.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "generated/autoexamples/example02_stacked.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_generated_autoexamples_example02_stacked.py: ========================================================= Batched and Stacked Reconstructions with PyGROG ========================================================= This example focuses on stack/batch behavior and trajectory handling. We demonstrate three cases: 1. Same trajectory for all images in a stack (vectorized in one call). 2. Different trajectory for each image in the stack (one plan per image). 3. Two stack axes: one shared trajectory axis and one per-image trajectory axis. .. GENERATED FROM PYTHON SOURCE LINES 14-29 .. code-block:: Python import matplotlib.pyplot as plt import numpy as np from brainweb_dl import get_mri from mrinufft import get_operator, initialize_2D_spiral from mrinufft.density import voronoi from pygrog.calib import GrogInterpolator from pygrog.operator import SparseFFT .. GENERATED FROM PYTHON SOURCE LINES 131-134 .. code-block:: Python vol = get_mri(0, "T1") .. GENERATED FROM PYTHON SOURCE LINES 151-157 Case 1: Shared trajectory across one stack axis ================================================ When all images in a stack use the same trajectory, we can initialize a single :class:`~pygrog.calib.GrogInterpolator` and call :meth:`~pygrog.calib.GrogInterpolator.interpolate` once with batch dimension. .. GENERATED FROM PYTHON SOURCE LINES 157-197 .. code-block:: Python B = 3 images_case1 = vol[88 : 88 + B] density_base = voronoi(samples_base) nufft_shared = get_operator("finufft")( samples=samples_base, shape=shape, n_coils=n_coils, smaps=smaps, density=density_base, squeeze_dims=True, ) ksp_case1 = np.stack( [nufft_shared.op(images_case1[b].astype(np.complex64)) for b in range(B)], axis=0, ) # (B, C, n_samples) ksp_case1 = ksp_case1.reshape(B, n_coils, n_shots, n_read) coords_base = (samples_base * np.asarray(shape, dtype=np.float32)).astype(np.float32) grog_shared = GrogInterpolator( shape=shape, coords=coords_base, kernel_width=2, oversamp=1.25, image_shape=shape, ) grog_shared.calc_interp_table(calib_cart, lamda=0.01, precision=1) sparse_case1 = grog_shared.interpolate(ksp_case1, ret_image=False) sqrt_w = np.asarray(grog_shared.plan.pre_weights) sparse_case1_w = sparse_case1 * sqrt_w op_shared = SparseFFT(plan=grog_shared.plan, smaps=smaps) recon_case1 = np.abs(op_shared.adjoint(sparse_case1_w)) print(f"Case 1 (shared trajectory): {recon_case1.shape}") .. rst-class:: sphx-glr-script-out .. code-block:: none /home/docs/checkouts/readthedocs.org/user_builds/pygrog/envs/latest/lib/python3.12/site-packages/mrinufft/_utils.py:67: UserWarning: Samples will be rescaled to [-pi, pi), assuming they were in [-0.5, 0.5) warnings.warn( Case 1 (shared trajectory): (3, 217, 181) .. GENERATED FROM PYTHON SOURCE LINES 198-202 .. code-block:: Python fig, axes = plt.subplots(2, B, figsize=(4 * B, 6), constrained_layout=True) .. image-sg:: /generated/autoexamples/images/sphx_glr_example02_stacked_001.png :alt: GT #1, GT #2, GT #3, Shared traj recon #1, Shared traj recon #2, Shared traj recon #3 :srcset: /generated/autoexamples/images/sphx_glr_example02_stacked_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 213-219 Case 2: Different trajectory per image in one stack axis ========================================================= Different trajectory per image is handled in one stacked call. ``coords_case2`` carries a non-singleton stack axis (B), so GROG builds one stacked plan and applies all trajectory variants in a single interpolate(). .. GENERATED FROM PYTHON SOURCE LINES 219-241 .. code-block:: Python images_case2 = vol[92 : 92 + B] angles = np.linspace(0.0, np.pi / 6.0, B, dtype=np.float32) grog_case2 = GrogInterpolator( shape=shape, coords=coords_case2, kernel_width=2, oversamp=1.25, image_shape=shape, ) grog_case2.calc_interp_table(calib_cart, lamda=0.01, precision=1) sparse_case2 = grog_case2.interpolate(ksp_case2, ret_image=False) pre_w_case2 = np.asarray(grog_case2.plan.pre_weights)[:, np.newaxis, :] sparse_case2_w = sparse_case2 * pre_w_case2 op_case2 = SparseFFT(plan=grog_case2.plan, smaps=smaps) recon_case2 = np.abs(op_case2.adjoint(sparse_case2_w)) print(f"Case 2 (per-image trajectory): {recon_case2.shape}") .. rst-class:: sphx-glr-script-out .. code-block:: none /home/docs/checkouts/readthedocs.org/user_builds/pygrog/envs/latest/lib/python3.12/site-packages/mrinufft/_utils.py:67: UserWarning: Samples will be rescaled to [-pi, pi), assuming they were in [-0.5, 0.5) warnings.warn( /home/docs/checkouts/readthedocs.org/user_builds/pygrog/envs/latest/lib/python3.12/site-packages/mrinufft/_utils.py:67: UserWarning: Samples will be rescaled to [-pi, pi), assuming they were in [-0.5, 0.5) warnings.warn( /home/docs/checkouts/readthedocs.org/user_builds/pygrog/envs/latest/lib/python3.12/site-packages/mrinufft/_utils.py:67: UserWarning: Samples will be rescaled to [-pi, pi), assuming they were in [-0.5, 0.5) warnings.warn( Case 2 (per-image trajectory): (3, 217, 181) .. GENERATED FROM PYTHON SOURCE LINES 247-251 .. code-block:: Python fig, axes = plt.subplots(2, B, figsize=(4 * B, 6), constrained_layout=True) .. image-sg:: /generated/autoexamples/images/sphx_glr_example02_stacked_002.png :alt: GT #1, GT #2, GT #3, Per-image traj recon #1, Per-image traj recon #2, Per-image traj recon #3 :srcset: /generated/autoexamples/images/sphx_glr_example02_stacked_002.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 262-268 Case 3: Two stack axes (T, B) ============================= Demonstrate 2D stacking: T (time/temporal) and B (trajectory variants). ``coords_case3`` is stacked along B only, while data carries (T, B). T is treated as batch and B as stacked trajectories in a single call. .. GENERATED FROM PYTHON SOURCE LINES 268-293 .. code-block:: Python T = 2 B2 = 3 images_case3 = vol[96 : 96 + T * B2].reshape(T, B2, *shape) angles_b = np.linspace(0.0, np.pi / 5.0, B2, dtype=np.float32) grog_case3 = GrogInterpolator( shape=shape, coords=coords_case3, kernel_width=2, oversamp=1.25, image_shape=shape, ) grog_case3.calc_interp_table(calib_cart, lamda=0.01, precision=1) sparse_case3 = grog_case3.interpolate(ksp_case3, ret_image=False) pre_w_case3 = np.asarray(grog_case3.plan.pre_weights)[np.newaxis, :, np.newaxis, :] sparse_case3_w = sparse_case3 * pre_w_case3 op_case3 = SparseFFT(plan=grog_case3.plan, smaps=smaps) recon_case3 = np.abs(op_case3.adjoint(sparse_case3_w)) print(f"Case 3 (2D stack TxB): {recon_case3.shape}") .. rst-class:: sphx-glr-script-out .. code-block:: none /home/docs/checkouts/readthedocs.org/user_builds/pygrog/envs/latest/lib/python3.12/site-packages/mrinufft/_utils.py:67: UserWarning: Samples will be rescaled to [-pi, pi), assuming they were in [-0.5, 0.5) warnings.warn( /home/docs/checkouts/readthedocs.org/user_builds/pygrog/envs/latest/lib/python3.12/site-packages/mrinufft/_utils.py:67: UserWarning: Samples will be rescaled to [-pi, pi), assuming they were in [-0.5, 0.5) warnings.warn( /home/docs/checkouts/readthedocs.org/user_builds/pygrog/envs/latest/lib/python3.12/site-packages/mrinufft/_utils.py:67: UserWarning: Samples will be rescaled to [-pi, pi), assuming they were in [-0.5, 0.5) warnings.warn( Case 3 (2D stack TxB): (2, 3, 217, 181) .. GENERATED FROM PYTHON SOURCE LINES 299-301 .. code-block:: Python fig, axes = plt.subplots(T, B2, figsize=(4 * B2, 3.5 * T), constrained_layout=True) .. image-sg:: /generated/autoexamples/images/sphx_glr_example02_stacked_003.png :alt: T=0, B=0, T=0, B=1, T=0, B=2, T=1, B=0, T=1, B=1, T=1, B=2 :srcset: /generated/autoexamples/images/sphx_glr_example02_stacked_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 4.690 seconds) .. _sphx_glr_download_generated_autoexamples_example02_stacked.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: example02_stacked.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: example02_stacked.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: example02_stacked.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_