update docs

seispy/ccpprofile.py

@@ -24,6 +24,7 @@ def _prof_range(lat, lon):
 
 def create_center_bin_profile(stations, val=5, method='linear'):
     """Create bins along a profile with given stations
+
     :param stations: Stations along a profile
     :type stations: :class:`seispy.rf2depth_makedata.Station`
     :param val: The interval between two points in km
@@ -109,6 +110,7 @@ def init_profile(lat1, lon1, lat2, lon2, val):
 class CCPProfile():
     def __init__(self, cfg_file=None, log:SetupLog=SetupLog()):
         """CCPProfile class for CCP stacking along a profile
+
         :param cfg_file: Configure file for CCP stacking
         :type cfg_file: str
         :param log: Log class for logging
@@ -118,12 +120,12 @@ def __init__(self, cfg_file=None, log:SetupLog=SetupLog()):
         if cfg_file is None:
             self.cpara = CCPPara()
         elif isinstance(cfg_file, str):
-            self.load_para(cfg_file)
+            self._load_para(cfg_file)
         else:
             raise ValueError('cfg_file must be str format.')
         self.stack_data = []
 
-    def load_para(self, cfg_file):
+    def _load_para(self, cfg_file):
         try:
             self.cpara = ccppara(cfg_file)
         except Exception as e:
@@ -277,12 +279,19 @@ def stack(self):
             self.stack_data.append(boot_stack)   
 
     def save_stack_data(self, format='npz'):
-        """If format is \'npz\', saving stacked data and parameters to local as a npz file. To load the file, please use data = np.load(fname, allow_pickle=True).
-        data['cpara'] is the parameters when CCP stacking.
-        data['stack_data'] is the result of stacked data.
+        """If format is ``npz``, saving stacked data and parameters to local as a npz file. To load the file, please use data = np.load(fname, allow_pickle=True).
+        ``data['cpara']`` is the parameters when CCP stacking.
+        ``data['stack_data']`` is the result of stacked data.
 
-        If format is \'dat\' the stacked data will be save into a txt file with 8 columns, including bin_lat, bin_lon, profile_dis, depth, amp, ci_low, ci_high and count.
-        where bin_lat and bin_lon represent the position of each bin; profile_dis represents the distance in km between each bin and the start point of the profile; depth represents depth of each bin; amp means the stacked amplitude; ci_low and ci_high mean confidence interval with bootstrap method; count represents stacking number of each bin.
+        If format is ``dat`` the stacked data will be save into a txt file with 8 columns,
+        including ``bin_lat``, ``bin_lon``, ``profile_dis``, ``depth``, ``amp``, ``ci_low``, ``ci_high`` and ``count``.
+        
+        - ``bin_lat`` and ``bin_lon`` represent the position of each bin; 
+        - ``profile_dis`` represents the distance in km between each bin and the start point of the profile;
+        - ``depth`` represents depth of each bin;
+        - ``amp`` means the stacked amplitude; 
+        - ``ci_low`` and ``ci_high`` mean confidence interval with bootstrap method;
+        - ``count`` represents stacking number of each bin.
 
         :param format: Format for stacked data
         :type format: str

seispy/distaz.py

@@ -2,59 +2,15 @@
 import numpy as np
 
 
-def sind(deg):
-    rad = math.radians(deg)
-    return math.sin(rad)
-
-
-def cosd(deg):
-    rad = math.radians(deg)
-    return math.cos(rad)
-
-
-def tand(deg):
-    rad = math.radians(deg)
-    return math.tan(rad)
-
-
-def cotd(deg):
-    rad = math.radians(deg)
-    return math.cos(rad) / math.sin(rad)
-
-
-def asind(x):
-    rad = math.asin(x)
-    return math.degrees(rad)
-
-
-def acosd(x):
-    rad = math.acos(x)
-    return math.degrees(rad)
-
-
-def atand(x):
-    rad = math.atan(x)
-    return math.degrees(rad)
-
-
-def km2deg(kilometers):
-    return kilometers / 111.19
-
-
-def deg2km(degree):
-    return degree * 111.19
-
-
 class distaz:
     """
-    c Subroutine to calculate the Great Circle Arc distance
-    c    between two sets of geographic coordinates
-    c
-    c Equations take from Bullen, pages 154, 155
-    c
-    c T. Owens, September 19, 1991
-    c           Sept. 25 -- fixed az and baz calculations
-    c
+    Subroutine to calculate the Great Circle Arc distance
+        between two sets of geographic coordinates
+    
+    Equations take from Bullen, pages 154, 155
+    
+    T. Owens, September 19, 1991
+              Sept. 25 -- fixed az and baz calculations
     P. Crotwell, Setember 27, 1995
     Converted to c to fix annoying problem of fortran giving wrong
     answers if the input doesn't contain a decimal point.

