[merge] merge branch 'improve-util-utils' of pull request #35 into develop

PyLoT.py

@@ -72,11 +72,11 @@ from pylot.core.util.errors import DatastructureError, \
     OverwriteError
 from pylot.core.util.connection import checkurl
 from pylot.core.util.dataprocessing import Metadata, restitute_data
-from pylot.core.util.utils import fnConstructor, getLogin, \
+from pylot.core.util.utils import fnConstructor, get_login, \
     full_range, readFilterInformation, pick_color_plt, \
     pick_linestyle_plt, identifyPhaseID, excludeQualityClasses, \
     transform_colors_mpl, transform_colors_mpl_str, getAutoFilteroptions, check_all_obspy, \
-    check_all_pylot, get_bool, get_None, get_pylot_eventfile_with_extension
+    check_all_pylot, get_bool, get_none, get_pylot_eventfile_with_extension
 from pylot.core.util.gui import make_pen
 from pylot.core.util.event import Event
 from pylot.core.io.location import create_creation_info, create_event
@@ -196,7 +196,7 @@ class MainWindow(QMainWindow):
                 if settings.value("user/FullName", None) is None:
                     fulluser = QInputDialog.getText(self, "Enter Name:", "Full name")
                     settings.setValue("user/FullName", fulluser)
-                    settings.setValue("user/Login", getLogin())
+                    settings.setValue("user/Login", get_login())
                 if settings.value("agency_id", None) is None:
                     agency = QInputDialog.getText(self,
                                                   "Enter authority/institution name:",
@@ -1990,8 +1990,8 @@ class MainWindow(QMainWindow):
 
         if len(curr_event.origins) > 0:
             origin_time = curr_event.origins[0].time
-            tstart = settings.value('tstart') if get_None(settings.value('tstart')) else 0
-            tstop = settings.value('tstop') if get_None(settings.value('tstop')) else 0
+            tstart = settings.value('tstart') if get_none(settings.value('tstart')) else 0
+            tstop = settings.value('tstop') if get_none(settings.value('tstop')) else 0
             tstart = origin_time + float(tstart)
             tstop = origin_time + float(tstop)
         else:
@@ -2306,7 +2306,7 @@ class MainWindow(QMainWindow):
         # wfst += self.get_data().getWFData().select(component=alter_comp)
         plotWidget = self.getPlotWidget()
         self.adjustPlotHeight()
-        if get_bool(settings.value('large_dataset')):
+        if get_bool(settings.value('large_dataset')) == True:
             self.plot_method = 'fast'
         else:
             self.plot_method = 'normal'

autoPyLoT.py

@@ -28,7 +28,7 @@ from pylot.core.util.dataprocessing import restitute_data, Metadata
 from pylot.core.util.defaults import SEPARATOR
 from pylot.core.util.event import Event
 from pylot.core.util.structure import DATASTRUCTURE
-from pylot.core.util.utils import get_None, trim_station_components, check4gapsAndRemove, check4doubled, \
+from pylot.core.util.utils import get_none, trim_station_components, check4gapsAndRemove, check4doubled, \
     check4rotated
 from pylot.core.util.version import get_git_version as _getVersionString
 
@@ -91,9 +91,9 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
                                                               sp=sp_info)
     print(splash)
 
-    parameter = get_None(parameter)
-    inputfile = get_None(inputfile)
-    eventid = get_None(eventid)
+    parameter = get_none(parameter)
+    inputfile = get_none(inputfile)
+    eventid = get_none(eventid)
 
     fig_dict = None
     fig_dict_wadatijack = None
@@ -154,7 +154,7 @@ def autoPyLoT(input_dict=None, parameter=None, inputfile=None, fnames=None, even
         datastructure.setExpandFields(exf)
 
         # check if default location routine NLLoc is available and all stations are used
-        if get_None(parameter['nllocbin']) and station == 'all':
+        if get_none(parameter['nllocbin']) and station == 'all':
             locflag = 1
             # get NLLoc-root path
             nllocroot = parameter.get('nllocroot')

pylot/core/io/location.py

@@ -1,7 +1,7 @@
 from obspy import UTCDateTime
 from obspy.core import event as ope
 
-from pylot.core.util.utils import getLogin, getHash
+from pylot.core.util.utils import get_login, get_hash
 
 
 def create_amplitude(pickID, amp, unit, category, cinfo):
@@ -61,7 +61,7 @@ def create_creation_info(agency_id=None, creation_time=None, author=None):
     :return:
     '''
     if author is None:
-        author = getLogin()
+        author = get_login()
     if creation_time is None:
         creation_time = UTCDateTime()
     return ope.CreationInfo(agency_id=agency_id, author=author,
@@ -210,7 +210,7 @@ def create_resourceID(timetohash, restype, authority_id=None, hrstr=None):
     '''
     assert isinstance(timetohash, UTCDateTime), "'timetohash' is not an ObsPy" \
                                                 "UTCDateTime object"
-    hid = getHash(timetohash)
+    hid = get_hash(timetohash)
     if hrstr is None:
         resID = ope.ResourceIdentifier(restype + '/' + hid[0:6])
     else:

pylot/core/io/phases.py

@@ -16,7 +16,7 @@ from pylot.core.io.inputs import PylotParameter
 from pylot.core.io.location import create_event, \
     create_magnitude
 from pylot.core.pick.utils import select_for_phase, get_quality_class
-from pylot.core.util.utils import getOwner, full_range, four_digits, transformFilterString4Export, \
+from pylot.core.util.utils import get_owner, full_range, four_digits, transformFilterString4Export, \
     backtransformFilterString, loopIdentifyPhase, identifyPhase
 
