Merge branch 'main' into feature/vmonitor

Author: georgevigelette

README.rst

@@ -58,14 +58,14 @@ Dev mode
 Installing Meshroom
 -------------------
 
-If you are using ``openlifu.nav.photoscan`` to reconstruct meshes from photo collections, then you will need to set up **Meshroom**.
+If you are using ``openlifu.nav.photoscan`` to reconstruct meshes from photo collections, then you will need to set up **Meshroom 2023.3.0**.
 
 Ubuntu
 ~~~~~~
 
 Download and Extract
 ^^^^^^^^^^^^^^^^^^^^
-1. Download Meshroom for Linux from `<https://alicevision.org/#meshroom>`_.
+1. Download Meshroom 2023.3.0 for Linux from `<https://github.com/alicevision/Meshroom/releases/tag/v2023.3.0>`_.
 2. Extract the downloaded archive:
 
    .. code:: bash
@@ -98,7 +98,7 @@ Windows
 Download and Extract
 ^^^^^^^^^^^^^^^^^^^^
 
-1. Download Meshroom for Windows from `<https://alicevision.org/#meshroom>`_.
+1. Download Meshroom 2023.3.0 for Windows from `<https://github.com/alicevision/Meshroom/releases/tag/v2023.3.0>`_.
 2. Extract the downloaded archive to a directory of your choice.
 
 Add Meshroom to PATH

pyproject.toml

@@ -51,6 +51,7 @@ dependencies = [
   "trimesh",
   "embreex; platform_machine=='x86_64' or platform_machine=='AMD64'",
   "onnxruntime==1.18.0",
+  "pydicom",
 ]
 
 [project.optional-dependencies]
@@ -250,6 +251,7 @@ messages_control.disable = [
   "duplicate-code",
   "cyclic-import",
   "unreachable", # This is to allow marking of TODO items with a NotImplementedError
+  "c-extension-no-member",
 ]
 
 [tool.setuptools.package-data]

src/openlifu/db/database.py

@@ -5,16 +5,22 @@
 import logging
 import os
 import shutil
+import tempfile
 from enum import Enum
 from pathlib import Path
 from typing import Dict, List
 
 import h5py
+import nibabel as nib
 
 from openlifu.nav.photoscan import Photoscan, load_data_from_photoscan
 from openlifu.plan import Protocol, Run, Solution
 from openlifu.util.json import PYFUSEncoder
 from openlifu.util.types import PathLike
+from openlifu.util.volume_conversion import (
+    convert_dicom_to_nifti,
+    is_dicom_file_or_directory,
+)
 from openlifu.xdc import Transducer, TransducerArray
 from openlifu.xdc.util import load_transducer_from_file
 
@@ -24,6 +30,7 @@
 
 OnConflictOpts = Enum('OnConflictOpts', ['ERROR', 'OVERWRITE', 'SKIP'])
 
+
 class Database:
     def __init__(self, path: str | None = None):
         if path is None:
@@ -378,35 +385,57 @@ def write_volume(self, subject_id, volume_id, volume_name, volume_data_filepath,
         if not Path(volume_data_filepath).exists():
             raise ValueError(f'Volume data filepath does not exist: {volume_data_filepath}')
 
-        volume_ids = self.get_volume_ids(subject_id)
-        if volume_id in volume_ids:
-            if on_conflict == OnConflictOpts.ERROR:
-                raise ValueError(f"Volume with ID {volume_id} already exists for subject {subject_id}.")
-            elif on_conflict == OnConflictOpts.OVERWRITE:
-                self.logger.info(f"Overwriting volume with ID {volume_id} for subject {subject_id}.")
-            elif on_conflict == OnConflictOpts.SKIP:
-                self.logger.info(f"Skipping volume with ID {volume_id} for subject {subject_id} as it already exists.")
-                return
-            else:
-                raise ValueError("Invalid 'on_conflict' option. Use 'error', 'overwrite', or 'skip'.")
-
-        # Create volume metadata
-        volume_metadata_dict = {"id": volume_id, "name": volume_name, "data_filename": Path(volume_data_filepath).name}
-        volume_metadata_json = json.dumps(volume_metadata_dict, separators=(',', ':'), cls=PYFUSEncoder)
-
-        # Save the volume metadata to a JSON file and copy volume data file to database
-        volume_metadata_filepath = self.get_volume_metadata_filepath(subject_id, volume_id) #subject_id/volume/volume_id/volume_id.json
-        Path(volume_metadata_filepath).parent.parent.mkdir(exist_ok=True) # volume directory
-        Path(volume_metadata_filepath).parent.mkdir(exist_ok=True)
-        with open(volume_metadata_filepath, 'w') as file:
-            file.write(volume_metadata_json)
-        shutil.copy(Path(volume_data_filepath), Path(volume_metadata_filepath).parent)
-
-        if volume_id not in volume_ids:
-            volume_ids.append(volume_id)
-            self.write_volume_ids(subject_id, volume_ids)
-
-        self.logger.info(f"Added volume with ID {volume_id} for subject {subject_id} to the database.")
+        path = Path(volume_data_filepath)
+        if path.is_dir() and not is_dicom_file_or_directory(volume_data_filepath):
