paprica.loader

Submodule containing classes and functions relative to data loading.

Usually, tileLoader objects are instantiated directly by iterating over the parser. Alternatively, they can be instantiated directly by the constructor by calling tile = paprica.loader.tileLoader().

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class paprica.loader.tileLoader(path, row, col, ftype, neighbors, neighbors_tot, neighbors_path, frame_size, folder_root, channel)[source]

Bases: object

Class to load each tile, neighboring tiles, segmentation and neighboring segmentation.

__init__(path, row, col, ftype, neighbors, neighbors_tot, neighbors_path, frame_size, folder_root, channel)[source]

Constructor of tileLoader object.

Parameters

path (string) – path to the tile (APR and tiff3D) or the folder containing the frames (tiff2D)
row (int) – vertical position of the tile (for multi-tile acquisition)
col (int) – horizontal position of the tile (for multi-tile acquisition)
ftype (str) – tile file type (‘apr’, ‘tiff3D’, ‘colm’, ‘clearscope’)
neighbors (list) –
neighbors list containing the neighbors position [row, col] of only the EAST and SOUTH neighbors to avoid the redundancy computation when stitching. For example, below the tile [0, 1] is represented by an ‘o’ while other tile are represented by an ‘x’:
```
x --- o --- x --- x
|     |     |     |
x --- x --- x --- x
|     |     |     |
x --- x --- x --- x
|     |     |     |
x --- x --- x --- x
```
in this case neighbors = [[0, 2], [1, 1]]
neighbors_tot (list) –
neighbors list containing all the neighbors position [row, col]. For example, below the tile [0, 1] is represented by an ‘o’ while other tile are represented by an ‘x’:
```
x --- o --- x --- x
|     |     |     |
x --- x --- x --- x
|     |     |     |
x --- x --- x --- x
|     |     |     |
x --- x --- x --- x
```
in this case neighbors_tot = [[0, 0], [0, 2], [1, 1]]
neighbors_path (list) – path of the neighbors whose coordinates are stored in neighbors
frame_size (int) – camera frame size (only square sensors are supported for now).
folder_root (str) – root folder where everything should be saved.
channel (int) – fluorescence channel for multi-channel acquisition. This is used to load the right data in the case of COLM acquisition where all the channel are saved in the same folder as tiff2D.

_erase_from_disk()[source]

Delete tile from disk, use with caution!

Return type: None

_load_clearscope(path)[source]

Load a sequence of images in a folder and return it as a 3D array.

Parameters: path (string) – path to folder where the data should be loaded.
Returns: v – numpy array containing the data.
Return type: array_like

_load_colm(path)[source]

Load a sequence of images in a folder and return it as a 3D array.

Parameters: path (string) – path to folder where the data should be loaded.
Returns: v – numpy array containing the data.
Return type: array_like

_load_data(path)[source]

Load data at given path.

Parameters: path (string) – path to the data to be loaded.
Returns: u – numpy array containing the data.
Return type: array_like

_load_raw(path)[source]

Load raw data at given path.

Parameters: path (string) – path to the data to be loaded.
Returns: u – numpy array containing the data.
Return type: array_like

lazy_load_segmentation(level_delta=0)[source]

Load the parts_cc lazily at the given resolution.

Parameters: level_delta (int) – parameter controlling the resolution at which the APR will be read lazily
Return type: None

lazy_load_tile(level_delta=0)[source]

Load the tile lazily at the given resolution.

Parameters: level_delta (int) – parameter controlling the resolution at which the APR will be read lazily
Return type: None

load_neighbors()[source]

Load the current tile neighbors if not already loaded.

Return type: None

load_neighbors_segmentation(load_tree=False)[source]

Load the current tile neighbors connected component (cc) if not already loaded.

Return type: None

load_segmentation(load_tree=False)[source]

Load the current tile connected component (cc) if not already loaded.

Return type: None

load_tile()[source]

Load the current tile if not already loaded.

Return type: None

plot_particles_size_distribution()[source]

Plot the particle size distribution of the tile.

Return type: None

view_tile(**kwargs)[source]

Display tile using napari.

Return type: None

paprica.loader.tile_from_apr(apr, parts)[source]

Function to generate a tile object from an APR object.

Parameters

apr (pyapr.APR) – APR to generate a tile from
parts (pyapr.ParticleData) – ParticleData to generate a tile from

Returns

tile – tile containing the given APR

Return type

tileLoader

paprica.loader.tile_from_path(path)[source]

Function to generate a tile object from the path of an APR object.

Parameters: path (string) – path to the stored APR object
Returns: tile – tile containing the given APR
Return type: tileLoader