coordination#

The coordination module contains functions related to extracting pore coordination numbers.

coordination_nums_3D()#

pore2chip.coordination.coordination_nums_3D(img_list=None, pn=None, alt=True)#

This function calculates the coordination number of each pore in a 3D image.

Parameters:

  • img_list (list) – A list of 3D images represented as NumPy arrays.

  • pn (openpnm.network.Network) – An optional OpenPNM network object. If provided, the function will directly calculate coordination numbers from the network instead of processing images.

Returns:

A list containing the coordination number for each pore in the image(s).

Return type:

list

Functionality:

  1. Check for OpenPNM network:

    • If pn is not None (i.e., an OpenPNM network is provided), the function extracts the coordination numbers directly from the network using op.models.network.coordination_number(pn).

    • This bypasses the image processing step and leverages the existing information in the network.

  2. Image processing (if no network provided):

    • If pn is None, the function assumes img_list contains 3D image data as NumPy arrays.

    • It utilizes the porespy library to process the images:

    • ps.networks.snow2(img_list, voxel_size=1): This function likely performs segmentation and network extraction from the images.

      • voxel_size=1 is assumed to be a unit voxel size (adjust if needed).

    • The processed network is then converted to an OpenPNM network using op.io.network_from_porespy(snow_output.network).

  3. Coordination number calculation:

    • Regardless of the input (image or network), the function calculates the coordination number of each pore using:

    • op.models.network.coordination_number(pn2): This function calculates the coordination number for each pore in the OpenPNM network pn2.

  4. Return coordination numbers:

    • The function returns the calculated coordination numbers (coordination_nums) as a list.

  • This function assumes the porespy and openpnm libraries are installed and imported.

  • The specific implementation of ps.networks.snow2 might require further investigation depending on the exact functionality of the PoresPy library.

coordination_nums_2D()#

pore2chip.coordination.coordination_nums_2D(img_list)#

This function calculates the coordination number of each pore in a series of 2D images.

Parameters:

img_list (list) – A list of 2D images represented as NumPy arrays. Each image is assumed to be a single slice from a 3D volume.

Returns:

A list containing the coordination number for each pore across all the 2D images.

Return type:

list

Functionality:

  1. Iterate through image slices:

    • The function loops through each image in img_list using a for loop.

  2. Process individual image:

    • Inside the loop, for each image slice (img_list[k]), it extracts a 2D portion using slicing (img_list[k, :, :]).

    • ps.networks.snow2(img_slice, voxel_size=1) likely performs segmentation and network extraction specifically for the 2D slice.

    • voxel_size=1 is assumed to be a unit voxel size (adjust if needed).

    • The processed network information is stored in snow_output.network.

    • An OpenPNM network object (pn) is created by converting the PoresPy network using op.io.network_from_porespy(snow_output.network).

  3. Coordination number calculation:

    • The coordination number for each pore in the current image slice’s network (pn) is calculated using op.models.network.coordination_number(pn).

    • This function from OpenPNM provides the coordination numbers as a list.

  4. Accumulate coordination numbers:

    • The calculated coordination numbers for the current slice (temp_coordination) are appended to the coordination_nums_2D list using np.concatenate.

    • This accumulates coordination numbers from all processed slices into a single list.

  5. Return results:

    • After iterating through all images, the function returns the final coordination_nums_2D list containing coordination numbers for all pores across the entire 2D image series.

  • This function assumes the porespy and openpnm libraries are installed and imported.

  • The specific implementation of ps.networks.snow2 might require further investigation depending on the exact functionality of the PoresPy library.

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