 
@@ -58,7 +58,7 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
     if phasfn is not None and os.path.isfile(phasfn):
         phases = sio.loadmat(phasfn)
         phasctime = UTCDateTime(os.path.getmtime(phasfn))
-        phasauthor = getOwner(phasfn)
+        phasauthor = get_owner(phasfn)
     else:
         phases = None
         phasctime = None
@@ -66,7 +66,7 @@ def readPILOTEvent(phasfn=None, locfn=None, authority_id='RUB', **kwargs):
     if locfn is not None and os.path.isfile(locfn):
         loc = sio.loadmat(locfn)
         locctime = UTCDateTime(os.path.getmtime(locfn))
-        locauthor = getOwner(locfn)
+        locauthor = get_owner(locfn)
     else:
         loc = None
         locctime = None

pylot/core/pick/autopick.py

@@ -22,7 +22,7 @@ from pylot.core.pick.picker import AICPicker, PragPicker
 from pylot.core.pick.utils import checksignallength, checkZ4S, earllatepicker, \
     getSNR, fmpicker, checkPonsets, wadaticheck, get_quality_class, PickingFailedException, MissingTraceException
 from pylot.core.util.utils import getPatternLine, gen_Pool, \
-    get_bool, identifyPhaseID, get_None, correct_iplot
+    get_bool, identifyPhaseID, get_none, correct_iplot
 
 
 def autopickevent(data, param, iplot=0, fig_dict=None, fig_dict_wadatijack=None, ncores=0, metadata=None, origin=None):
@@ -258,7 +258,7 @@ class AutopickStation(object):
         self.pickparams = copy.deepcopy(pickparam)
         self.verbose = verbose
         self.iplot = correct_iplot(iplot)
-        self.fig_dict = get_None(fig_dict)
+        self.fig_dict = get_none(fig_dict)
         self.metadata = metadata
         self.origin = origin
 

pylot/core/pick/utils.py

@@ -15,7 +15,7 @@ import numpy as np
 from obspy.core import Stream, UTCDateTime
 from scipy.signal import argrelmax
 
-from pylot.core.util.utils import get_bool, get_None, SetChannelComponents
+from pylot.core.util.utils import get_bool, get_none, SetChannelComponents
 
 
 def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecolor='k'):
@@ -136,7 +136,7 @@ def earllatepicker(X, nfac, TSNR, Pick1, iplot=0, verbosity=1, fig=None, linecol
     PickError = symmetrize_error(diffti_te, diffti_tl)
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -275,7 +275,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
             try:
                 P1 = np.polyfit(xslope1, xraw[islope1], 1)
                 datafit1 = np.polyval(P1, xslope1)
-            except Exception as e:
+            except ValueError as e:
                 print("fmpicker: Problems with data fit! {}".format(e))
                 print("Skip first motion determination!")
                 return FM
@@ -321,7 +321,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
             try:
                 P2 = np.polyfit(xslope2, xfilt[islope2], 1)
                 datafit2 = np.polyval(P2, xslope2)
-            except Exception as e:
+            except ValueError as e:
                 emsg = 'fmpicker: polyfit failed: {}'.format(e)
                 print(emsg)
                 return FM
@@ -344,7 +344,7 @@ def fmpicker(Xraw, Xfilt, pickwin, Pick, iplot=0, fig=None, linecolor='k'):
         print("fmpicker: Found polarity %s" % FM)
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -868,7 +868,7 @@ def checksignallength(X, pick, minsiglength, pickparams, iplot=0, fig=None, line
             returnflag = 0
 
     if iplot > 1:
-        if get_None(fig) is None:
+        if get_none(fig) is None:
             fig = plt.figure()  # iplot)
             plt_flag = 1
         fig._tight = True
@@ -1213,14 +1213,14 @@ def checkZ4S(X, pick, pickparams, iplot, fig=None, linecolor='k'):
             t = np.linspace(diff_dict[key], trace.stats.endtime - trace.stats.starttime + diff_dict[key],
                             trace.stats.npts)
             if i == 0:
-                if get_None(fig) is None:
+                if get_none(fig) is None:
                     fig = plt.figure()  # self.iplot) ### WHY? MP MP
                     plt_flag = 1
                 ax1 = fig.add_subplot(3, 1, i + 1)
                 ax = ax1
                 ax.set_title('CheckZ4S, Station %s' % zdat[0].stats.station)
             else:
-                if get_None(fig) is None:
+                if get_none(fig) is None:
                     fig = plt.figure()  # self.iplot) ### WHY? MP MP
                     plt_flag = 1
                 ax = fig.add_subplot(3, 1, i + 1, sharex=ax1)
@@ -1494,7 +1494,7 @@ def getQualityFromUncertainty(uncertainty, Errors):
     # set initial quality to 4 (worst) and change only if one condition is hit
     quality = 4
 
