Merge branch 'master' into rtd

attune/workup/_intensity.py

@@ -37,6 +37,7 @@ def intensity(
     cutoff_factor=0.1,
     autosave=True,
     save_directory=None,
+    **spline_kwargs,
 ):
     """Workup a generic intensity plot for a single dependent.
 
@@ -72,8 +73,11 @@ def intensity(
     cutoff = channel.max() * cutoff_factor
     channel.clip(min=cutoff)
 
-    offsets = _intensity(data, channel.natural_name, setpoints[:])
-    print(offsets)
+    offsets = _intensity(data, channel.natural_name, setpoints[:], **spline_kwargs)
+    try:
+        raw_offsets = _intensity(data, channel.natural_name, setpoints[:], spline=False)
+    except ValueError:
+        raw_offsets = None
 
     units = data.axes[1].units
     if units == "None":
@@ -91,7 +95,7 @@ def intensity(
     # Why did we have to map setpoints?
     curve.map_setpoints(setpoints[:])
 
-    fig, _ = plot_intensity(data, channel.natural_name, dependent, curve, old_curve)
+    fig, _ = plot_intensity(data, channel.natural_name, dependent, curve, old_curve, raw_offsets)
 
     if autosave:
         if save_directory is None:

attune/workup/_plot.py

@@ -3,35 +3,40 @@
 import numpy as np
 
 
-def plot_intensity(data, channel, dependent, curve, prior_curve=None):
+def plot_intensity(data, channel, dependent, curve, prior_curve=None, raw_offsets=None):
     fig, gs = wt.artists.create_figure(
-        width="double", nrows=2, cols=[1, "cbar"], default_aspect=.5
+        width="single", nrows=2, cols=[1, "cbar"], default_aspect=.5
     )
     ax = plt.subplot(gs[0, 0])
-    curve_plot_kwargs = {"lw": 4, "c": "k", "alpha": .75}
+    curve_plot_kwargs = {"lw": 5, "c": "k", "alpha": .5}
     prior_curve_plot_kwargs = {"lw": 2, "c": "k"}
     ax.plot(curve.setpoints[:], curve[dependent][:], **curve_plot_kwargs)
     if prior_curve:
         ax.plot(prior_curve.setpoints[:], prior_curve[dependent][:], **prior_curve_plot_kwargs)
     ax.set_ylabel(dependent)
     wt.artists.plot_gridlines()
+    ax.set_xlim(*curve.get_limits())
+    ax.xaxis.set_tick_params(label1On=False)
 
     ax = plt.subplot(gs[1, 0])
     ax.pcolor(data, channel=channel)
-    xlim = ax.get_xlim()
     if prior_curve:
         ypoints = (
-            prior_curve(curve.setpoints[:], curve.setpoints.units, full=False)[dependent]
-            - curve[dependent][:]
+            curve[dependent][:]
+            - prior_curve(curve.setpoints[:], curve.setpoints.units, full=False)[dependent]
         )
     else:
         ypoints = curve[dependent][:]
+
+    if raw_offsets is not None:
+        ax.plot(curve.setpoints[:], raw_offsets, c="grey", lw=5, alpha=0.5)
+
     ax.plot(curve.setpoints[:], ypoints, **curve_plot_kwargs)
     ax.axhline(0, **prior_curve_plot_kwargs)
     wt.artists.plot_gridlines()
     ax.set_ylabel(r"$\mathsf{{\Delta {dependent}}}$".format(dependent=dependent))
     ax.set_xlabel(f"Setpoint ({curve.setpoints.units})")
-    ax.set_xlim(xlim)
+    ax.set_xlim(*curve.get_limits())
 
     cax = plt.subplot(gs[1, 1])
     ticks = np.linspace(data[channel].null, data[channel].max(), 11)

attune/workup/_tune_test.py

@@ -75,7 +75,10 @@ def tune_test(
     channel.clip(min=cutoff)
 
     offsets = _offsets(data, channel.natural_name, setpoints[:])
-    raw_offsets = _offsets(data, channel.natural_name, data.axes[0].points, spline=False)
+    try:
+        raw_offsets = _offsets(data, channel.natural_name, data.axes[0].points, spline=False)
+    except ValueError:
+        raw_offsets = None
 
