From 34771daa0441760ef7f5a74878291e2698c62462 Mon Sep 17 00:00:00 2001
From: Ameya Khot <90050951+ameyakhot@users.noreply.github.com>
Date: Sat, 8 Jun 2024 17:57:17 -0500
Subject: [PATCH 1/3] Issue410: Added groundtruth comparion flags to
 ./Python/tigre/algorithms/iterative_recon_alg.py and
 ./Python/tigre/algorithms/single_pass_algorithms.py

---
 Python/tigre/algorithms/iterative_recon_alg.py    | 9 +++++++++
 Python/tigre/algorithms/single_pass_algorithms.py | 5 ++++-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/Python/tigre/algorithms/iterative_recon_alg.py b/Python/tigre/algorithms/iterative_recon_alg.py
index b882b97b..47b7487b 100644
--- a/Python/tigre/algorithms/iterative_recon_alg.py
+++ b/Python/tigre/algorithms/iterative_recon_alg.py
@@ -92,6 +92,12 @@ class IterativeReconAlg(object):
             OS_SART_TV
             FISTA
 
+            
+    :keyword groundtruth: ()
+        groundtruth image for comparison with the reconstruction.
+        Default is None
+
+
     Usage
     --------
     >>> import numpy as np
@@ -133,6 +139,9 @@ def __init__(self, proj, geo, angles, niter, **kwargs):
         self.angles = angles
         self.geo = geo
         self.niter = niter
+        
+        # adding groundtruth comparison
+        self.groundtruth = None if "groundtruth" not in kwargs else kwargs["groundtruth"]
 
         self.geo.check_geo(angles)
 
diff --git a/Python/tigre/algorithms/single_pass_algorithms.py b/Python/tigre/algorithms/single_pass_algorithms.py
index 7ab33f71..f2442268 100644
--- a/Python/tigre/algorithms/single_pass_algorithms.py
+++ b/Python/tigre/algorithms/single_pass_algorithms.py
@@ -70,9 +70,10 @@ def FDK(proj, geo, angles, **kwargs):
                         PYTHON : Reuben Lindroos
     """
     verbose = kwargs["verbose"] if "verbose" in kwargs else False
-
     gpuids = kwargs["gpuids"] if "gpuids" in kwargs else None
     dowang = kwargs["dowang"] if "dowang" in kwargs else False
+    # adding groundtruth comparison
+    groundtruth = None if "groundtruth" not in kwargs else kwargs["groundtruth"]
 
     def zeropadding(proj, geo):
         zgeo = copy.deepcopy(geo)
@@ -192,4 +193,6 @@ def fbp(proj, geo, angles, **kwargs):  # noqa: D103
     gpuids = kwargs["gpuids"] if "gpuids" in kwargs else None
     proj_filt = filtering(copy.deepcopy(proj), geox,
                           angles, parker=False, verbose=verbose)
+    # adding groundtruth comparison 
+    groundtruth = None if "groundtruth" not in kwargs else kwargs["groundtruth"]
     return Atb(proj_filt, geo, angles, gpuids=gpuids) * geo.DSO / geo.DSD

From 69afbcf94ec3ffa20d1fcd15e800805540ff577a Mon Sep 17 00:00:00 2001
From: Ameya Khot <90050951+ameyakhot@users.noreply.github.com>
Date: Mon, 17 Jun 2024 17:18:19 -0500
Subject: [PATCH 2/3] Added a small functionality to Iterative_recon_alg - ref
 SART.m

---
 Python/tigre/algorithms/iterative_recon_alg.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/Python/tigre/algorithms/iterative_recon_alg.py b/Python/tigre/algorithms/iterative_recon_alg.py
index 47b7487b..9994ecca 100644
--- a/Python/tigre/algorithms/iterative_recon_alg.py
+++ b/Python/tigre/algorithms/iterative_recon_alg.py
@@ -212,6 +212,9 @@ def __init__(self, proj, geo, angles, niter, **kwargs):
             self.Quameasopts = (
                 [self.Quameasopts] if isinstance(self.Quameasopts, str) else self.Quameasopts
             )
+            # appending error_norm is groundtruth is Null
+            if self.groundtruth is not None:
+                self.Quameasopts.append('error_norm')
             setattr(self, "lq", np.zeros([len(self.Quameasopts), niter]))  # quameasoptslist
         else:
             setattr(self, "lq", np.zeros([0, niter]))  # quameasoptslist
@@ -320,7 +323,8 @@ def run_main_iter(self):
         Quameasopts = self.Quameasopts
 
         for i in range(self.niter):
-
+            # init Quameasopts
+            Quameasopts = self.Quameasopts
             res_prev = None
             if Quameasopts is not None:
                 res_prev = copy.deepcopy(self.res)
@@ -366,7 +370,10 @@ def minimizeAwTV(self, res_prev, dtvg):
 
     def error_measurement(self, res_prev, iter):
         if self.Quameasopts is not None:
-            self.lq[:, iter] = MQ(self.res, res_prev, self.Quameasopts)
+            if self.groundtruth is not None:
+                self.lq[:, iter] = MQ(self.res, self.groundtruth, self.Quameasopts)
+            else:
+                self.lq[:, iter] = MQ(self.res, res_prev, self.Quameasopts)
         if self.computel2:
             # compute l2 borm for b-Ax
             errornow = im3DNORM(

From 091f0fe83e487c1a8509b294395ebe864935cd5a Mon Sep 17 00:00:00 2001
From: Ameya Khot <90050951+ameyakhot@users.noreply.github.com>
Date: Wed, 19 Jun 2024 23:11:05 -0500
Subject: [PATCH 3/3] added a comment for now for tasklist

---
 Python/tigre/algorithms/iterative_recon_alg.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Python/tigre/algorithms/iterative_recon_alg.py b/Python/tigre/algorithms/iterative_recon_alg.py
index 9994ecca..898e5c3e 100644
--- a/Python/tigre/algorithms/iterative_recon_alg.py
+++ b/Python/tigre/algorithms/iterative_recon_alg.py
@@ -497,3 +497,5 @@ def iterativereconalg(proj, geo, angles, niter, **kwargs):
 
 
 iterativereconalg = decorator(IterativeReconAlg)
+
+# have to find a usecase to groundtruth comparing with matlab
\ No newline at end of file