implement subtract dark

zUtil_Python/pydct/orangecontrib/pydct/widgets/roi_selection.py

@@ -159,7 +159,7 @@ class ROISelectionWidget(qt.QWidget):
     def apply(self):
         """
         Function that replaces the dataset data with the data shown in the stack of images.
-        If the stack has a roi applied, it applies the same roi to the dark frames of the dataset.
+        If the stack has a roi applied, it applies the same roi to the data frames of the dataset.
         Signal emitted with the roi parameters.
         """
         if self.roi:

zUtil_Python/pydct/orangecontrib/pydct/widgets/subtract_dark.py

@@ -2,4 +2,104 @@
 
 import logging
 
+import numpy as np
+from numpy import ndarray
+from Orange.widgets import gui, settings, widget
+from Orange.widgets.utils.signals import Input, Output
+from Orange.widgets.widget import OWWidget
+from silx.gui.qt import QThread
+
 _logger = logging.getLogger("orangecontrib.pydct")
+
+
+class SubtractDarkThread(QThread):
+    """todo doc SubtractDarkThread"""
+
+    def __init__(self, parent, data, dark):
+        super().__init__(parent=parent)
+        self.data = data
+        self.dark = dark
+        self.data_processed = None
+
+    def run(self):
+        self.data_processed = self.data - self.dark
+
+
+class SubtractDark(OWWidget):
+
+    name = "subtract dark"
+    description = "Subtract the dark frame (z-length = 1) from all frames of dataset."
+    icon = "icons/subtract-dark.svg"  # todo get an icon
+
+    want_main_area = False
+    resizing_enabled = True
+
+    class Inputs:
+        data = Input("data", ndarray)
+        dark = Input("dark", ndarray)
+
+    class Outputs:
+        data = Output("data", ndarray)
+
+    def __init__(self):
+        super().__init__()
+        self.dark = None
+        self.data = None
+        self._computing = False
+        self.information("waiting for inputs")
+
+    @Inputs.data
+    def set_data(self, data):
+        # todo add validations here
+        self.data = data
+        self.information("needs to update")
+        self._update()
+
+    @Inputs.dark
+    def set_dark(self, dark):
+        # todo add validations here
+        self.dark = dark
+        self.information("needs to update")
+
+        if dark is not None:
+
+            nz, nx, ny = self.dark.shape
+
+            if nz != 1:
+                self.error("please squeeze the dark image on the z-axis first (use zwise median)")
+                return
+
+        self._update()
+
+    def _update(self):
+        _logger.debug("updating")
+
+        if self._computing:
+            _logger.warning("already updating")
+            return
+
+        if self.data is None or self.dark is None:
+            _logger.debug("still missing an input")
+            return
+
+        self._thread = SubtractDarkThread(parent=self, data=self.data, dark=self.dark)
+        self._thread.finished.connect(self._send_signal)
+
+        _logger.debug("computing dark subtraction")
+        self._computing = True
+        self.information("computing...")
+
+        self._thread.start()
+
+    def _send_signal(self):
+        self._thread.finished.disconnect(self._send_signal)
+        self._computing = False
+
+        _logger.info("done with dark subtraction")
+        self.information("done")
+
+        if self._thread.data_processed is not None:
+            self.Outputs.data.send(self._thread.data_processed)
+
+        else:
+            self.error("something went wrong and the thread did not return the dark correctly")

zUtil_Python/pydct/orangecontrib/pydct/widgets/zwise_median.py

@@ -28,7 +28,7 @@ class ZwiseMedianThread(QThread):
 class ZwiseMedian(OWWidget):
     """todo docstring of ZwiseMedian"""
 
-    name = "Z-wise median"
+    name = "z-wise median"
     description = (
         "Squeeze a volume on the z-axis to get a single frame where each pixel is the median of its position on the input."
     )