fixes for project module

mu_map/recon/project.py

@@ -7,9 +7,10 @@ from pydicom.dataset import FileDataset as DCMImage
 import stir
 
 from mu_map.file.interfile import (
+    Interfile,
+    InterfileKeys,
     load_interfile,
     write_interfile,
-    InterfileKeys,
 )
 
 
@@ -27,8 +28,8 @@ type of data := Tomographic
 imagedata byte order := LITTLEENDIAN
 number format := float
 number of bytes per pixel := 4
-patient orientation := feet_in
-patient rotation := supine
+patient orientation := {PATIENT_ORIENTATION}
+patient rotation := {PATIENT_ROTATION}
 
 SPECT STUDY (General) := 
 ;matrix axis label [2] := axial coordinate
@@ -52,21 +53,18 @@ END OF INTERFILE :=
 
 
 def forward_project(
-    recon_header: Dict[str, str],
-    recon_img: np.ndarray,
+    recon: Interfile,
     n_slices: Optional[int] = None,
     n_bins: Optional[int] = None,
     n_projections: int = 120,
     rotation: int = 360,
     start_angle: int = 180,
     radius: int = 150,
-    **kwargs,
-) -> Tuple[Dict[str, str], np.ndarray]:
+) -> Interfile:
     """
     Forward project a reconstruction in INTERFILE format.
 
-    :param recon_header: the header of the reconstruction
-    :param recon_img: the reconstruction image
+    :param recon: the reconstruction in Interfile format
     :param n_slices: the number of slices of the projection - defaults to the number of slices of the reconstruction
     :param n_bins: the number of bins of the projection - defaults to the number of rows in the reconstruction
     :param n_projections: the number of views used for the projection
@@ -75,6 +73,8 @@ def forward_project(
     :param radius: the radius of the detector circle in mm
     :return: an interfile image as a tuple of a header and a numpy array
     """
+    recon_header, recon_img = recon
+
     n_slices = recon_img.shape[0] if n_slices is None else n_slices
     n_bins = recon_img.shape[1] if n_bins is None else n_bins
     # work around a bug in STIR with start_angle = 0
@@ -89,12 +89,22 @@ def forward_project(
     header_proj = TEMPLATE_HEADER_PROJ.replace("{DATA_FILE}", filename_proj_data)
     header_proj = header_proj.replace("{SLICES}", str(n_slices))
     header_proj = header_proj.replace("{BINS}", str(n_bins))
-    header_proj = header_proj.replace("{SPACING_SLICES}", recon_header[InterfileKeys.spacing(3)])
-    header_proj = header_proj.replace("{SPACING_BINS}", recon_header[InterfileKeys.spacing(1)])
+    header_proj = header_proj.replace(
+        "{SPACING_SLICES}", recon_header[InterfileKeys.spacing(3)]
+    )
+    header_proj = header_proj.replace(
+        "{SPACING_BINS}", recon_header[InterfileKeys.spacing(1)]
+    )
     header_proj = header_proj.replace("{N_PROJECTIONS}", str(n_projections))
     header_proj = header_proj.replace("{ROTATION}", str(rotation))
     header_proj = header_proj.replace("{START_ANGLE}", str(start_angle))
     header_proj = header_proj.replace("{RADIUS}", str(radius))
+    header_proj = header_proj.replace(
+        "{PATIENT_ORIENTATION}", recon_header[InterfileKeys.patient_orientation]
+    )
+    header_proj = header_proj.replace(
+        "{PATIENT_ROTATION}", recon_header[InterfileKeys.patient_rotation]
+    )
     header_proj = header_proj.strip()
 
     # write temporary files to configure the projection with STIR
@@ -107,7 +117,7 @@ def forward_project(
         f.write(header_proj)
     with open(os.path.join(dir_tmp.name, filename_proj_data), mode="wb") as f:
         f.write(b"")
-    write_interfile(filename_recon, recon_header, recon_img)
+    write_interfile(filename_recon, recon)
 
     projdata = stir.ProjData.read_from_file(filename_proj_header)
     recon = stir.FloatVoxelsOnCartesianGrid.read_from_file(filename_recon)
@@ -177,6 +187,13 @@ if __name__ == "__main__":
 
     stir.Verbosity_set(args.verbosity)
 
-    header, image = load_as_interfile(args.recon)
-    header, image = forward_project(header, image, **vars(args))
-    write_interfile(args.out, header, image)
+    recon = load_as_interfile(args.recon)
+    projection = forward_project(
+        recon,
+        n_slices=args.n_slices,
+        n_projections=args.n_projections,
+        rotation=args.rotation,
+        start_angle=args.start_angle,
+        radius=args.radius,
+    )
+    write_interfile(args.out, projection)