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fix shape returned after zero filling #7

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fix shape returned after zero filling #7

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21 changes: 18 additions & 3 deletions src/twix_recon/twix.py
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Original file line number Diff line number Diff line change
Expand Up @@ -206,7 +206,7 @@ def _performNoiseDecorr(self, data):
def _fixShapeAndIFFT(self):
sz = self.sig.shape
trg_sz = [self.sig.shape[0], int(self.twix.hdr.Meas.iRoFTLength)//2, int(self.twix.hdr.Meas.iPEFTLength), int(self.twix.hdr.Meas.i3DFTLength)]
diff_sz = np.array(trg_sz) - np.array(sz)
diff_sz = np.array(sz) - np.array(trg_sz)
shift = np.floor(diff_sz / 2).astype(int)

ixin1 = np.maximum(shift, 0)
Expand All @@ -215,8 +215,7 @@ def _fixShapeAndIFFT(self):
ixout2 = np.abs(np.minimum(shift, 0)) + np.minimum(sz, trg_sz)

sig_r = np.zeros(trg_sz, dtype=self.sig.dtype)

sig_r[:, ixin1[1]:ixin2[1], ixin1[2]:ixin2[2], ixin1[3]:ixin2[3]] = self.sig[:, ixout1[1]:ixout2[1], ixout1[2]:ixout2[2], ixout1[3]:ixout2[3]]
sig_r[:, ixout1[1]:ixout2[1], ixout1[2]:ixout2[2], ixout1[3]:ixout2[3]] = self.sig[:, ixin1[1]:ixin2[1], ixin1[2]:ixin2[2], ixin1[3]:ixin2[3]]

for nc in range(sig_r.shape[0]):
sig_tmp = torch.from_numpy(sig_r[nc])
Expand All @@ -225,6 +224,22 @@ def _fixShapeAndIFFT(self):
sig_r[nc] = sig_tmp.cpu().numpy()

self.sig = sig_r
sz = trg_sz

# image space
trg_sz = [self.sig.shape[0], int(self.twix.hdr.Config.NImageCols), int(self.twix.hdr.Config.NImageLins), int(self.twix.hdr.Config.NoImagesPerSlab)]
diff_sz = sz - np.array(trg_sz)
shift = np.floor(diff_sz / 2).astype(int)

ixin1 = np.maximum(shift, 0)
ixin2 = np.maximum(shift, 0) + np.minimum(sz, trg_sz)
ixout1 = np.abs(np.minimum(shift, 0))
ixout2 = np.abs(np.minimum(shift, 0)) + np.minimum(sz, trg_sz)

sig_temp = np.zeros(trg_sz, dtype=self.sig.dtype)
sig_temp[:, ixout1[1]:ixout2[1], ixout1[2]:ixout2[2], ixout1[3]:ixout2[3]] = self.sig[:, ixin1[1]:ixin2[1], ixin1[2]:ixin2[2], ixin1[3]:ixin2[3]]

self.sig = sig_temp

def runReco(self):
if self.doNoiseDecorr:
Expand Down