-    if get_None(uncertainty) is None:
+    if get_none(uncertainty) is None:
         return quality
 
     if uncertainty <= Errors[0]:

pylot/core/util/utils.py

@@ -8,6 +8,7 @@ import platform
 import re
 import subprocess
 import warnings
+from typing import Literal, Tuple, Type
 from functools import lru_cache
 
 import numpy as np
@@ -20,6 +21,10 @@ from pylot.core.io.inputs import PylotParameter, FilterOptions
 from pylot.core.util.obspyDMT_interface import check_obspydmt_eventfolder
 from pylot.styles import style_settings
 
+Rgba: Type[tuple] = Tuple[int, int, int, int]
+Mplrgba: Type[tuple] = Tuple[float, float, float, float]
+Mplrgbastr: Type[tuple] = Tuple[str, str, str, str]
+
 
 def _pickle_method(m):
     if m.im_self is None:
@@ -83,25 +88,6 @@ def fit_curve(x, y):
     return splev, splrep(x, y)
 
 
-def getindexbounds(f, eta):
-    """
-    Get indices of values closest below and above maximum value in an array
-    :param f: array
-    :type f: `~numpy.ndarray`
-    :param eta: look for value in array that is closes to max_value * eta
-    :type eta: float
-    :return: tuple containing index of max value, index of value closest below max value,
-     index of value closest above max value
-    :rtype: (int, int, int)
-    """
-    mi = f.argmax()  # get indices of max values
-    m = max(f)  # get maximum value
-    b = m * eta  #
-    l = find_nearest(f[:mi], b)  # find closest value below max value
-    u = find_nearest(f[mi:], b) + mi  # find closest value above max value
-    return mi, l, u
-
-
 def gen_Pool(ncores=0):
     """
     Generate mulitprocessing pool object utilizing ncores amount of cores
@@ -167,11 +153,11 @@ def clims(lim1, lim2):
     """
     takes two pairs of limits and returns one pair of common limts
     :param lim1: limit 1
-    :type lim1: int
+    :type lim1: List[int]
     :param lim2: limit 2
-    :type lim2: int
+    :type lim2: List[int]
     :return: new upper and lower limit common to both given limits
-    :rtype: [int, int]
+    :rtype: List[int]
 
     >>> clims([0, 4], [1, 3])
     [0, 4]
@@ -303,7 +289,7 @@ def fnConstructor(s):
     if type(s) is str:
         s = s.split(':')[-1]
     else:
-        s = getHash(UTCDateTime())
+        s = get_hash(UTCDateTime())
 
     badchars = re.compile(r'[^A-Za-z0-9_. ]+|^\.|\.$|^ | $|^$')
     badsuffix = re.compile(r'(aux|com[1-9]|con|lpt[1-9]|prn)(\.|$)')
@@ -315,15 +301,32 @@ def fnConstructor(s):
     return fn
 
 
-def get_None(value):
+def get_none(value):
     """
     Convert "None" to None
     :param value:
-    :type value: str, bool
+    :type value: str, NoneType
     :return:
-    :rtype: bool
+    :rtype: type(value) or NoneType
+
+    >>> st = read()
+    >>> print(get_none(st))
+    3 Trace(s) in Stream:
+    BW.RJOB..EHZ | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    BW.RJOB..EHN | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    BW.RJOB..EHE | 2009-08-24T00:20:03.000000Z - 2009-08-24T00:20:32.990000Z | 100.0 Hz, 3000 samples
+    >>> get_none('Stream')
+    'Stream'
+    >>> get_none(0)
+    0
+    >>> get_none(0.)
+    0.0
+    >>> print(get_none('None'))
+    None
+    >>> print(get_none(None))
+    None
     """
-    if value == 'None':
+    if value is None or (type(value) is str and value == 'None'):
         return None
     else:
         return value
@@ -333,9 +336,26 @@ def get_bool(value):
     """
     Convert string representations of bools to their true boolean value
     :param value:
-    :type value: str, bool
+    :type value: str, bool, int, float
     :return: true boolean value
     :rtype: bool
+
+    >>> get_bool(True)
+    True
+    >>> get_bool(False)
+    False
+    >>> get_bool(0)
+    False
+    >>> get_bool(0.)
+    False
+    >>> get_bool(0.1)
+    True
+    >>> get_bool(2)
+    True
+    >>> get_bool(-1)
+    False
+    >>> get_bool(-0.3)
+    False
     """
     if type(value) is bool:
         return value
@@ -343,8 +363,11 @@ def get_bool(value):
         return True
     elif value in ['False', 'false']:
         return False
+    elif value > 0. or value > 0:
+        return True
     else:
-        return bool(value)
+        return False
+
 
 def four_digits(year):
     """
@@ -355,8 +378,8 @@ def four_digits(year):
     :return: four digit year correspondent
     :rtype: int
 
