Merge pull request #7 from gschramm/main

update README and clean up
ETSIhackers · Nov 16, 2023 · 9cc443d · 9cc443d
2 parents 72bbf60 + 2f07cc5
commit 9cc443d
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -50,6 +50,8 @@ jobs:
         run: |
           cd python
           python start.py
+          python 00_simulate_lm_data.py
+          python 01_reconstruct_lm_data.py
 
       - name: Cpp
         run: |

diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.12.0) # older would work, but could give warnings on policy CMP0074
-project(PETSIRDUseCaseTemplate VERSION 0.1.0)
+project(LMSimRecon VERSION 0.1.0)
 
 set(CMAKE_CXX_STANDARD 17)
 

diff --git a/python/00_simulate_lm_data.py b/python/00_simulate_lm_data.py
@@ -5,7 +5,7 @@
 
 import prd
 import parallelproj
-import utils
+import parallelproj_utils
 import array_api_compat.numpy as np
 import matplotlib.pyplot as plt
 from array_api_compat import to_device
@@ -41,7 +41,7 @@
 
 # setup a line of response descriptor that describes the LOR start / endpoints of
 # a "narrow" clinical PET scanner with 9 rings
-lor_descriptor = utils.DemoPETScannerLORDescriptor(
+lor_descriptor = parallelproj_utils.DemoPETScannerLORDescriptor(
     xp, dev, num_rings=4, radial_trim=141
 )
 
@@ -79,7 +79,7 @@
 res_model = parallelproj.GaussianFilterOperator(
     img_shape, sigma=4.5 / (2.355 * xp.asarray(voxel_size))
 )
-projector = utils.RegularPolygonPETProjector(
+projector = parallelproj_utils.RegularPolygonPETProjector(
     lor_descriptor, img_shape, voxel_size, resolution_model=res_model
 )
 projector.tof = True  # set this to True to get a time of flight projector

diff --git a/python/README.md b/python/README.md
@@ -1,6 +1,6 @@
-# PETSIRD basic Python example
+# Simulation and Reconstruction of PETSIRD listmode data
 
-This directory contains some instructions to wrote Python code to read/write PETSIRD data. You need to `yardl generate` in the `model` directory first.
+This repository contains minimal python examples that simulate and reconstruct
+PETSIRD listmode data using the [parallelproj](https://github.com/gschramm/parallelproj) projectors.
 
-As we currently do not have a `set_up.py` for PETSIRD yet, the example file hard-codes the path to the generated files.
-Alternatives would be to use the `PYTHONPATH` environment variable or symbolic links.
+Before running the example python scripts, make sure to generate the PETSIRD yardl model.
diff --git a/python/parallelproj_sim.py b/python/parallelproj_sim.py