Refactors plot_ref_sld to plot_ref_sld_helper, (#33)

Author: StephenNneji

RAT/events.py

@@ -26,8 +26,8 @@ def get_event_callback(event_type: EventTypes) -> List[Callable[[Union[str, Plot
     event_type : EventTypes
         The event type.
 
-    Retuns
-    ------
+    Returns
+    -------
     callback : Callable[[Union[str, PlotEventData, ProgressEventData]], None]
         The callback for the event type.
     """

RAT/utils/plotting.py

@@ -1,6 +1,7 @@
 """
 Plots using the matplotlib library
 """
+from typing import Optional
 import matplotlib.pyplot as plt
 import numpy as np
 from RAT.rat_core import PlotEventData, makeSLDProfileXY
@@ -11,15 +12,15 @@ class Figure:
     Creates a plotting figure.
     """
 
-    def __init__(self, row: int = 1, col: int = 2):
+    def __init__(self, row: int = 1, col: int = 1):
         """
         Initializes the figure and the subplots.
 
         Parameters
         ----------
-        row : int
+        row : int, default: 1
               The number of rows in subplot
-        col : int
+        col : int, default: 1
               The number of columns in subplot
         """
         self._fig, self._ax = \
@@ -55,7 +56,8 @@ def _close(self, _):
         self._close_clicked = True
 
 
-def plot_errorbars(ax, x, y, err, onesided, color):
+def plot_errorbars(ax: 'matplotlib.axes._axes.Axes', x: np.ndarray, y: np.ndarray, err: np.ndarray, 
+                   one_sided: bool, color: str):
     """
     Plots the error bars.
 
@@ -69,12 +71,12 @@ def plot_errorbars(ax, x, y, err, onesided, color):
         The shifted data y axis data
     err : np.ndarray
             The shifted data e data
-    onesided : bool
+    one_sided : bool
         A boolean to indicate whether to draw one sided errorbars
     color : str
             The hex representing the color of the errorbars
     """
-    y_error = [[0]*len(err), err] if onesided else err
+    y_error = [[0]*len(err), err] if one_sided else err
     ax.errorbar(x=x,
                 y=y,
                 yerr=y_error,
@@ -85,7 +87,7 @@ def plot_errorbars(ax, x, y, err, onesided, color):
     ax.scatter(x=x, y=y, s=3, marker="o", color=color)
 
 
-def plot_ref_sld(data: PlotEventData, fig: Figure = None, delay: bool = True):
+def plot_ref_sld_helper(data: PlotEventData, fig: Optional[Figure] = None, delay: bool = True):
     """
     Clears the previous plots and updates the ref and SLD plots.
 
@@ -94,9 +96,9 @@ def plot_ref_sld(data: PlotEventData, fig: Figure = None, delay: bool = True):
     data : PlotEventData
            The plot event data that contains all the information
            to generate the ref and sld plots
-    fig : Figure
+    fig : Figure, optional 
           The figure class that has two subplots
-    delay : bool
+    delay : bool, default: True
             Controls whether to delay 0.005s after plot is created
 
     Returns
@@ -105,7 +107,7 @@ def plot_ref_sld(data: PlotEventData, fig: Figure = None, delay: bool = True):
           The figure class that has two subplots
     """
     if fig is None:
-        fig = Figure()
+        fig = Figure(1, 2)
     elif fig._ax.shape != (2,):
         fig._fig.clf()
         fig._ax = fig._fig.subplots(1, 2)
@@ -121,9 +123,6 @@ def plot_ref_sld(data: PlotEventData, fig: Figure = None, delay: bool = True):
                                                 data.shiftedData,
                                                 data.sldProfiles,
                                                 data.resampledLayers)):
-
-        sld, layer = map(lambda x: x[0], (sld, layer))
-
         # Calculate the divisor
         div = 1 if i == 0 else 2**(4*(i+1))
 
@@ -154,25 +153,29 @@ def plot_ref_sld(data: PlotEventData, fig: Figure = None, delay: bool = True):
             plot_errorbars(ref_plot, sd_x_s, sd_y_s, sd_e_s, True, color)
 
