Process SLIM Mapper

All of the below functions can be found in the process_slim_mapper module of the package.

The below functions can be used to post-process SLIM (spacer layer imaging method) mapper bitmap files created by MTM or EHD test rigs by PCS Instruments.

load_npz(file)

Load an npz database file into a mutable dictionary.

Parameters:file (str) – Path to npz database file. Returns:dat_cop – Loaded data. Return type:dict

slim2thick(file, rgb_map, rads=None, skip=1, crop=0.0, aperture=None)

Extract film thickness data from a PCS Instruments SLIM image file in BMP format. To obtain the thickness data, the color information of the BMP is converted to thickness information according to the rgb color map (Spacer Calibration file) provided by the instrument.

The center point of the relevant (circular) contact area between the ball and the glass window is automatically detected. The radius of the contact area is automatically detected if rads is not provided. Thickness information outside of the detected area is discarded. The crop and aperture parameters can be used to further constrain the area of interest.

The skip parameter determines the number of data points that is evaluated. For example, for skip = 1, every pixel within the area of interest is evaluated; for skip = 10 every 10th pixel is evaluated.

Parameters:

• file (str) – Path to a PCS bitmap 3D SLIM mapper output file

• rgb_map (str) – Path to a PCS Spacer Calibration file in npz format. The original instrument output file needs to be imported into npz database format using the import_del function of the data_import module first.

• rads (int, float, list, ndarray, optional) – The contact radius (in pixels) of the circular contact area between ball and glass window. If several radii are provided, the mean value will be used.

• skip (positive int, optional) – The number of pixels to skip (in both x and y direction). Higher skip numbers will lead to faster processing; lower skip numbers to higher accuracies.

• crop (float, optional) – Determines by how much the radius of the contact area is cropped during the data processing step. Value needs to be in the range [0, 1]. A crop value of 0.5 will reduce the radius by 50 %.

• aperture (dict, optional) – A dictionary defining a rectangular area relative to the crop radius. Data points outside the rectangular area are not evaluated. The borders of the rectangle are defined relative to the crop radius. Values in the range [0, 1] may be defined for the following keys:

  • top
  • right
  • bottom
  • left

  If the aperture value is 0, the borders of the rectangle intersect with the crop radius on all four sides (i.e., the aperture has no effect). The following will reduce the crop radius on the top and bottom by 30 %:

  aperture = {‘top’: 0.3, ‘bottom’: 0.3}

Returns:

• thick (ndarray) – Film thickness in nanometer for each evaluated pixel.
• rgb (ndarray) – Best matching RGB tuple for each evaluated pixel obtained by comparison of bitmap image and SLIM Spacer Calibration file.
• rads (ndarray) – The automatically detected radii of the contact between ball and window. If rads is provided as an argument, rads is simply returned.
• x_vals (tuple) – Minimum and maximum evaluated pixel coordinate (in x-direction)
• y_vals (tuple) – Minimum and maximum evaluated pixel coordinate (in y-direction)
• dist (ndarray) – Array of distance values between actual color and closest known color in the RGB space, normalized to 255.

slim2thick_batch(bitmaps, zero_bmp, rgb_map, mtm_file, relative=False, pcs_vars=('time_accumulated_s', ), plot=False, plt_dir='', print_prog=True, skip=1, crop=0.0, aperture=None)

Batch process a number of PCS Spacer Layer image files that share the same zero step, instrument output file and spacer layer calibration file.

This function is a wrapper function for slim2thick. See docstring for more information.

Returns a dictionary containing mean film thickness values and, depending on user input, corresponding MTM variable values at the time of the film thickness measurement step.

Parameters:

• bitmaps (tuple, list) – Paths to spacer layer bitmap files as list/tuple of strings.
• zero_bmp (str) – Path to bitmap image that corresponds to initial zero step of experiment.
• rgb_map (str) – Path to the shared spacer layer calibration file, imported into npz database format using the import_del function of the import_data module.
• mtm_file (str) – Path to the shared instrument output file, imported into npz database format using the import_del function of the import_data module.
• relative (bool, optional) – If True, the mean film thickness value is calculated relative to the mean film thickness of the zero step; if False, the absolute mean film thickness is calculated.
• pcs_vars (list, optional) – A list of MTM variables. Variable names must match those used in npz database created using the import_del function of the import_data module. By default, values for variable time_accumulated_s are included.
• plot (bool, optional) – If True, film thickness plots will be created for each image.
• plt_dir (str, optional) – Path to the output directroy in which to store plots.
• print_prog (bool) – If true, status updates are printed to the command line.
• skip (positive int, optional) – See function slim2thick
• crop (float, optional) – See function slim2thick
• aperture (dict, optional) – See function slim2thick

Returns:

outdict – The mean film thickness data for each bitmap file, along with extracted data from instrument output files (depending on user inputs).

Return type:

dict