Use unreleased whippersnappy from git

Address github co-pilot suggestions
replace libegl with libmesa in docker for no-gpu rendering

Author: dkuegler

CorpusCallosum/cc_visualization.py

@@ -5,11 +5,11 @@
 
 import nibabel as nib
 import numpy as np
-from nibabel.affines import apply_affine
 
 from CorpusCallosum.data.fsaverage_cc_template import load_fsaverage_cc_template
 from CorpusCallosum.shape.contour import CCContour
 from CorpusCallosum.shape.mesh import CCMesh
+from FastSurferCNN.utils import AffineMatrix4x4
 from FastSurferCNN.utils.logging import get_logger, setup_logging
 from FastSurferCNN.utils.lta import read_lta
 
@@ -221,8 +221,8 @@ def main(
     # we need to get the upright image header, which is the same as cc_up.lta applied to orig.
     elif Path(template_dir / "mri/orig.mgz").exists() and Path(template_dir / "mri/transforms/cc_up.lta").exists():
         image = nib.load(template_dir / "mri" / "orig.mgz")
-        lta_mat = read_lta(template_dir / "mri/transforms/cc_up.lta")["lta"]
-        image.affine = apply_affine(lta_mat, image.affine)
+        lta_mat: AffineMatrix4x4 = read_lta(template_dir / "mri/transforms/cc_up.lta")["lta"]
+        image.affine = lta_mat @ image.affine
         header = image.header
     else:
         header = None
@@ -245,9 +245,10 @@ def main(
     try:
         cc_mesh.snap_cc_picture(str(output_dir / "cc_mesh_snap.png"), ref_header=header)
         logger.info(f"Writing 3D snapshot image to {output_dir / 'cc_mesh_snap.png'}")
-    except RuntimeError:
+    except Exception:
         logger.warning("The cc_visualization script requires whippersnappy>=2.0 to makes screenshots, install with "
-                "`pip install whippersnappy>=2.0` !")
+                       "`pip install whippersnappy>=2.0` !")
+        raise
     return 0
 
 if __name__ == "__main__":

CorpusCallosum/shape/mesh.py

@@ -477,7 +477,7 @@ def __create_cc_viewmat() -> "Matrix44":
             - -8 degrees around z-axis
         3. Adds a small translation for better centering
         """
-        from whippersnappy.gl.views import ViewType, get_view_matrix
+        from whippersnappy import ViewType, get_view_matrix
 
         if not HAS_PYRR:
             raise ImportError("Pyrr not installed, install pyrr with `pip install pyrr`.")
@@ -511,12 +511,14 @@ def snap_cc_picture(
         ----------
         output_path : Path, str
             Path where to save the snapshot image.
-        ref_header : Path, str, nibabelImage, optional
-            Path to reference image to use for tkr creation. If None, ignores the file for saving.
+        ref_header : Path, str, nibabelHeader, optional
+            Path to reference image header to use for tkr creation. If None, ignores the file for saving.
 
         Raises
         ------
-        Warning
+        ImportError
+            If whippersnappy is not installed or if the version is too old.
+        ValueError
             If the mesh has no faces and cannot create a snapshot.
         """
         from packaging.version import parse
@@ -539,20 +541,26 @@ def snap_cc_picture(
             )
         # Skip snapshot if there are no faces
         if len(self.t) == 0:
-            logger.warning("Cannot create snapshot - no faces in mesh")
-            return
+            raise ValueError("Cannot create snapshot - no faces in mesh")
 
         self.__make_parent_folder(output_path)
 
-        if ref_header is not None:
-            v = apply_affine(ref_header.get_vox2ras_tkr(), self.v)
-        else:
+        if ref_header is None:
             v = self.v
+        else:
+            from nibabel.freesurfer.mghformat import MGHHeader
+
+            # if header is a file, load its header from the file
+            if isinstance(ref_header, (str, Path)):
+                ref_header = nib.load(ref_header).header
+            # if header is not already an MGHHeader, convert it to MGHHeader, so we have the get_vox2ras_tkr function
+            mgh_header = ref_header if isinstance(ref_header, MGHHeader) else MGHHeader.from_header(ref_header)
+            v = apply_affine(mgh_header.get_vox2ras_tkr(), self.v)
+
         whippersnappy.snap1(
             mesh=(v, self.t),
             overlay=self.mesh_vertex_colors,
-            view=None,
-            viewmat=self.__create_cc_viewmat(),
+            view=self.__create_cc_viewmat(),
             width=3 * 500,
             height=3 * 300,
             outpath=str(output_path),

pyproject.toml

@@ -60,7 +60,8 @@ dependencies = [
 
 [project.optional-dependencies]
 qc  = [
-    'whippersnappy>=2.0',
+    'whippersnappy@git+https://github.com/Deep-MI/WhipperSnapPy@main',
+#    'whippersnappy>=2.0.1',
 ]
 doc = [
     'fastsurfer[qc]',
@@ -171,3 +172,6 @@ exclude_lines = [
     'if __name__ == .__main__.:',
 ]
 precision = 2
+
+[tool.uv.sources]
+whippersnappy = { git = "https://github.com/Deep-MI/WhipperSnapPy", rev = "main" }

tools/Docker/Dockerfile

@@ -272,7 +272,7 @@ RUN <<EOF
 apt-get update
 shell_deps="time bc"
 freesurfer_deps="gawk libgomp1 libquadmath0 tcsh"
-whippersnappy_egl_deps="libegl1 libgl1 libfontconfig1"
+whippersnappy_egl_deps="libosmesa6 libgl1 libfontconfig1"
 apt-get install -y --no-install-recommends \
     $shell_deps \
     $freesurfer_deps \