From 8cd006849be73376e58ef4b526b398413bd2a166 Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Thu, 24 Jun 2021 14:46:28 +0100
Subject: [PATCH] fixed simplistic_petmr.py example

- replace constructor from sirf.Gadgetron.ImageData with "manual" construction
- fix sirf.STIR.ImageData doc for constructor

Fixes #974
---
 examples/Python/PETMR/simplistic_petmr.py | 18 ++++++++++++++----
 src/xSTIR/pSTIR/STIR.py                   |  3 ++-
 2 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/examples/Python/PETMR/simplistic_petmr.py b/examples/Python/PETMR/simplistic_petmr.py
index acc20732e..19bfe3874 100644
--- a/examples/Python/PETMR/simplistic_petmr.py
+++ b/examples/Python/PETMR/simplistic_petmr.py
@@ -3,6 +3,8 @@
 Usage:
   simplistic_petmr [--help | options]
 
+This demo currently only shows how to convert an MR image to a PET object.
+
 Options:
   -f <file>, --file=<file>  raw data file
                             [default: simulated_MR_2D_cartesian.h5]
@@ -14,7 +16,7 @@
 
 ## SyneRBI Synergistic Image Reconstruction Framework (SIRF)
 ## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC
-## Copyright 2015 - 2017 University College London.
+## Copyright 2015 - 2017, 2021 University College London.
 ##
 ## This is software developed for the Collaborative Computational
 ## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR)
@@ -31,10 +33,11 @@
 ##   limitations under the License.
 
 # import common (engine-independent) utilities
-import pUtilities as pUtil
+import sirf.Utilities as pUtil
+import numpy
 
 # get command-line arguments
-__version__ = '0.1.0'
+__version__ = '0.2.0'
 from docopt import docopt
 args = docopt(__doc__, version=__version__)
 
@@ -66,7 +69,14 @@ def main():
 
 # PET
     # convert MR image into PET image
-    image = PET.ImageData(complex_image)
+    # At present, we cannot do the following yet
+    #image = PET.ImageData(complex_image)
+    # So, instead we do it "by hand".
+    # Note however that the lines below ignore any orientation (TODO)
+    image = PET.ImageData()
+    image.initialise(complex_image.dimensions(), complex_image.get_geometrical_info().get_spacing())
+    image.fill(numpy.abs(complex_image.as_array()))
+    # should give the same values as the MR ones
     print(image.norm())
     print(image.dot(image))
     # apply filter that zeroes the image outside a cylinder of the same
diff --git a/src/xSTIR/pSTIR/STIR.py b/src/xSTIR/pSTIR/STIR.py
index 86276c9ca..ef0fe1b02 100644
--- a/src/xSTIR/pSTIR/STIR.py
+++ b/src/xSTIR/pSTIR/STIR.py
@@ -286,9 +286,10 @@ def __init__(self, arg=None):
             arg : Python str or AcquisitionData or None, interpreted as follows:
         str            : read the object from a file specified by <arg>
                          (the file format has to be support by STIR).
-        AcquisitionData: create an object compatible with the scanner data
+        STIR.AcquisitionData: create an object compatible with the scanner data
                          recorded in an AcquisitionData object <arg>.
                          This sets default voxel sizes.
+        SIRF.ImageData : (attempt to) convert data from another SIRF ImageData container.
         None           : create an empty ImageData object. Call initialise()
                          method before using it.
         """