7.3. Plotting component maps

Component maps are calculated by integrating the spectroscopic image over user-selected spectral ROIs, resulting in spatial maps that show the spatial distribution of each component. They can be visualized with the following command:

plot_comp_maps.sh -spect_imfile spect_imfile_name -spectmaskfile spectmaskfile_name -outprefix outprefix_name

plot_comp_maps('spect_imfile','___','spectmaskfile','___','outprefix','___')
roi_avgspect

Example spectral ROIs.

Workflow overview

Example component maps.

When using optional arguments, the following syntax should be used:

plot_comp_maps.sh -spect_imfile spect_imfile_name -spectmaskfile spectmaskfile -outprefix outprefix_name -color color_name -weights weights_values -cbar tf -file_types file_types_name

plot_comp_maps('spect_imfile','___','spectmaskfile','___','outprefix','___','color','___','weights','___','cbar','___','file_types','___')

7.3.1. Required inputs

  • spect_imfile::

    The spectroscopic image to be visualized. The spectroscopic image must be in the spectImagefile format (e.g., as generated through DRSuite’s spectroscopic image estimation tool) as described here.

  • specMaskfile:

    A set of binary spectral ROI masks used to calculate component maps. This must be in the spectmaskfile format as described here, with the same spectral dimensions as the spectroscopic image.

  • outprefix:

    A string specifying the filename prefix to use for the saved output images.

7.3.2. Optional Inputs

  • file_types: char | string | cellstr | string array

    Output formats (case-insensitive). Allowed: fig, m, eps, epsc, ai, pdf, bmp, jpg, jpeg, png, tif, tiff. Default: "png". Invalid entries are ignored.

  • color: char | string

    Path to .mat file with variable color of size 3×Nc (values are RGB in [0,1], columns correspond to components). If omitted, a built-in 13-color set is used. See here for more information.

  • weights: numeric vector

    Length Nc. Visualization weight for each component (affects color scaling). Default: all ones.

  • cbar: numeric (0/1)

    Show colorbar for individual component maps. Default: 0 (no colorbar).

7.3.3. Outputs

This function writes two files:

  • Figures: <outprefix>_<slice>.<ext> for each requested extension.

  • Data file: <outprefix>.mat containing:

    data         % Nc × Nx × Ny × Nz numeric array (component maps)
resolution   % [dx dy dz] in physical units
transform    % 4×4 (as provided in input spectfile)
spatial_dim  % [Nx Ny] or [Nx Ny Nz]

Note

  • spectral_dim must have length 1 or 2. The function errors if length(spectral_dim) >= 3.

  • The built-in colormap supports up to 13 components. Provide a custom color file if Nc > 13.