Raw

add_basic_info_no_save(nb)

This adds the basic_info page to the notebook without saving the notebook.

Parameters:

Name	Type	Description	Default
nb	Notebook	Notebook with no basic_info page.	required

Source code in coppafish/plot/raw.py

def add_basic_info_no_save(nb: Notebook):
    """
    This adds the `basic_info` page to the notebook without saving the notebook.

    Args:
        nb: Notebook with no `basic_info` page.

    """
    if not nb.has_page("basic_info"):
        nb._no_save_pages['basic_info'] = {}  # don't save if add basic_info page
        config = nb.get_config()
        nbp_basic = set_basic_info(config['file_names'], config['basic_info'])
        nb += nbp_basic

get_raw_images(nb, tiles, rounds, channels, use_z)

This loads in raw images for the experiment corresponding to the Notebook.

Parameters:

Name	Type	Description	Default
nb	Notebook	Notebook for experiment	required
tiles	List[int]	npy (as opposed to nd2 fov) tile indices to view. For an experiment where the tiles are arranged in a 4 x 3 (ny x nx) grid, tile indices are indicated as below: | 2 | 1 | 0 | | 5 | 4 | 3 | | 8 | 7 | 6 | | 11 | 10 | 9 |	required
rounds	List[int]	Rounds to view.	required
channels	List[int]	Channels to view.	required
use_z	List[int]	Which z-planes to load in from raw data.	required

Returns:

Type	Description
np.ndarray	raw_images - [len(tiles) x len(rounds) x len(channels) x n_y x n_x x len(use_z)] uint16 array.
np.ndarray	raw_images[t, r, c] is the [n_y x n_x x len(use_z)] image for tile tiles[t], round rounds[r] and channel
np.ndarray	channels[c].

Source code in coppafish/plot/raw.py

def get_raw_images(nb: Notebook, tiles: List[int], rounds: List[int],
                   channels: List[int], use_z: List[int]) -> np.ndarray:
    """
    This loads in raw images for the experiment corresponding to the *Notebook*.

    Args:
        nb: Notebook for experiment
        tiles: npy (as opposed to nd2 fov) tile indices to view.
            For an experiment where the tiles are arranged in a 4 x 3 (ny x nx) grid, tile indices are indicated as
            below:

            | 2  | 1  | 0  |

            | 5  | 4  | 3  |

            | 8  | 7  | 6  |

            | 11 | 10 | 9  |
        rounds: Rounds to view.
        channels: Channels to view.
        use_z: Which z-planes to load in from raw data.

    Returns:
        `raw_images` - `[len(tiles) x len(rounds) x len(channels) x n_y x n_x x len(use_z)]` uint16 array.
        `raw_images[t, r, c]` is the `[n_y x n_x x len(use_z)]` image for tile `tiles[t]`, round `rounds[r]` and channel
        `channels[c]`.
    """
    n_tiles = len(tiles)
    n_rounds = len(rounds)
    n_channels = len(channels)
    n_images = n_rounds * n_tiles * n_channels
    ny = nb.basic_info.tile_sz
    nx = ny
    nz = len(use_z)

    raw_images = np.zeros((n_tiles, n_rounds, n_channels, ny, nx, nz), dtype=np.uint16)
    with tqdm(total=n_images) as pbar:
        pbar.set_description(f'Loading in raw data')
        for r in range(n_rounds):
            round_dask_array = raw.load(nb.file_names, nb.basic_info, r=rounds[r])
            # TODO: Can get rid of these two for loops, when round_dask_array is always a dask array.
            #  At the moment though, is not dask array when using nd2_reader (On Mac M1).
            for t in range(n_tiles):
                for c in range(n_channels):
                    pbar.set_postfix({'round': rounds[r], 'tile': tiles[t], 'channel': channels[c]})
                    raw_images[t, r, c] = raw.load(nb.file_names, nb.basic_info, round_dask_array,
                                                   rounds[r], tiles[t], channels[c], use_z)
                    pbar.update(1)
    return raw_images

view_raw(nb=None, tiles=0, rounds=0, channels=None, use_z=None, config_file=None)

Function to view raw data in napari. There will upto 4 scrollbars for each image to change tile, round, channel and z-plane.

Requires access to nb.file_names.input_dir

Parameters:

Name	Type	Description	Default
nb	Optional[Notebook]	Notebook for experiment. If no Notebook exists, pass config_file instead.	None
tiles	Union[int, List[int]]	npy (as opposed to nd2 fov) tile indices to view. For an experiment where the tiles are arranged in a 4 x 3 (ny x nx) grid, tile indices are indicated as below: | 2 | 1 | 0 | | 5 | 4 | 3 | | 8 | 7 | 6 | | 11 | 10 | 9 |	0
rounds	Union[int, List[int]]	rounds to view (anchor will be nb.basic_info.n_rounds i.e. the last round.)	0
channels	Optional[Union[int, List[int]]]	Channels to view. If None, will load all channels.	None
use_z	Optional[Union[int, List[int]]]	Which z-planes to load in from raw data. If None, will use load all z-planes (except from first one if config['basic_info']['ignore_first_z_plane'] == True).	None
config_file	Optional[str]	path to config file for experiment.	None

Source code in coppafish/plot/raw.py

def view_raw(nb: Optional[Notebook] = None, tiles: Union[int, List[int]] = 0, rounds: Union[int, List[int]] = 0,
             channels: Optional[Union[int, List[int]]] = None,
             use_z: Optional[Union[int, List[int]]] = None, config_file: Optional[str] = None):
    """
    Function to view raw data in napari.
    There will upto 4 scrollbars for each image to change tile, round, channel and z-plane.

    !!! warning "Requires access to `nb.file_names.input_dir`"

    Args:
        nb: *Notebook* for experiment. If no *Notebook* exists, pass `config_file` instead.
        tiles: npy (as opposed to nd2 fov) tile indices to view.
            For an experiment where the tiles are arranged in a 4 x 3 (ny x nx) grid, tile indices are indicated as
            below:

            | 2  | 1  | 0  |

            | 5  | 4  | 3  |

            | 8  | 7  | 6  |

            | 11 | 10 | 9  |
        rounds: rounds to view (`anchor` will be `nb.basic_info.n_rounds` i.e. the last round.)
        channels: Channels to view. If `None`, will load all channels.
        use_z: Which z-planes to load in from raw data. If `None`, will use load all z-planes (except from first
            one if `config['basic_info']['ignore_first_z_plane'] == True`).
        config_file: path to config file for experiment.
    """
    if nb is None:
        nb = Notebook(config_file=config_file)
    add_basic_info_no_save(nb)  # deal with case where there is no notebook yet
    if channels is None:
        channels = np.arange(nb.basic_info.n_channels)
    if use_z is None:
        use_z = nb.basic_info.use_z
    tiles, rounds, channels, use_z = number_to_list([tiles, rounds, channels, use_z])

    raw_images = get_raw_images(nb, tiles, rounds, channels, use_z)
    viewer = napari.Viewer()
    viewer.add_image(np.moveaxis(raw_images, -1, 3), name='Raw Images')

    @viewer.dims.events.current_step.connect
    def update_slider(event):
        viewer.status = f'Tile: {tiles[event.value[0]]}, Round: {rounds[event.value[1]]}, ' \
                        f'Channel: {channels[event.value[2]]}, Z: {use_z[event.value[3]]}'

    viewer.dims.axis_labels = ['Tile', 'Round', 'Channel', 'z', 'y', 'x']
    viewer.dims.set_point([0, 1, 2], [0, 0, 0])  # set to first tile, round and channel initially
    napari.run()