slitflow.loc.convert module

class LocalMax2Xy(info_path=None)[source]

Bases: Table

Convert nonzero local max pixels to X,Y-coordinate.

Caution

The input image should be split into a single frame image. In other words, the shape of reqs[0] in process() should be (1, height, width).

Parameters:

  • reqs[0] (LocalMax) – Local max images to pick up coordinates. Required params; length_unit, pitch.

  • param["split_depth"] (int) – File split depth number.

Returns:

X,Y-coordinate of local max pixels

Return type:

Table

set_info(param)[source]

Copy info from reqs[0] and add columns.

static process(reqs, param)[source]

Convert nonzero local max pixels to X,Y-coordinate.

Parameters:

  • reqs[0] (numpy.ndarray) – Numpy 3D array with the shape of (1, height, width).

  • param["length_unit"] (str) – Unit string for column names such as “um” and “nm”.

  • param["pitch"] (float) – Length per pixel.

Returns:

X,Y-coordinate of local max pixels

Return type:

pandas.DataFrame

post_run()[source]

Index columns should be added on the upper level of the DataFrame.

class LocalMax2XyWithDoG(info_path=None)[source]

Bases: Table

Convert nonzero local max pixels to X,Y-coordinate with DoG filter.

Parameters:

  • reqs[0] (Image) – Image to apply the filter to. Required parameters; length_unit, pitch.

  • param["wavelength"] (int) – Emission wavelength in length_unit.

  • param["NA"] (float) – Numerical aperture.

  • param["size_factor"] (float, optional) – Particle size factor to multiply PSF size. Defaults to 1.

  • param["mask_factor"] (float, optional) – Mask size factor to multiply PSF diameter. Defaults to 1.

  • param["split_depth"] (int) – File split depth number.

Returns:

X,Y-coordinate of detected local max

Return type:

Table

set_info(param)[source]

Copy info from reqs[0] and add params.

static process(reqs, param)[source]

Convert nonzero local max pixels to X,Y-coordinate with DoG filter.

Parameters:

  • reqs[0] (numpy.ndarray) – Image to apply the filter to. The image should have the shape of (frame number, height, width).

  • param["dog_sd1"] (float) – Standard deviation of the first Gaussian filter.

  • param["dog_sd2"] (float) – Standard deviation of the second Gaussian filter.

  • param["mask_size"] (int) – Mask size factor to multiply PSF diameter.

  • param["length_unit"] (str) – Unit string for column names such as “um” and “nm”.

  • param["pitch"] (float) – Length per pixel.

Returns:

X,Y-coordinate of local max pixels

Return type:

pandas.DataFrame

post_run()[source]

Index columns should be added on the upper level of the DataFrame.