update to version 2.0 - Full Python !

README.md

@@ -1,6 +1,5 @@
-![version](https://img.shields.io/badge/version-1.4.2-blue)
+![version](https://img.shields.io/badge/version-2.0-blue)
 ![pythonversion](https://img.shields.io/badge/Python-3.7-blue)
-![idlversion](https://img.shields.io/badge/IDL-8.3-blue)
 
 # OMEGA-Py : Python tools for OMEGA data
 

docs/doc.md

@@ -1,24 +1,25 @@
-# OMEGA-Py documentation - v1.2
+# OMEGA-Py documentation - v2.0
 
 ## [`omegapy.omega_data`](doc_omega_data.md)
 
-Importation of OMEGA observations in the OMEGAdata class.
-Using IDL routines containing in omegapy/omega_routines/*.
+Importation and correction of OMEGA/MEx observations from binaries files.
 
-`class OMEGAdata(obs='', empty=False, data_path=_omega_bin_path)`
+`class OMEGAdata(obs='', empty=False, data_path=_omega_bin_path, corrV=True, corrL=True)`
 
-`find_cube(lat, lon, cmin=0, cmax=10000, out=False)`
+`find_cube(lon0, lat0, cmin=0, cmax=10000, out=False)`
 
 `autosave_omega(omega, folder='auto', base_folder=_omega_py_path, security=True, disp=True)`
 
-`autoload_omega(obs_name, folder='auto', version=Version, base_folder=_omega_py_path, therm_corr=None, atm_corr=None, disp=True)`
+`autoload_omega(obs_name, folder='auto', version=_Version, base_folder=_omega_py_path, therm_corr=None, atm_corr=None, disp=True)`
 
 `save_omega(omega, savname='auto', folder='', base_folder=_omega_py_path, pref ='', suff='', disp=True)`
 
 `load_omega(filename, disp=True)`
 
 `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, npool=1)`
@@ -45,28 +46,32 @@ Using IDL routines containing in omegapy/omega_routines/*.
 
 `get_ls(omega_list)`
 
-`update_cube_quality(obs_name='ORB*.pkl', folder='auto', version=Version, base_folder=_omega_py_path)`
+`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)`
 
+`shared_lam(lam_list)`
+
+`shared_lam_omegalist(omega_list)`
+
 
 ## [`omegapy.omega_plots`](doc_omega_plots.md)
 
 Display of OMEGAdata cubes.
 
 `show_omega(omega, lam, refl=True, lam_unit='m', cmap='Greys_r', vmin=None, vmax=None, title='auto', xlim=(None, None), ylim=(None, None), Nfig=None)`
 
-`show_omega_v2(omega, lam, refl=True, lam_unit='m', cmap='Greys_r', vmin=None, vmax=None, alpha=None, title='auto', lonlim=(None, None), latlim=(None, None), Nfig=None, polar=False, cbar=True)`
+`show_omega_v2(omega, lam, refl=True, lam_unit='m', cmap='Greys_r', vmin=None, vmax=None, alpha=None, title='auto', lonlim=(None, None), latlim=(None, None), Nfig=None, polar=False, cbar=True, grid=True, mask=None, negatives_longitudes='auto')`
 
 `show_omega_interactif(omega, lam, refl=True, lam_unit='m', cmap='Greys_r', vmin=None, vmax=None, title='auto', autoyscale=True, xlim=(None, None), ylim=(None, None))`
 
-`show_omega_interactif_v2(omega, lam=1.085, refl=True, lam_unit='m', data=None, cmap='Greys_r', cb_title='IBD', title='auto', vmin=None, vmax=None, autoyscale=True, ylim_sp=(None, None), alpha=None, lonlim=(None, None), latlim=(None, None), polar=False, cbar=True, grid=True)`
+`show_omega_interactif_v2(omega, lam=1.085, refl=True, lam_unit='m', data=None, cmap='Greys_r', cb_title='data', title='auto', vmin=None, vmax=None, autoyscale=True, ylim_sp=(None, None), alpha=None, lonlim=(None, None), latlim=(None, None), polar=False, cbar=True, grid=True, mask=None, lam_mask=None, negatives_longitudes='auto')`
 
-`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_data_v2(omega, data, cmap='viridis', vmin=None, vmax=None, alpha=None, title='auto', cb_title = 'data', lonlim=(None, None), latlim=(None, None), Nfig=None, polar=False, cbar=True, grid=True, mask=None, negatives_longitudes='auto')`
 
 `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)`
 
@@ -76,6 +81,8 @@ Display of OMEGAdata cubes.
 
 `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)`
 
+`plot_psp(sp1_id, *args, sp2_id=(None, None), Nfig=None, sp_dict=picked_spectra, **kwargs)`
+
 
 ## [`omegapy.useful_functions`](doc_useful_functions.md)
 

docs/doc_omega_data.md

@@ -1,13 +1,12 @@
-# OMEGA-Py documentation - v1.2
+# OMEGA-Py documentation - v2.0
 
 ## `omegapy.omega_data`
 
-Importation of OMEGA observations in the OMEGAdata class.
-Using IDL routines containing in omegapy/omega_routines/*.
+Importation and correction of OMEGA/MEx observations from binaries files.
 
