diff --git a/mu_map/recon/project.py b/mu_map/recon/project.py index fbf76861a1c88337c85d8d45011bee74f074f545..5aaaa900a69717e7fd6bb9c206a46f212aab0e46 100644 --- a/mu_map/recon/project.py +++ b/mu_map/recon/project.py @@ -18,37 +18,35 @@ from mu_map.file.interfile import ( A template for a header of a projection in INTERFILE format. """ TEMPLATE_HEADER_PROJ = """ -!INTERFILE := -!imaging modality := nucmed -!version of keys := 3.3 +INTERFILE := +imaging modality := nucmed +version of keys := 3.3 name of data file := {DATA_FILE} -;data offset in bytes := 0 -!GENERAL IMAGE DATA := -!type of data := Tomographic +GENERAL IMAGE DATA := +type of data := Tomographic imagedata byte order := LITTLEENDIAN -!number format := float -!number of bytes per pixel := 4 +number format := float +number of bytes per pixel := 4 -!SPECT STUDY (General) := -;number of dimensions := 2 +SPECT STUDY (General) := ;matrix axis label [2] := axial coordinate -!matrix size [2] := {SLICES} -!scaling factor (mm/pixel) [2] := {SPACING_SLICES} +matrix size [2] := {SLICES} +scaling factor (mm/pixel) [2] := {SPACING_SLICES} ;matrix axis label [1] := bin coordinate -!matrix size [1] := {BINS} -!scaling factor (mm/pixel) [1] := {SPACING_BINS} -!number of projections := {N_PROJECTIONS} -!extent of rotation := {ROTATION} -!process status := acquired - -!SPECT STUDY (acquired data) := -!direction of rotation := CW +matrix size [1] := {BINS} +scaling factor (mm/pixel) [1] := {SPACING_BINS} +number of projections := {N_PROJECTIONS} +extent of rotation := {ROTATION} +process status := acquired + +SPECT STUDY (acquired data) := +direction of rotation := CW start angle := {START_ANGLE} orbit := circular radius := {RADIUS} -!END OF INTERFILE := +END OF INTERFILE := """ @@ -133,8 +131,7 @@ def forward_project( if __name__ == "__main__": import argparse - from mu_map.file.dicom import load_dcm - from mu_map.file.dicom_to_interfile import to_interfile + from mu_map.file import load_as_interfile parser = argparse.ArgumentParser( description="Forward project a reconstruction with STIR", @@ -179,11 +176,6 @@ if __name__ == "__main__": stir.Verbosity_set(args.verbosity) - _, ext = os.path.splitext(args.recon) - if ext == ".dcm": - header, image = to_interfile(*load_dcm(args.recon)) - else: - header, image = load_interfile(args.recon) - + header, image = load_as_interfile(args.recon) header, image = forward_project(header, image, **vars(args)) write_interfile(args.out, header, image)