From 75dac3f99cdf7dc82591be771c716207b3a0fefc Mon Sep 17 00:00:00 2001
From: David Rotermund <54365609+davrot@users.noreply.github.com>
Date: Sat, 3 Feb 2024 19:24:32 +0100
Subject: [PATCH] Add files via upload

---
 .../functions/align_cameras.py                | 175 ++++++++++++++++++
 1 file changed, 175 insertions(+)
 create mode 100644 reproduction_effort/functions/align_cameras.py

diff --git a/reproduction_effort/functions/align_cameras.py b/reproduction_effort/functions/align_cameras.py
new file mode 100644
index 0000000..6cbb36b
--- /dev/null
+++ b/reproduction_effort/functions/align_cameras.py
@@ -0,0 +1,175 @@
+import torch
+import torchvision as tv  # type: ignore
+import numpy as np
+import json
+import scipy.io as sio  # type: ignore
+
+from functions.align_refref import align_refref
+from functions.perform_donor_volume_rotation import perform_donor_volume_rotation
+from functions.perform_donor_volume_translation import perform_donor_volume_translation
+from functions.ImageAlignment import ImageAlignment
+
+
+@torch.no_grad()
+def align_cameras(
+    filename_raw_json: str,
+    filename_bin_mat: str,
+    device: torch.device,
+    dtype: torch.dtype,
+    batch_size: int,
+    fill_value: float = 0,
+) -> tuple[
+    torch.Tensor, torch.Tensor, torch.Tensor, torch.Tensor, torch.Tensor, torch.Tensor
+]:
+    image_alignment = ImageAlignment(default_dtype=dtype, device=device)
+
+    # --- Load data ---
+    with open(filename_raw_json, "r") as file_handle:
+        metadata: dict = json.load(file_handle)
+    channels: list[str] = metadata["channelKey"]
+
+    data = torch.tensor(
+        sio.loadmat(filename_bin_mat)["nparray"].astype(np.float32),
+        device=device,
+        dtype=dtype,
+    )
+    # --==-- DONE --==--
+
+    # --- Get reference image ---
+    acceptor_index: int = channels.index("acceptor")
+    donor_index: int = channels.index("donor")
+    oxygenation_index: int = channels.index("oxygenation")
+    volume_index: int = channels.index("volume")
+
+    # --==-- DONE --==--
+
+    # --- Sort data ---
+    acceptor = data[..., acceptor_index].moveaxis(-1, 0).clone()
+    donor = data[..., donor_index].moveaxis(-1, 0).clone()
+    oxygenation = data[..., oxygenation_index].moveaxis(-1, 0).clone()
+    volume = data[..., volume_index].moveaxis(-1, 0).clone()
+    del data
+    # --==-- DONE --==--
+
+    # --- Calculate translation and rotation between the reference images ---
+    angle_refref, tvec_refref, ref_image_acceptor, ref_image_donor = align_refref(
+        ref_image_acceptor=acceptor[
+            acceptor.shape[2] // 2,
+            :,
+            :,
+        ],
+        ref_image_donor=donor[
+            donor.shape[2] // 2,
+            :,
+            :,
+        ],
+        image_alignment=image_alignment,
+        batch_size=batch_size,
+        fill_value=fill_value,
+    )
+
+    ref_image_oxygenation = tv.transforms.functional.affine(
+        img=oxygenation[
+            oxygenation.shape[2] // 2,
+            :,
+            :,
+        ].unsqueeze(0),
+        angle=-float(angle_refref),
+        translate=[0, 0],
+        scale=1.0,
+        shear=0,
+        interpolation=tv.transforms.InterpolationMode.BILINEAR,
+        fill=fill_value,
+    )
+
+    ref_image_oxygenation = tv.transforms.functional.affine(
+        img=ref_image_oxygenation,
+        angle=0,
+        translate=[tvec_refref[1], tvec_refref[0]],
+        scale=1.0,
+        shear=0,
+        interpolation=tv.transforms.InterpolationMode.BILINEAR,
+        fill=fill_value,
+    )
+
+    ref_image_oxygenation = ref_image_oxygenation.squeeze(0)
+
+    ref_image_volume = volume[
+        volume.shape[2] // 2,
+        :,
+        :,
+    ].clone()
+
+    # --==-- DONE --==--
+
+    # --- Rotate and translate the acceptor and oxygenation data accordingly ---
+    acceptor = tv.transforms.functional.affine(
+        img=acceptor,
+        angle=-float(angle_refref),
+        translate=[0, 0],
+        scale=1.0,
+        shear=0,
+        interpolation=tv.transforms.InterpolationMode.BILINEAR,
+        fill=fill_value,
+    )
+
+    acceptor = tv.transforms.functional.affine(
+        img=acceptor,
+        angle=0,
+        translate=[tvec_refref[1], tvec_refref[0]],
+        scale=1.0,
+        shear=0,
+        interpolation=tv.transforms.InterpolationMode.BILINEAR,
+        fill=fill_value,
+    )
+
+    oxygenation = tv.transforms.functional.affine(
+        img=oxygenation,
+        angle=-float(angle_refref),
+        translate=[0, 0],
+        scale=1.0,
+        shear=0,
+        interpolation=tv.transforms.InterpolationMode.BILINEAR,
+        fill=fill_value,
+    )
+
+    oxygenation = tv.transforms.functional.affine(
+        img=oxygenation,
+        angle=0,
+        translate=[tvec_refref[1], tvec_refref[0]],
+        scale=1.0,
+        shear=0,
+        interpolation=tv.transforms.InterpolationMode.BILINEAR,
+        fill=fill_value,
+    )
+    # --==-- DONE --==--
+
+    acceptor, donor, oxygenation, volume, angle_donor_volume = (
+        perform_donor_volume_rotation(
+            acceptor=acceptor,
+            donor=donor,
+            oxygenation=oxygenation,
+            volume=volume,
+            ref_image_donor=ref_image_donor,
+            ref_image_volume=ref_image_volume,
+            image_alignment=image_alignment,
+            batch_size=batch_size,
+            fill_value=fill_value,
+        )
+    )
+
+    acceptor, donor, oxygenation, volume, tvec_donor_volume = (
+        perform_donor_volume_translation(
+            acceptor=acceptor,
+            donor=donor,
+            oxygenation=oxygenation,
+            volume=volume,
+            ref_image_donor=ref_image_donor,
+            ref_image_volume=ref_image_volume,
+            image_alignment=image_alignment,
+            batch_size=batch_size,
+            fill_value=fill_value,
+        )
+    )
+
+    return acceptor, donor, oxygenation, volume, angle_donor_volume, tvec_donor_volume