-    >>> four_digits(20)
-    1920
+    >>> four_digits(75)
+    1975
     >>> four_digits(16)
     2016
     >>> four_digits(00)
@@ -438,36 +461,53 @@ def backtransformFilterString(st):
     return st
 
 
-def getHash(time):
+def get_hash(time):
     """
     takes a time object and returns the corresponding SHA1 hash of the formatted date string
     :param time: time object for which a hash should be calculated
     :type time: `~obspy.core.utcdatetime.UTCDateTime`
     :return: SHA1 hash
     :rtype: str
+
+    >>> time = UTCDateTime(0)
+    >>> get_hash(time)
+    '7627cce3b1b58dd21b005dac008b34d18317dd15'
+    >>> get_hash(0)
+    Traceback (most recent call last):
+    ...
+    AssertionError: 'time' is not an ObsPy UTCDateTime object
     """
+    assert isinstance(time, UTCDateTime), '\'time\' is not an ObsPy UTCDateTime object'
     hg = hashlib.sha1()
-    hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f'))
+    hg.update(time.strftime('%Y-%m-%d %H:%M:%S.%f').encode('utf-8'))
     return hg.hexdigest()
 
 
-def getLogin():
+def get_login():
     """
-    returns the actual user's login ID
-    :return: login ID
+    returns the actual user's name
+    :return: login name
     :rtype: str
     """
     import getpass
     return getpass.getuser()
 
 
-def getOwner(fn):
+def get_owner(fn):
     """
     takes a filename and return the login ID of the actual owner of the file
     :param fn: filename of the file tested
     :type fn: str
     :return: login ID of the file's owner
     :rtype: str
+
+    >>> import tempfile
+    >>> with tempfile.NamedTemporaryFile() as tmpfile:
+    ...     tmpfile.write(b'') and True
+    ...     tmpfile.flush()
+    ...     get_owner(tmpfile.name) == os.path.expanduser('~').split('/')[-1]
+    0
+    True
     """
     system_name = platform.system()
     if system_name in ["Linux", "Darwin"]:
@@ -513,6 +553,11 @@ def is_executable(fn):
     :param fn: path to the file to be tested
     :return: True or False
     :rtype: bool
+
+    >>> is_executable('/bin/ls')
+    True
+    >>> is_executable('/var/log/system.log')
+    False
     """
     return os.path.isfile(fn) and os.access(fn, os.X_OK)
 
@@ -539,24 +584,36 @@ def isSorted(iterable):
     >>> isSorted([2,3,1,4])
     False
     """
-    assert isIterable(iterable), 'object is not iterable; object: {' \
-                                 '}'.format(iterable)
+    assert is_iterable(iterable), "object is not iterable; object: {}".format(iterable)
     if type(iterable) is str:
         iterable = [s for s in iterable]
     return sorted(iterable) == iterable
 
 
-def isIterable(obj):
+def is_iterable(obj):
     """
     takes a python object and returns True is the object is iterable and
     False otherwise
     :param obj: a python object
-    :type obj: object
+    :type obj: obj
     :return: True of False
     :rtype: bool
+
+    >>> is_iterable(1)
+    False
+    >>> is_iterable(True)
+    False
+    >>> is_iterable(0.)
+    False
+    >>> is_iterable((0,1,3,4))
+    True
+    >>> is_iterable([1])
+    True
+    >>> is_iterable('a')
+    True
     """
     try:
-        iterator = iter(obj)
+        iter(obj)
     except TypeError as te:
         return False
     return True
@@ -565,13 +622,19 @@ def isIterable(obj):
 def key_for_set_value(d):
     """
     takes a dictionary and returns the first key for which's value the
-    boolean is True
+    boolean representation is True
     :param d: dictionary containing values
     :type d: dict
     :return: key to the first non-False value found; None if no value's
     boolean equals True
-    :rtype:
+    :rtype: bool or NoneType
+
+    >>> key_for_set_value({'one': 0, 'two': 1})
+    'two'
+    >>> print(key_for_set_value({1: 0, 2: False}))
+    None
     """
+    assert type(d) is dict, "Function only defined for inputs of type 'dict'."
     r = None
     for k, v in d.items():
         if v:
@@ -579,32 +642,53 @@ def key_for_set_value(d):
     return r
 