seispy/eq.py

@@ -25,6 +25,8 @@ def __str__(self):
         return '{}'.format(self.matchkey)
 
 def rotateZNE(st):
+    """Rotate Z, N, E components to Z, N, E components
+    """
     try:
         zne = rotate2zne(
             st[0], st[0].stats.sac.cmpaz, st[0].stats.sac.cmpinc,
@@ -92,6 +94,7 @@ def _cleanstream(self):
     @classmethod
     def from_stream(cls, stream):
         """Create EQ object from obspy stream
+
         :param stream: obspy stream
         :type stream: obspy.Stream
         :return: EQ object
@@ -138,6 +141,13 @@ def channel_correct(self, switchEN=False, reverseE=False, reverseN=False):
             self.st.select(channel='*[N1]')[0].stats.channel = chE
 
     def write(self, path, evt_datetime):
+        """Write raw stream to SAC files
+
+        :param path: path to save SAC files
+        :type path: str
+        :param evt_datetime: event datetime
+        :type evt_datetime: obspy.core.utcdatetime.UTCDateTime
+        """
         for tr in self.st:
             sac = SACTrace.from_obspy_trace(tr)
             sac.b = 0
@@ -158,6 +168,7 @@ def detrend(self):
 
     def filter(self, freqmin=0.05, freqmax=1, order=4):
         """Bandpass filter
+
         :param freqmin: minimum frequency, defaults to 0.05
         :type freqmin: float, optional
         :param freqmax: maximum frequency, defaults to 1
@@ -169,6 +180,7 @@ def filter(self, freqmin=0.05, freqmax=1, order=4):
 
     def get_arrival(self, model, evdp, dis, phase='P'):
         """Get arrival time, ray parameter and incident angle from TauP model
+
         :param model: TauP model
         :type model: TauPyModel
         :param evdp: focal depth
@@ -192,6 +204,7 @@ def get_arrival(self, model, evdp, dis, phase='P'):
 
     def search_inc(self, bazi):
         """Search incident angle for S wave
+
         :param bazi: back azimuth
         :type bazi: float
         :return: incident angle
@@ -211,6 +224,7 @@ def search_inc(self, bazi):
 
     def search_baz(self, bazi, time_b=10, time_e=20, offset=90):
         """Search back azimuth for P wave
+
         :param bazi: back azimuth
         :type bazi: float
         :param time_b: time before P arrival, defaults to 10
@@ -261,6 +275,7 @@ def fix_channel_name(self):
 
     def rotate(self, baz, inc=None, method='NE->RT', search_inc=False, baz_shift=0):
         """Rotate to radial and transverse components
+
         :param baz: back azimuth
         :type baz: float
         :param inc: incident angle, defaults to None
@@ -294,6 +309,7 @@ def rotate(self, baz, inc=None, method='NE->RT', search_inc=False, baz_shift=0):
 
     def snr(self, length=50):
         """Calculate SNR
+
         :param length: length for noise, defaults to 50
         :type length: int, optional
         :return: SNR of E, N, Z components
@@ -317,6 +333,7 @@ def snr(self, length=50):
 
     def get_time_offset(self, event_time=None):
         """Get time offset from SAC header
+
         :param event_time: event time, defaults to None
         :type event_time: obspy.core.utcdatetime.UTCDateTime, optional
         """
@@ -347,6 +364,7 @@ def _get_time(self, time_before, time_after):
 
     def phase_trigger(self, time_before, time_after, prepick=True, stl=5, ltl=10):
         """ Trigger P or S phase
+
         :param time_before: time before P or S arrival
         :type time_before: float
         :param time_after: time after P or S arrival
@@ -445,6 +463,7 @@ def deconvolute(self, shift, time_after, f0=2.0, method='iter', only_r=False,
 
     def decon_p(self, tshift, tcomp=False, **kwargs):
         """Deconvolution for P wave
+
         :param tshift: Time shift before P arrival
         :type tshift: float
         :param tcomp: Whether calculate transverse component, defaults to False
@@ -468,6 +487,7 @@ def decon_p(self, tshift, tcomp=False, **kwargs):
 
     def decon_s(self, tshift, **kwargs):
         """Deconvolution for S wave
+
         :param tshift: Time shift before P arrival
         :type tshift: float
         """
@@ -487,6 +507,7 @@ def saverf(self, path, evtstr=None, shift=0, evla=-12345.,
                evlo=-12345., evdp=-12345., mag=-12345.,
                gauss=0, baz=-12345., gcarc=-12345., only_r=False, **kwargs):
         """Save receiver function to SAC file
+
         :param path: path to save SAC file
         :type path: str
         :param evtstr: event string, defaults to None
@@ -560,6 +581,7 @@ def _s_condition(self, trrf, shift):
 
     def judge_rf(self, gauss, shift, npts, criterion='crust', rmsgate=None):
         """Judge whether receiver function is valid
+        
         :param gauss: Gaussian factor
         :type gauss: float
         :param shift: time shift before P arrival

seispy/hk.py

@@ -136,6 +136,7 @@ def ci(allstack, h, kappa, ev_num):
     """
     Search best H and kappa from stacked matrix.
     Calculate error for H and kappa
+
     :param allstack: stacked HK matrix
     :param h: 1-D array of H
     :param kappa: 1-D array of kappa

seispy/rf2depth_makedata.py

@@ -74,6 +74,8 @@ class RFDepth():
     def __init__(self, cpara:CCPPara, log:Logger=SetupLog().RF2depthlog,
                  raytracing3d=False, velmod3d=None, modfolder1d=None) -> None:
         """
+        Convert receiver function to depth axis
+        
         :param cpara: CCPPara object
         :type cpara: CCPPara
         :param log: Log object