Basic reconstruction with nabu

In this notebook, we see how to use the different building blocks of nabu to parse a dataset and perform a basic reconstruction.

This notebook uses a dataset of a bamboo stick (acquired at ESRF ID19, courtesy Ludovic Broche). The projections were binned by a factor of 4 in each dimension, and the angular range was also subsampled by 4.

Browse the dataset

We use nabu utility analyze_dataset which builds a data structure with all information on the dataset.

import numpy as np
from tempfile import mkdtemp
from nabu.resources.dataset_analyzer import analyze_dataset
from nabu.resources.nxflatfield import update_dataset_info_flats_darks
from nabu.testutils import get_file

print("Getting dataset (downloading if necessary) ...")
data_path = get_file("bamboo_reduced.nx")
print("... OK")
output_dir = mkdtemp(prefix="nabu_reconstruction")

Getting dataset (downloading if necessary) ...
... OK

# Parse the ".nx" file. This NX file is our entry point when it comes to data,
# as it's only the format which is remotely stable
# From this .nx file, build a data structure with readily available information
dataset_info = analyze_dataset(data_path)

Estimate the center of rotation

from nabu.pipeline.estimators import estimate_cor

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-4-778b8223ed36> in <module>
----> 1 from nabu.pipeline.estimators import estimate_cor

~/.local/lib/python3.8/site-packages/nabu/pipeline/estimators.py in <module>
      5 import inspect
      6 import numpy as np
----> 7 import scipy.fft  #  pylint: disable=E0611
      8 from silx.io import get_data
      9 from ..preproc.flatfield import FlatFieldDataUrls

ModuleNotFoundError: No module named 'scipy.fft'

cor = estimate_cor(
    "sliding-window", # estimator name
    dataset_info,
    do_flatfield=True,
)
print("Estimated center of rotation: %.2f" % cor)

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-5-3c8173a018f1> in <module>
----> 1 cor = estimate_cor(
      2     "sliding-window", # estimator name
      3     dataset_info,
      4     do_flatfield=True,
      5 )

NameError: name 'estimate_cor' is not defined

Define how the data should be processed

Instantiate the various components of the pipeline.

from nabu.io.reader import NXTomoReader
from nabu.preproc.flatfield import FlatField
from nabu.preproc.phase import PaganinPhaseRetrieval
from nabu.reconstruction.fbp import Backprojector

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-6-b70f0fd6c8e2> in <module>
----> 1 from nabu.io.reader import NXTomoReader
      2 from nabu.preproc.flatfield import FlatField
      3 from nabu.preproc.phase import PaganinPhaseRetrieval
      4 from nabu.reconstruction.fbp import Backprojector

ImportError: cannot import name 'NXTomoReader' from 'nabu.io.reader' (/var/lib/gitlab-runner/.local/lib/python3.8/site-packages/nabu/io/reader.py)

# Define the sub-region to read (and reconstruct)
# Read all projections, from row 270 to row 288
sub_region = (
    slice(None),
    slice(270, 289),
    slice(None)
)

reader = NXTomoReader(
    data_path,
    sub_region=sub_region,
)
radios_shape = reader.output_shape
n_angles, n_z, n_x = radios_shape

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-8-3f7b6efb6350> in <module>
----> 1 reader = NXTomoReader(
      2     data_path,
      3     sub_region=sub_region,
      4 )
      5 radios_shape = reader.output_shape

NameError: name 'NXTomoReader' is not defined

flatfield = FlatField(
    radios_shape,
    dataset_info.get_reduced_flats(sub_region=sub_region),
    dataset_info.get_reduced_darks(sub_region=sub_region),
    radios_indices=sorted(list(dataset_info.projections.keys())),
)

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-9-43a589e0d43e> in <module>
----> 1 flatfield = FlatField(
      2     radios_shape,
      3     dataset_info.get_reduced_flats(sub_region=sub_region),
      4     dataset_info.get_reduced_darks(sub_region=sub_region),
      5     radios_indices=sorted(list(dataset_info.projections.keys())),

NameError: name 'FlatField' is not defined

paganin = PaganinPhaseRetrieval(
    radios_shape[1:],
    distance=dataset_info.distance,
    energy=dataset_info.energy,
    delta_beta=250., # should be tuned
    pixel_size=dataset_info.pixel_size * 1e-6,
)

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-10-4ae2eb148aef> in <module>
----> 1 paganin = PaganinPhaseRetrieval(
      2     radios_shape[1:],
      3     distance=dataset_info.distance,
      4     energy=dataset_info.energy,
      5     delta_beta=250., # should be tuned

NameError: name 'PaganinPhaseRetrieval' is not defined

reconstruction = Backprojector(
    (n_angles, n_x),
    angles=dataset_info.rotation_angles,
    rot_center=cor,
    halftomo=dataset_info.is_halftomo,
    padding_mode="edges",
    scale_factor=1/(dataset_info.pixel_size * 1e-4), # mu/cm
    extra_options={"centered_axis": True, "clip_outer_circle": True}
)

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-11-c08982cb1f66> in <module>
----> 1 reconstruction = Backprojector(
      2     (n_angles, n_x),
      3     angles=dataset_info.rotation_angles,
      4     rot_center=cor,
      5     halftomo=dataset_info.is_halftomo,

NameError: name 'Backprojector' is not defined

Read data

radios = reader.load_data()

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-12-ad4922173686> in <module>
----> 1 radios = reader.load_data()

NameError: name 'reader' is not defined

Pre-processing

flatfield.normalize_radios(radios) # in-place
print()

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-13-b9e4a1f57ebe> in <module>
----> 1 flatfield.normalize_radios(radios) # in-place
      2 print()

NameError: name 'flatfield' is not defined

radios_phase = np.zeros_like(radios)
for i in range(radios.shape[0]):
    paganin.retrieve_phase(radios[i], output=radios_phase[i])

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-14-8b41c1a1caa6> in <module>
----> 1 radios_phase = np.zeros_like(radios)
      2 for i in range(radios.shape[0]):
      3     paganin.retrieve_phase(radios[i], output=radios_phase[i])

NameError: name 'radios' is not defined

Reconstruction

volume = np.zeros((n_z, n_x, n_x), "f")

for i in range(n_z):
    volume[i] = reconstruction.fbp(radios[:, i, :])

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-15-00222c7e518f> in <module>
----> 1 volume = np.zeros((n_z, n_x, n_x), "f")
      2
      3 for i in range(n_z):
      4     volume[i] = reconstruction.fbp(radios[:, i, :])

NameError: name 'n_z' is not defined

import matplotlib.pyplot as plt

plt.figure()
plt.imshow(volume[0], cmap="gray")
plt.show()

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-17-394cfad5f2ae> in <module>
      1 plt.figure()
----> 2 plt.imshow(volume[0], cmap="gray")
      3 plt.show()

NameError: name 'volume' is not defined

<Figure size 432x288 with 0 Axes>

Going further: GPU processing

All the above components have a Cuda backend: SinoBuilder becomes CudaSinoBuilder, PaganinPhaseRetrieval becomes CudaPaganinPhaseRetrieval, and so on. Importantly, the cuda counterpart of these classes have the same API.