From 3370f8c1fd3bfced0f7a5ab345a354fb1275bf2c Mon Sep 17 00:00:00 2001
From: Brenden <brenden.kadota@gmail.com>
Date: Fri, 17 Jun 2022 12:27:39 -0700
Subject: [PATCH] created addphase function

---
 processingTools/MRSI/op_CSIaddPhase.m | 53 +++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 processingTools/MRSI/op_CSIaddPhase.m

diff --git a/processingTools/MRSI/op_CSIaddPhase.m b/processingTools/MRSI/op_CSIaddPhase.m
new file mode 100644
index 00000000..e29da464
--- /dev/null
+++ b/processingTools/MRSI/op_CSIaddPhase.m
@@ -0,0 +1,53 @@
+% op_CSIaddPhase.m
+% Brenden Kadota, Sunnybrook 2022
+%
+% CSI version of op_addPhase. Takes in MRSI structure, zeroth order phase,
+% second order phase, and pivot to apply phase corrections. Adds phase to either
+% time domain or frequency domain depending on the data dype in the data field.
+%
+% Input:
+% MRSIStuct       = MRSI structure used in FID-A
+% ph0             = First order phase in degrees (deg)
+% ph1             = Second order phase in seconds (s) [default: 0]
+% ppm0            = Frequency reference point (ppm) [default: 4.65]
+% suppressPlot    = Plotting of frequency corrected (boolean) [default: 1]. Be
+%                   careful with this option! Plots one figure for each voxel!!!
+%
+% Output:
+% MRSIStruct      = MRSI structure used in FID-A
+
+
+function MRSIStruct = op_CSIaddPhase(MRSIStruct, ph0, ph1, ppm0, suppressPlot)
+arguments
+    MRSIStruct (1, 1) struct
+    ph0 (1, 1) double 
+    ph1 (1, 1) double = 0
+    ppm0 (1, 1) double = 4.65
+    suppressPlot (1, 1) logical = 1
+end
+    checkArguments(MRSIStruct);
+    [MRSIStruct, prevPermute, prevShape] = reshapeDimensions(MRSIStruct, {'t', 'y', 'x'});
+    data = getData(MRSIStruct);
+    for e = 1:getSizeFromDimensions(MRSIStruct, {'extras'})
+        for x = 1:getSizeFromDimensions(MRSIStruct, {'x'})
+            for y = 1:getSizeFromDimensions(MRSIStruct, {'y'})
+                mrs = op_CSItoMRS(MRSIStruct, x, y, 'extraIndex', e); 
+                mrs = op_addphase(mrs, ph0, ph1, ppm0, suppressPlot);
+                if(getFlags(MRSIStruct, 'spectralFT'))
+                    data(:, y, x, e) = mrs.specs;
+                else
+                    data(:, y, x, e) = mrs.fids;
+                end
+            end
+        end
+    end
+    MRSIStruct = setData(MRSIStruct, data);
+    MRSIStruct = reshapeBack(MRSIStruct, prevPermute, prevShape);
+
+end
+
+function checkArguments(MRSIStruct)
+    if(getFlags(MRSIStruct, 'spatialFT') == 0)
+        error('Please fourier transform along the spectral dimension')
+    end
+end