Merge pull request #227 from rmodrak/master

Graphics fixes

docs/install/index.rst

@@ -40,11 +40,16 @@ Finally, install PyGMT:
 
 .. code::
 
-    conda install pygmt
+    conda install 'pygmt>=0.9'
 
 .. note::
 
-    PyGMT is only used for generating figures. If `conda install pygmt` fails, MTUQ will attempt to fall back to GMT or ObsPy.  We note that some versions of GMT and ObsPy do not plot full moment tensors `correctly <https://github.com/obspy/obspy/issues/2388>`_.
+    PyGMT installation has been finicky at times, so we include it as a separate step after the main env.yaml-based installation. 
+
+
+.. note::
+
+    If PyGMT installation fails, most MTUQ functions will still work, but some plotting functions will fall back to GMT or ObsPy.  We note that some versions of GMT and ObsPy do not plot `full moment tensors <https://github.com/obspy/obspy/issues/2388>`_ correctly.
 
 
 

mtuq/graphics/uq/_gmt.py

@@ -162,6 +162,7 @@ def _plot_depth_gmt(filename, depths, values,
 
     data = np.column_stack((depths, values))
     minval, maxval, exp = _parse_limits(data[:,-1])
+    data[:,-1] /= 10.**exp
 
     # write values to be plotted as ASCII table
     _savetxt(ascii_file_1, data)

mtuq/graphics/waveforms.py

@@ -104,7 +104,7 @@ def plot_waveforms1(filename,
 
         ir += 1
 
-    pyplot.savefig(filename)
+    _save(filename)
     pyplot.close()
 
 
@@ -221,7 +221,7 @@ def plot_waveforms2(filename,
 
         ir += 1
 
-    pyplot.savefig(filename)
+    _save(filename)
     pyplot.close()
 
 
@@ -418,22 +418,7 @@ def _plot_ZR(axes, ic, dat, syn, component,
 
     _plot(axis, dat, syn)
 
-    # THIS PART WAS COMMENTED OUT BEFORE THE WORKSHOP FOR A QUICK WORKAROUND
-    # WE NEED A PROPER WAY OF DEALING WITH CUSTOM AMPLITUDE BY ADDING AN OPTION
-    # # normalize amplitudes
-    # if normalize=='trace_amplitude':
-    #     max_trace = _max(dat, syn)
-    #     ylim = [-3*max_trace, +3*max_trace]
-    #     axis.set_ylim(*ylim)
-    # elif normalize=='station_amplitude':
-    #     max_stream = _max(stream_dat, stream_syn)
-    #     ylim = [-3*max_stream, +3*max_stream]
-    #     axis.set_ylim(*ylim)
-    # elif normalize=='maximum_amplitude':
-    #     ylim = [-2*max_amplitude, +2*max_amplitude]
-    #     axis.set_ylim(*ylim)
-
-    # normalize amplitude - using same scaling parameters as surface waves
+    # normalize amplitude
     if normalize=='trace_amplitude':
         max_trace = _max(dat, syn)
         ylim = [-1.5*max_trace, +1.5*max_trace]
@@ -446,6 +431,7 @@ def _plot_ZR(axes, ic, dat, syn, component,
         ylim = [-0.75*max_amplitude, +0.75*max_amplitude]
         axis.set_ylim(*ylim)
 
+
     if trace_label_writer is not None:
         trace_label_writer(axis, dat, syn, total_misfit)
 
@@ -467,9 +453,6 @@ def _plot(axis, dat, syn, label=None):
     axis.plot(t, s[start:stop], 'r', linewidth=1.25, 
         clip_on=False, zorder=10)
 
-    # prevents traces from getting clipped
-    axis.patch.set_alpha(0.)
-
 
 def _add_component_labels1(axes, body_wave_labels=True, surface_wave_labels=True):
     """ Displays component name above each column
@@ -580,6 +563,7 @@ def _hide_axes(axes):
             col.spines['left'].set_visible(False)
             col.get_xaxis().set_ticks([])
             col.get_yaxis().set_ticks([])
+            col.patch.set_visible(False)
 
 
 def _prepare_header(model, solver, source, source_dict, origin, *args):
@@ -600,6 +584,10 @@ def _prepare_header(model, solver, source, source_dict, origin, *args):
         raise TypeError
 
 
+def _save(filename):
+    pyplot.savefig(filename)
+
+
 def _get_tag(tags, pattern):
     for tag in tags:
         parts = tag.split(':')

mtuq/process_data.py

@@ -63,20 +63,20 @@ class ProcessData(object):
     ``pick_type`` (`str`)
 
     - ``'taup'``
-      calculates P, S arrival times from Tau-P model
+      calculates P, S travel times from Tau-P model
       (uses `obspy.taup.TauPyModel.get_arrival_times`)
 
     - ``'FK_metadata'``
-      reads P, S arrival times from FK metadata
+      reads P, S travel times from FK metadata
 
     - ``'SAC_metadata'``
-      reads P, S arrival times from SAC metadata fields `t5`, `t6`
+      reads P, S travel times from SAC metadata fields `t5`, `t6`
 
     - ``'user_supplied'``
-      reads P, S arrival times from columns 8, 10 of `capuaf_file`
+      reads P, S travel times from columns 8, 10 of `capuaf_file`
 
     - ``None``
-      no phase picks will be calculated
+      no P,S travel times will be calculated
 
 
     ``window_type`` (`str`)
@@ -121,6 +121,9 @@ class ProcessData(object):
     ``freq`` (`float`)
     Required for `filter_type=lowpass` or `filter_type=highpass`
 
+    ``window_length`` (`float`)
+    Window length in seconds
+
     ``group_velocity`` (`float`)
     Group velocity in m/s, required for `window_type=group_velocity`
 
@@ -134,11 +137,8 @@ class ProcessData(object):
     ``v_max`` (`float`)
     Maximum velocity in m/s, required for `window_type=min_max`
 
-    ``window_length`` (`float`)
-    window length in seconds
-
     ``padding`` (`list`)
-    amount by which Green's functions will be padded relative to data
+    Amount by which Green's functions will be padded relative to data
 
     ``taup_model`` (`str`)
     Name of built-in ObsPy TauP model or path to custom ObsPy TauP model,