update omegapy to v2.1

AStcherbinine · Feb 15, 2021 · 4452281 · 4452281
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-![version](https://img.shields.io/badge/version-2.0-blue)
+![version](https://img.shields.io/badge/version-2.1-blue)
 ![pythonversion](https://img.shields.io/badge/Python-3.7-blue)
 
 # OMEGA-Py : Python tools for OMEGA data
@@ -57,4 +57,4 @@ See [`docs/*.md`](docs/) or the interactive IPython help for more details.
 ## Credits
 Developped at the Institut d'Astrophysique Spatiale (IAS), Université Paris-Saclay, Orsay, France  
 
-© Aurélien Stcherbinine (2020)
+© Aurélien Stcherbinine (2020–2021)
diff --git a/omegapy/omega_data.py b/omegapy/omega_data.py
@@ -3,7 +3,7 @@
 
 ## omega_data.py
 ## Created by Aurélien STCHERBININE
-## Last modified by Aurélien STCHERBININE : 15/10/2020
+## Last modified by Aurélien STCHERBININE : 15/02/2021
 
 ##----------------------------------------------------------------------------------------
 """Importation and correction of OMEGA/MEx observations from binaries files.
@@ -34,7 +34,7 @@
 
 # Name of the current file
 _py_file = 'omega_data.py'
-_Version = 2.0
+_Version = 2.1
 
 # Path of the package files
 package_path = os.path.abspath(os.path.dirname(__file__))
@@ -263,7 +263,7 @@ def _readomega(cube_id, disp=True, corrV=True, corrL=True):
     Parameters
     ==========
     cube_id : str
-        The observation ID (format XXXX_X).
+        The observation ID (format ORBXXXX_X).
     disp : bool, optional (default True)
         Enable or disable the display of informations during the file reading.
         | True -> Enable display.
@@ -285,7 +285,8 @@ def _readomega(cube_id, disp=True, corrV=True, corrL=True):
     nomfic0 = cube_id + '.QUB'
     nomfic = os.path.join(_omega_bin_path, nomfic0)
     nomgeo = os.path.join(_omega_bin_path, nomgeo0)
-    print('\n\033[1mComputing OMEGA observation {0:s}\033[0m'.format(cube_id))
+    if disp:
+        print('\n\033[1mComputing OMEGA observation {0:s}\033[0m'.format(cube_id))
     # Orbit number in base 10
     orbnum = int.from_bytes(str.encode(nomfic0[3]), byteorder='big') - 48
     if orbnum > 9:
@@ -730,6 +731,9 @@ class OMEGAdata:
         If True, compute the correction on the visible channel (Vis).
     corrL : bool, optional (default True)
         If True, compute the correction on the long-IR channel (L).
+    disp : bool, optional (default True)
+        Enable or disable the display of informations during the file reading.
+        | True -> Enable display.
 
     Attributes
     ==========
@@ -831,16 +835,16 @@ class OMEGAdata:
         | False -> No atmospheric correction.
     atm_corr_infos : dict
         Information about the atmospheric correction (date, method).
-    version : float
-        The version of the omegapy.omega_data.py file used.
+    version : int
+        The major release version of the omegapy.omega_data.py file used.
     add_infos : str
         Additional informations about the observation.
         Show in the OMEGAdata representation.
     """
 
-    def __init__(self, obs='', empty=False, data_path=_omega_bin_path, corrV=True, corrL=True):
+    def __init__(self, obs='', empty=False, data_path=_omega_bin_path, corrV=True, corrL=True, disp=True):
         # Infos
-        self.version = _Version
+        self.version = int(_Version)
         self.therm_corr = False
         self.atm_corr = False
         self.therm_corr_infos = {'datetime': None, 'method': None}
@@ -903,9 +907,10 @@ def __init__(self, obs='', empty=False, data_path=_omega_bin_path, corrV=True, c
                 print("\033[1;33mAborted\033[0m")
                 return None
             nomfic0 = obs_name[obs_name.rfind('/')+1:-4]    # Récupération nom + décodage UTF-8
-            data_dict, geom_dict = _readomega(nomfic0, disp=True, corrV=corrV, corrL=corrL)
+            data_dict, geom_dict = _readomega(nomfic0, disp=disp, corrV=corrV, corrL=corrL)
 
