C04B21 Dual Energy Carbonate Core CT

This project is a set of dual energy medical CT scans of 3 ft carbonate core samples, made available by Rodolfo Victor at Digital Rocks Portal, acquired with (0.488 X 0.488 X 1.25) mm voxel length at Petrobras Research Center. We will download the vuggy C04B21 sample.

Note

If you plan to use this data, please remember to cite the data and the related publications.

Go to the Dual-energy medical CT in carbonate rocks project in the Digital Rocks Portal: https://www.digitalrocksportal.org/projects/102. Click on the low-energy image C04B21_Raw100keV.

Pay attention to the metadata! We’ll need it later. An extra piece of information: this is ImageJ/Fiji exported raw data, so it is in Fortran file order. Click Action->Download File.

Repeat the procedure and download the high-energy image C04B21_Raw140keV.

Let’s import the raw files into RockVerse. In this example we’ll use 8 chunks by halving the number of voxels in each direction:

import rockverse as rv

C04B21_Raw100keV =  rv.voxel_image.import_raw(
    rawfile='/path/to/rawdata/dual_energy_carbonate/C04B21Raw100keV.raw',
    store='/path/to/imported/dual_energy_carbonate/C04B21Raw100keV',
    shape=(512, 512, 738),               #<- From metadata, image size
    chunks=(256, 256, 369),              #<- Our choice of chunk size will give a 2x2x2 chunk grid
    dtype='<i2',                         #<- From metadata, little-endian 16-bit signed integer
    offset=0,                            #<- From metadata
    voxel_length=(0.488, 0.488, 1.25),   #<- From metadata
    voxel_unit='mm',                     #<- From metadata
    raw_file_order='F',                  #<- Fortran file order
    field_name='Low attenuation',            #<- Our choice for field name (X-ray attenuation)
    field_unit='H.U.',                   #<- field units (Hounsfield units)
    description='Low energy X-ray CT attenuation',
    overwrite=True                       #<- Overwrite if file exists in disk
    )

C04B21_Raw140keV =  rv.voxel_image.import_raw(
    rawfile='/path/to/rawdata/dual_energy_carbonate/C04B21Raw140keV.raw',
    store='/path/to/imported/dual_energy_carbonate/C04B21Raw140keV',
    shape=(512, 512, 738),               #<- From metadata, image size
    chunks=(256, 256, 369),              #<- Our choice of chunk size will give a 2x2x2 chunk grid
    dtype='<i2',                         #<- From metadata, little-endian 16-bit signed integer
    offset=0,                            #<- From metadata
    voxel_length=(0.488, 0.488, 1.25),   #<- From metadata
    voxel_unit='mm',                     #<- From metadata
    raw_file_order='F',                  #<- Fortran file order
    field_name='High attenuation',            #<- Our choice for field name (X-ray attenuation)
    field_unit='H.U.',                   #<- field units (Hounsfield units)
    description='High energy X-ray CT attenuation',
    overwrite=True                       #<- Overwrite if file exists in disk
    )

[2025-01-09 12:31:54] (Low attenuation) Importing raw file: 100%|>>>>>>>>>>| 8/8 [00:04<00:00,  1.68chunk/s]
[2025-01-09 12:31:59] (High attenuation) Importing raw file: 100%|>>>>>>>>>>| 8/8 [00:06<00:00,  1.25chunk/s]

The images are now available as a RockVerse voxel image in disk, at the path given in the store parameters. Lets do a quick visualization:

import matplotlib.pyplot as plt
fig = plt.figure(layout='constrained', figsize=(10, 4))
subfigs = fig.subfigures(2, 1, wspace=0.07)
viewer_low = rv.OrthogonalViewer(C04B21_Raw100keV,
                                 show_xz_plane=False,
                                 show_histogram=False,
                                 image_dict={'clim': (-1200, 4000)}
                                 )
viewer_high = rv.OrthogonalViewer(C04B21_Raw140keV,
                                 show_xz_plane=False,
                                 show_histogram=False,
                                 image_dict={'clim': (-1200, 4000)},
                                 )

[2025-01-09 12:32:06] Histogram Low attenuation (min/max): 100%|>>>>>>>>>>| 8/8 [00:00<00:00, 20.36chunk/s]
[2025-01-09 12:32:06] Histogram Low attenuation (counting voxels): 100%|>>>>>>>>>>| 8/8 [00:03<00:00,  2.25chunk/s]
[2025-01-09 12:32:12] Histogram High attenuation (min/max): 100%|>>>>>>>>>>| 8/8 [00:00<00:00, 21.73chunk/s]
[2025-01-09 12:32:12] Histogram High attenuation (counting voxels): 100%|>>>>>>>>>>| 8/8 [00:02<00:00,  2.68chunk/s]

<Figure size 1000x400 with 0 Axes>