cellpack.autopack.writers package

Submodules

cellpack.autopack.writers.ImageWriter module

class cellpack.autopack.writers.ImageWriter.ImageWriter(env, name=None, output_path=None, voxel_size=None, hollow=False, convolution_options=None, projection_axis='z')

Bases: object

concatenate_image_data()

Creates a voxelized representation of the current scene

static convolve_channel(channel, psf)

Convolves a channel with a psf

Parameters:

• channel (numpy.ndarray) – channel to be convolved

• psf (numpy.ndarray) – psf

Returns:

convolved channel

Return type:

numpy.ndarray

convolve_image(image, psf='gaussian', psf_parameters=None)

Convolves the image with a psf

Parameters:

• image (numpy.ndarray) – image to be convolved

• psf (str or numpy.ndarray) – psf type

• psf_parameters (dict) – psf parameters

Returns:

convolved image

Return type:

numpy.ndarray

static create_box_psf(size=None)

Creates a box psf

Parameters:

size (np.ndarray) – size of the psf

Returns:

psf

Return type:

numpy.ndarray

static create_gaussian_psf(sigma=1.5, size=None)

Creates a gaussian psf

Parameters:

• sigma (float) – sigma of the gaussian

• size (np.ndarray) – size of the psf

Returns:

psf

Return type:

numpy.ndarray

export_image()

Saves the results as a tiff file

static transpose_image_for_projection(image, projection_axis)

cellpack.autopack.writers.MarkdownWriter module

class cellpack.autopack.writers.MarkdownWriter.MarkdownWriter(title: str, output_path: Path, output_image_location: Path, report_name: str)

Bases: object

add_header(header, level: int = 2)

add_images(header, image_text, filepaths)

add_inline_image(text, filepath)

add_line(line)

add_list(list_items)

add_table(header, table, text_align='center')

add_table_from_csv(header, filepath, text_align='center')

write_file()

Module contents

Write out data for cellpack.

class cellpack.autopack.writers.IOingredientTool(env=None)

Bases: object

ingrJsonNode(ingr, result=False, kwds=None, transpose=False)

write(ingr, filename, ingr_format='xml', kwds=None, result=False)

class cellpack.autopack.writers.NumpyArrayEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)

Bases: JSONEncoder

default(obj)

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return super().default(o)

class cellpack.autopack.writers.Writer(format='simularium')

Bases: object

static return_object_value(data)

save(env, kwds=None, result=False, grid=False, packing_options=False, indent=False, quaternion=False, transpose=False, seed_to_results_map=None)

save_Mixed_asJson(env, useXref=True, kwds=None, result=False, grid=False, packing_options=False, indent=True, quaternion=False, transpose=False)

Save the current environment setup as an json file. env is the environment / recipe to be exported.

save_as_simularium(env, seed_to_results_map)

static setValueToJsonNode(value, attrname)

cellpack.autopack.writers.updatePositionsRadii(ingr)