papylio.Movie#

class papylio.Movie(filepath, rot90=0)#

__init__(filepath, rot90=0)#

Methods

`__init__`(filepath[, rot90])
`apply_corrections`(frames, frame_indices)
`determine_general_background_correction`([...])
`determine_spatial_background_correction`([...])
`determine_temporal_background_correction`([...])
`flatten_channels`(frames)
`frames_to_xarray_dataarray`(frames, frame_indices)
`get_channel`(image[, channel])
`get_channel_from_name`(channel_name)	Get the channel index belonging to a specific channel (name) If
`get_channel_indices_from_names`(channel_names)
`get_channels_from_names`(channel_names)	Get the channel index belonging to a specific channel (name) If
`get_illumination_from_name`(illumination_name)	Get the channel index belonging to a specific channel (name) If
`get_illumination_indices_from_names`(...)
`get_illuminations_from_names`(illumination_names)	Get the channel index belonging to a specific channel (name) If
`image_info_from_filename`(filename)
`image_info_to_filename`(filename[, ...])
`make_average_image`(**kwargs)	Construct an average image Determine average image for a number_of_frames starting at start_frame.
`make_maximum_projection`(**kwargs)	Construct a maximum projection image Determine maximum projection image for a number_of_frames starting at start_frame.
`make_projection_image`([projection_type, ...])	Construct a projection image Determine a projection image for a number_of_frames starting at start_frame.
`make_projection_images`([projection_type, ...])
`read_frame`(frame_index, **kwargs)
`read_frames`([frame_indices, ...])
`read_header`()
`reset_corrections`()
`save_corrections`(**kwargs)
`saveas_tif`()
`separate_channels`(frames)
`show`()
`show_correction`(correction_name[, save])
`type_dict`()

Attributes

`bitdepth`
`boundaries_metric`
`boundaries_stage`
`bytes_per_frame`
`channel_arrangement`
`channel_columns`
`channel_indices`
`channel_rows`
`configuration`
`corrections`
`corrections_filepath`
`data_type`
`frame_indices`
`height_metric`
`illumination_arrangement`
`illumination_index_per_frame`
`illumination_indices`
`illumination_indices_in_movie`
`illuminations`
`number_of_channels`	number of channels in the movie
`number_of_channels_per_frame`
`number_of_illuminations`	number of channels in the movie
`number_of_illuminations_in_movie`	number of channels in the movie
`pixel_to_stage_coordinates_transformation`
`pixels_per_frame`
`time`
`width_metric`

apply_corrections(frames, frame_indices)#

property bitdepth#

property boundaries_metric#

property boundaries_stage#

property bytes_per_frame#

property channel_arrangement#

property channel_columns#

property channel_indices#

property channel_rows#

property configuration#

property corrections#

property corrections_filepath#

property data_type#

determine_general_background_correction(method='median', frame_range=(0, 20), use_existing=False)#

determine_spatial_background_correction(method='median_filter', frame_range=(0, 20), use_existing=False, **kwargs)#

determine_temporal_background_correction(method='median', use_existing=False)#

flatten_channels(frames)#

property frame_indices#

frames_to_xarray_dataarray(frames, frame_indices)#

get_channel(image, channel='d')#

get_channel_from_name(channel_name)#

Get the channel index belonging to a specific channel (name) If

Parameters:: channel (str or int) – The name or number of a channel
Returns:: i (int) – The index of the channel to which the channel name belongs

get_channel_indices_from_names(channel_names)#

get_channels_from_names(channel_names)#

Get the channel index belonging to a specific channel (name) If

Parameters:: channel (str or int) – The name or number of a channel
Returns:: i (int) – The index of the channel to which the channel name belongs

classmethod get_illumination_from_name(illumination_name)#

Get the channel index belonging to a specific channel (name) If

Parameters:: channel (str or int) – The name or number of a channel
Returns:: i (int) – The index of the channel to which the channel name belongs

classmethod get_illumination_indices_from_names(illumination_names)#

classmethod get_illuminations_from_names(illumination_names)#

Get the channel index belonging to a specific channel (name) If

Parameters:: channel (str or int) – The name or number of a channel
Returns:: i (int) – The index of the channel to which the channel name belongs

property height_metric#

property illumination_arrangement#

property illumination_index_per_frame#

property illumination_indices#

property illumination_indices_in_movie#

illuminations = [Illumination(green), Illumination(red)]#

classmethod image_info_from_filename(filename)#

classmethod image_info_to_filename(filename, fov_index=None, projection_type=None, frame_range=None, illumination=None, apply_corrections=None)#

make_average_image(**kwargs)#

Construct an average image Determine average image for a number_of_frames starting at start_frame. i.e. [start_frame, start_frame + number_of_frames)

Parameters:

start_frame (int) – Frame to start with
number_of_frames (int) – Number of frames to average over
write (bool) – If true, the a tif file will be saved in the writepath

Returns:

np.ndarray – 2d image array with the average image

make_maximum_projection(**kwargs)#

Construct a maximum projection image Determine maximum projection image for a number_of_frames starting at start_frame. i.e. [start_frame, start_frame + number_of_frames)

Parameters:

start_frame (int) – Frame to start with
number_of_frames (int) – Number of frames to average over
write (bool) – If true, the a tif file will be saved in the writepath

Returns:

np.ndarray – 2d image array with the maximum projection image

make_projection_image(projection_type='average', frame_range=(0, 20), apply_corrections=True, illumination=None, write=False, return_image=True, flatten_channels=True, intensity_range=None, color_map='gray')#

Construct a projection image Determine a projection image for a number_of_frames starting at start_frame. i.e. [start_frame, start_frame + number_of_frames)

Parameters:

projection_type (str) – ‘average’ for average image ‘maximum’ for maximum projection image
start_frame (int) – Frame to start with
number_of_frames (int) – Number of frames to average over
write (bool) – If true, a tif file will be saved in writepath

Returns:

np.ndarray – 2d image array with the projected image

make_projection_images(projection_type='average', frame_range=(0, 20))#

property number_of_channels#

number of channels in the movie

Setting the number of channels will divide the image horizontally in equally spaced channels.

Type:: int

property number_of_channels_per_frame#

property number_of_illuminations#

number of channels in the movie

Setting the number of channels will divide the image horizontally in equally spaced channels.

Type:: int

property number_of_illuminations_in_movie#

number of channels in the movie

Setting the number of channels will divide the image horizontally in equally spaced channels.

Type:: int

property pixel_to_stage_coordinates_transformation#

property pixels_per_frame#

read_frame(frame_index, **kwargs)#

read_frames(frame_indices=None, apply_corrections=True, xarray=True, flatten_channels=False)#

read_header()#

reset_corrections()#

save_corrections(**kwargs)#

saveas_tif()#

separate_channels(frames)#

show()#

show_correction(correction_name, save=True, **kwargs)#

property time#

classmethod type_dict()#

property width_metric#