     # make curve ----------------------------------------------------------------------------------
     new_curve = old_curve.copy()

docs/.gitignore

@@ -0,0 +1,4 @@
+auto_examples/
+_build/
+gen_modules/
+modules/

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python3 -msphinx
+SPHINXPROJ    = WrightTools
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/api/.gitignore

@@ -0,0 +1,9 @@
+*.rst
+!modules.rst
+!attune.curve.rst
+!attune.curve.Curve.rst
+!attune.curve.Dependents.rst
+!attune.curve.Setpoints.rst
+!attune.curve.TopasCurve.rst
+!attune.interpolator.rst
+!attune.workup.rst

docs/api/attune.curve.Curve.rst

@@ -0,0 +1,43 @@
+attune.curve.Curve
+==================
+
+.. currentmodule:: attune.curve
+
+.. autoclass:: Curve
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~Curve.__init__
+      ~Curve.coerce_dependents
+      ~Curve.convert
+      ~Curve.copy
+      ~Curve.get_dependent_positions
+      ~Curve.get_limits
+      ~Curve.get_source_setpoint
+      ~Curve.interpolate
+      ~Curve.map_setpoints
+      ~Curve.offset_by
+      ~Curve.offset_to
+      ~Curve.plot
+      ~Curve.read
+      ~Curve.save
+      ~Curve.sort
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~Curve.dependent_names
+      ~Curve.dependent_units
+
+

docs/api/attune.curve.Setpoints.rst

@@ -0,0 +1,23 @@
+attune.curve.Setpoints
+======================
+
+.. currentmodule:: attune.curve
+
+.. autoclass:: Setpoints
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~Setpoints.__init__
+      ~Setpoints.convert
+
+
+
+
+
+

docs/api/attune.curve.TopasCurve.rst

@@ -0,0 +1,44 @@
+attune.curve.TopasCurve
+=======================
+
+.. currentmodule:: attune.curve
+
+.. autoclass:: TopasCurve
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~TopasCurve.__init__
+      ~TopasCurve.coerce_dependents
+      ~TopasCurve.convert
+      ~TopasCurve.copy
+      ~TopasCurve.get_dependent_positions
+      ~TopasCurve.get_limits
+      ~TopasCurve.get_source_setpoint
+      ~TopasCurve.interpolate
+      ~TopasCurve.map_setpoints
+      ~TopasCurve.offset_by
+      ~TopasCurve.offset_to
+      ~TopasCurve.plot
+      ~TopasCurve.read
+      ~TopasCurve.read_all
+      ~TopasCurve.save
+      ~TopasCurve.sort
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~TopasCurve.dependent_names
+      ~TopasCurve.dependent_units
+
+

docs/api/attune.curve.rst

@@ -0,0 +1,18 @@
+attune.curve package
+====================
+
+Module contents
+---------------
+
+.. automodule:: attune.curve
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+.. autosummary::
+   :toctree: ../api
+
+   Curve
+   Dependent
+   Setpoints
+   TopasCurve

docs/api/attune.interpolator.rst

@@ -0,0 +1,15 @@
+attune.interpolator package
+===========================
+
+Module contents
+---------------
+
+.. automodule:: attune.interpolator
+
+.. autosummary::
+   :toctree: ../api
+
+    Interpolator
+    Linear
+    Poly
+    Spline

docs/api/attune.workup.rst

@@ -0,0 +1,13 @@
+attune.workup package
+=====================
+
+Module contents
+---------------
+
+.. automodule:: attune.workup
+
+.. autosummary::
+   :toctree: ../api
+
+    intensity
+    tune_test

docs/api/modules.rst

@@ -0,0 +1,9 @@
+attune API
+==========
+
+.. toctree::
+   :maxdepth: 6
+
+   attune.curve
+   attune.interpolator
+   attune.workup