-`class OMEGAdata(obs='', empty=False, data_path=_omega_bin_path)`
+`class OMEGAdata(obs='', empty=False, data_path=_omega_bin_path, corrV=True, corrL=True)`
 
-`find_cube(lat, lon, cmin=0, cmax=10000, out=False)`
+`find_cube(lon0, lat0, cmin=0, cmax=10000, out=False)`
 
 `autosave_omega(omega, folder='auto', base_folder=_omega_py_path, security=True, disp=True)`
 
@@ -55,11 +54,15 @@ Using IDL routines containing in omegapy/omega_routines/*.
 
 `utc_to_my(dt)`
 
+`shared_lam(lam_list)`
+
+`shared_lam_omegalist(omega_list)`
+
 
 ### OMEGAdata class
 ~~~python
-class omegapy.omega_data.OMEGAdata(obs='', empty=False, data_path=_omega_bin_path):
-    Importation of OMEGA/MEx observation, using the readomega_vpy.pro IDL routine.
+class omegapy.omega_data.OMEGAdata(obs='', empty=False, data_path=_omega_bin_path, corrV=True, corrL=True):
+    Importation of OMEGA/MEx observation.
 
     Parameters
     ==========
@@ -70,6 +73,10 @@ class omegapy.omega_data.OMEGAdata(obs='', empty=False, data_path=_omega_bin_pat
     data_path : str, optional (default _omega_py_path)
         The path of the directory containing the data (.QUB) and 
         navigation (.NAV) files.
+    corrV : bool, optional (default True)
+        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).
 
     Attributes
     ==========
@@ -93,6 +100,8 @@ class omegapy.omega_data.OMEGAdata(obs='', empty=False, data_path=_omega_bin_pat
         The elevation of the pixel footprint center point (km).
     loct : 2D array of floats
         The array of the local time for each pixel of the observation.
+    my : int
+        The Martian Year number at the time of the observation.
     emer : 2D array
         The angle of emergent line (from the surface) (deg).
     inci : 2D array
@@ -117,7 +126,7 @@ class omegapy.omega_data.OMEGAdata(obs='', empty=False, data_path=_omega_bin_pat
         Information about the saturation of the Vis-channel.
     summation : int
         The downtrack summing.
-    bits_per_data : int
+    bits_per_data : float
         The compression rate in bits per data.
     data_quality : int
         Information about the data quality, from 0 to 5 depending on missing lines and
@@ -190,16 +199,16 @@ class omegapy.omega_data.OMEGAdata(obs='', empty=False, data_path=_omega_bin_pat
 
 ### Observation search
 ~~~python
-omegapy.omega_data.find_cube(lat, lon, cmin=0, cmax=10000, out=False):
+omegapy.omega_data.find_cube(lon0, lat0, cmin=0, cmax=10000, out=False):
     Display the available OMEGA/MEx cubes with observations of the target
-    latitude and longitude, using the IDL procedure `findcub.pro`.
+    latitude and longitude, Python translation of the IDL procedure `findcub.pro`.
 
     Parameters
     ==========
-    lat : float
-        The target latitude (in degrees).
-    lon : float
+    lon0 : float
         The target longitude (in degrees).
+    lat0 : float
+        The target latitude (in degrees).
     cmin : float, optional (default 0)
         The minimum orbit number.
     cmax : float, optional (default 10000)
@@ -211,7 +220,7 @@ omegapy.omega_data.find_cube(lat, lon, cmin=0, cmax=10000, out=False):
     =======
     cub_list : array-like
         List of matching observations.
-        Format : (orbit, x, y, dmin, altMEx, inci, emer, phas, Ls)
+        Format : (orbit, x, y, dmin, altMEx, inci, emer, phas, loct, Ls, MY)
 ~~~
 
 ### OMEGAdata files handling
@@ -678,3 +687,37 @@ omegapy.omega_data.utc_to_my(dt):
     my : int
         The corresponding Martian Year.
 ~~~
+
+### Shared wavelength array between different observations
+~~~python
+omegapy.omega_data.shared_lam(lam_list):
+    Return a list of wavelength shared by all the input wavelength arrays.
+
+    Parameters
+    ==========
+    lam_list : list of 1D np.array
+        The list of wavelength array.
+
+    Returns
+    =======
+    lam2 : 1D np.array
+        The wavelength array that contains only wavelength shared by all the arrays of
+        lam_list.
+~~~
+
+~~~python
+omegapy.omega_data.shared_lam_omegalist(omega_list):
+    Return a list of wavelength shared by all the wavelength arrays of the input
+    OMEGA/MEx observations.
+
+    Parameters
+    ==========
+    omega_list : list of OMEGAdata
+        The list of OMEGA/MEx observations.
+
+    Returns
+    =======
+    lam2 : 1D np.array
+        The wavelength array that contains only wavelength shared by all the arrays of
+        lam_list.
+~~~