update to version 1.4.2

AStcherbinine · May 13, 2020 · e260407 · e260407
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-![version](https://img.shields.io/badge/version-1.4-blue)
+![version](https://img.shields.io/badge/version-1.4.2-blue)
 ![pythonversion](https://img.shields.io/badge/Python-3.7-blue)
 ![idlversion](https://img.shields.io/badge/IDL-8.3-blue)
 

diff --git a/docs/doc.md b/docs/doc.md
@@ -21,17 +21,17 @@ Using IDL routines containing in omegapy/omega_routines/*.
 
 `import_list_obs_csv(filename)`
 
-`corr_therm(omega)`
+`corr_therm(omega, npool=1)`
 
 `corr_therm2(omega)`
 
 `corr_atm(omega)`
 
 `corr_atm2(omega)`
 
-`corr_save_omega(obsname, folder='auto', base_folder=_omega_py_path, security=True, overwrite=True, compress=True)`
+`corr_save_omega(obsname, folder='auto', base_folder=_omega_py_path, security=True, overwrite=True, compress=True, npool=1)`
 
-`corr_save_omega_list(liste_obs, folder='auto', base_folder=_omega_py_path, security=True, overwrite=True, compress=True)`
+`corr_save_omega_list(liste_obs, folder='auto', base_folder=_omega_py_path, security=True, overwrite=True, compress=True, npool=1)`
 
 `set_omega_bin_path(new_path)`
 
@@ -47,6 +47,12 @@ Using IDL routines containing in omegapy/omega_routines/*.
 
 `update_cube_quality(obs_name='ORB*.pkl', folder='auto', version=Version, base_folder=_omega_py_path)`
 
+`test_cube(obs)`
+
+`compute_list_good_observations(savfilename='liste_good_obs.csv', folder='../data/OMEGA/liste_obs', security=True)`
+
+`utc_to_my(dt)`
+
 
 ## [`omegapy.omega_plots`](doc_omega_plots.md)
 
@@ -62,7 +68,13 @@ Display of OMEGAdata cubes.
 
 `show_ibd_v2(omega, ibd, cmap='viridis', vmin=None, vmax=None, alpha=None, title='auto', cb_title = 'IBD', lonlim=(None, None), latlim=(None, None), Nfig=None, polar=False, cbar=True)`
 
-`show_omega_list_v2(omega_list, lam=1.085, lat_min=-90, lat_max=90, lon_min=0, lon_max=360, pas_lat=0.1, pas_lon=0.1, cmap='Greys_r', vmin=None, vmax=None, title='auto', Nfig=None, polar=False, cbar=True, cb_title='auto', data_list=None, plot=True, grid=True, out=False, **kwargs)`
+`show_omega_list_v2(omega_list, lam=1.085, lat_min=-90, lat_max=90, lon_min=0, lon_max=360, pas_lat=0.1, pas_lon=0.1, cmap='Greys_r', vmin=None, vmax=None, title='auto', Nfig=None, polar=False, cbar=True, cb_title='auto', data_list=None, mask_list=None, plot=True, grid=True, out=False, negatives_longitudes=False, **kwargs)`
+
+`save_map_omega_list(omega_list, lat_min=-90, lat_max=90, lon_min=0, lon_max=360, pas_lat=0.1, pas_lon=0.1, lam=1.085, data_list=None, data_desc='', mask_list=None, sav_filename='auto', base_folder='../data/OMEGA/sav_map_list_v2/', ext='')`
+
+`load_map_omega_list(filename)`
+
+`show_omega_list_v2_man(data, grid_lat, grid_lon, infos, cmap='Greys_r', vmin=None, vmax=None, title='auto', Nfig=None, polar=False, cbar=True, cb_title='auto', grid=True, negatives_longitudes=False, **kwargs)`
 
 
 ## [`omegapy.useful_functions`](doc_useful_functions.md)
@@ -81,6 +93,8 @@ Some useful generic functions.
 
 `load_pickle(filename, disp=True)`
 
+`test_security_overwrite(path)`
+
 `reg_lin(X, Y)`
 
 `planck(lam, T)`

diff --git a/docs/doc_omega_data.md b/docs/doc_omega_data.md
@@ -19,19 +19,21 @@ Using IDL routines containing in omegapy/omega_routines/*.
 
