Foam¶

Challenge¶

These phantoms were first added to TomoBank to be used as part of TomoChallenge, please see https://tomochallenge.github.io/ for more details and for information about how you can participate. The phantoms were generated using the foam_ct_phantom package, version 1.0.0. Projection data was generated for a virtual PCO.edge 5.5 detector in 2x2 binning mode, resulting in projections of 1080x1280 pixels. Data is provided for multiple simulated phantoms, with various types of data limitations. For one sample (Foam 1), data is provided for all data limitations, in addition to a high-quality dataset with many projections and limited noise. For other samples, only limited data is given.

Each dataset consists of a HDF5 file with two entries: projs is the projections data (already flatfielded and linearized) and angs is a list of projection angles in radians. An example script that reconstructs a dataset with the ASTRA toolbox is available here.

Data for the following acquisition modes are included:

Acquisition mode	Number of projections	Noise level	Comments
HQ	1536	Low
Limited angle	128	Low
Noisy	1536	High
Missing wedge	1024	Low	Angular range of 120 degrees
Blur	128	Low	Simulates continuous rotation
Artifacts	512	Medium	Additional ring artifacts and outliers
Expanding	3072 (24 sets of 128)	Low	Sample expands during acquisition over 24 x 180 degrees

The following datasets are provided:

Data ID	Sample name	Acquisition mode
phan_00016	Foam 1	HQ
phan_00017	Foam 1	Limited angle
phan_00018	Foam 1	Noisy
phan_00019	Foam 1	Missing wedge
phan_00020	Foam 1	Blur
phan_00021	Foam 1	Artifacts
phan_00022	Foam 1	Expanding
phan_00023	Foam 2	Limited angle
phan_00024	Foam 3	Noisy
phan_00025	Foam 4	Missing wedge
phan_00026	Foam 5	Blur
phan_00027	Foam 6	Artifacts
phan_00028	Foam 7	Expanding

Further information about the generation of the various datasets is deliberately not given until the associated reconstruction challenge has concluded.

XDesign¶

These phantom use XDesign version 0.2.0.dev0+1d67599 are generated as follows:

ccd_x = 256
ccd_y = 1
n_proj = 512

phantom_00008 = xdesign.Foam(size_range=[0.05, 0.01], gap=0, porosity=1)
phantom_00009 = xdesign.Foam(size_range=[0.07, 0.01], gap=0, porosity=0.75)
phantom_00010 = xdesign.Foam(size_range=[0.1, 0.01], gap=0, porosity=0.5)
phantom_00011 = xdesign.Foam(size_range=[0.1, 0.01], gap=0.015, porosity=0.5)

The ground truth, sinogram and projection are obtained with:

ground_truth = discrete_phantom(phantom, ccd_x, prop='mass_atten')

sino, probe = sinogram(n_proj, ccd_x, phantom)
proj = np.expand_dims(sino, 1)

To load the phantom data sets and perform a basic reconstruction using tomopy use the tomopy_rec.py python script:

tomopy recon --file-name phantom_00008.h5

Phantom ID	Facility	Sample	Ground Truth	Grirec	Downloads
phan_00008	XDesign	Foam 00008			`gen_script.py`
phan_00009	XDesign	Foam 00009			`gen_script.py`
phan_00010	XDesign	Foam 00010			`gen_script.py`
phan_00011	XDesign	Foam 00011			`gen_script.py`