Merge pull request #145 from falconstryker/devel

bypass shtools for new tide decomp

Author: rurata

amescap/Spectral_utils.py

@@ -31,27 +31,40 @@
 #                           DEFINITIONS
 # ======================================================================
 
-# Try to import pyshtools with proper error handling
-try:
-    import pyshtools
-    PYSHTOOLS_AVAILABLE = True
-except ImportError:
-    PYSHTOOLS_AVAILABLE = False
-    print(
-        f"{Yellow}__________________\n"
-        f"Tidal decomposition relies on the pyshtools library, "
-        f"referenced at:\n\n"
-        f"Mark A. Wieczorek and Matthias Meschede (2018). "
-        f"SHTools - Tools for working with spherical harmonics,"
-        f"Geochemistry, Geophysics, Geosystems, 2574-2592, "
-        f"doi:10.1029/2018GC007529\n\nPlease consult pyshtools  "
-        f"documentation at:\n"
-        f" {Cyan}https://pypi.org/project/pyshtools\n"
-        f"{Yellow}And installation instructions for CAP with pyshtools:\n"
-        f" {Cyan}https://amescap.readthedocs.io/en/latest/installation."
-        f"html#_spectral_analysis{Yellow}\n"
-        f"__________________{Nclr}\n\n"
-    )
+def import_pyshtools():
+    """
+    Attempt to import pyshtools and set the global variable
+    PYSHTOOLS_AVAILABLE accordingly.
+    Check if pyshtools is available and return its availability status
+
+    :return: True if pyshtools is available, False otherwise
+    :rtype: bool
+    """
+
+    global PYSHTOOLS_AVAILABLE
+    # Try to import pyshtools with proper error handling
+    try:
+        import pyshtools
+        global pyshtools
+        PYSHTOOLS_AVAILABLE = True
+    except ImportError:
+        PYSHTOOLS_AVAILABLE = False
+        print(
+            f"{Yellow}__________________\n"
+            f"Tidal decomposition relies on the pyshtools library, "
+            f"referenced at:\n"
+            f"{Cyan}Mark A. Wieczorek and Matthias Meschede (2018). "
+            f"SHTools - Tools for working with spherical harmonics, "
+            f"Geochemistry, Geophysics, Geosystems, 2574-2592, "
+            f"doi:10.1029/2018GC007529\n\n"
+            f"Please consult pyshtools documentation at:\n"
+            f"{Cyan}https://pypi.org/project/pyshtools\n\n"
+            f"{Yellow}And installation instructions for CAP with pyshtools:\n"
+            f"{Cyan}https://amescap.readthedocs.io/en/latest/installation."
+            f"html#_spectral_analysis{Yellow}\n"
+            f"__________________{Nclr}\n\n"
+        )
+    return PYSHTOOLS_AVAILABLE
 
 
 def diurn_extract(VAR, N, tod, lon):
@@ -74,7 +87,8 @@ def diurn_extract(VAR, N, tod, lon):
         (e.g., size ``[Nh, time, lat, lon]``)
     :rtype: ND arrays
     """
-
+    import_pyshtools()
+    
     dimsIN = VAR.shape
     nsteps = len(tod)
     period = 24
@@ -140,6 +154,7 @@ def diurn_extract(VAR, N, tod, lon):
     # Return the phase and amplitude
     return amp.reshape(dimsOUT), phas.reshape(dimsOUT)
 
+
 def reconstruct_diurn(amp, phas, tod, lon, sumList=[]):
     """
     Reconstructs a field wave based on its diurnal harmonics
@@ -162,7 +177,8 @@ def reconstruct_diurn(amp, phas, tod, lon, sumList=[]):
         aggregated (i.e., size = ``[tod, time, lat, lon]``)
     :rtype: _type_
     """
-
+    import_pyshtools()
+    
     dimsIN = amp.shape
     N = dimsIN[0]
     dimsSUM = np.append([len(tod)], dimsIN[1:])
@@ -207,6 +223,7 @@ def reconstruct_diurn(amp, phas, tod, lon, sumList=[]):
         # Return harmonics separately
         return varOUT
 
+
 def extract_diurnal_harmonics(kmx, tmx, varIN, tod, lon):
     """
     Obtain west and east propagating waves. This is a Python
@@ -344,6 +361,7 @@ def zeroPhi_filter(VAR, btype, low_highcut, fs, axis=0, order=4,
     .. note:: ``Wn=[low, high]`` are expressed as a function of the
         Nyquist frequency
     """
+    import_pyshtools()
 
     # Create the filter
     low_highcut = np.array(low_highcut)
@@ -381,6 +399,7 @@ def zonal_decomposition(VAR):
     .. note:: Output size is (``[...,lat/2, lat/2]``) as lat is the
         smallest dimension. This matches the Nyquist frequency.
     """
+    import_pyshtools()
 
     if not PYSHTOOLS_AVAILABLE:
         raise ImportError(
@@ -440,6 +459,7 @@ def zonal_construct(COEFFS_flat, VAR_shape, btype=None, low_highcut=None):
         print("(kmin,kmax) = ({kmin}, {kmax})
               -> dx min = {L_min} km, dx max = {L_max} km")
     """
+    import_pyshtools()
 
     if not PYSHTOOLS_AVAILABLE:
         raise ImportError(
@@ -472,12 +492,3 @@ def zonal_construct(COEFFS_flat, VAR_shape, btype=None, low_highcut=None):
     return  VAR.reshape(VAR_shape)
 