+            raise ValueError(f'Volume data filepath is a directory without DICOM files: {volume_data_filepath}')
+
+        # convert dicom to nifti if needed
+        temp_nifti_path = None
+        if is_dicom_file_or_directory(volume_data_filepath):
+            self.logger.info(f"Detected DICOM input for volume {volume_id}, converting to NIfTI format")
+            with tempfile.NamedTemporaryFile(suffix='.nii.gz', delete=False) as temp_file:
+                temp_nifti_path = Path(temp_file.name)
+
+            try:
+                convert_dicom_to_nifti(volume_data_filepath, temp_nifti_path)
+                volume_data_filepath = temp_nifti_path
+            except Exception as e:
+                if temp_nifti_path.exists():
+                    temp_nifti_path.unlink()
+                raise RuntimeError(f"Failed to convert DICOM to NIfTI: {e}") from e
+
+        try:
+            volume_ids = self.get_volume_ids(subject_id)
+            if volume_id in volume_ids:
+                if on_conflict == OnConflictOpts.ERROR:
+                    raise ValueError(f"Volume with ID {volume_id} already exists for subject {subject_id}.")
+                elif on_conflict == OnConflictOpts.OVERWRITE:
+                    self.logger.info(f"Overwriting volume with ID {volume_id} for subject {subject_id}.")
+                elif on_conflict == OnConflictOpts.SKIP:
+                    self.logger.info(f"Skipping volume with ID {volume_id} for subject {subject_id} as it already exists.")
+                    return
+                else:
+                    raise ValueError("Invalid 'on_conflict' option. Use 'error', 'overwrite', or 'skip'.")
+
+            volume_metadata_dict = {"id": volume_id, "name": volume_name, "data_filename": Path(volume_data_filepath).name}
+            volume_metadata_json = json.dumps(volume_metadata_dict, separators=(',', ':'), cls=PYFUSEncoder)
+
+            volume_metadata_filepath = self.get_volume_metadata_filepath(subject_id, volume_id)
+            Path(volume_metadata_filepath).parent.parent.mkdir(exist_ok=True)
+            Path(volume_metadata_filepath).parent.mkdir(exist_ok=True)
+            with open(volume_metadata_filepath, 'w') as file:
+                file.write(volume_metadata_json)
+            shutil.copy(Path(volume_data_filepath), Path(volume_metadata_filepath).parent)
+
+            if volume_id not in volume_ids:
+                volume_ids.append(volume_id)
+                self.write_volume_ids(subject_id, volume_ids)
+
+            self.logger.info(f"Added volume with ID {volume_id} for subject {subject_id} to the database.")
+        finally:
+            # cleanup temp nifti file
+            if temp_nifti_path is not None and temp_nifti_path.exists():
+                temp_nifti_path.unlink()
 
     def write_photocollection(self, subject_id, session_id, reference_number: str, photo_paths: List[PathLike], on_conflict=OnConflictOpts.ERROR):
         """ Writes a photocollection to database and copies the associated
@@ -980,7 +1009,6 @@ def load_volume(self, subject, volume_id):
         if not volume_data_filepath.exists() or not volume_data_filepath.is_file():
             self.logger.error(f"Volume data file not found for volume {volume_id}, subject {subject.id}")
             raise FileNotFoundError(f"Volume data file not found for volume {volume_id}, subject {subject.id}")
-        import nibabel as nib
         # Load the volume data using nibabel
         volume_data = nib.load(volume_data_filepath)
         self.logger.info(f"Loaded volume {volume_id} for subject {subject.id}")

src/openlifu/util/volume_conversion.py

@@ -0,0 +1,160 @@
+"""Utilities for converting between different medical imaging formats."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+import nibabel as nib
+import numpy as np
+import pydicom
+
+from openlifu.util.types import PathLike
+
+
+def is_dicom_file_or_directory(path: PathLike) -> bool:
+    """
+    Check if a path is a DICOM file or directory containing DICOM files.
+
+    Args:
+        path: Path to check
+
+    Returns:
+        True if path is a DICOM file or directory with DICOM files, False otherwise
+    """
+    path = Path(path)
+
+    if path.is_file():
+        # check for 'DICM' magic bytes at offset 128
+        try:
+            with open(path, 'rb') as f:
+                f.seek(128)
+                return f.read(4) == b'DICM'
+        except OSError:
+            return False
+
+    elif path.is_dir():
+        for file in path.iterdir():
+            if file.is_file():
+                try:
