made pixel size optional so that inputs can just be specified in pixe…

…ls if desired

src/ttmask/cone.py

@@ -15,7 +15,7 @@ def cone(
     cone_height: float = typer.Option(...),
     cone_base_diameter: float = typer.Option(...),
     soft_edge_width: int = typer.Option(0),
-    pixel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(1),
     output: Path = typer.Option(Path("cone.mrc"))
 ):
     c = sidelength // 2

src/ttmask/cube.py

@@ -14,7 +14,7 @@ def cube(
     sidelength: int = typer.Option(...),
     cube_sidelength: float = typer.Option(...),
     soft_edge_width: float = typer.Option(0),
-    pixel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(1),
     output: Path = typer.Option(Path("cube.mrc")),
     wall_thickness: float = typer.Option(0),
 ):

src/ttmask/cuboid.py

@@ -18,7 +18,7 @@ def cuboid(
     sidelength: int = typer.Option(...),
     cuboid_sidelengths: Annotated[Tuple[float, float, float], typer.Option()] = (None, None, None),
     soft_edge_width: float = typer.Option(0),
-    pixel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(1),
     output: str = typer.Option(Path("cuboid.mrc")),
     wall_thickness: float = typer.Option(0),
 ):

src/ttmask/cylinder.py

@@ -16,7 +16,7 @@ def cylinder(
     cylinder_diameter: float = typer.Option(...),
     wall_thickness: float = typer.Option(0),
     soft_edge_width: int = typer.Option(0),
-    pixel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(1),
     output: Path = typer.Option(Path("cylinder.mrc"))
 ):
     cylinder_radius = cylinder_diameter / 2

src/ttmask/ellipsoid.py

@@ -16,7 +16,7 @@ def ellipsoid(
     height: float = typer.Option(...),
     depth: float = typer.Option(...),
     soft_edge_width: int = typer.Option(0),
-    pixel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(1),
     output: Path = typer.Option(Path("ellipsoid.mrc")),
     wall_thickness: float = typer.Option(0),
 ):

src/ttmask/sphere.py

@@ -15,7 +15,7 @@ def sphere(
     sidelength: int = typer.Option(...),
     sphere_diameter: float = typer.Option(...),
     soft_edge_width: int = typer.Option(0),
-    pixel_size: float = typer.Option(...),
+    pixel_size: float = typer.Option(1),
     output: Path = typer.Option(Path("sphere.mrc")),
     wall_thickness: float = typer.Option(0),
 ):