8.3.4. Solid Files

Generating solid (.pfsol) files for a ParFlow run can be somewhat of a pain. PFTools has a few features that can help with this process.

8.3.4.1. Example

To see the how Python can help generate solid files, navigate to $PARFLOW_SOURCE/test/python/pfsol/simple-mask/ and open the Python script simple-mask.py. Here, you’ll see the following lines at the top of the script:

from parflow import Run
from parflow.tools.fs import get_absolute_path
from parflow.tools.io import load_patch_matrix_from_sa_file, load_patch_matrix_from_asc_file, load_patch_matrix_from_image_file
from parflow.tools.builders import SolidFileBuilder

By now, you should be familiar with the first two modules and functions. The load_patch_matrix... functions handle different file types to generate solid files. The SolidFileBuilder class imported from the parflow.tools.builders module handles the matrices of patches, converting them to ASCII files and passing those to the pfmask-to-pfsol converter in ParFlow. This way, the user doesn’t have to deal with the more complicated steps.

Lines 52 through 55 show examples of how the patch_matrix functions are used for different types of files:

sabino_mask = load_patch_matrix_from_sa_file(get_absolute_path('Sabino_Mask.sa'))
# sabino_mask = load_patch_matrix_from_asc_file(get_absolute_path('Sabino_Mask.asc'))
# sabino_mask = load_patch_matrix_from_image_file(get_absolute_path('Sabino_Mask.png'))
# sabino_mask = load_patch_matrix_from_image_file(get_absolute_path('Sabino_Mask.tiff'))

Note that only one is used at a time, but all four will work. These functions return a matrix, which is assigned to sabino_mask. The input files are located in the same directory as the example, so feel free to reference them. Several of these functions have extra optional arguments, which are described in the full API below.

Next, we’ll show some examples of the SolidFileBuilder class to demonstrate the arguments and methods that can be called on the object:

# Example of using unique ids for each surface [top/bottom/side]
SolidFileBuilder(top=1, bottom=2, side=3) \ # Initializing the SolidFileBuilder
    .mask(sabino_mask) \                      # Setting the 2D mask
    .write('sabino_domain.pfsol', cellsize=90) \  # Write pfsol file
    .for_key(sabino.GeomInput.domaininput)  # Setting keys to "sabino" Run object that relate to the solid file

# Example using an id mask for the top patches
SolidFileBuilder(bottom=2, side=3) \ # Initializing the SolidFileBuilder
    .mask(sabino_mask) \               # Setting the 2D mask
    .top_ids(id_array) \                  # Using a 2D numpy array to provide patch ids
    .write('sabino_domain.pfsol', cellsize=90) # Write pfsol file

# Example using the same matrix to write multiple solid files
SolidFileBuilder(top=1, bottom=2, side=3) \
    .mask(sabino_mask) \                      # Setting the 2D mask
    .write('sabino_domain.pfsol', cellsize=90) \  # Write first pfsol file
    .mask(sabino_mask_2) \                      # Setting another 2D mask
    .side_ids(id_array) \              # Using a 2D numpy array to provide new patch ids (possibly to change boundary conditions)
    .write('sabino_domain_2.pfsol', cellsize=90)   # Write second pfsol file

8.3.4.2. Full API: IO tools (from parflow.tools.io)

  1. load_patch_matrix_from_pfb_file(file_name, layer=None)

    Reads in a 2D or 3D ParFlow binary (PFB) file and converts it to a patch matrix.

    param file_name

    Path to PFB file.

    param layer

    If 3D PFB file, layer corresponds to a vertical layer of the file to convert to the matrix. If no layer is specified, the function will use the top layer of the file.

    return

    An ndarray containing patch matrix data.

  2. load_patch_matrix_from_image_file(file_name, color_to_patch=None, fall_back_id=0)

    Reads in an image file file_name and converts it to a patch matrix.

    param file_name

    Path to image file.

    param color_to_patch

    A dictionary with hexidecimal colors as keys with their corresponding ID numbers as values. See $PARFLOW_SOURCE/test/python/pfsol/image-as-mask/image-as-mask.py for an example. If color_to_patch is not provided, it will default to assume that everything in white is not part of the mask and everything else is part of the mask.

    param fall_back_id

    The ID number for colors that are found in the image but are not specified in the color_to_patch dictionary. Its default value is zero.

    return

    An ndarray containing patch matrix data.

  3. load_patch_matrix_from_asc_file(file_name)

    Reads in an ASCII file and converts it to a patch matrix.

    param file_name

    Path to ASCII file.

    return

    An ndarray containing patch matrix data.

