Extend shift spectra

orangecontrib/spectroscopy/preprocess/__init__.py

@@ -730,28 +730,40 @@ def __call__(self, data):
         return data.transform(domain)
 
 
-class CurveShiftFeature(SelectColumn):
+class LinearTransformFeature(SelectColumn):
     InheritEq = True
 
 
-class _CurveShiftCommon(CommonDomain):
+class _LinearTransformCommon(CommonDomain):
 
-    def __init__(self, amount, domain):
+    def __init__(self, amount, scale, domain):
         super().__init__(domain)
         self.amount = amount
+        self.scale = scale
+
 
     def transformed(self, data):
-        return data.X + self.amount
+        return self.scale * data.X + self.amount
+
 
+class LinearTransform(Preprocess):
+    """
+    Linear transformation of the data into the form:
+    y = scale * x + amount
 
-class CurveShift(Preprocess):
+    Parameters
+    ----------
+    amount : float
+    scale  : float
+    """
 
-    def __init__(self, amount=0.):
+    def __init__(self, amount=0., scale=1.):
         self.amount = amount
+        self.scale = scale
 
     def __call__(self, data):
-        common = _CurveShiftCommon(self.amount, data.domain)
-        atts = [a.copy(compute_value=CurveShiftFeature(i, common))
+        common = _LinearTransformCommon(self.amount, self.scale, data.domain)
+        atts = [a.copy(compute_value=LinearTransformFeature(i, common))
                 for i, a in enumerate(data.domain.attributes)]
         domain = Orange.data.Domain(atts, data.domain.class_vars,
                                     data.domain.metas)

orangecontrib/spectroscopy/tests/test_preprocess.py

@@ -11,7 +11,7 @@
 from orangecontrib.spectroscopy.preprocess import Absorbance, Transmittance, \
     Integrate, Interpolate, Cut, SavitzkyGolayFiltering, \
     GaussianSmoothing, PCADenoising, RubberbandBaseline, \
-    Normalize, LinearBaseline, CurveShift, EMSC, MissingReferenceException, \
+    Normalize, LinearBaseline, LinearTransform, EMSC, MissingReferenceException, \
     WrongReferenceException, NormalizeReference, XASnormalization, ExtractEXAFS, \
     PreprocessException, NormalizePhaseReference, Despike, SpSubtract
 from orangecontrib.spectroscopy.preprocess.als import ALSP, ARPLS, AIRPLS
@@ -58,7 +58,7 @@ def preprocessor_data(preproc):
     Normalize(method=Normalize.Vector),
     Normalize(method=Normalize.Area, int_method=Integrate.PeakMax, lower=0, upper=10000),
     Normalize(method=Normalize.MinMax),
-    CurveShift(1),
+    LinearTransform(1, 2),
     Despike(threshold=5, cutoff=60, dis=5),
     ALSP(lam=100E+6, itermax=5, p=0.5),
     ARPLS(lam=100E+5, itermax=5, ratio=0.5),
@@ -588,14 +588,14 @@ def test_iris(self):
                                         [4.75015528, 3.15366444, 1.46254138, 0.23693223]])
 
 
-class TestCurveShift(unittest.TestCase):
+class TestLinearTransform(unittest.TestCase):
 
     def test_simple(self):
         data = Table.from_numpy(None, [[1.0, 2.0, 3.0, 4.0]])
-        f = CurveShift(amount=1.1)
+        f = LinearTransform(amount=1.1, scale=2.)
         fdata = f(data)
         np.testing.assert_almost_equal(fdata.X,
-                                       [[2.1, 3.1, 4.1, 5.1]])
+                                       [[3.1, 5.1, 7.1, 9.1]])
 
 
 class TestUtils(unittest.TestCase):

orangecontrib/spectroscopy/widgets/preprocessors/misc.py

@@ -16,7 +16,7 @@
 from orangecontrib.spectroscopy.preprocess import (
     PCADenoising, GaussianSmoothing, Cut, SavitzkyGolayFiltering,
     Absorbance, Transmittance,
-    CurveShift, SpSubtract
+    LinearTransform, SpSubtract
 )
 from orangecontrib.spectroscopy.preprocess.transform import SpecTypes
 from orangecontrib.spectroscopy.widgets.gui import lineEditFloatRange, MovableVline, \
@@ -295,34 +295,40 @@ def createinstance(cls, params):
         return SavitzkyGolayFiltering(window=window, polyorder=polyorder, deriv=deriv)
 
 
-class CurveShiftEditor(BaseEditorOrange):
+class LinearTransformEditor(BaseEditorOrange):
     """
-    Editor for CurveShift
+    Editor for LinearTransform
     """
     # TODO: the layout changes when I click the area of the preprocessor
     #       EFFECT: the sidebar snaps in
 
-    name = "Shift Spectra"
-    qualname = "orangecontrib.infrared.curveshift"
+    name = "Linear Transformation"
+    qualname = "orangecontrib.infrared.lineartransform"
+    replaces = ["orangecontrib.infrared.curveshift"]
 
     def __init__(self, parent=None, **kwargs):
         super().__init__(parent, **kwargs)
 
         self.amount = 0.
+        self.scale = 1.
 
         form = QFormLayout()
         amounte = lineEditFloatRange(self, self, "amount", callback=self.edited.emit)
         form.addRow("Shift Amount", amounte)
+        scale_input = lineEditFloatRange(self, self, "scale", callback=self.edited.emit)
+        form.addRow("Scale Factor", scale_input)
         self.controlArea.setLayout(form)
 
     def setParameters(self, params):
         self.amount = params.get("amount", 0.)
+        self.scale = params.get("scale", 1.)
 
     @staticmethod
     def createinstance(params):
         params = dict(params)
         amount = float(params.get("amount", 0.))
-        return CurveShift(amount=amount)
+        scale = float(params.get("scale", 1.))
+        return LinearTransform(amount=amount, scale=scale)
 
 
 class PCADenoisingEditor(BaseEditor):
@@ -462,5 +468,5 @@ def update_reference_info(self):
 preprocess_editors.register(SavitzkyGolayFilteringEditor, 100)
 preprocess_editors.register(PCADenoisingEditor, 200)
 preprocess_editors.register(SpectralTransformEditor, 225)
-preprocess_editors.register(CurveShiftEditor, 250)
+preprocess_editors.register(LinearTransformEditor, 250)
 preprocess_editors.register(SpSubtractEditor, 275)