Remove baseline

.github/workflows/tests.yml

@@ -75,7 +75,8 @@ jobs:
       - name: Install HyperSpy (RELEASE_next_minor)
         if: contains( matrix.LABEL, 'RnM')
         run: |
-          pip install git+https://github.com/hyperspy/hyperspy.git@RELEASE_next_minor
+          # pip install git+https://github.com/hyperspy/hyperspy.git@RELEASE_next_minor
+          pip install "hyperspy[all] @ git+https://github.com/ericpre/hyperspy.git@remove_baselines"
 
       - name: Install HyperSpy (RELEASE_next_patch)
         if: contains( matrix.LABEL, 'RnP')

hyperspy_gui_traitsui/hyperspy_extension.yaml

@@ -43,6 +43,9 @@ GUI:
       hyperspy.Signal1D.remove_background:
         module: hyperspy_gui_traitsui.tools
         function: remove_background_traitsui
+      hyperspy.Signal1D.remove_baseline:
+        module: hyperspy_gui_traitsui.tools
+        function: remove_baseline_traitsui
       hyperspy.SimpleMessage:
         module: hyperspy_gui_traitsui.messages
         function: simple_message

hyperspy_gui_traitsui/tests/test_tools.py

@@ -25,6 +25,7 @@
     BackgroundRemoval,
     Signal2DCalibration,
     )
+from hyperspy.utils.baseline_removal_tool import BaselineRemoval
 
 from hyperspy_gui_traitsui.tests.utils import KWARGS
 
@@ -69,6 +70,21 @@ def test_remove_background_tool():
     assert s.isig[:500.0].data.mean() < 1
 
 
+def test_remove_baseline():
+    pytest.importorskip("pybaselines")
+
+    s = hs.data.two_gaussians().inav[:5, :5]
+    s.plot()
+
+    br = BaselineRemoval(s)
+    br.gui(**KWARGS)
+    br.algorithm = "Asymmetric Least Squares"
+    br.algorithm = "Adaptive Smoothness Penalized Least Squares"
+    br.lam = 1e7
+    br.apply()
+    assert s.isig[:10].data.mean() < 5
+
+
 def test_signal_2d_calibration():
     s = hs.signals.Signal2D(np.zeros((100, 100)))
     s.plot()

hyperspy_gui_traitsui/tools.py

@@ -9,7 +9,7 @@
 from hyperspy_gui_traitsui.utils import add_display_arg
 
 
-class SmoothingHandler(tu.Handler):
+class GenericHandler(tu.Handler):
 
     def close(self, info, is_ok):
         # Removes the span selector from the plot
@@ -263,7 +263,7 @@
             # 'line_color',
         ),
         kind='live',
-        handler=SmoothingHandler,
+        handler=GenericHandler,
         buttons=OKCancelButtons,
         title='Savitzky-Golay Smoothing',
     )
@@ -279,7 +279,7 @@
             # 'line_color',
         ),
         kind='live',
-        handler=SmoothingHandler,
+        handler=GenericHandler,
         buttons=OKCancelButtons,
         title='Lowess Smoothing',)
     return obj, {"view": view}
@@ -293,7 +293,7 @@
             # 'line_color',
         ),
         kind='live',
-        handler=SmoothingHandler,
+        handler=GenericHandler,
         buttons=OKCancelButtons,
         title='Total Variation Smoothing',)
     return obj, {"view": view}
@@ -307,7 +307,7 @@
             'order',
             'type'),
         kind='live',
-        handler=SmoothingHandler,
+        handler=GenericHandler,
         buttons=OKCancelButtons,
         title='Butterworth filter',)
     return obj, {"view": view}
@@ -449,6 +449,117 @@
     return obj, {"view": view}
 
 
+@add_display_arg
+def remove_baseline_traitsui(obj, **kwargs):
+    view = tu.View(
+        tu.Item(
+            'algorithm',
+            label="Method",
+        ),
+        tu.Item(
+            '_time_per_pixel',
+            style='readonly',
+            label="Time per pixel (ms)",
+            format_str='%.3g',
+        ),
+        tu.Group(
+            tu.Group(
+                tu.Item(
+                    'lam',
+                    enabled_when="_enable_lam",
+                ),
+                tu.Item(
+                    'diff_order',
+                    enabled_when="_enable_diff_order",
+                ),
+                tu.Item(
+                    'p',
+                    enabled_when="_enable_p",
+                ),
+                tu.Item(
+                    'lam_1',
+                    enabled_when="_enable_lam_1",
+                ),
+                tu.Item(
+                    'eta',
+                    enabled_when="_enable_eta",
+                ),
+                tu.Item(
+                'penalized_spline',
+                enabled_when="_enable_penalized_spline",
+                ),
+                label="Whittaker",
+            ),
+            tu.Group(
+                # Enabled when a polynomial baseline is selected
+                tu.Item(
+                    'poly_order',
+                    enabled_when="_enable_poly_order",
+                ),
+                tu.Item(
+                    'peak_ratio',
+                    enabled_when="_enable_peak_ratio",
+                ),
+                label="Polynomial",
+            ),
+            tu.Group(
+                tu.Item(
+                    'num_knots',
+                    enabled_when="_enable_num_knots",
+                ),
+                tu.Item(
+                    'spline_degree',
+                    enabled_when="_enable_spline_degree",
+                ),
+                tu.Item(
+                    'symmetric',
+                    enabled_when="_enable_symmetric",
+                ),
+                tu.Item(
+                    'quantile',
+                    enabled_when="_enable_quantile",
+                ),
+                label="Spline",
+            ),
+            tu.Group(
+                tu.Item(
+                    'smooth_half_window',
+                    enabled_when="_enable_smooth_half_window",
+                ),
+                tu.Item(
+                    'num_std',
+                    enabled_when="_enable_num_std",
+                ),
+                tu.Item(
+                    'interp_half_window',
+                    enabled_when="_enable_interp_half_window",
+                ),
+                tu.Item(
+                    'half_window',
+                    enabled_when="_enable_half_window",
+                ),
+                tu.Item(
+                    'section',
+                    enabled_when="_enable_section",
+                ),
+                tu.Item(
+                    'segments',
+                    enabled_when="_enable_segments",
+                ),
+                label="Classification",
+            ),
+        ),
+        buttons=OKCancelButtons,
+        handler=GenericHandler,
+        close_result=False, # is_ok=False when using window close button.
+        title='Baseline removal tool',
+        resizable=True,
+        width=300,
+    )
+    return obj, {"view": view}
+
+
+
 class SpikesRemovalHandler(tu.Handler):
 
     def close(self, info, is_ok):