 `load_omega_list(basename, disp=True)`
 
+`load_omega_list2(liste_obs, therm_corr=True, atm_corr=True, **kwargs)`
+
 `import_list_obs_csv(filename)`
 
-`corr_therm(omega)`
+`corr_therm(omega, npool=1)`
 
 `corr_therm2(omega)`
 
 `corr_atm(omega)`
 
 `corr_atm2(omega)`
 
-`corr_save_omega(obsname, folder='auto', base_folder=_omega_py_path, security=True, overwrite=True, compress=True)`
+`corr_save_omega(obsname, folder='auto', base_folder=_omega_py_path, security=True, overwrite=True, compress=True, npool=1)`
 
-`corr_save_omega_list(liste_obs, folder='auto', base_folder=_omega_py_path, security=True, overwrite=True, compress=True)`
+`corr_save_omega_list(liste_obs, folder='auto', base_folder=_omega_py_path, security=True, overwrite=True, compress=True, npool=1)`
 
 `set_omega_bin_path(new_path)`
 
@@ -47,6 +49,12 @@ Using IDL routines containing in omegapy/omega_routines/*.
 
 `update_cube_quality(obs_name='ORB*.pkl', folder='auto', version=_Version, base_folder=_omega_py_path)`
 
+`test_cube(obs)`
+
+`compute_list_good_observations(savfilename='liste_good_obs.csv', folder='../data/OMEGA/liste_obs', security=True)`
+
+`utc_to_my(dt)`
+
 
 ### OMEGAdata class
 ~~~python
@@ -335,6 +343,31 @@ omegapy.omega_data.load_omega_list(basename, disp=True):
         The array of loaded objects of OMEGA/MEx observation.
 ~~~
 
+~~~python
+omegapy.omega_data.load_omega_list2(liste_obs, therm_corr=True, atm_corr=True, **kwargs)
+    Load a list of saved OMEGAdata objects, using load_omega().
+
+    Parameters
+    ==========
+    liste_obs : array of str
+        List of OMEGA/MEx observations ID.
+    therm_corr : bool or None, optional (default None)
+        | True -> Only results with thermal correction.
+        | False -> Only results without thermal correction.
+        | None -> Both with and without thermal correction.
+    atm_corr : bool or None, optional (default None)
+        | True -> Only results with atmospheric correction.
+        | False -> Only results without atmospheric correction.
+        | None -> Both with and without atmospheric correction.
+    **kwargs:
+        Optional arguments for autoload_omega().
+
+    Returns
+    =======
+    omega_list : list of OMEGAdata objects
+        The list of loaded objects of OMEGA/MEx observation.
+~~~
+
 ~~~python
 omegapy.omega_data.import_list_obs_csv(filename):
     Import a list of observations ID from a csv file generated by JMars.
@@ -354,13 +387,18 @@ omegapy.omega_data.import_list_obs_csv(filename):
 Correction thermique 1 - Détermitation réflectance à 5µm à partir de celle à 2.4µm puis CN -- Méthode historique (Calvin & Erard 1997)
 
 ~~~python
-omegapy.omega_data.corr_therm(omega):
+omegapy.omega_data.corr_therm(omega, npool=1):
     Remove the thermal component in the OMEGA hyperspectral cube.
+
+    Parallelization is implemented using the multiprocessing module. The number of
+    process to run is controlled by the npool argument.
 
     Parameters
     ==========
     omega : OMEGAdata
         The OMEGA observation data.
+    npool : int, optional (default 1)
+        Number of parallelized worker process to use.
 
     Returns
     =======
@@ -428,10 +466,13 @@ omegapy.omega_data.corr_atm2(omega):
 ### Correction & Saving
 Import an OMEGA/MEx observation, apply a thermal and atmospheric correction (M1) and save the OMEGAdata object at each step.
 
-~~~
+~~~python
 omegapy.omega_data.corr_save_omega(obsname, folder='auto', base_folder=_omega_py_path, security=True,
-                    overwrite=True, compress=True):
+                    overwrite=True, compress=True, npool=1):
     Correction and saving of OMEGA/MEx observations.
+
+    Parallelization is implemented using the multiprocessing module. The number of
+    process to run is controlled by the npool argument.
 
