Pyatoa v0.4.2 (#49)

* Bugfi: measure with no windows (#47)

* bugfix: when component list does not match the internal streams (e.g., seisflows inversion that is processing one component at a time), and no windows are selected, measure fails to run and throws an IndexError because it's tries to index out of the Stream. fixed to remove dependence on component list

* bump version and update changelog

* Bugfix Incorrectly scaled waveform plots (#48)

* allow Manager.load() to work without the need for a StationXML attribute, which happens for synthetic only cases

* removed plotting axis formatter which was forcing axis bounds [0,1] when the fraction between min and max y lim values was <1, which will happen if only have positive or negative values, but we don't want this to happen because we will likely always want plots to straddle 0, especially when showing adjoint sources which will straddle 0 even if waveforms are all one value

* bugfix label for synthetic waveforms was incorrect

* change misfit label formatting on waveform plots from floating point to sci notation as misfit is usually << 1

* updating test figure

* bump patch version and update changelog

Author: bch0w

CHANGELOG.md

@@ -1,5 +1,18 @@
 # CHANGELOG
 
+
+## v0.4.2 (#48)
+
+- Remove plot axis formatter which forced axis bounds [0,1] in some instances
+- Bugfix synthetic waveform label was being incorrectly set
+- Changed misfit label $\chi$ format from float to scientific notation as misfit can be << 1
+- Allow Manager.load() to work even without valid StationXML attribute in ASFDataSet
+
+## v0.4.1
+
+- Bugfix: no window selection did not allow measure to be called due to some
+  incorrect referencing
+
 ## v0.4.0
 
 >__Note__: Mainly improvements to the Inspector class and its ability to

pyatoa/core/manager.py

@@ -492,11 +492,14 @@ def load(self, code=None, path=None, ds=None, synthetic_tag=None,
             net, sta = code.split('.')
             sta_tag = f"{net}.{sta}"
             if sta_tag in ds.waveforms.list():
-                self.inv = ds.waveforms[sta_tag].StationXML
                 self.st_syn = ds.waveforms[sta_tag][synthetic_tag or
                                                     self.config.synthetic_tag]
                 self.st_obs = ds.waveforms[sta_tag][observed_tag or
                                                     self.config.observed_tag]
+                try:
+                    self.inv = ds.waveforms[sta_tag].StationXML
+                except AttributeError:
+                    logger.warning("no StationXML attribute found for station")
                 if windows:
                     self.windows = load_windows(ds, net, sta, iter_, step, 
                                                 return_previous=False)
@@ -1239,7 +1242,8 @@ def _format_windows(self):
         else:
             logger.debug("no windows given, adjoint sources will be "
                          "calculated on full trace")
-            for comp in self.config.component_list:
+            component_list = list(set(_.stats.component for _ in self.st_syn))
+            for comp in component_list:
                 dt = self.st_obs.select(component=comp)[0].stats.delta
                 npts = self.st_obs.select(component=comp)[0].stats.npts
                 # We offset the bounds of the entire trace by 1s to play nice

pyatoa/tests/test_data/baseline_images/default_manager_plot_wav.png

@@ -6,6 +6,7 @@
 Flexible to allow for only waveform plots, or for the addition of objects
 based on inputs.
 """
+from re import I
 import numpy as np
 import matplotlib as mpl
 import matplotlib.pyplot as plt
@@ -227,7 +228,7 @@ def plot_waveforms(self, ax, obs, syn, normalize=False):
                       label=f"{obs.id} ({self.config.st_obs_type.upper()})",
                       linewidth=linewidth)
         a2, = ax.plot(self.time_axis, syn.data, syn_color, zorder=10, 
-                      label=f"{syn.id} ({self.config.st_obs_type.upper()})",
+                      label=f"{syn.id} ({self.config.st_syn_type.upper()})",
                       linewidth=linewidth)
 
         return [a1, a2]
@@ -485,7 +486,7 @@ def plot_adjsrcs(self, ax, adjsrc):
         b1, = ax.plot(self.time_axis, adjsrc.adjoint_source[::-1], color, 
                       alpha=alpha, linewidth=linewidth, linestyle=linestyle, 
                       zorder=9,
-                      label=fr"Adjoint Source ($\chi$={adjsrc.misfit:.2f})"
+                      label=fr"Adjoint Source ($\chi$={adjsrc.misfit:.3E})"
                       )
         return [b1]
 
@@ -773,13 +774,11 @@ def format_axis(input_ax, percent_over=0.125):
     :param percent_over: the percentage above the peak value that the bounds
         of the axis will be set
     """
-    ymin, ymax = input_ax.get_ylim()
     maxvalue = max([abs(_) for _ in input_ax.get_ylim()])
     percent_over = maxvalue * percent_over
-    if abs(round(ymin / ymax)) != 0:
-        # Set bounds to be the same positive and negative
-        bounds = (-1 * (maxvalue + percent_over), (maxvalue + percent_over))
-    else: 
-        bounds = (-0.05, 1.05)
+
+    # Set bounds to be the same positive and negative
+    bounds = (-1 * (maxvalue + percent_over), (maxvalue + percent_over))
+
     input_ax.set_ylim(bounds)
 

pyatoa/visuals/wave_maker.py

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyatoa"
-version = "0.4.0"
+version = "0.4.2"
 description = "Python's Adjoint Tomography Operations Assistant"
 readme = "README.md"
 requires-python = ">=3.7"