+                    with open(file, 'rb') as f:
+                        f.seek(128)
+                        if f.read(4) == b'DICM':
+                            return True
+                except OSError:
+                    continue
+
+    return False
+
+
+def extract_affine_from_dicom(
+    dicom_slices: list[tuple[int, np.ndarray, pydicom.Dataset]]
+) -> np.ndarray:
+    """
+    Extract the affine transformation matrix from DICOM header information.
+    Converts from DICOM LPS (Left-Posterior-Superior) to NIfTI RAS.
+
+    Args:
+        dicom_slices: List of tuples (instance_number, pixel_array, header) where
+            header is a pydicom.Dataset containing DICOM metadata tags
+
+    Returns:
+        4x4 affine transformation matrix mapping voxel coordinates to RAS world coordinates
+
+    Raises:
+        RuntimeError: If required DICOM tags are missing
+    """
+    # use the first slice to extract most parameters
+    first_header = dicom_slices[0][2]
+
+    try:
+        # ImageOrientationPatient (0020,0037): direction cosines for row and column
+        orientation = np.array(first_header.ImageOrientationPatient, dtype=float)
+        row_cosine = orientation[:3]  # direction cosines for rows
+        col_cosine = orientation[3:]  # direction cosines for columns
+
+        # ImagePositionPatient (0020,0032): position of the upper-left voxel
+        position = np.array(first_header.ImagePositionPatient, dtype=float)
+
+        # PixelSpacing is [row_spacing, col_spacing], so map to dy, dx
+        dy, dx = np.array(first_header.PixelSpacing, dtype=float)
+
+    except AttributeError as e:
+        raise RuntimeError(
+            f"Missing required DICOM tag for affine calculation: {e}"
+        ) from e
+
+    # Compute Z direction and spacing (handling potential gantry tilt)
+    slice_cosine = np.cross(row_cosine, col_cosine)
+
+    # calculate slice spacing
+    if len(dicom_slices) > 1:
+        # calculate from the distance between first two slices
+        first_pos = np.array(dicom_slices[0][2].ImagePositionPatient, dtype=float)
+        second_pos = np.array(dicom_slices[1][2].ImagePositionPatient, dtype=float)
+        dz = np.dot(second_pos - first_pos, slice_cosine)
+    else:
+        # single slice - try to get from SliceThickness or default to 1.0
+        dz = float(getattr(first_header, 'SliceThickness', 1.0))
+
+    # Construct affine in DICOM LPS space
+    affine = np.eye(4)
+    affine[:3, 0] = row_cosine * dx
+    affine[:3, 1] = col_cosine * dy
+    affine[:3, 2] = slice_cosine * dz
+    affine[:3, 3] = position
+
+    # Convert LPS to RAS by flipping X and Y axes
+    return np.diag([-1, -1, 1, 1]) @ affine
+
+
+def convert_dicom_to_nifti(input_path: PathLike, output_filepath: PathLike) -> None:
+    """
+    Convert DICOM file(s) to NIfTI format using pydicom and nibabel.
+
+    Args:
+        input_path: Path to either a DICOM file or directory containing DICOM files
+        output_filepath: Path where the output NIfTI file should be saved
+
+    Raises:
+        RuntimeError: If the conversion fails
+    """
+    input_path = Path(input_path)
+    output_filepath = Path(output_filepath)
+
+    try:
+        if input_path.is_file():
+            dicom_files = [input_path]
+        else:
+            # dicom files may not have .dcm extension
+            dicom_files = [f for f in input_path.iterdir() if f.is_file()]
+
+        if not dicom_files:
+            raise RuntimeError("No DICOM files found")
+
+        slices = []
+        for dcm_file in dicom_files:
+            try:
+                header = pydicom.dcmread(dcm_file)
+                # Transpose to swap (Row, Col) -> (X, Y) for NIfTI
+                slices.append((header.get('InstanceNumber', 0), header.pixel_array.T, header))
+            except Exception:
+                # skip files that aren't valid dicom
+                continue
+
+        if not slices:
+            raise RuntimeError("No valid DICOM files found")
+
+        # sort by instance number - this is the slice order in the series
+        # so we reconstruct the 3D volume in the right order
+        slices.sort(key=lambda x: x[0])
+
+        # stack into 3D volume (handles both single and multiple slices)
+        volume = np.stack([s[1] for s in slices], axis=-1)
+
+        # extract affine from DICOM headers
+        affine = extract_affine_from_dicom(slices)
+
+        nib.save(nib.Nifti1Image(volume, affine), str(output_filepath))
+
+    except Exception as e:
+        raise RuntimeError(f"DICOM to NIfTI conversion failed: {e}") from e