Merge pull request #109 from hanjinliu/relative-image-path

Find image by relative path

cylindra/cli/run.py

@@ -28,7 +28,7 @@ def __init__(self):
         self.add_argument("--output", "-o", type=str, default=None)
 
     def run_action(
-        self, path: str, headless: bool = False, output: str = None, **kwargs
+        self, path: str, headless: bool = False, output: str | None = None, **kwargs
     ):
         from runpy import run_path
 

cylindra/project/_single.py

@@ -33,6 +33,7 @@ class CylindraProject(BaseProject):
     version: str
     dependency_versions: dict[str, str]
     image: PathLike | None
+    image_relative: PathLike | None = None
     scale: float
     invert: bool = False
     multiscales: list[int]
@@ -134,19 +135,12 @@ def from_gui(
                     continue
                 landscape_infos.append(LandscapeInfo.from_layer(gui, layer))
 
-        def as_relative(p: "Path | None"):
-            assert isinstance(p, Path) or p is None
-            try:
-                out = p.relative_to(project_dir)
-            except Exception:
-                out = p
-            return out
-
         return cls(
             datetime=datetime.now().strftime("%Y/%m/%d %H:%M:%S"),
             version=_versions.pop("cylindra", "unknown"),
             dependency_versions=_versions,
-            image=as_relative(tomo.metadata.get("source", None)),
+            image=tomo.metadata.get("source", None),
+            image_relative=_as_relative(tomo.metadata.get("source", None), project_dir),
             scale=tomo.scale,
             invert=tomo.is_inverted,
             multiscales=[x[0] for x in tomo.multiscaled],
@@ -476,6 +470,14 @@ def load_tomogram(
                     binsize=self.multiscales,
                     compute=compute,
                 )
+            elif _rpath := self._try_resolve_image_relative():
+                tomo = CylTomogram.imread(
+                    path=_rpath,
+                    scale=self.scale,
+                    tilt=self.missing_wedge.as_param(),
+                    binsize=self.multiscales,
+                    compute=compute,
+                )
             else:
                 LOGGER.warning(
                     f"Cannot find image file: {self.image.as_posix()}. "
@@ -497,6 +499,19 @@ def load_tomogram(
         tomo.splines.extend(self.iter_load_splines(dir))
         return tomo
 
+    def _try_resolve_image_relative(self) -> Path | None:
+        if self.image_relative is None or self.project_path is None:
+            return None
+        cur_dir = self.project_path.parent
+        for part in Path(self.image_relative).parts:
+            if part.startswith(".."):
+                cur_dir = cur_dir.parent
+            else:
+                cur_dir = cur_dir / part
+        if cur_dir.exists():
+            return cur_dir
+        return None
+
     def make_project_viewer(self):
         """Build a project viewer widget from this project."""
         from cylindra.project._widgets import ProjectViewer
@@ -611,6 +626,20 @@ def _get_instance(gui: "CylindraMainWidget | None" = None):
     return ui
 
 
+def _as_relative(p: Path | None, project_dir: Path | None):
+    if p is None or project_dir is None:
+        return None
+    elif isinstance(p, Path):
+        cur_path = project_dir
+        rel_path = Path("..")
+        for _ in range(5):
+            cur_path = cur_path.parent
+            if p.is_relative_to(cur_path):
+                return rel_path.parent / p.relative_to(cur_path)
+            rel_path = rel_path / ".."
+    return None
+
+
 def _drop_null_columns(df: pl.DataFrame) -> pl.DataFrame:
     nrows = df.shape[0]
     to_drop = list[str]()