-            print("\n\033[01;34mComputing data extraction and correction...\033[0m", end=' ')
+            if disp:
+                print("\n\033[01;34mComputing data extraction and correction...\033[0m", end=' ')
             # Extract values
             ldat = data_dict['ldat']
             jdat = data_dict['jdat']
@@ -1046,7 +1051,8 @@ def __init__(self, obs='', empty=False, data_path=_omega_bin_path, corrV=True, c
                 self.add_infos = corrupted_orbits_comments[i_obs]
             #--------------------------
             # End of data extraction & correction
-            print("\033[01;32m[done]\033[0m")
+            if disp:
+                print("\033[01;32m[done]\033[0m")
 
 
     def __copy__(self):
@@ -1565,7 +1571,7 @@ def autoload_omega(obs_name, folder='auto', version=_Version, base_folder=_omega
         The observation ID.
     folder : str, optional (default 'auto')
         The subfolder where the data is.
-        | If 'auto' -> folder = 'vX.X', where X.X is the given value of code version.
+        | If 'auto' -> folder = 'vX', where X is the major release version of the used code.
     version : float, optional (default _Version)
         The version of the target file (if folder is 'auto').
     base_folder : str, optional (default _omega_py_path)
@@ -1600,7 +1606,7 @@ def autoload_omega(obs_name, folder='auto', version=_Version, base_folder=_omega
         excl.append('atm')
     filename = '*{name}*{corr_ext}*.pkl'.format(name=obs_name, corr_ext=ext)
     if folder == 'auto':
-        folder = 'v' + str(version)
+        folder = 'v' + str(int(version))
     filename2 = uf.myglob(os.path.join(base_folder, folder, filename), exclude=excl)
     if filename2 is None:
         if (therm_corr in [None, False]) and (atm_corr in [None, False]):
@@ -2083,7 +2089,7 @@ def corr_save_omega(obsname, folder='auto', base_folder=_omega_py_path, security
         The name of the OMEGA observation.
     folder : str, optional (default 'auto')
         The subfolder to save the data.
-        | If 'auto' -> folder = 'vX.X', where X.X is the OMEGAdata version.
+        | If 'auto' -> folder = 'vX', where X is the major release version of the used code.
     base_folder : str, optional (default _omega_py_path)
         The base folder path.
     security : bool, optional (default True)
@@ -2100,7 +2106,7 @@ def corr_save_omega(obsname, folder='auto', base_folder=_omega_py_path, security
         Number of parallelized worker process to use.
     """
     if folder == 'auto':
-        folder = 'v' + str(_Version)
+        folder = 'v' + str(int(_Version))
     omega = OMEGAdata(obsname)
     name = omega.name
     # path synthax
@@ -2138,7 +2144,7 @@ def corr_save_omega_list(liste_obs, folder='auto', base_folder=_omega_py_path,
         The list of the name of the OMEGA observations.
     folder : str, optional (default 'auto')
         The subfolder to save the data.
-        | If 'auto' -> folder = 'vX.X', where X.X is the Version of the current code.
+        | If 'auto' -> folder = 'vX', where X is the major release version of the used code.
     base_folder : str, optional (default _omega_py_path)
         The base folder path.
     security : bool, optional (default True)
@@ -2156,7 +2162,7 @@ def corr_save_omega_list(liste_obs, folder='auto', base_folder=_omega_py_path,
     """
     N = len(liste_obs)
     if folder == 'auto':
-        folder = 'v' + str(_Version)
+        folder = 'v' + str(int(_Version))
     for i, obsname in enumerate(liste_obs):
         print('\n\033[01mComputing observation {0} / {1} : {2}\033[0m\n'.format(i+1, N, obsname))
         corr_save_omega(obsname, folder, base_folder, security, overwrite, compress, npool)
@@ -2280,7 +2286,7 @@ def update_cube_quality(obs_name='ORB*.pkl', folder='auto', version=_Version,
         The files basename.
     folder : str, optional (default 'auto')
         The subfolder where the data is.
-        | If 'auto' -> folder = 'vX.X', where X.X is the given value of code version.
+        | If 'auto' -> folder = 'vX', where X is the major release version of the used code.
     version : float, optional (default _Version)
         The version of the target file (if folder is 'auto').
         Default is the current code version.
@@ -2291,7 +2297,7 @@ def update_cube_quality(obs_name='ORB*.pkl', folder='auto', version=_Version,
     if obs_name[-4] != '.pkl':
         obs_name += '.pkl'
     if folder == 'auto':
-        folder = 'v' + str(version)
+        folder = 'v' + str(int(version))
     basename = uf.myglob(os.path.join(base_folder, folder, obs_name))
     # Load list corrupted obs
     OBC = readsav(os.path.join(package_path, 'OMEGA_dataref', 'OBC_OMEGA_OCT2017.sav'))

