Merge pull request #718 from brnovasco/extend-shift-spectra

Extend shift spectra

orangecontrib/spectroscopy/preprocess/__init__.py

@@ -730,28 +730,40 @@ def __call__(self, data):
         return data.transform(domain)
 
 
-class CurveShiftFeature(SelectColumn):
+class ShiftAndScaleFeature(SelectColumn):
     InheritEq = True
 
 
-class _CurveShiftCommon(CommonDomain):
+class _ShiftAndScaleCommon(CommonDomain):
 
-    def __init__(self, amount, domain):
+    def __init__(self, offset, scale, domain):
         super().__init__(domain)
-        self.amount = amount
+        self.offset = offset
+        self.scale = scale
+
 
     def transformed(self, data):
-        return data.X + self.amount
+        return self.scale * data.X + self.offset
 
 
-class CurveShift(Preprocess):
+class ShiftAndScale(Preprocess):
+    """
+    Shift and scale of the data into the form:
+    y = scale * x + offset
 
-    def __init__(self, amount=0.):
-        self.amount = amount
+    Parameters
+    ----------
+    offset : float
+    scale  : float
+    """
+
+    def __init__(self, offset=0., scale=1.):
+        self.offset = offset
+        self.scale = scale
 
     def __call__(self, data):
-        common = _CurveShiftCommon(self.amount, data.domain)
-        atts = [a.copy(compute_value=CurveShiftFeature(i, common))
+        common = _ShiftAndScaleCommon(self.offset, self.scale, data.domain)
+        atts = [a.copy(compute_value=ShiftAndScaleFeature(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, ShiftAndScale, 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),
+    ShiftAndScale(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 TestShiftAndScale(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 = ShiftAndScale(offset=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/owpreprocess.py

@@ -14,7 +14,7 @@
 from Orange.widgets.data.utils.preprocess import SequenceFlow, Controller, \
     StandardItemModel
 from Orange.widgets.data.owpreprocess import (
-    PreprocessAction, Description, icon_path, DescriptionRole, ParametersRole, blocked
+    PreprocessAction, Description, icon_path, DescriptionRole, ParametersRole
 )
 from Orange.widgets.utils.sql import check_sql_input
 from Orange.widgets.utils.overlay import OverlayWidget
@@ -988,6 +988,10 @@ def migrate_preprocessor(cls, preprocessor, version):
         if name == "orangecontrib.infrared.cutinverse":
             name = "orangecontrib.spectroscopy.cut"
             settings["inverse"] = True
+        if name == "orangecontrib.infrared.curveshift":
+            name = "orangecontrib.spectroscopy.shiftandscale"
+            settings["offset"] = settings.get("amount", 0.)
+            settings["scale"] = 1.
         return [((name, settings), version)]
 
     @classmethod

orangecontrib/spectroscopy/widgets/preprocessors/misc.py

@@ -15,7 +15,7 @@
 from orangecontrib.spectroscopy.preprocess import (
     PCADenoising, GaussianSmoothing, Cut, SavitzkyGolayFiltering,
     Absorbance, Transmittance,
-    CurveShift, SpSubtract
+    ShiftAndScale, SpSubtract
 )
 from orangecontrib.spectroscopy.preprocess.transform import SpecTypes
 from orangecontrib.spectroscopy.widgets.gui import lineEditFloatRange, MovableVline, \
@@ -294,34 +294,40 @@ def createinstance(cls, params):
         return SavitzkyGolayFiltering(window=window, polyorder=polyorder, deriv=deriv)
 
 
-class CurveShiftEditor(BaseEditorOrange):
+class ShiftAndScaleEditor(BaseEditorOrange):
     """
-    Editor for CurveShift
+    Editor for ShiftAndScale
     """
     # 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 = "Shift and scale"
+    qualname = "orangecontrib.spectroscopy.shiftandscale"
+    replaces = ["orangecontrib.infrared.curveshift"]
 
     def __init__(self, parent=None, **kwargs):
         super().__init__(parent, **kwargs)
 
-        self.amount = 0.
+        self.offset = 0.
+        self.scale = 1.
 
         form = QFormLayout()
-        amounte = lineEditFloatRange(self, self, "amount", callback=self.edited.emit)
-        form.addRow("Shift Amount", amounte)
+        offset_input = lineEditFloatRange(self, self, "offset", callback=self.edited.emit)
+        form.addRow("Vertical offset", offset_input)
+        scale_input = lineEditFloatRange(self, self, "scale", callback=self.edited.emit)
+        form.addRow("Vertical scaling", scale_input)
         self.controlArea.setLayout(form)
 
     def setParameters(self, params):
-        self.amount = params.get("amount", 0.)
+        self.amount = params.get("offset", 0.)
+        self.scale = params.get("scale", 1.)
 
     @staticmethod
     def createinstance(params):
         params = dict(params)
-        amount = float(params.get("amount", 0.))
-        return CurveShift(amount=amount)
+        offset = float(params.get("offset", 0.))
+        scale = float(params.get("scale", 1.))
+        return ShiftAndScale(offset=offset, scale=scale)
 
 
 class PCADenoisingEditor(BaseEditorOrange):
@@ -453,5 +459,5 @@ 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(ShiftAndScaleEditor, 250)
 preprocess_editors.register(SpSubtractEditor, 275)