inout

pysmFISH.stitching_package.inout.display_tiles(tiles, tile_set, fig_nr=1, block=True, maximize=False, main_title=None, rgb=False)

Plot tiles in subplots

tiles: list

List of tiles

tile_set: np.array

Tiles organization

fig_nr: int

number of the figure window.

block: bool

Block causes the program to stop running after plotting the figure, until the figure window is closed.

maximize: bool

Maximize plots the figure full screen.

main_title: str

Main title adds a title text in the figure.

rgb: bool

define the color standard used

pysmFISH.stitching_package.inout.extract_hdf5_refs(hdf5_group, image_inds)

Make a list of the dataset is hdf5_group.

When image_inds is not empty this function returns only the data sets corresponding to the numbers in image_inds.

hdf5_group: pointer

HDF5 group reference. Reference to the group from which we should extract the dataset names. The data sets are expected to be numbered.

image_inds: iterable

Iterable containing ints. Should contain the names of the datasets that will be selected. This list could also contain strings, as long as it’s contents reflect a subset of dataset names.

tile_refs: list

List of strings. The references to the data sets.

pysmFISH.stitching_package.inout.free_hdf5_space(f)

Clean up the hdf5 file after deleting a dataset

After deleting a data set from an hdf5-file, the disk space taken up by that data is not freed. Flushing the hfd5-file may help to keep the file smaller after deleting several data sets.

f: pointer

HDF5 file handle. The opened file that needs flushing.

pysmFISH.stitching_package.inout.get_image_names(hdf5_file, image_list=array([], dtype=float64), hyb_nr=1, gene='Nuclei', pre_proc_level='FilteredData')

Get the references to the tiles from the hdf5 file.

If no matching data set was found, None will be used instead of a string reference.

hdf5_file: pointer

HDF5 file handle. The file containing the tiles.

image_list: iterable

Iterable containing ints. Should contain the names of the data sets that will be selected. This list could also contain strings, as long as it’s contents reflect a subset of dataset names.

hyb_nr: int

The number of the hybridization where the data sets can be found. This will be used to navigate tile_file and find the correct tiles. (Default: 1)

gene: str

The name of the gene where the data sets can be found. This will be used to navigate tile_file and find the correct tiles. (Default: ‘Nuclei’)

pre_proc_level: str

The name of the pre processing group where the data sets can be found. This will be used to navigate tile_file and find the correct tiles. (Default: ‘Filtered’)

pysmFISH.stitching_package.inout.load_stitching_coord(file_name)

Load pickled variables

file_name: str

The name of a pickled data file. Should be given without extension.

: dict

Unpickled data found in <file_name>’.pkl’

pysmFISH.stitching_package.inout.load_tile(file_name, hdf5_file=None)

Load a tile into memory as 2D image.

file_name: str

Hdf5 reference to tile data set.

hdf5_file: pointer

HDF5 file handle. Opened HDF5 file containing the tile.

: np.array

The tile as 2D image. Or an empty array when the file_name is None.

pysmFISH.stitching_package.inout.load_tile_3D(file_name, hdf5_file=None)

Load a tile into memory as 3D image.

file_name: str

Hdf5 reference to tile data set.

hdf5_file: pointer

HDF5 file handle. Opened HDF5 file containing the tile.

: np.array

The tile as 3D image. Or an empty array when the file_name is None.

pysmFISH.stitching_package.inout.plot_coordinates(micData, ind_coord_list=None, block=True, name='coordinates', file_name=None, invert_yaxis=True)

Plot top-left coordinates with their tile numbers

Coordinates are assumed to be in pixels.

micData: object

MicroscopeData object. Containing the coordinates to be plotted.

block: bool

Plot blocks the running program untill the plotting window is closed if true (default: True)

name: str

Name of the plotting window (default: “coordinates”)

file_name: str

Name of the file the image should be saved to. The name should list the complete absolute map. Default/None causes the image to not be saved. (Default: None)

invert_yaxis: bool

Invert the y-axis when plotting. (default: True)

pysmFISH.stitching_package.inout.plot_stitched_coordinates(corner_list, image_list, block=True, name='stitched_coordinates', file_name=None, invert_yaxis=True)

Plot top-left coordinates with their tile numbers

Coordinates are assumed to be in pixels.

corner_list : list

List with as many elements as there are tiles. Each element contains the tile index (as int) and y and x coordinate of the top left corner (as a numpy array)

image_list: list

The list of the numbers of the tiles as they are found in the file names, but reordered to match the order of corner_list.

block: bool

Plot blocks the running program untill the plotting window is closed if true (default: True)

name: str

Name of the plotting window (default: “coordinates”)

file_name: str

Name of the file the image should be saved to. The name should list the complete absolute map. Default/None causes the image to not be saved. (Default: None)

invert_yaxis: bool

Invert the y-axis when plotting. (default: True)

pysmFISH.stitching_package.inout.read_IJ_corners(folder)

Read Preibisch corners

Read previously determined global corners from the Preibisch imageJ plugin data. This code starts reading below the line: ‘# Define the image coordinates’ and the file should not contain empty lines after this line.

folder: str Exact path to the folder, including trailing “/”

compare_corners: list

List, each element is a list containing the tile_ind and a numpy arrray with the corresponding corner’s y and x coordinates.

pysmFISH.stitching_package.inout.save_image(im_file, hyb_nr, gene, pre_proc_level, image_name, save_file_name)

Save hdf5 file as a tiff image

Save the data found in im_file_name[hyb_nr][gene][pre_proc_level][ image_name] as an image in a tiff-file called save_file_name. im_file should be an hdf5-file and image_name should be a variable in that file.

im_file: pointer

HDF5 file handle. Opened HDF5 file containing the image to be saved.

hyb_nr: int

Number of the current hybridization.

gene: str

The name of the gene where the image to be saved can be found. This will be used to navigate im_file and find the correct image.

pre_proc_level: str

The name of the pre processing group where the image to be saved can be found. This will be used to navigate im_file and find the correct image.

image_name: str

The name of the dataset containing the image to be saved.

save_file_name: str

The name of the image file that is going to be generated, should be given without extension.

pysmFISH.stitching_package.inout.save_to_file(file_name, **kwargs)

Save pickled stitching info to file_name

file_name: str

The name of the file where the data will be saved. Should be given without extension.

**kwarg

All keyword argument values will be gathered in a dictionary, with the variable name as their key in the dictionary. This dictionary will then be saved in the pickled file.