  4. load_patch_matrix_from_sa_file(file_name)

    Reads in a simple ASCII file file_name and converts it to a patch matrix.

    param file_name

    Path to simple ASCII file.

    return

    An ndarray containing patch matrix data.

  5. write_patch_matrix_as_asc(matrix, file_name, xllcorner=0.0, yllcorner=0.0, cellsize=1.0, NODATA_value=0)

    Writes a patch matrix to an ASCII file.

    param matrix

    Patch matrix that you want to write out.

    param file_name

    Filename to write the patch matrix to.

    param xllcorner

    X-coordinate of the origin (by lower left corner of the cell). Written to the header of the ASCII file.

    param yllcorner

    Y-coordinate of the origin (by lower left corner of the cell). Written to the header of the ASCII file.

    param cellsize

    Cell size. Written to the header of the ASCII file.

    param NODATA_value

    The input values to be NoData in the output raster. Written to the header of the ASCII file.

  6. write_patch_matrix_as_sa(matrix, file_name)

    Writes a patch matrix to a simple ASCII file.

    param matrix

    Patch matrix that you want to write out.

    param file_name

    Filename to write the patch matrix to.

8.3.4.3. Full API: SolidFileBuilder

  1. SolidFileBuilder(top=1, bottom=2, side=3)

    Initializes a SolidFileBuilder object with default values for the top, bottom, and sides of a domain, respectively.

    param top

    ID of the top patch of the domain.

    param bottom

    ID of the bottom patch of the domain.

    param side

    ID of the side patch of the domain.

  2. mask(mask_array)

    Applies the matrix array mask_array to the SolidFileBuilder object.

    param mask_array

    Array of values to define the mask.

  3. write(self, name, xllcorner=0, yllcorner=0, cellsize=0, vtk=False, extra=None, generate_asc_files=False)

    Writes the SolidFileBuilder object data to the .pfsol file name.

    param name

    Name of the solid file to write.

    param xllcorner

    X-coordinate of the origin (by lower left corner of the cell).

    param yllcorner

    Y-coordinate of the origin (by lower left corner of the cell).

    param cellsize=0

    Cell size.

    param vtk

    If vtk is set to True, it will write a VTK file name.vtk that you can view in ParaView or another VTK viewer to check that the solid file is correct.

    param extra

    If there are any extra arguments you want to pass to the pfmask-to-pfsol converter in Parflow, specify them using the extra parameter, as a list of strings.

    param generate_asc_files

    When generate_asc_files is set to True, this method generates .asc files for top/bottom/sides, with filenames <name>_top.asc, <name>_bottom.asc, <name>_front.asc, <name>_back.asc, <name>_left.asc, <name>_right.asc, and calls pfmask-to-pfsol with individual mask-* flags with these files.

  4. for_key(self, geomItem)
    Sets two keys on the Run object passed in as the geomItem argument:

    1. geomItem.InputType = 'SolidFile'

    2. geomItem.FileName = 'name.pfsol'.

    'name.pfsol' is implicitly referenced from the name argument of the write method.

    param geom_item

    String name of the geometric unit in the ParFlow run that will be used as a token for the ParFlow key.

  5. top(patch_id)

    Sets the ID number of the top of the solid file domain to the integer patch_id. This will override the top argument passed to the SolidFileBuilder object.

    param patch_id

    Integer ID of top patch in mask array.

  6. bottom(patch_id)

    Sets the ID number of the bottom of the solid file domain to the integer patch_id. This will override the bottom argument passed to the SolidFileBuilder object.

    param patch_id

    Integer ID of bottom patch in mask array.

  7. side(patch_id)

    Sets the ID number of the side of the solid file domain to the integer patch_id. This will override the side argument passed to the SolidFileBuilder object.

    param patch_id

    Integer ID of side patch in mask array.

  8. top_ids(top_patch_ids)

    Sets the ID numbers of the top of the solid file domain to the values in the numpy array top_patch_ids.

    param top_patch_ids

    Numpy array of top patch IDs.

  9. bottom_ids(bottom_patch_ids)

    Sets the ID numbers of the bottom of the solid file domain to the values in the numpy array bottom_patch_ids.

    param bottom_patch_ids

    Numpy array of bottom patch IDs.

  10. side_ids(side_patch_ids) Sets the ID numbers of the side of the solid file domain to the values in the numpy array side_patch_ids.

    param side_patch_ids

    Numpy array of side patch IDs.

8.3.4.4. More examples

Other example scripts showing how to use the SolidFileBuilder can be found in $PARFLOW_SOURCE/test/python/pfsol/. If you have an idea for a new feature or improvement to the functionality, please let us know, or better yet, become a contributor!