diff --git a/omegapy/omega_plots.py b/omegapy/omega_plots.py
@@ -3,7 +3,7 @@
 
 ## omega_plots.py
 ## Created by Aurélien STCHERBININE
-## Last modified by Aurélien STCHERBININE : 07/10/2020
+## Last modified by Aurélien STCHERBININE : 15/02/2021
 
 ##----------------------------------------------------------------------------------------
 """Display of OMEGAdata cubes.
@@ -846,7 +846,7 @@ def show_data_v2(omega, data, cmap='viridis', vmin=None, vmax=None, alpha=None,
 ##----------------------------------------------------------------------------------------
 ## Projection grille
 def proj_grid(omega, data, lat_min=-90, lat_max=90, lon_min=0, lon_max=360,
-              pas_lat=0.1, pas_lon=0.1):
+              pas_lat=0.1, pas_lon=0.1, negative_values=False):
     """Sample the data from the input OMEGA/MEx observation on a given lat/lon grid.
 
     Parameters
@@ -868,6 +868,8 @@ def proj_grid(omega, data, lat_min=-90, lat_max=90, lon_min=0, lon_max=360,
         The latitude intervals of the grid.
     pas_lon : float, optional (default 0.1)
         The longitude intervals of the grid.
+    negative_values : bool, optional (default False)
+        Set if the negative values are considered as relevant data or not.
 
     Returns
     =======
@@ -897,9 +899,15 @@ def proj_grid(omega, data, lat_min=-90, lat_max=90, lon_min=0, lon_max=360,
             i_lon = int(longi/pas_lon - lon_min/pas_lon)
             j_lat = int(lati/pas_lat - lat_min/pas_lat)
             data_tmp = data[i,j]
-            if (not np.isnan(data_tmp)) & (data_tmp > 0):   # Filtrage régions sans données
-                grid_data[i_lon,j_lat] += data_tmp
-                mask[i_lon,j_lat] += 1
+            # if (not np.isnan(data_tmp)) & (data_tmp > 0):   # Filtrage régions sans données
+            if negative_values:
+                if (not np.isnan(data_tmp)) & (not np.isinf(data_tmp)):   # Filtrage régions sans données
+                    grid_data[i_lon,j_lat] += data_tmp
+                    mask[i_lon,j_lat] += 1
+            else:   # negative values = No data
+                if (not np.isnan(data_tmp)) & (data_tmp > 0) & (not np.isinf(data_tmp)):   # Filtrage régions sans données
+                    grid_data[i_lon,j_lat] += data_tmp
+                    mask[i_lon,j_lat] += 1
     grid_data[grid_data==0] = np.nan
     grid_data2 = grid_data / mask       # Normalisation
     mask2 = np.clip(mask, 0, 1)
@@ -952,8 +960,8 @@ def check_list_mask_omega(omega_list, mask_list, disp=True):
 def 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):
+                       data_list=None, mask_list=None, negative_values=False, plot=True, 
+                       grid=True, out=False, negatives_longitudes=False, **kwargs):
     """Display an composite map from a list OMEGA/MEx observations, sampled on a new lat/lon grid.
 
