utils package

The utils package contains different useful but not essential scripts such as plotting scripts and scripts to compute criterias to evaluate the performance of the inference.

utils.generate_gif module

utils.generate_gif.generate_gif(images_path='./plot/plot_all_timestep/', save_path='./plot/', file_name='output')

generate a gif file from png files contained in a given directory * images_path: string, ‘./plot/plot_all_timestep/’ by default, contains the path of the directory in which the figures are * save_path: string, ‘./plot/’ by default, contains the path of the directory in which the gif file will be saved * file_name string, ‘output’ by default, name of the file in which the gif will be saved

• do:

  • open and concatenate in the alphabetic order the files contained in the given images’ directory

  • save the array of images as a gif in the given save directory

utils.geom_to_shapefile module

utils.geom_to_shapefile.geom_to_shapefile(msh, name_file_out, path_out)

method to save the geometry in a shapefile with the domain as a shapely.box for visualization

• input:

  • msh: object of the class MeshRect2D, the mesh containing the geometry to save

  • path_out: str, path to the folder in which the geometry will be saved

  • name_file_out: str, name of the file in which the geometry will be saved

• do:

  • generate a shapely.box corresponding the the domain

  • save the geometry contained in msh and the domain’s box in the file and folder given as input

utils.plot_colormap module

utils.plot_colormap.plot_colormap(msh, xy_map, label, unit, cmap='jet', title=None, map_bound=None, save_path=None, file_name=None, file_format='pdf', figsize=(20, 15))

Plot a given physical quantity

• input:

  • msh: object of the class MeshRect2D

  • xy_map: numpy array of shape (mesh.y.size, mesh.x.size), contains the mean value of the physical quantity in the cells

  • label: string, contains the label of the physical quantity, can be in LaTeX format

  • unit: string, contains the unit of the physical quantity, can be in LaTeX format

  • cmap: string, “jet” by default, contains the name of the colormap to use

  • title: string, None by default, contains the title of the figure, can be in LaTeX format

  • map_bound: tuple, contains the lower and upper boundary we want to impose to the colormap

  • save_path: string, None by default, contains the path to directory in which the figure is saved if not None

  • file_name: string, None by default, contains the name of the filein which the figure is saved if save_path is not None

  • file_format: string, ‘pdf’ by default, contains the format of the file in which the figure is saved if save_path is not None

  • figsize: tuple, (20, 15) by default, contains the size of the figure

• do:

  • plot on the whole domain the given physical quantity

  • save the figure in a file if the save_path input is not None, show the figure otherwise

utils.plot_colormap.plot_colormap_all_timestep(msh, t, txy_map, label, unit, cmap='jet', save_path='./plot/plot_all_timestep/', figsize=(20, 15), restart_ite=0)

Plot and save a given physical quantity at every time step

• input:

  • msh: object of the class MeshRect2D

  • t: numpy array, contains all the time at which the physical quantity is plotted

  • txy_map:

    numpy array of shape (t.size, mesh.y.size, mesh.x.size), contains the mean value of the physical quantity in the cells at every time step

  • label: string, contains the label of the physical quantity, can be in LaTeX format

  • unit: string, contains the unit of the physical quantity, can be in LaTeX format

  • cmap: string, “jet” by default, contains the name of the colormap to use

  • save_path: string, ‘./plot/plot_all_timestep/’ by default, contains the path to directory in which all the figures are saved

• do:

  • plot on the whole domain and at every time step the given physical quantity

  • save the figures in png files

utils.plot_cost module

utils.plot_cost.plot_cost(j_obs, j_reg, norm_noise, label_reg, ls_reg, save_path=None, file_name=None, file_format='pdf', figsize=(20, 15))

Plot cost

Parameters:

• j_obs (array) – observation cost

• j_reg (dict of arrays) – cost of the regularization terms

• norm_noise (float) – noise level

• label_reg (dict of strings) – labels of the regularization terms

• ls_reg (dict of string) – line styles

• save_path (str, optional) – Save path. Defaults to None.

• file_name (str, optional) – plot file name. Defaults to None.

• file_format (str, optional) – file format. Defaults to ‘pdf’.

