Reference Image handling and self referencing

orangecontrib/snom/preprocess/utils.py

@@ -2,7 +2,11 @@
 
 from Orange.data import Domain
 from Orange.preprocess import Preprocess
-from orangecontrib.spectroscopy.preprocess import CommonDomain, SelectColumn
+from orangecontrib.spectroscopy.preprocess import (
+    CommonDomain,
+    SelectColumn,
+    WrongReferenceException,
+)
 from orangecontrib.spectroscopy.utils import (
     InvalidAxisException,
     values_to_linspace,
@@ -32,21 +36,60 @@ def __call__(self, data):
         return np.full(len(data), np.nan)
 
 
+def _prepare_domain_for_image(data, image_opts):
+    at = data.domain[image_opts["attr_value"]].copy(compute_value=NoComputeValue())
+    return domain_with_single_attribute_in_x(at, data.domain)
+
+
+def _prepare_table_for_image(data, image_opts):
+    odata = data
+    domain = _prepare_domain_for_image(data, image_opts)
+    data = data.transform(domain)
+    if len(data):
+        with data.unlocked(data.X):
+            data.X[:, 0] = odata.get_column(image_opts["attr_value"], copy=True)
+    return data
+
+
+def _image_from_table(data, image_opts):
+    hypercube, _, indices = get_ndim_hyperspec(
+        data, (image_opts["attr_y"], image_opts["attr_x"])
+    )
+    return hypercube[:, :, 0], indices
+
+
 class PreprocessImageOpts2DOnlyWhole(PreprocessImageOpts):
     def __call__(self, data, image_opts):
-        at = data.domain[image_opts["attr_value"]].copy(compute_value=NoComputeValue())
-        odata = data
-        domain = domain_with_single_attribute_in_x(at, data.domain)
-        data = data.transform(domain)
+        data = _prepare_table_for_image(data, image_opts)
+        try:
+            image, indices = _image_from_table(data, image_opts)
+            transformed = self.transform_image(image, data)
+            col = transformed[indices].reshape(-1)
+        except InvalidAxisException:
+            col = np.full(len(data), np.nan)
         if len(data):
             with data.unlocked(data.X):
-                data.X[:, 0] = odata.get_column(image_opts["attr_value"], copy=True)
+                data.X[:, 0] = col
+        return data
+
+    def transform_image(self, image, data):
+        """
+        image: a numpy 2D array where image[y,x] is the value in image row y and column x
+        data: image data set (used for passing meta data)
+        """
+        raise NotImplementedError
+
+
+class PreprocessImageOpts2DOnlyWholeReference(PreprocessImageOpts):
+    def __call__(self, data, image_opts):
+        data = _prepare_table_for_image(data, image_opts)
+        reference = _prepare_table_for_image(self.reference, image_opts)
         try:
-            hypercube, _, indices = get_ndim_hyperspec(
-                data, (image_opts["attr_y"], image_opts["attr_x"])
-            )
-            image = hypercube[:, :, 0]
-            transformed = self.transform_image(image, odata)
+            image, indices = _image_from_table(data, image_opts)
+            ref_image, _ = _image_from_table(reference, image_opts)
+            if image.shape != ref_image.shape:
+                raise WrongReferenceException("Reference data should have length 1")
+            transformed = self.transform_image(image, ref_image, data)
             col = transformed[indices].reshape(-1)
         except InvalidAxisException:
             col = np.full(len(data), np.nan)
@@ -55,10 +98,11 @@ def __call__(self, data, image_opts):
                 data.X[:, 0] = col
         return data
 
