print settings and add updates option for run_OSEM

SyneRBI · Oct 9, 2024 · 5b86e1a · 5b86e1a
1 parent 0436d4d
commit 5b86e1a
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Showing 3 changed files with 14 additions and 7 deletions.
diff --git a/SIRF_data_preparation/create_Hoffman_VOIs.py b/SIRF_data_preparation/create_Hoffman_VOIs.py
@@ -65,9 +65,10 @@
 os.makedirs(downloaddir, exist_ok=True)
 os.makedirs(intermediate_data_path, exist_ok=True)
 
-print(
-    f"srcdir: {srcdir}\ndownloaddir: {downloaddir}\nprocessingdir: {intermediate_data_path}\nwrite_VOIs: {write_PETRIC_VOIs}"
-)
+print("srcdir:", srcdir)
+print("downloaddir:", downloaddir)
+print("processingdir:", intermediate_data_path)
+print("write_VOIs:", write_PETRIC_VOIs)
 
 
 # %% Function to find the n-th connected component (counting by size)

diff --git a/SIRF_data_preparation/run_BSREM.py b/SIRF_data_preparation/run_BSREM.py
@@ -32,7 +32,6 @@
 
 scanID = args['<data_set>']
 num_updates = int(args['--updates'])
-print(f"num_updates {num_updates}")
 
 if not all((SRCDIR.is_dir(), OUTDIR.is_dir())):
     PETRICDIR = Path('~/devel/PETRIC').expanduser()
@@ -46,6 +45,9 @@
 settings = get_settings(scanID)
 
 data = get_data(srcdir=srcdir, outdir=outdir)
+print("Penalisation factor:", data.prior.get_penalisation_factor())
+print("num_subsets:", settings.num_subsets)
+print("num_updates:", num_updates)
 data_sub, acq_models, obj_funs = partitioner.data_partition(data.acquired_data, data.additive_term, data.mult_factors,
                                                             settings.num_subsets, mode="staggered",
                                                             initial_image=data.OSEM_image)

diff --git a/SIRF_data_preparation/run_OSEM.py b/SIRF_data_preparation/run_OSEM.py
@@ -6,12 +6,13 @@
 Arguments:
   <data_set>  path to data files as well as prefix to use
 
+Options:
+  --updates=<u>  number of updates to run [default: 400]
 """
 # Copyright 2024 Rutherford Appleton Laboratory STFC
 # Copyright 2024 University College London
 # Licence: Apache-2.0
-__version__ = '0.1.0'
-
+__version__ = '0.2.0'
 from pathlib import Path
 
 import matplotlib.pyplot as plt
@@ -27,6 +28,7 @@
 # logging.basicConfig(level=logging.INFO)
 
 scanID = args['<data_set>']
+num_updates = int(args['--updates'])
 
 if not all((SRCDIR.is_dir(), OUTDIR.is_dir())):
     PETRICDIR = Path('~/devel/PETRIC').expanduser()
@@ -40,9 +42,11 @@
 settings = get_settings(scanID)
 
 data = get_data(srcdir=srcdir, outdir=outdir)
+print("num_subsets:", settings.num_subsets)
+print("num_updates:", num_updates)
 # %%
 algo = main_OSEM.Submission(data, settings.num_subsets, update_objective_interval=20)
-algo.run(400, callbacks=[MetricsWithTimeout(**settings.slices, seconds=5000, outdir=outdir)])
+algo.run(num_updates, callbacks=[MetricsWithTimeout(**settings.slices, seconds=5000, outdir=outdir)])
 # %%
 fig = plt.figure()
 data_QC.plot_image(algo.get_output(), **settings.slices)