     Parameters
     ==========
@@ -452,12 +493,17 @@ omegapy.omega_data.corr_save_omega(obsname, folder='auto', base_folder=_omega_py
     compress : bool, optional (default True)
         If True, the radiance cube after correction is removed (i.e. set to None)
         in order to reduce the size of the saved file.
+    npool : int, optional (default 1)
+        Number of parallelized worker process to use.
 ~~~
 
 ~~~
 omegapy.omega_data.corr_save_omega_list(liste_obs, folder='auto', base_folder=_omega_py_path,
-                         security=True, overwrite=True, compress=True):
+                         security=True, overwrite=True, compress=True, npool=1):
     Correction and saving of a list of OMEGA/MEx observations.
+
+    Parallelization is implemented using the multiprocessing module. The number of
+    process to run is controlled by the npool argument.
 
     Parameters
     ==========
@@ -478,6 +524,8 @@ omegapy.omega_data.corr_save_omega_list(liste_obs, folder='auto', base_folder=_o
     compress : bool, optional (default True)
         If True, the radiance cube after correction is removed (i.e. set to None)
         in order to reduce the size of the saved file.
+    npool : int, optional (default 1)
+        Number of parallelized worker process to use.
 ~~~
 
 ~~~python
@@ -537,7 +585,7 @@ omegapy.omega_data.get_names(omega_list):
 
 ~~~python
 omegapy.omega_data.get_ls(omega_list):
-    """Return the array of the Solar longitude of each OMEGA/MEx observation in omega_list.
+    Return the array of the Solar longitude of each OMEGA/MEx observation in omega_list.
 
     Parameters
     ==========
@@ -552,7 +600,7 @@ omegapy.omega_data.get_ls(omega_list):
 
 
 ### Update quality
-~~python
+~~~Python
 omegapy.omega_data.update_cube_quality(obs_name='ORB*.pkl', folder='auto', version=_Version, 
                         base_folder=_omega_py_path):
     Update the quality attribute of previously saved OMEGAdata objects.
@@ -571,3 +619,62 @@ omegapy.omega_data.update_cube_quality(obs_name='ORB*.pkl', folder='auto', versi
         The base folder path.
 ~~~
 
+
+### Testing observations quality
+~~~python
+omegapy.omega_data.test_cube(obs):
+    Test the quality of an OMEGA/MEx observation from the header informations
+    witout open it.
+
+    Parameters
+    ==========
+    obs : str
+        The name of the OMEGA observation.
+
+    Returns
+    =======
+    test_quality : bool
+        | True -> Accepted observation.
+        | False -> Rejected observation.
+~~~
+
+~~~python
+omegapy.omega_data.compute_list_good_observations(savfilename='liste_good_obs.csv', 
+                                   folder='../data/OMEGA/liste_obs', security=True):
+    Scan the available OMEGA/MEx data cubes and list the observations considered as 
+    good quality.
+    The results are saved in the specified csv file.
+
+    Parameters
+    ==========
+    savfilename : str
+        The name of the csv file to save the data.
+    folder : str
+        The name of the folder where the saved file will be located.
+        Final saved file path = folder + savfilename
+    security : bool, optional (default True)
+        Enable / disable checking before overwriting a file.
+        | True -> Check if the target file already exists before overwriting on it.
+                  And if is the case, you will be asked for a confirmation.
+        | False -> Didn't care about the already existing files.
+~~~
+
+### Conversion UTC to MY
+~~~python
+omegapy.omega_data.utc_to_my(dt):
+    Convert a UTC datetime to the corresponding Martian Year (MY).
+
+    Martian Years are numbered according to the calendar proposed by R. Todd Clancy 
+    (Clancy et al., Journal of Geophys. Res 105, p 9553, 2000): Martian Year 1 begins 
+    (at a time such that Ls=0) on April 11th, 1955.
+
+    Parameters
+    ==========
+    dt : datetime.datetime
+        The UTC datetime object.
+
+    Returns
+    =======
+    my : int
+        The corresponding Martian Year.
+~~~