• figsize (tuple, optional) – size of the figure. Defaults to (20, 15).

utils.plot_cost.plot_cost_obs_comparison(case_dict, save_path=None, file_name=None, file_format='pdf', figsize=(20, 15))

Plot observation cost in different cases

Parameters:

• case_dict (dict) – The different cases

• save_path (str, optional) – Save path. Defaults to None.

• file_name (str, optional) – File name. Defaults to None.

• file_format (str, optional) – file format. Defaults to ‘pdf’.

• figsize (tuple, optional) – figure size. Defaults to (20, 15).

utils.plot_ctrl module

utils.plot_ctrl.plot_ctrl(msh, t, ctrl, ctrl_target=None, obs=None, trajectory_U=None, cmap='jet', title=None, map_bound=None, label='s', save_path=None, file_name=None, file_format='pdf', figsize=(20, 15))

plot of the control

Parameters:

• msh (mesh2D) – 2D mesh

• t (float) – time

• ctrl (array) – control

• ctrl_target (array, optional) – target. Defaults to None.

• obs (array, optional) – observations. Defaults to None.

• trajectory_U (array, optional) – trajectory. Defaults to None.

• cmap (str, optional) – color map. Defaults to “jet”.

• title (str, optional) – title. Defaults to None.

• map_bound (array like, optional) – boundaries. Defaults to None.

• label (str, optional) – label. Defaults to ‘s’.

• save_path (str, optional) – save path. Defaults to None.

• file_name (str, optional) – file name. Defaults to None.

• file_format (str, optional) – file format. Defaults to ‘pdf’.

• figsize (tuple, optional) – figure size. Defaults to (20, 15).

utils.plot_ctrl.plot_ctrl_all_timestep(msh, ctrl, ctrl_target=None, obs=None, label='s', cmap='jet', save_path='./plot/plot_all_timestep/')

Plot and save a given physical quantity at every time step

• input:

  • msh: object of the class MeshRect2D

  • t: numpy array, contains all the time at which the physical quantity is plotted

  • txy_map:

    numpy array of shape (t.size, mesh.y.size, mesh.x.size), contains the mean value of the physical quantity in the cells at every time step

  • label: string, contains the label of the physical quantity, can be in LaTeX format

  • unit: string, contains the unit of the physical quantity, can be in LaTeX format

  • cmap: string, “jet” by default, contains the name of the colormap to use

  • save_path: string, ‘./plot/plot_all_timestep/’ by default, contains the path to directory in which all the figures are saved

• do:

  • plot on the whole domain and at every time step the given physical quantity

  • save the figures in png files

utils.plot_ctrl.plot_ctrl_map(msh, t, ctrl_map, ctrl_target_map=None, obs=None, trajectory_U=None, cmap='jet', title=None, map_bound=None, label='s', save_path=None, file_name=None, file_format='pdf', figsize=(20, 15))

Plot the control map

Parameters:

• msh (mesh2D) – 2D mesh

• t (float) – time

• ctrl_map (array) – map of the control

• ctrl_target_map (array, optional) – map of the target. Defaults to None.

• obs (array, optional) – observations. Defaults to None.

• trajectory_U (array, optional) – trajectory. Defaults to None.

• cmap (str, optional) – color map. Defaults to “jet”.

• title (str, optional) – title. Defaults to None.

• map_bound (array like, optional) – boundaries. Defaults to None.

• label (str, optional) – label. Defaults to ‘s’.

• save_path (str, optional) – save path. Defaults to None.

• file_name (str, optional) – file name. Defaults to None.

• file_format (str, optional) – file format. Defaults to ‘pdf’.

• figsize (tuple, optional) – figure size. Defaults to (20, 15).

utils.plot_ctrl.trajectory(x, y, msh, U)

Computes a trajectory

Parameters:

• x (float) – seed (x coordinates)

• y (float) – seed (y coordinates)

• msh (mesh2D) – 3D mesh

• U (array) – velocity field

Returns:

trajectories

Return type:

tuple of lists

utils.plot_ctrl_error module

utils.plot_ctrl_error.plot_mean_error_ctrl_comparison_vs_ite(case_dict, ctrl_target, optim_iter_start=0, optim_iter_end=-1, flag_domain=None, ordre_norm=2, ylabel=None, save_path=None, file_name=None, file_format='pdf', figsize=(20, 15))

Plot mean error with control, comparison with different cases

Parameters:

• case_dict (dict of cases) – the different cases

• ctrl_target (dataframe) – control target

• optim_iter_start (int, optional) – iter start. Defaults to 0.

