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Store tissue map in SimData object #152

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Store tissue map in SimData object #152

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35 changes: 12 additions & 23 deletions python/MRzeroCore/phantom/voxel_grid_phantom.py
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Original file line number Diff line number Diff line change
Expand Up @@ -181,7 +181,7 @@ def dephasing_func(t, _): return identity(t)
recover_func=lambda data: recover(mask, data),
phantom_motion=self.phantom_motion,
voxel_motion=self.voxel_motion,
tissue_masks=self.tissue_masks
tissue_masks=mask
)

@classmethod
Expand Down Expand Up @@ -312,11 +312,6 @@ def select(tensor: torch.Tensor):
return tensor[..., slices].view(
*list(self.PD.shape[:2]), len(slices)
)
def select_multicoil(tensor: torch.Tensor):
coils = tensor.shape[0]
return tensor[..., slices].view(
coils, *list(self.PD.shape[:2]), len(slices)
)

return VoxelGridPhantom(
select(self.PD),
Expand All @@ -325,8 +320,8 @@ def select_multicoil(tensor: torch.Tensor):
select(self.T2dash),
select(self.D),
select(self.B0),
select_multicoil(self.B1),
select_multicoil(self.coil_sens),
select(self.B1).unsqueeze(0),
select(self.coil_sens).unsqueeze(0),
self.size.clone(),
tissue_masks={
key: mask[..., slices] for key, mask in self.tissue_masks.items()
Expand Down Expand Up @@ -438,7 +433,7 @@ def resample_masks(tensors: Dict) -> Optional[Dict]:
tissue_masks=resample_masks(self.tissue_masks)
)

def plot(self, plot_masks=False, plot_slice="center", time_unit='s') -> None:
def plot(self, plot_masks=False, plot_slice="center") -> None:
"""
Print and plot all data stored in this phantom.

Expand All @@ -449,8 +444,6 @@ def plot(self, plot_masks=False, plot_slice="center", time_unit='s') -> None:
slice : str | int
If int, the specified slice is plotted. "center" plots the center
slice and "all" plots all slices as a grid.
time_unit : str
Time unit to use for T1, T2, and T2' maps (default: 's'). Supported 's' and 'ms'.
"""
print("VoxelGridPhantom")
print(f"size = {self.size}")
Expand All @@ -459,7 +452,7 @@ def plot(self, plot_masks=False, plot_slice="center", time_unit='s') -> None:
s = self.PD.shape[2] // 2
elif plot_slice == "all":
s = slice(None)
elif isinstance(plot_slice, int):
elif plot_slice is int:
s = plot_slice
else:
raise ValueError("expected plot_slice to be 'all', 'center' or an integer")
Expand All @@ -471,10 +464,6 @@ def plot(self, plot_masks=False, plot_slice="center", time_unit='s') -> None:
if self.PD.shape[2] > 1:
print(f"Plotting slice {s} / {self.PD.shape[2]}")


# Get time unit scaling factor
time_factor = 1000 if time_unit == 'ms' else 1

# Determine the number of subplots needed
num_plots = 9 # Base number of plots without masks
if plot_masks:
Expand All @@ -494,18 +483,18 @@ def plot(self, plot_masks=False, plot_slice="center", time_unit='s') -> None:
plt.colorbar()

plt.subplot(rows, cols, 2)
plt.title("T1 (%s)" % time_unit)
imshow(self.T1[:, :, s]*time_factor, vmin=0)
plt.title("T1")
imshow(self.T1[:, :, s], vmin=0)
plt.colorbar()

plt.subplot(rows, cols, 3)
plt.title("T2 (%s)" % time_unit)
imshow(self.T2[:, :, s]*time_factor, vmin=0)
plt.title("T2")
imshow(self.T2[:, :, s], vmin=0)
plt.colorbar()

plt.subplot(rows, cols, 4)
plt.title("T2' (%s)" % time_unit)
imshow(self.T2dash[:, :, s]*time_factor, vmin=0)
plt.title("T2'")
imshow(self.T2dash[:, :, s], vmin=0)
plt.colorbar()

plt.subplot(rows, cols, 5)
Expand Down Expand Up @@ -564,7 +553,7 @@ def plot3D(self, data2print: int = 0) -> None:

def recover(mask, sim_data: SimData) -> VoxelGridPhantom:
"""Provided to :class:`SimData` to reverse the ``build()``"""

mask = mask.to(sim_data.device)

def to_full(sparse):
Expand Down
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