From 4bda72739f01c1e79fc21c4f33b84e6e7c7854d5 Mon Sep 17 00:00:00 2001
From: Casper da Costa-Luis <casper.dcl@physics.org>
Date: Wed, 11 Sep 2024 14:33:51 +0100
Subject: [PATCH] slight lint

---
 SIRF_data_preparation/Mediso_NEMA_IQ/README.md  | 2 +-
 SIRF_data_preparation/Mediso_NEMA_IQ/prepare.py | 5 +++--
 SIRF_data_preparation/plot_BSREM_metrics.py     | 4 ++--
 petric.py                                       | 3 ++-
 4 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/SIRF_data_preparation/Mediso_NEMA_IQ/README.md b/SIRF_data_preparation/Mediso_NEMA_IQ/README.md
index 670bce5..3aaec0a 100644
--- a/SIRF_data_preparation/Mediso_NEMA_IQ/README.md
+++ b/SIRF_data_preparation/Mediso_NEMA_IQ/README.md
@@ -12,7 +12,7 @@ cd Mediso_NEMA_IQ/
 # trim sinograms to avoid "corner" problems in mult_factors
 # TODO for next data: use 30 (as some problems remain)
 for f in additive_term.hs  mult_factors.hs  prompts.hs; do
-   SSRB -t 20 $f $orgpath/sinograms/$f; 
+   SSRB -t 20 $f $orgpath/sinograms/$f
 done
 # alternative if we don't need to trim
 #cp -rp $orgpath/sinograms/* .
diff --git a/SIRF_data_preparation/Mediso_NEMA_IQ/prepare.py b/SIRF_data_preparation/Mediso_NEMA_IQ/prepare.py
index 68c2f42..82ad5f6 100644
--- a/SIRF_data_preparation/Mediso_NEMA_IQ/prepare.py
+++ b/SIRF_data_preparation/Mediso_NEMA_IQ/prepare.py
@@ -1,10 +1,11 @@
 # Set NaNs to zero in additive_term
-import sirf.STIR
 import numpy as np
+
+import sirf.STIR
+
 additive = sirf.STIR.AcquisitionData('additive_term.hs')
 add_arr = additive.as_array()
 add_arr = np.nan_to_num(add_arr)
 new_add = additive.clone()
 new_add.fill(add_arr)
 new_add.write('additive_term.hs')
-
diff --git a/SIRF_data_preparation/plot_BSREM_metrics.py b/SIRF_data_preparation/plot_BSREM_metrics.py
index a5d0606..39bb828 100644
--- a/SIRF_data_preparation/plot_BSREM_metrics.py
+++ b/SIRF_data_preparation/plot_BSREM_metrics.py
@@ -1,4 +1,4 @@
-#%%
+# %%
 # """Preliminary file to check evolution of metrics as well as pass_index"""
 # %load_ext autoreload
 # %autoreload 2
@@ -71,7 +71,7 @@
     reference_image = STIR.ImageData(str(datadir / 'iter_final.hv'))
 qm = QualityMetrics(reference_image, data.whole_object_mask, data.background_mask, tb_summary_writer=None,
                     voi_mask_dict=data.voi_masks)
-#%% get update ("iteration") numbers from objective functions
+# %% get update ("iteration") numbers from objective functions
 last_iteration = int(objs[-1, 0] + .5)
 # find interval(don't use last value, as that interval can be smaller)
 iteration_interval = int(objs[-2, 0] - objs[-3, 0] + .5)
diff --git a/petric.py b/petric.py
index 18fb47a..bef5936 100755
--- a/petric.py
+++ b/petric.py
@@ -141,7 +141,8 @@ def keys(self):
 
 class MetricsWithTimeout(cil_callbacks.Callback):
     """Stops the algorithm after `seconds`"""
-    def __init__(self, seconds=600, outdir=OUTDIR, transverse_slice=None, coronal_slice=None, sagittal_slice=None, **kwargs):
+    def __init__(self, seconds=600, outdir=OUTDIR, transverse_slice=None, coronal_slice=None, sagittal_slice=None,
+                 **kwargs):
         super().__init__(**kwargs)
         self._seconds = seconds
         self.callbacks = [