 
-def prepTimeAxis(stime, trace, verbosity=0):
+def prep_time_axis(offset, trace, verbosity=0):
     """
-    takes a starttime and a trace object and returns a valid time axis for
+    takes an offset and a trace object and returns a valid time axis for
     plotting
-    :param stime: start time of the actual seismogram as UTCDateTime
-    :type stime: `~obspy.core.utcdatetime.UTCDateTime`
+    :param offset: offset of the actual seismogram on plotting axis
+    :type offset: float or int
     :param trace: seismic trace object
     :type trace: `~obspy.core.trace.Trace`
     :param verbosity: if != 0, debug output will be written to console
     :type verbosity: int
     :return: valid numpy array with time stamps for plotting
     :rtype: `~numpy.ndarray`
+
+    >>> tr = read()[0]
+    >>> prep_time_axis(0., tr)
+    array([0.00000000e+00, 1.00033344e-02, 2.00066689e-02, ...,
+           2.99799933e+01, 2.99899967e+01, 3.00000000e+01])
+    >>> prep_time_axis(22.5, tr)
+    array([22.5       , 22.51000333, 22.52000667, ..., 52.47999333,
+           52.48999667, 52.5       ])
+    >>> prep_time_axis(tr.stats.starttime, tr)
+    Traceback (most recent call last):
+    ...
+    AssertionError: 'offset' is not of type 'float' or 'int'; type: <class 'obspy.core.utcdatetime.UTCDateTime'>
+    >>> tr.stats.npts -= 1
+    >>> prep_time_axis(0, tr)
+    array([0.00000000e+00, 1.00033356e-02, 2.00066711e-02, ...,
+           2.99699933e+01, 2.99799967e+01, 2.99900000e+01])
+    >>> tr.stats.npts += 2
+    >>> prep_time_axis(0, tr)
+    array([0.00000000e+00, 1.00033333e-02, 2.00066667e-02, ...,
+           2.99899933e+01, 2.99999967e+01, 3.00100000e+01])
     """
+    assert isinstance(offset, (float, int)), "'offset' is not of type 'float' or 'int'; type: {}".format(type(offset))
     nsamp = trace.stats.npts
     srate = trace.stats.sampling_rate
     tincr = trace.stats.delta
-    etime = stime + nsamp / srate
-    time_ax = np.linspace(stime, etime, nsamp)
+    etime = offset + nsamp / srate
+    time_ax = np.linspace(offset, etime, nsamp)
     if len(time_ax) < nsamp:
         if verbosity:
             print('elongate time axes by one datum')
-        time_ax = np.arange(stime, etime + tincr, tincr)
+        time_ax = np.arange(offset, etime + tincr, tincr)
     elif len(time_ax) > nsamp:
         if verbosity:
             print('shorten time axes by one datum')
-        time_ax = np.arange(stime, etime - tincr, tincr)
+        time_ax = np.arange(offset, etime - tincr, tincr)
     if len(time_ax) != nsamp:
         print('Station {0}, {1} samples of data \n '
               '{2} length of time vector \n'
@@ -620,13 +704,13 @@ def find_horizontals(data):
     :param data: waveform data
     :type data: `obspy.core.stream.Stream`
     :return: components list
-    :rtype: list
+    :rtype: List(str)
 
     ..example::
 
     >>> st = read()
     >>> find_horizontals(st)
-    [u'N', u'E']
+    ['N', 'E']
     """
     rval = []
     for tr in data:
@@ -637,7 +721,7 @@ def find_horizontals(data):
     return rval
 
 
-def pick_color(picktype, phase, quality=0):
+def pick_color(picktype: Literal['manual', 'automatic'], phase: Literal['P', 'S'], quality: int = 0) -> Rgba:
     """
     Create pick color by modifying the base color by the quality.
 
@@ -650,7 +734,7 @@ def pick_color(picktype, phase, quality=0):
     :param quality: quality of pick. Decides the new intensity of the modifier color
     :type quality: int
     :return: tuple containing modified rgba color values
-    :rtype: (int, int, int, int)
+    :rtype: Rgba
     """
     min_quality = 3
     bpc = base_phase_colors(picktype, phase)  # returns dict like {'modifier': 'g', 'rgba': (0, 0, 255, 255)}
@@ -706,17 +790,17 @@ def pick_linestyle_plt(picktype, key):
     return linestyles[picktype][key]
 
 
-def modify_rgba(rgba, modifier, intensity):
+def modify_rgba(rgba: Rgba, modifier: Literal['r', 'g', 'b'], intensity: float) -> Rgba:
     """
     Modify rgba color by adding the given intensity to the modifier color
     :param rgba: tuple containing rgba values
-    :type rgba: (int, int, int, int)
-    :param modifier: which color should be modified, eg. 'r', 'g', 'b'
-    :type modifier: str
+    :type rgba: Rgba
+    :param modifier: which color should be modified; options: 'r', 'g', 'b'
+    :type modifier: Literal['r', 'g', 'b']
     :param intensity: intensity to be added to selected color
     :type intensity: float
     :return: tuple containing rgba values
-    :rtype: (int, int, int, int)
+    :rtype: Rgba
     """
     rgba = list(rgba)
     index = {'r': 0,
@@ -750,18 +834,20 @@ def transform_colors_mpl_str(colors, no_alpha=False):
     Transforms rgba color values to a matplotlib string of color values with a range of [0, 1]
     :param colors: tuple of rgba color values ranging from [0, 255]
     :type colors: (float, float, float, float)
-    :param no_alpha: Wether to return a alpha value in the matplotlib color string
+    :param no_alpha: Whether to return an alpha value in the matplotlib color string
     :type no_alpha: bool
     :return: String containing r, g, b values and alpha value if no_alpha is False (default)
     :rtype: str
+
+    >>> transform_colors_mpl_str((255., 255., 255., 255.), True)
+    '(1.0, 1.0, 1.0)'
+    >>> transform_colors_mpl_str((255., 255., 255., 255.))
+    '(1.0, 1.0, 1.0, 1.0)'
     """
-    colors = list(colors)
-    colors_mpl = tuple([color / 255. for color in colors])
     if no_alpha:
-        colors_mpl = '({}, {}, {})'.format(*colors_mpl)
+        return '({}, {}, {})'.format(*transform_colors_mpl(colors))
     else:
-        colors_mpl = '({}, {}, {}, {})'.format(*colors_mpl)
-    return colors_mpl
+        return '({}, {}, {}, {})'.format(*transform_colors_mpl(colors))
 
