filters
Contains filter functions that take a 2D array representing an image as an input, as well as necessary parameters, and return a 2D array of the same size representing the filtered image.
- topostats.filters.align_rows(image: numpy.array, mask: Optional[numpy.array] = None) numpy.array[source]
Returns the input image with rows aligned by median height
- Parameters
image (np.array) – Numpy array representing image.
mask (np.array) – Mask array to apply.
- Returns
Numpy array of image but with any linear plane slant removed.
- Return type
np.array
- topostats.filters.amplify(image: numpy.array, level: float) numpy.array[source]
The amplify filter mulitplies the value of all pixels by the level argument.
Parameters
- image: np.array
Numpy array representing image.
- level: np.array
Factor by which to amplify the array.
- Returns
Numpy array of image amplified by level.
- Return type
np.array
- topostats.filters.average_background(image: numpy.array, mask: Optional[numpy.array] = None) numpy.array[source]
Zero the background based on the median.
- Parameters
image (np.array) – Numpy array representing image.
mask (np.array) – Mask of the array, should have the same dimensions as image.
- Returns
Numpy array of image zero averaged.
- Return type
np.array
- topostats.filters.calc_diff(array: numpy.array) numpy.array[source]
Calculate the difference of an array.
- Parameters
image (np.array) – Numpy array representing image.
- Return type
np.array
- topostats.filters.calc_gradient(array: numpy.array, shape: int) numpy.array[source]
Calculate the gradient of an array.
- Parameters
image (np.array) – Numpy array representing image.
shape (int) – Shape of the array in terms of the number of rows, typically it will be array[0].
- Return type
np.array
- topostats.filters.extract_channel(scan_raw: pySPM.Bruker, channel: str = 'Height') pySPM.SPM.SPM_image[source]
Extract the given channel from the image.
- Parameters
scan_raw (pySPM.Bruker) – Raw scan loaded by pySPM.
channel (str) – Channel to extract (default is ‘Height’).
filename (str) – File being processed.
- Returns
SPM image.
- Return type
SPM_image
Examples
FIXME: Add docs.
- topostats.filters.extract_img_name(img_path: Union[str, pathlib.Path]) str[source]
Extract the image name from the image path.
- Parameters
img_path (Union[str, Path]) – Path to image being processed.
- Returns
Filename of processed image.
- Return type
str
Examples
FIXME: Add docs.
- topostats.filters.extract_pixel_to_nm_scaling(extracted_channel: pySPM.SPM.SPM_image) float[source]
Extract the pixel to nanometer scaling from the image metadata.
- Parameters
extracted_channel (SPM_image) – Channel extracted from an image.
- Returns
Scaling factor for pixels to nanometers.
- Return type
float
- topostats.filters.extract_pixels(extracted_channel: pySPM.SPM.SPM_image) numpy.array[source]
Flatten the scan to a Numpy Array
- Parameters
extracted_channel (SPM_image) – Channel extracted from an image.
- Returns
Numpy array representation of the channel of interest.
- Return type
np.array
Examples
FIXME: Add docs.
- topostats.filters.remove_x_y_tilt(image: numpy.array, mask: Optional[numpy.array] = None) numpy.array[source]
Returns the input image after removing any linear plane slant
- Parameters
image (np.array) – Numpy array representing image.
mask (np.array) – Mask array to apply.
- Returns
Numpy array of image but with any linear plane slant removed.
- Return type
np.array
- topostats.filters.row_col_quantiles(image: numpy.array, mask: Optional[numpy.array] = None) numpy.array[source]
Returns the height value quantiles for the rows and columns.
- Parameters
image (np.array) – Numpy array representing image.
mask (np.array) – Mask array to apply.
- Returns
Numpy array of image but with any linear plane slant removed.
- Return type
np.array