 
-def init_shtools():
-    """
-    Check if pyshtools is available and return its availability status
-
-    :return: True if pyshtools is available, False otherwise
-    :rtype: bool
-    """
-
-    return PYSHTOOLS_AVAILABLE

bin/MarsFiles.py

@@ -444,7 +444,7 @@ def wrapper(*args, **kwargs):
         f"in Sols.\n"
         f"{Yellow}Generates a new file ending in ``_hps.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 01336.atmos_daily.nc -hps 10 -add_trend\n"
+        f"> MarsFiles 01336.atmos_daily.nc -hps 10\n"
         f"{Nclr}\n\n"
     )
 )
@@ -464,7 +464,7 @@ def wrapper(*args, **kwargs):
         f"cutoff frequency in Sols.\n"
         f"{Yellow}Generates a new file ending in ``_lps.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 01336.atmos_daily.nc -lps 20 -add_trend\n"
+        f"> MarsFiles 01336.atmos_daily.nc -lps 20\n"
         f"{Nclr}\n\n"
     )
 )
@@ -484,7 +484,7 @@ def wrapper(*args, **kwargs):
         f"cutoff frequency in Sols.\nData detrended before filtering.\n"
         f"{Yellow}Generates a new file ending in ``_bps.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 01336.atmos_daily.nc -bps 10 20 -add_trend\n"
+        f"> MarsFiles 01336.atmos_daily.nc -bps 10 20\n"
         f"{Nclr}\n\n"
     )
 )
@@ -539,21 +539,25 @@ def wrapper(*args, **kwargs):
     parser=parser,
     nargs=2, type=int,
     help=(
-        f"{Yellow}This is separate from -tide and does not provide "
-        f"total amplitude and phase. It does not work with the options "
-        f"normalize and reconstruct.\n"
+        f"{Yellow}This function is separate distinct from [-tide "
+        f"--tide_decomp] and therefore does not return total amplitude \n"
+        f"and phase nor does it work with [-norm --normalize] or [-recon "
+        f"--reconstruct].\n"
+        f"For 'diurn' files only.\n"
         f"{Nclr}\n"
-        f"Use fourier decomposition to break down the signal into kmx longitudinal harmonics "
-        f"and tmx diurnal harmonics.\nOnly works with 'diurn' files.\nReturns the normalized phases "
-        f"and amplitudes (not percent) of the propagating tides for the variables.\n"
-        f"kmx = 1 wavenumber 1, kmx = 2 wavenumber 2, etc.\n"
-        f"tmx = 1 diurnal tide, tmx = 2 semi-diurnal, etc.\n"
-        f"Works on 'diurn' files only.\n"
-        f"{Yellow}Generates a new file ending in ``_prop_tides.nc``\n"
+        f"Use fourier decomposition to break down a variable into `kmx` "
+        f"longitudinal (spatial) harmonics and `tmx` \n"
+        f"diurnal (time) harmonics. This returns the normalized phases and "
+        f"amplitudes (not percent) of the \n"
+        f"propagating tides for a variable.\n"
+        f"{Yellow}Generates a new file ending in ``_prop_tides.nc``{Nclr}\n"
+        f"`kmx = 1` for wavenumber 1, `kmx = 2` for wavenumber 2, etc.\n"
+        f"`tmx = 1` for diurnal tide, `tmx = 2` for semi-diurnal tide, etc.\n"
         f"{Green}Example:\n"
+        f"> MarsFiles 01336.atmos_diurn.nc -prop kmx tmx -incl ps temp\n"
         f"> MarsFiles 01336.atmos_diurn.nc -prop 2 2 -incl ps temp\n"
-        f"{Blue}(extracts eastward and westward tide components of ps and\ntemp "
-        f"variables up to semi-dirunal wavenumber 2)"
+        f"{Blue}(extracts the eastward and westward tide components of ps and"
+        f"temp up to semi-diurnal wavenumber 2)"
         f"{Nclr}\n\n"
     )
 )
@@ -1795,9 +1799,9 @@ def main():
           args.band_pass_spatial):
         from amescap.Spectral_utils import (zonal_decomposition,
                                             zonal_construct,
-                                            init_shtools)
+                                            import_pyshtools)
         # Load the module
-        init_shtools()
+        import_pyshtools()
         if args.high_pass_spatial:
             btype = "high"
             nk = np.asarray(args.high_pass_spatial).astype(int)

docs/source/installation.rst

@@ -469,7 +469,7 @@ The pip installation method is less recommended as it requires manual installati
    # Activate your virtual environment
 
    # Install CAP with spectral analysis support
-   pip install "amescap[spectral] @ git+https://github.com/NASA-Planetary-Science/AmesCAP.git@pyshtools"
+   pip install "amescap[spectral] @ git+https://github.com/NASA-Planetary-Science/AmesCAP.git"
 
    # Don't forget to copy the profile file to your home directory
    cp amescap/mars_templates/amescap_profile ~/.amescap_profile