• optim_iter_end (int, optional) – iter end. Defaults to -1.

• flag_domain (_type_, optional) – flag of the domain. Defaults to None.

• ordre_norm (int, optional) – error norm order. Defaults to 2.

• ylabel (str, optional) – ylabel. Defaults to None.

• save_path (str, optional) – save path. Defaults to None.

• file_name (str, optional) – file name. Defaults to None.

• file_format (str, optional) – file format. Defaults to ‘pdf’.

• figsize (tuple, optional) – figure size. Defaults to (20, 15).

utils.plot_env_param module

utils.plot_env_param.plot_diffusion_tensor(msh, diffu_coeff, save_path=None, figsize=(20, 15))

Plot the diffusion tensor

• input:

  • msh: object of the class MeshRect2D

  • diffu_coeff: object of the class DiffusionTensor

  • save_path: string, None by default, contains the path to directory in which the figure is saved if not None

  • figsize: tuple, (20, 15) by default, contains the size of the figure

• do:

  • plot on the whole domain the four component of the diffusion tensor

  • save the figure in a pdf file if the save_path input is not None, show the figure otherwise

utils.plot_env_param.plot_velocity_field(msh, vel, save_path=None, file_name=None, figsize=(20, 15), space_subsampling_rate=10, scale_arrow=0.9756097560975611, width_arrow=0.2, vlim=None, title=None, format_out='pdf')

Plot the velocity field

• input:

  • msh: object of the class MeshRect2D

  • vel: object of the class Velocity

  • save_path: string, None by default, contains the path to directory in which the figure is saved if not None

  • figsize: tuple, (20, 15) by default, contains the size of the figure

• do:

  • plot on the whole domain the velocity field with an arrow representation of the velocity vector

  • save the figure in a pdf file if the save_path input is not None, show the figure otherwise

utils.plot_obs module

utils.plot_obs.plot_obs(msh, t, obs, figsize=(20, 15), cmap='jet', save_path=None, file_format='pdf', cbar_dim=[0.92, 0.15, 0.02, 0.69])

Plot and save the observations at a given time step

• input:

  • msh: object of the class MeshRect2D

  • t: float, contains the time at which the observations plotted

  • obs: object of the class Obs, contains the observations we want to plot

  • cmap: string, “jet” by default, contains the name of the colormap to use

  • save_path: string, ‘./plot/plot_all_timestep/’ by default, contains the path to directory in which all the figures are saved

  • file_format: string, ‘pdf’ by default, contains the format of the file in which the figure is saved if save_path is not None

  • figsize: tuple, (20, 15) by default, contains the size of the figure

• do:

  • plot on the observations at a given time step, the points not observed are left white

  • save the figures in a file

utils.superlevel_set module

utils.superlevel_set.intersection_superlevel_set(threshold, s_array)

Define superlevel set intersections

Parameters:

• threshold (float) – threshold

• s_array (array) – value

Returns:

returns point superior to the threshold

Return type:

array

utils.superlevel_set.superlevel_set(threshold, s)

Defines the superlevel set

Parameters:

• threshold (float) – threshold

• s (array) – value

Returns:

returns point superior to the threshold

Return type:

array

utils.superlevel_set.volume(domain, volume_cell)

Cmpute volumem

Parameters:

• domain (array like) – domain definition

• volume_cell (array_like) – volume celles

Returns:

domain volume

Return type:

float

utils.superlevel_set.volume_intersection_superlevel_set(threshold, s_array, volume_cell)

Volume of intersection of superlevel sets

Parameters:

• threshold (float) – threshold

• s_array (array_like) – control

• volume_cell (array_like) – volume of the cells

Returns:

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Return type:

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