         # Plot the slds on plot (1,2)
-        for j in range(1, sld.shape[1]):
-            sld_plot.plot(sld[:, 0],
-                          sld[:, j],
+        for j in range(len(sld)):
+            sld_plot.plot(sld[j][:, 0],
+                          sld[j][:, 1],
                           label=f'sld {i+1}',
-                          color=color,
-                          linewidth=2)
+                          linewidth=1)
 
         if data.resample[i] == 1 or data.modelType == 'custom xy':
-            new = makeSLDProfileXY(layer[0, 1],
-                                   layer[-1, 1],
-                                   data.subRoughs[i],
-                                   layer,
-                                   len(layer),
-                                   1.0)
-
-            sld_plot.plot([row[0]-49 for row in new],
-                          [row[1] for row in new],
-                          color=color,
-                          linewidth=1)
+            layers = data.resampledLayers[i][0]
+            for j in range(len(data.resampledLayers[i])):
+                layer = data.resampledLayers[i][j]
+                if layers.shape[1] == 4:
+                    layer = np.delete(layer, 2, 1)
+                new_profile = makeSLDProfileXY(layers[0, 1],      # Bulk In
+                                               layers[-1, 1],     # Bulk Out
+                                               data.subRoughs[i], # roughness
+                                               layer,
+                                               len(layer),
+                                               1.0)
+
+                sld_plot.plot([row[0]-49 for row in new_profile],
+                              [row[1] for row in new_profile],
+                              color=color,
+                              linewidth=1)
 
     # Format the axis
     ref_plot.set_yscale('log')
@@ -191,3 +194,33 @@ def plot_ref_sld(data: PlotEventData, fig: Figure = None, delay: bool = True):
         plt.pause(0.005)
 
     return fig
+
+
+def plot_ref_sld(problem, results, block: bool = False):
+    """
+    Plots the reflectivity and SLD profiles.
+
+    Parameters
+    ----------
+    problem : ProblemDefinition
+              An instance of the ProblemDefinition class
+    results : OutputResult
+              The result from the calculation
+    block : bool, default: False
+            Indicates the plot should block until it is closed
+    """
+    data = PlotEventData()
+
+    data.reflectivity = results.reflectivity
+    data.shiftedData = results.shiftedData
+    data.sldProfiles = results.sldProfiles
+    data.resampledLayers = results.resampledLayers
+    data.dataPresent = problem.dataPresent
+    data.subRoughs = results.contrastParams.subRoughs
+    data.resample = problem.resample
+
+    figure = Figure(1, 2)
+
+    plot_ref_sld_helper(data, figure)
+    if block:
+        figure.wait_for_close()

tests/test_plotting.py

@@ -6,7 +6,7 @@
 from unittest.mock import MagicMock
 import matplotlib.pyplot as plt
 from RAT.rat_core import PlotEventData
-from RAT.utils.plotting import Figure, plot_ref_sld
+from RAT.utils.plotting import Figure, plot_ref_sld_helper
 
 
 TEST_DIR_PATH = os.path.join(os.path.dirname(os.path.realpath(__file__)),
@@ -40,7 +40,7 @@ def fig() -> Figure:
     """
     plt.close('all')
     figure = Figure(1, 3)
-    fig = plot_ref_sld(fig=figure, data=data())
+    fig = plot_ref_sld_helper(fig=figure, data=data())
     return fig
 
 
@@ -155,7 +155,7 @@ def test_sld_profile_function_call(mock: MagicMock) -> None:
     Tests the makeSLDProfileXY function called with
     correct args.
     """
-    plot_ref_sld(data())
+    plot_ref_sld_helper(data())
 
     assert mock.call_count == 3
     assert mock.call_args_list[0].args[0] == 2.07e-06

tests/test_wrappers.py

@@ -5,8 +5,9 @@
 
 
 def test_matlab_wrapper() -> None:
-    with pytest.raises(ImportError):
-        RAT.wrappers.MatlabWrapper('demo.m')
+    with mock.patch.dict('sys.modules', {'matlab': mock.MagicMock(side_effect=ImportError)}):
+        with pytest.raises(ImportError):
+            RAT.wrappers.MatlabWrapper('demo.m')
     mocked_matlab_module = mock.MagicMock()
     mocked_engine = mock.MagicMock()
     mocked_matlab_module.engine.start_matlab.return_value = mocked_engine