 
 def transform_colors_mpl(colors):
@@ -771,27 +857,16 @@ def transform_colors_mpl(colors):
     :type colors: (float, float, float, float)
     :return: tuple of rgba color values ranging from [0, 1]
     :rtype: (float, float, float, float)
+
+    >>> transform_colors_mpl((127.5, 0., 63.75, 255.))
+    (0.5, 0.0, 0.25, 1.0)
+    >>> transform_colors_mpl(())
     """
     colors = list(colors)
     colors_mpl = tuple([color / 255. for color in colors])
     return colors_mpl
 
 
-def remove_underscores(data):
-    """
-    takes a `obspy.core.stream.Stream` object and removes all underscores
-    from station names
-    :param data: stream of seismic data
-    :type data: `~obspy.core.stream.Stream`
-    :return: data stream
-    :rtype: `~obspy.core.stream.Stream`
-    """
-    # for tr in data:
-    #    # remove underscores
-    #    tr.stats.station = tr.stats.station.strip('_')
-    return data
-
-
 def trim_station_components(data, trim_start=True, trim_end=True):
     """
     cut a stream so only the part common to all three traces is kept to avoid dealing with offsets
@@ -928,11 +1003,11 @@ def get_possible_pylot_eventfile_extensions(event, fext):
 
 def get_stations(data):
     """
-    Get list of all station names in data stream
+    Get list of all station names in data-stream
     :param data: stream containing seismic traces
     :type data: `~obspy.core.stream.Stream`
     :return: list of all station names in data, no duplicates
-    :rtype: list of str
+    :rtype: List(str)
     """
     stations = []
     for tr in data:
@@ -959,66 +1034,87 @@ def check4rotated(data, metadata=None, verbosity=1):
     :rtype: `~obspy.core.stream.Stream`
     """
 
-    def rotate_components(wfstream, metadata=None):
+    def rotation_required(trace_ids):
+        """
+        Derive if any rotation is required from the orientation code of the input.
+
+        :param trace_ids: string identifier of waveform data trace
+        :type trace_ids: List(str)
+        :return: boolean representing if rotation is necessary for any of the traces
+        :rtype: bool
+        """
+        orientations = [trace_id[-1] for trace_id in trace_ids]
+        return any([orientation.isnumeric() for orientation in orientations])
+
+    def rotate_components(wfs_in, metadata=None):
         """
         Rotate components if orientation code is numeric (= non traditional orientation).
 
         Azimut and dip are fetched from metadata. To be rotated, traces of a station have to be cut to the same length.
         Returns unrotated traces of no metadata is provided
-        :param wfstream: stream containing seismic traces of a station
-        :type wfstream: `~obspy.core.stream.Stream`
+        :param wfs_in: stream containing seismic traces of a station
+        :type wfs_in: `~obspy.core.stream.Stream`
         :param metadata: tuple containing metadata type string and metadata parser object
         :type metadata: (str, `~obspy.io.xseed.parser.Parser`)
         :return: stream object with traditionally oriented traces (ZNE)
         :rtype: `~obspy.core.stream.Stream`
         """
 