     Parameters
@@ -998,6 +1006,8 @@ def show_omega_list_v2(omega_list, lam=1.085, lat_min=-90, lat_max=90, lon_min=0
         corrupted pixels of each observaiton, in the **same order** than the observations of 
         `omega_list`.
         Each mask is a 2D array, filled with 1 for good pixels and NaN for bad ones.
+    negative_values : bool, optional (default False)
+        Set if the negative values are considered as relevant data or not.
     plot : bool, optional (default True)
         If True -> Diplay the final figure.
     grid : bool, optional (default True)
@@ -1042,7 +1052,7 @@ def show_omega_list_v2(omega_list, lam=1.085, lat_min=-90, lat_max=90, lon_min=0
             else:
                 data_tmp = omega.cube_rf[:,:,i_lam] * mask_list[i]  # Reflectance with mask
             data0, mask0 = proj_grid(omega, data_tmp, lat_min, lat_max,
-                                     lon_min, lon_max, pas_lat, pas_lon)[:2]
+                                     lon_min, lon_max, pas_lat, pas_lon, negative_values)[:2]
             data += np.nan_to_num(data0)    # Conversion NaN -> 0 pour somme des images
             mask += mask0
             mask_obs[mask0 == 1] += (omega.name + ',')
@@ -1054,7 +1064,7 @@ def show_omega_list_v2(omega_list, lam=1.085, lat_min=-90, lat_max=90, lon_min=0
             else:
                 data_tmp = data_list[i] * mask_list[i]  # Data with mask
             data0, mask0 = proj_grid(omega, data_tmp, lat_min, lat_max,
-                                     lon_min, lon_max, pas_lat, pas_lon)[:2]
+                                     lon_min, lon_max, pas_lat, pas_lon, negative_values)[:2]
             data += np.nan_to_num(data0)    # Conversion NaN -> 0 pour somme des images
             mask += mask0
             mask_obs[mask0 == 1] += (omega.name + ',')
@@ -1136,7 +1146,7 @@ def show_omega_list_v2(omega_list, lam=1.085, lat_min=-90, lat_max=90, lon_min=0
 ## Sauvegarde résultats
 def 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', ext='',
+                        mask_list=None, negative_values=False, sav_filename='auto', ext='',
                         base_folder='../data/OMEGA/sav_map_list_v2/', sub_folder=''):
     """Save the output of the omega_plots.show_omega_list_v2() function with the requested
     parameters as a dictionary.
@@ -1169,6 +1179,8 @@ def save_map_omega_list(omega_list, lat_min=-90, lat_max=90, lon_min=0, lon_max=
         corrupted pixels of each observaiton, in the **same order** than the observations of 
         `omega_list`.
         Each mask is a 2D array, filled with 1 for good pixels and NaN for bad ones.
+    negative_values : bool, optional (default False)
+        Set if the negative values are considered as relevant data or not.
     sav_filename : str, optional (default 'auto')
         The saving file name.
         | If 'auto' -> Automatically generated.
@@ -1193,7 +1205,8 @@ def save_map_omega_list(omega_list, lat_min=-90, lat_max=90, lon_min=0, lon_max=
     # Compute the data sampling
     data, mask, grid_lat, grid_lon, mask_obs = show_omega_list_v2(omega_list,
                 lam, lat_min, lat_max, lon_min, lon_max, pas_lat, pas_lon,
-                data_list=data_list, mask_list=mask_list, plot=False, out=True)
+                data_list=data_list, mask_list=mask_list, negative_values=negative_values,
+                plot=False, out=True)
     # Sav file
     input_params = {
         'omega_list' : od.get_names(omega_list),

diff --git a/omegapy/useful_functions.py b/omegapy/useful_functions.py
@@ -3,7 +3,7 @@
 
 ## useful_functions.py
 ## Created by Aurélien STCHERBININE
-## Last modified by Aurélien STCHERBININE : 06/10/2020
+## Last modified by Aurélien STCHERBININE : 15/02/2021
 
 ##-----------------------------------------------------------------------------------
 """Useful generics functions.
@@ -239,7 +239,7 @@ def where_closer(value, array):
         The index of the closer value to value in array.
     """
     array2 = np.abs(array - value)
-    i_closer = np.where(array2 == array2.min())[0][0]
+    i_closer = np.where(array2 == np.nanmin(array2))[0][0]
     return i_closer
 
 def where_closer_array(values, array):

diff --git a/setup.py b/setup.py
@@ -11,7 +11,7 @@
 
 setuptools.setup(
     name='omegapy',
-    version='2.0.1',
+    version='2.1',
     author='Aurélien Stcherbinine',
     author_email='[email protected]',
     description='Python tools for OMEGA/MEx observations analysis',