-    def transform_image(self, image, data):
+    def transform_image(self, image, ref_image, data):
         """
         image: a numpy 2D array where image[y,x] is the value in image row y and column x
-        data: original data set (used for passing meta data)
+        ref_image: a numpy 2D array where image[y,x] is the value in image row y and column x
+        data: image data set (used for passing meta data)
         """
         raise NotImplementedError
 

orangecontrib/snom/widgets/owpreprocessimage.py

@@ -12,7 +12,7 @@
 
 import Orange.data
 from Orange import preprocess
-from Orange.widgets.widget import Output
+from Orange.widgets.widget import Output, Input
 
 from orangecontrib.spectroscopy.widgets.owhyper import BasicImagePlot
 
@@ -132,7 +132,16 @@ def progress_interrupt(i: float):
         return orig_data, data
 
 
-class OWPreprocessImage(SpectralImagePreprocess):
+class SpectralImagePreprocessReference(SpectralImagePreprocess, openclass=True):
+    class Inputs(SpectralImagePreprocess.Inputs):
+        reference = Input("Reference", Orange.data.Table)
+
+    @Inputs.reference
+    def set_reference(self, reference):
+        self.reference_data = reference
+
+
+class OWPreprocessImage(SpectralImagePreprocessReference):
     name = "Preprocess image"
     id = "orangecontrib.snom.widgets.preprocessimage"
     description = "Process image"

orangecontrib/snom/widgets/preprocessors/__init__.py

@@ -6,3 +6,4 @@
 from orangecontrib.snom.widgets.preprocessors import phase_rotation  # noqa: F401
 from orangecontrib.snom.widgets.preprocessors import simple_normalize  # noqa: F401
 from orangecontrib.snom.widgets.preprocessors import linelevel  # noqa: F401
+from orangecontrib.snom.widgets.preprocessors import self_reference  # noqa: F401

orangecontrib/snom/widgets/preprocessors/self_reference.py

@@ -0,0 +1,72 @@
+from AnyQt.QtWidgets import QFormLayout, QLabel
+
+from orangecontrib.spectroscopy.preprocess import MissingReferenceException
+from orangecontrib.spectroscopy.widgets.preprocessors.utils import (
+    BaseEditorOrange,
+    REFERENCE_DATA_PARAM,
+)
+
+from pySNOM.images import SelfReference
+
+from orangecontrib.snom.preprocess.utils import (
+    PreprocessImageOpts2DOnlyWholeReference,
+)
+from orangecontrib.snom.widgets.preprocessors.registry import preprocess_image_editors
+
+
+class SelfRef(PreprocessImageOpts2DOnlyWholeReference):
+    def __init__(self, reference):
+        self.reference = reference
+        if self.reference is None:
+            raise MissingReferenceException("Self-referencing needs a reference")
+
+    def transform_image(self, image, ref_image, data):
+        d = SelfReference(referencedata=ref_image).transform(image)
+        return d
+
+
+class SelfRefEditor(BaseEditorOrange):
+    name = "Self-referencing"
+    qualname = "orangecontrib.snom.self_reference"
+
+    def __init__(self, parent=None, **kwargs):
+        super().__init__(parent, **kwargs)
+
+        self.reference = None
+
+        form = QFormLayout()
+        self.reference_info = QLabel("Reference data from input!")
+        form.addRow(self.reference_info)
+        self.controlArea.setLayout(form)
+
+    def activateOptions(self):
+        pass  # actions when user starts changing options
+
+    def setParameters(self, params):
+        self.update_reference_info()
+
+    def set_reference_data(self, reference):
+        self.reference = reference
+        self.update_reference_info()
+
+    def update_reference_info(self):
+        if not self.reference:
+            self.reference_info.setText("Reference: missing!")
+            self.reference_info.setStyleSheet("color: red")
+        else:
+            rinfo = "Reference order: N"
+            self.reference_info.setText(rinfo)
+            self.reference_info.setStyleSheet("color: black")
+
+    @classmethod
+    def createinstance(cls, params):
+        params = dict(params)
+        reference = params.get(REFERENCE_DATA_PARAM, None)
+        return SelfRef(reference=reference)
+
+    def set_preview_data(self, data):
+        if data:
+            pass  # TODO any settings
+
+
+preprocess_image_editors.register(SelfRefEditor, 400)