+        if len(wfs_in) < 3:
+            print(f"Stream {wfs_in=}, has not enough components to rotate.")
+            return wfs_in
+
         # check if any traces in this station need to be rotated
-        trace_ids = [trace.id for trace in wfstream]
-        orientations = [trace_id[-1] for trace_id in trace_ids]
-        rotation_required = [orientation.isnumeric() for orientation in orientations]
-        if any(rotation_required):
-            t_start = full_range(wfstream)
+        trace_ids = [trace.id for trace in wfs_in]
+        if not rotation_required(trace_ids):
+            print(f"Stream does not need any rotation: Traces are {trace_ids=}")
+            return wfs_in
+
+        # check metadata quality
+        t_start = full_range(wfs_in)
         try:
-                azimuts = []
+            azimuths = []
             dips = []
             for tr_id in trace_ids:
-                    azimuts.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
+                azimuths.append(metadata.get_coordinates(tr_id, t_start)['azimuth'])
                 dips.append(metadata.get_coordinates(tr_id, t_start)['dip'])
-            except (KeyError, TypeError) as e:
-                print('Failed to rotate trace {}, no azimuth or dip available in metadata'.format(tr_id))
-                return wfstream
-            if len(wfstream) < 3:
-                print('Failed to rotate Stream {}, not enough components available.'.format(wfstream))
-                return wfstream
+        except (KeyError, TypeError) as err:
+            print(f"{type(err)=} occurred: {err=} Rotating not possible, not all azimuth and dip information "
+                  f"available in metadata. Stream remains unchanged.")
+            return wfs_in
+        except Exception as err:
+            print(f"Unexpected {err=}, {type(err)=}")
+            raise
+
         # to rotate all traces must have same length, so trim them
-            wfstream = trim_station_components(wfstream, trim_start=True, trim_end=True)
+        wfs_out = trim_station_components(wfs_in, trim_start=True, trim_end=True)
         try:
-                z, n, e = rotate2zne(wfstream[0], azimuts[0], dips[0],
-                                     wfstream[1], azimuts[1], dips[1],
-                                     wfstream[2], azimuts[2], dips[2])
+            z, n, e = rotate2zne(wfs_out[0], azimuths[0], dips[0],
+                                 wfs_out[1], azimuths[1], dips[1],
+                                 wfs_out[2], azimuths[2], dips[2])
             print('check4rotated: rotated trace {} to ZNE'.format(trace_ids))
             # replace old data with rotated data, change the channel code to ZNE
             z_index = dips.index(min(
-                    dips))  # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90 being vertical)
-                wfstream[z_index].data = z
-                wfstream[z_index].stats.channel = wfstream[z_index].stats.channel[0:-1] + 'Z'
+                dips))  # get z-trace index, z has minimum dip of -90 (dip is measured from 0 to -90, with -90
+            # being vertical)
+            wfs_out[z_index].data = z
+            wfs_out[z_index].stats.channel = wfs_out[z_index].stats.channel[0:-1] + 'Z'
             del trace_ids[z_index]
             for trace_id in trace_ids:
                 coordinates = metadata.get_coordinates(trace_id, t_start)
                 dip, az = coordinates['dip'], coordinates['azimuth']
-                    trace = wfstream.select(id=trace_id)[0]
-                    if az > 315 or az <= 45 or az > 135 and az <= 225:
+                trace = wfs_out.select(id=trace_id)[0]
+                if az > 315 or az <= 45 or 135 < az <= 225:
                     trace.data = n
                     trace.stats.channel = trace.stats.channel[0:-1] + 'N'
-                    elif az > 45 and az <= 135 or az > 225 and az <= 315:
+                elif 45 < az <= 135 or 225 < az <= 315:
                     trace.data = e
                     trace.stats.channel = trace.stats.channel[0:-1] + 'E'
-            except (ValueError) as e:
-                print(e)
-                return wfstream
+        except ValueError as err:
+            print(f"{err=} Rotation failed. Stream remains unchanged.")
+            return wfs_in
 
-        return wfstream
+        return wfs_out
 
     if metadata is None:
         if verbosity:
@@ -1032,38 +1128,6 @@ def check4rotated(data, metadata=None, verbosity=1):
     return data
 
 
-def scaleWFData(data, factor=None, components='all'):
-    """
-    produce scaled waveforms from given waveform data and a scaling factor,
-    waveform may be selected by their components name
-    :param data: waveform data to be scaled
-    :type data: `~obspy.core.stream.Stream` object
-    :param factor: scaling factor
-    :type factor: float
-    :param components: components labels for the traces in data to be scaled by
-     the scaling factor (optional, default: 'all')
-    :type components: tuple
-    :return:  scaled waveform data
-    :rtype: `~obspy.core.stream.Stream` object
-    """
-    if components != 'all':
-        for comp in components:
-            if factor is None:
-                max_val = np.max(np.abs(data.select(component=comp)[0].data))
-                data.select(component=comp)[0].data /= 2 * max_val
-            else:
-                data.select(component=comp)[0].data /= 2 * factor
-    else:
-        for tr in data:
-            if factor is None:
-                max_val = float(np.max(np.abs(tr.data)))
-                tr.data /= 2 * max_val
-            else:
-                tr.data /= 2 * factor
-
-    return data
-
-
 def runProgram(cmd, parameter=None):
     """
     run an external program specified by cmd with parameters input returning the

pylot/core/util/widgets.py

@@ -7,6 +7,7 @@ Created on Wed Mar 19 11:27:35 2014
 import copy
 import datetime
 import getpass
+import glob
 import multiprocessing
 import os
 import subprocess
@@ -16,6 +17,7 @@ import traceback
 
 import matplotlib
 import numpy as np
+from pylot.core.io.phases import getQualitiesfromxml
 
 matplotlib.use('QT5Agg')
 
