From e46b35ba1ff01bbbbdbb2016eea19ee50c5becea Mon Sep 17 00:00:00 2001
From: Pawel Markiewicz <p.markiewicz@gmail.com>
Date: Tue, 9 Jan 2024 00:41:55 +0000
Subject: [PATCH] added storing dictionary in break dyanamic alignment with CT

---
 amypet/align_brkdyn_ct.py | 28 ++++++++++++++++++++--------
 1 file changed, 20 insertions(+), 8 deletions(-)

diff --git a/amypet/align_brkdyn_ct.py b/amypet/align_brkdyn_ct.py
index 9ef79bf1..082d47fc 100644
--- a/amypet/align_brkdyn_ct.py
+++ b/amypet/align_brkdyn_ct.py
@@ -19,7 +19,7 @@
 
 
 
-def align_break_petct(niidat, cts, Cnt, qcpth=None, refpetidx=None):
+def align_break_petct(niidat, cts, Cnt, qcpth=None, refpetidx=None, use_stored=False):
     '''
     Align PET images in break dynamic acquisition
     using the CT for aligning all frames within each acquisition
@@ -39,6 +39,23 @@ def align_break_petct(niidat, cts, Cnt, qcpth=None, refpetidx=None):
                 used as reference instead.
     '''
 
+    # > output path from the input dictionary
+    opth = niidat['outpath'].parent
+
+    # > output path for alignment of CTs
+    algnFpth = opth/(f'aligned_full')
+    affsF = algnFpth/'combined_affines'
+    
+    nimpa.create_dir(algnFpth)
+    nimpa.create_dir(affsF)
+
+    # > output dictionary file
+    fout = algnFpth/'aligned_full_output.npy'
+    if use_stored and fout.is_file():
+        outdct = np.load(fout, allow_pickle=True)
+        outdct = outdct.item()
+        return outdct
+
     # > number of frames for break dynamic acquisitions A and B
     nfrmA = len(niidat['series'][0])
     nfrmB = len(niidat['series'][1])
@@ -65,14 +82,7 @@ def align_break_petct(niidat, cts, Cnt, qcpth=None, refpetidx=None):
     # > alignment results
     algn_frm = [None, None]
 
-    opth = niidat['outpath'].parent
-
-    # > output path for alignment of CTs
-    algnFpth = opth/(f'aligned_full')
-    affsF = algnFpth/'combined_affines'
     
-    nimpa.create_dir(algnFpth)
-    nimpa.create_dir(affsF)
 
     if qcpth is None:
         qcpth = opth/'QC-output'
@@ -343,5 +353,7 @@ def align_break_petct(niidat, cts, Cnt, qcpth=None, refpetidx=None):
     outdct['faffines'] = faffines
     outdct['fnii_com'] = algn_frm[0]['fnii_com'] + algn_frm[1]['fnii_com']
 
+    np.save(fout, outdct)
+
     return outdct