miop.image_helper.image¶

Classes

Image(image_path, image_name, metadata_type)

Represents an image with associated metadata, and provides tools for preprocessing, transformation, and visualization.

class miop.image_helper.image.Image(image_path, image_name, metadata_type, metadata=None, tilt_axis=[1.0, 0, 0])[source]¶

Bases: object

Represents an image with associated metadata, and provides tools for preprocessing, transformation, and visualization.

The image is loaded from the given path and may include metadata in ‘fei’, ‘custom’, or ‘none’ formats. Basic image transformations such as cropping, rotation, and downsampling are supported.

image_path¶

Path to the image file.

Type:: str

image_name¶

Name of the image file.

Type:: str

image¶

Image data as a NumPy array, loaded using OpenCV.

Type:: np.ndarray

metadata_type¶

Type of metadata used (‘fei’, ‘custom’, or ‘none’).

Type:: str

tilt_axis¶

Axis about which the tilt is defined. Default is [1., 0, 0].

Type:: list of float

tilt¶

Tilt angle in radians.

Type:: float

rotation_z¶

In-plane rotation angle (around z-axis) in radians. Automatically snapped to closest multiple of 90°.

Type:: float

tilt_rad¶

Whether the tilt is in radians (always True after init).

Type:: bool

metadata¶

Parsed metadata from the image (if available).

Type:: dict

crop(dim, top_left_corner)[source]¶

Crops the image based on given dimensions and top-left coordinates.

Parameters:

dim (list of int) – Width and height of the cropped region [width, height].
top_left_corner (list of int) – X and Y coordinates of the top-left corner of the cropping box.

Returns:

The image object after cropping (for method chaining).

Return type:

Self

downsample(factor_x, factor_y)[source]¶

Downsamples the image using nearest-neighbor interpolation.

Parameters:

factor_x (float) – Downsampling factor in the x-direction (width).
factor_y (float) – Downsampling factor in the y-direction (height).

Returns:

The image object after downsampling (for method chaining).

Return type:

Self

rotate(angle, rad=False)[source]¶

Rotates the image by a given angle.

Parameters:

angle (float) – Angle to rotate the image.
rad (bool, optional) – If True, the angle is interpreted as radians. Default is False (degrees).

Returns:

Rotated image.

Return type:

np.ndarray

rotate_by_transpose()[source]¶

Rotates the image using matrix transposition based on rotation_z, which is expected to be a multiple of 90 degrees (in radians). Uses NumPy’s rot90.

Returns:: Rotated image.
Return type:: np.ndarray
Raises:: ValueError – If rotation_z exceeds 2π radians.

save(path_to_dir)[source]¶

Saves the image to the specified directory as a PNG file.

Parameters:: path_to_dir (str) – Directory where the image should be saved.
Returns:: True if the image is successfully saved, False otherwise.
Return type:: bool

property shape¶

Returns the shape of the image.

Returns:: The shape of the image (height, width, channels).
Return type:: tuple

show()[source]¶

Displays the image using matplotlib.

If the image is not loaded, a warning message is printed.