation lines",
     )
-    parser.add_argument("--version", action="version", version="%(prog)s 0.4.0")
+    parser.add_argument(
+        "--log-level",
+        default="WARNING",
+        metavar="LEVEL",
+        help="sets the logging level (default: %(default)s)",
+    )
+    parser.add_argument(
+        "--version", action="version", version="%(prog)s " + version("oct_to_tiff")
+    )
     args = parser.parse_args()
 
+    numeric_level = getattr(logging, args.log_level.upper(), None)
+    if not isinstance(numeric_level, int):
+        raise ValueError(f"Invalid log level: {args.log_level}")
+    logging.basicConfig(
+        level=numeric_level,
+        format="%(asctime)s %(name)s:%(funcName)s %(levelname)s - %(message)s",
+    )
+
     input_path = args.input
     if args.output:
         dir_name = args.output
@@ -172,18 +209,22 @@ def main():
     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:
@@ -227,6 +268,32 @@ def main():
             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
@@ -435,7 +502,7 @@ def main():
         )
 
         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-0.4.0.dist-info → oct_to_tiff-0.6.0.dist-info}/METADATA

@@ -1,30 +1,43 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: oct-to-tiff
-Version: 0.4.0
+Version: 0.6.0
 Summary: A command line tool for converting optical coherence tomography angiography (OCTA) data.
-Home-page: https://github.com/camlloyd/oct-to-tiff
-Author: Cameron Lloyd
-Author-email: lloyd@med.unideb.hu
+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
 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 :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
+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
+Provides-Extra: dev
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: types-defusedxml; extra == "dev"
+Dynamic: license-file
 
 # oct-to-tiff
 
 [![DOI](https://zenodo.org/badge/382486199.svg)](https://zenodo.org/badge/latestdoi/382486199)
+[![PyPI - Version](https://img.shields.io/pypi/v/oct-to-tiff)](https://pypi.org/project/oct-to-tiff)
+[![PyPI - License](https://img.shields.io/pypi/l/oct-to-tiff)](https://github.com/camlloyd/oct-to-tiff/blob/main/LICENSE.txt)
+[![PyPI Downloads](https://static.pepy.tech/badge/oct-to-tiff)](https://pepy.tech/projects/oct-to-tiff)
+
 
 A command line tool for converting optical coherence tomography angiography (OCTA) data.
 
@@ -33,9 +46,9 @@ via pip:
 
     pip install oct-to-tiff
 
-via conda:
+via mamba:
 
-    conda install -c conda-forge oct-to-tiff
+    mamba install -c conda-forge oct-to-tiff
 
 ## Getting started
     oct-to-tiff /path/to/image.OCT
@@ -51,6 +64,12 @@ By default, the output file will be written with the same name as the input file
 
 To specify a custom output directory, see [Optional arguments](#optional-arguments) below.
 
+## Batch processing
+``` bash
+for file in *.OCT; do oct-to-tiff "${file}"; done
+```
+will convert all OCT volumes in the current directory to OME-TIFF files, including voxel size in the metadata.
+
 ## Supported scan patterns
 
 This tool has been developed by reverse engineering data from the Optovue RTVue XR Avanti System.
@@ -113,6 +132,13 @@ Sets the correct voxel size for scan patterns with adjustable length.
 
     oct-to-tiff /path/to/image.OCT --size 4.5
 
+#### `--log-level LEVEL`
+**Description**: sets the logging level (default: `WARNING`)
+
+**Usage**:
+
+    oct-to-tiff /path/to/image.OCT --log-level INFO
+
 #### `--version`
 **Description**: show program's version number and exit.
 
@@ -156,8 +182,8 @@ Requires `--size SIZE`.
 
 ## Contributing
 
-This project uses [black](https://github.com/psf/black) for formatting and [isort](https://github.com/PyCQA/isort) for sorting imports.
+This project uses [Ruff](https://github.com/astral-sh/ruff) for linting and formatting.
 
 ## Requirements
 
-Requires Python 3.8 or higher.
+Requires Python 3.11 or higher.

oct_to_tiff-0.6.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+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-0.4.0.dist-info → oct_to_tiff-0.6.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.40.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

oct_to_tiff-0.4.0.dist-info/RECORD

@@ -1,8 +0,0 @@
-oct_to_tiff/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-oct_to_tiff/cli.py,sha256=Ct0yG2iALYWAyYMZJZDa7FusQbm6yoYXHQYF5sC8zxc,15115
-oct_to_tiff-0.4.0.dist-info/LICENSE.txt,sha256=8KO0dluzLStmIF0HM18BOP9T2miIcX8q-GOfMOw6Ngk,1521
-oct_to_tiff-0.4.0.dist-info/METADATA,sha256=RZGGDg3QPgTxAi3OxfVz-KjXCtP0Bh0yfmfIekIKtlE,3903
-oct_to_tiff-0.4.0.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-oct_to_tiff-0.4.0.dist-info/entry_points.txt,sha256=mKWNdkTThZm2JKtLwp4PGMpXkvAWk-xnQDAOyRsCo9Y,53
-oct_to_tiff-0.4.0.dist-info/top_level.txt,sha256=_ovqm7f48yb_IAiVqWzB3VPnHXwzkkEqQQ_ZJz_McSY,12
-oct_to_tiff-0.4.0.dist-info/RECORD,,