@@ -49,11 +51,11 @@ from pylot.core.pick.utils import getSNR, earllatepicker, getnoisewin, \
 from pylot.core.pick.compare import Comparison
 from pylot.core.pick.autopick import fmpicker
 from pylot.core.util.defaults import OUTPUTFORMATS, FILTERDEFAULTS
-from pylot.core.util.utils import prepTimeAxis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
+from pylot.core.util.utils import prep_time_axis, full_range, demeanTrace, isSorted, findComboBoxIndex, clims, \
     pick_linestyle_plt, pick_color_plt, \
     check4rotated, check4doubled, check_for_gaps_and_merge, check_for_nan, identifyPhase, \
     loopIdentifyPhase, trim_station_components, transformFilteroptions2String, \
-    identifyPhaseID, get_bool, get_None, pick_color, getAutoFilteroptions, SetChannelComponents, \
+    identifyPhaseID, get_bool, get_none, pick_color, getAutoFilteroptions, SetChannelComponents, \
     station_id_remove_channel, get_pylot_eventfile_with_extension, get_possible_pylot_eventfile_extensions
 from autoPyLoT import autoPyLoT
 from pylot.core.util.thread import Thread
@@ -936,10 +938,10 @@ class WaveformWidgetPG(QtWidgets.QWidget):
                 msg = 'plotting %s channel of station %s' % (channel, station)
                 print(msg)
             stime = trace.stats.starttime - self.wfstart
-            time_ax = prepTimeAxis(stime, trace)
+            time_ax = prep_time_axis(stime, trace)
             if st_syn:
                 stime_syn = trace_syn.stats.starttime - self.wfstart
-                time_ax_syn = prepTimeAxis(stime_syn, trace_syn)
+                time_ax_syn = prep_time_axis(stime_syn, trace_syn)
 
             if method == 'fast':
                 trace.data, time_ax = self.minMax(trace, time_ax)
@@ -1422,7 +1424,7 @@ class PylotCanvas(FigureCanvas):
                 msg = 'plotting %s channel of station %s' % (channel, station)
                 print(msg)
             stime = trace.stats.starttime - wfstart
-            time_ax = prepTimeAxis(stime, trace)
+            time_ax = prep_time_axis(stime, trace)
             if time_ax is not None:
                 if scaleToChannel:
                     st_scale = wfdata.select(channel=scaleToChannel)
@@ -1460,7 +1462,7 @@ class PylotCanvas(FigureCanvas):
                 if not scaleddata:
                     trace.detrend('constant')
                     trace.normalize(np.max(np.abs(trace.data)) * 2)
-                time_ax = prepTimeAxis(stime, trace)
+                time_ax = prep_time_axis(stime, trace)
                 times = [time for index, time in enumerate(time_ax) if not index % nth_sample]
                 p_data = compare_stream[0].data
                 # #normalize
@@ -2267,7 +2269,7 @@ class PickDlg(QDialog):
 
                 # create action and add to menu
                 # phase name transferred using lambda function
-                slot = lambda phase=phase, phaseID=phaseID: phaseSelect[phaseID](phase)
+                slot = lambda ph=phase, phID=phaseID: phaseSelect[phID](ph)
                 picksAction = createAction(parent=self, text=phase,
                                            slot=slot,
                                            shortcut=shortcut)
@@ -2671,7 +2673,7 @@ class PickDlg(QDialog):
 
         # prepare plotting of data
         for trace in data:
-            t = prepTimeAxis(trace.stats.starttime - stime, trace)
+            t = prep_time_axis(trace.stats.starttime - stime, trace)
             inoise = getnoisewin(t, ini_pick, noise_win, gap_win)
             trace = demeanTrace(trace, inoise)
             # upscale trace data in a way that each trace is vertically zoomed to noiselevel*factor
@@ -4794,8 +4796,8 @@ class InputsTab(PropTab):
         self.tstopBox = QSpinBox()
         for spinbox in [self.tstartBox, self.tstopBox]:
             spinbox.setRange(-99999, 99999)
-        self.tstartBox.setValue(float(settings.value('tstart')) if get_None(settings.value('tstart')) else 0)
-        self.tstopBox.setValue(float(settings.value('tstop')) if get_None(settings.value('tstop')) else 1e6)
+        self.tstartBox.setValue(float(settings.value('tstart')) if get_none(settings.value('tstart')) else 0)
+        self.tstopBox.setValue(float(settings.value('tstop')) if get_none(settings.value('tstop')) else 1e6)
         self.cuttimesLayout.addWidget(self.tstartBox, 10)
         self.cuttimesLayout.addWidget(QLabel('[s] and'), 0)
         self.cuttimesLayout.addWidget(self.tstopBox, 10)
@@ -5791,7 +5793,7 @@ class ChooseWaveFormWindow(QWidget):
         #self.currentSpectro = self.traces[
         #    self.chooseBoxTraces.currentText()[3:]][self.chooseBoxComponent.currentText()].spectrogram(show=False, title=t)
         #self.currentSpectro.show()
-        applyFFT()
+        self.applyFFT()
 
     def applyFFT(self, trace):
         tra = self.traces[self.chooseBoxTraces.currentText()[3:]]['Z']