Merge pull request #158 from timwahoo/main

Adding brkrecon CLI and minor updates

brkraw/lib/recoFunctions.py

@@ -68,7 +68,6 @@ def reco_phase_rotate(frame, Reco, actual_framenumber):
 
     # import variables
     RECO_rotate_all = get_value(Reco,'RECO_rotate')
-
 
     if RECO_rotate_all.shape[1] > actual_framenumber:
         RECO_rotate =  get_value(Reco,'RECO_rotate')[:, actual_framenumber]
@@ -89,13 +88,12 @@ def reco_phase_rotate(frame, Reco, actual_framenumber):
     phase_matrix = np.ones_like(frame)
     for index in range(len(RECO_rotate)):
         f = np.arange(dims[index])
-        #print(f)
+
         if RECO_ft_mode in ['COMPLEX_FT', 'COMPLEX_FFT']:
             phase_vector = np.exp(1j*2*np.pi*RECO_rotate[index]*f)
         elif RECO_ft_mode in ['NO_FT', 'NO_FFT']:
             phase_vector = np.ones_like(f)
         elif RECO_ft_mode in ['COMPLEX_IFT', 'COMPLEX_IFFT']:
-            #print(RECO_rotate[index])
             phase_vector = np.exp(1j*2*np.pi*(1-RECO_rotate[index])*f)
         else:
             raise ValueError('Your RECO_ft_mode is not supported')
@@ -192,7 +190,7 @@ def reco_FT(frame, Reco, actual_framenumber):
     elif RECO_ft_mode in ['NO_FT', 'NO_FFT']:
         pass
     elif RECO_ft_mode in ['COMPLEX_IFT', 'COMPLEX_IFFT']:
-        frame = np.fft.fftn(frame)
+        frame = np.fft.ifftn(frame)
         #frame = sp.ifft(frame, axes=[0,1,2], center=False)
     else:
         raise ValueError('Your RECO_ft_mode is not supported')
@@ -236,20 +234,20 @@ def reco_cutoff(frame, Reco, actual_framenumber):
     # Use function only if Reco.RECO_size is not equal to size(frame)
     dim_equal = True
     for i,j in zip(get_value(Reco,'RECO_size'), frame.shape):
-        dim_equal = (i==j)
-
-    if not dim_equal:
-
+        if i!=j:
+            dim_equal = False
+
+    if not dim_equal:      
         # Import variables
         RECO_offset = get_value(Reco,'RECO_offset')[:, actual_framenumber]
         RECO_size = get_value(Reco, 'RECO_size')
 
         # Cut the new part with RECO_size and RECO_offset
         pos_ges = []
         for i in range(len(RECO_size)):
-
             pos_ges.append(slice(RECO_offset[i], RECO_offset[i] + RECO_size[i]))
         newframe = frame[tuple(pos_ges)]
+
     else:
         newframe = frame
 

brkraw/lib/recoSigpy.py

@@ -0,0 +1,52 @@
+"""
+Created on Sat Feb 08 2024
+ DEVELOPED FOR BRUKER PARAVISION 360 datasets
+ Below code will work for 3D cartesian sequence 
+ undersampled in the y-z phase view
+ Reconstructions are completed with SIGPY
+
+ THIS IS A WORK IN PROGRESS due to a lack of CS 
+ datasets from PV360.3.3 or higher
+
+@author: Tim Ho (UVA) 
+"""
+
+import sigpy as sp 
+import sigpy.mri as mr
+import numpy as np 
+
+from .utils import get_value
+
+def compressed_sensing_recon(data, acqp, meth, reco, lamda=0.01, method=None):
+    # Meta Variables
+    ky = get_value(meth,'PVM_EncGenSteps1')
+    kz = get_value(meth,'PVM_EncGenSteps2')
+    PVM_EncGenTotalSteps = get_value(meth, 'PVM_EncGenTotalSteps')
+
+    kspaceShape = [1 for _ in range(7)] 
+    RECO_ft_size = get_value(reco, 'RECO_ft_size')
+    NI = get_value(acqp, 'NI')
+    NR = get_value(acqp, 'NR')
+    kspaceShape[1:len(RECO_ft_size)+1] = RECO_ft_size
+    kspaceShape[0] = data.shape[1]
+    kspaceShape[5] = NI 
+    kspaceShape[6] = NR
+
+    # Resort Raw Sorted to K-SPACE
+    frame_sort = data.reshape((NR, PVM_EncGenTotalSteps, NI, kspaceShape[0], RECO_ft_size[0]))
+
+    k_space = np.zeros(shape=kspaceShape, dtype=complex)
+    for index, (i,j) in enumerate(zip(ky,kz)):
+        k_space[:,:,int(i+max(ky)), j+max(kz)+1,0,:,:]= frame_sort[:,index,:,:,:].transpose(2,3,1,0)
+
+
+    N1, N2, N3, N4, N5, N6, N7 = k_space.shape
+    output = np.zeros(shape=(N2,N3,N4,N6,N7), dtype=complex)
+    for NR in range(N7):
+        for NI in range(N6):
+            k_space = np.squeeze(k_space[:,:,:,:,:,NI,NR])
+            # Compressed Sensing
+            sens = mr.app.EspiritCalib(k_space).run()
+            output[:,:,:,NI,NR] = mr.app.L1WaveletRecon(k_space, sens, lamda=lamda).run()
+
+    return output