[core][process][noiseremoval] Add step and chunks properties

darfix/core/process.py

@@ -41,6 +41,7 @@ from silx.gui import qt
 from darfix.core import utils
 from darfix.gui.blindSourceSeparationWidget import Method
 from darfix.gui.grainPlotWidget import GrainPlotWidget
+from darfix.gui.rsmWidget import PixelSize
 
 _input_desc = namedtuple("_input_desc", ["name", "type", "handler", "doc"])
 
@@ -73,14 +74,17 @@ class _NoiseRemoval:
         dataset, indices, li_indices, bg_dataset = dataset
         method = self._properties['method'] if 'method' in self._properties else ''
         background_type = self._properties['background_type'] if 'background_type' in self._properties else ''
+        step = int(self._properties['step']) if 'step' in self._properties and self._properties['step'] != '' else None
+        chunks = self._properties['chunks'] if 'chunks' in self._properties and self._properties['chunks'] else None
         bg = None
         if background_type == "Dark data":
             bg = bg_dataset
         elif background_type == "Low intensity data":
             bg = li_indices
         size = self._properties['kernel_size'] if 'kernel_size' in self._properties else ''
+        print(step, chunks)
         if method != '':
-            dataset = dataset.apply_background_subtraction(indices=indices, method=method, background=bg)
+            dataset = dataset.apply_background_subtraction(indices=indices, method=method, background=bg, step=step, chunk_shape=chunks)
         if size != '':
             dataset = dataset.apply_hot_pixel_removal(indices=indices, kernel=int(size))
         return dataset, indices, li_indices, bg_dataset
@@ -262,3 +266,30 @@ class _GrainPlot:
         widget.show()
         app.exec_()
         return dataset
+
+
+class _Transformation:
+    inputs = [_input_desc(name='dataset', type=tuple, handler='process',
+                          doc='dataset to process'), ]
+
+    outputs = [
+        _output_desc(name='dataset', type=tuple, doc='dataset to process'), ]
+
+    def __init__(self):
+        self._properties = {}
+
+    def process(self, dataset):
+        dataset, indices, li_indices, bg_dataset = dataset
+        magnification = self._properties['magnification'] if 'magnification' in self._properties else None
+        pixelSize = self._properties['pixelSize'] if 'pixelSize' in self._properties else None
+        rotate = self._properties['rotate'] if 'rotate' in self._properties else None
+        if dataset and dataset.dims.ndim:
+            if dataset.dims.ndim == 1:
+                dataset.compute_transformation(PixelSize[pixelSize].value,
+                                               rotate)
+            else:
+                dataset.compute_transformation(magnification)
+        return dataset, indices, li_indices, bg_dataset
+
+    def set_properties(self, properties):
+        self._properties = properties