[com] rework operation.Com amd Com gui to work with n dim

id06workflow/core/operation/com.py

@@ -30,7 +30,7 @@ __date__ = "15/10/2018"
 
 
 from . import AdditiveOperation
-from .mapping import _MappingBase
+from .mapping import _MappingBase, _IMap
 from collections import namedtuple
 import numpy
 import logging
@@ -53,22 +53,22 @@ class COM(AdditiveOperation):
         AdditiveOperation.__init__(self, experiment=map.experiment,
                                    name=COM._NAME)
         self._map = map
-        self.__maps = []
+        self.__maps = {}
 
     def key(self):
         return COM._NAME
 
     def compute(self):
-        assert self._map.ndim is 1
-        self.__maps = []
-
-        for dim in self._map.dims:
-            _map1 = dim[:, :, 0]
-            _map1 = _map1 - numpy.nan_to_num(_map1.mean())
-
-            _map2 = dim[:, :, 1]
-            _map2 = _map2 - numpy.nan_to_num(_map2.mean())
-            self.__maps.append(_MapsCom(map1=_map1, map2=_map2))
+        self.__maps = {}
+        for axis, _map in self._map.dims.items():
+            assert _map.mean.ndim is 2
+            _mean = _map.mean - numpy.nan_to_num(_map.mean.mean())
+            _variance = _map.variance - numpy.nan_to_num(_map.variance.mean())
+            _skewness = _map.skewness - numpy.nan_to_num(_map.skewness.mean())
+            _kurtosis = _map.kurtosis - numpy.nan_to_num(_map.kurtosis.mean())
+            self.__maps[axis] = _IMap(name=_map.name, kind=_map.kind,
+                                      mean=_mean, variance=_variance,
+                                      skewness=_skewness, kurtosis=_kurtosis)
         self.registerOperation()
 
     @property

id06workflow/core/test/test_stream_operations.py

@@ -30,10 +30,9 @@ __date__ = "21/11/2018"
 
 import os
 import unittest
-
 from id06workflow.core.operation.mapping import IntensityMapping, \
     GradientRemoval
-
+from id06workflow.core.operation.com import COM
 from id06workflow.core.experiment import Dataset, POSITIONER_METADATA
 from id06workflow.core.experiment import Experiment, Dim
 from id06workflow.core.geometry.TwoThetaGeometry import TwoThetaGeometry
@@ -114,9 +113,9 @@ class TestOperationStream(unittest.TestCase):
         ope_intensity_map.compute()
         ope_gradient_removal = GradientRemoval(self.experiment)
         ope_gradient_removal.compute()
-        ope_intensity_map_2 = IntensityMapping(experiment=self.experiment)
-        ope_intensity_map_2.compute()
 
+        com_operation = COM(map=ope_gradient_removal)
+        com_operation.compute()
         # TODO: should be call at one moment if the 'project file' is not storing
         # each results
         # self.experiment.save('myProjectFile.h5')

id06workflow/gui/com.py

@@ -29,11 +29,11 @@ __date__ = "04/10/2018"
 
 
 import logging
-from collections import OrderedDict
 from silx.gui import qt
 from silx.gui.plot import Plot2D
-
+from id06workflow.core.mapping import MEAN, VARIANCE, SKEWNESS, KURTOSIS
 from id06workflow.core.operation.com import COM as COMOperation
+from id06workflow.gui.settings import DEFAULT_COLORMAP
 
 _logger = logging.getLogger(__file__)
 
@@ -48,6 +48,7 @@ class ComWidget(qt.QWidget):
         self._control = _ComControlWidget(parent=self)
         self.layout().addWidget(self._control)
         self._plot = Plot2D(parent=self)
+        self._plot.setDefaultColormap(DEFAULT_COLORMAP)
         self.layout().addWidget(self._plot)
 
         # connect signal
@@ -64,30 +65,20 @@ class ComWidget(qt.QWidget):
     def _update(self):
         self._plot.clear()
         dim = self._control.getDim()
-        _iMap = self._control.getMapType()
-        if dim >= 0:
-            # TODO: maps[dims] should be also a list with key values: 'value',
-            # 'mean', 'gradients' ...
-            if len(self._operation.maps[dim]) <= _iMap:
-                _logger.error('map of index %s has not been created' % _iMap)
-                self._plot.clear()
-                return
-            else:
-                _map = self._operation.maps[dim][_iMap]
-                self._plot.addImage(_map)
+        map_type = self._control.getMapType()
 
+        if dim is None:
+            return
 
-class _ComControlWidget(qt.QWidget):
+        self._plot.clear()
+        try:
+            _map = getattr(self._operation.maps[dim], map_type)
+            self._plot.addImage(_map)
+        except Exception as e:
+            _logger.error(e)
 
-    _COM_VALUE = 'com value'
-    _COM_VARIANCE = 'com mean variance'
-    _COM_GRADIENTS = 'com gradients'
 
-    _MAP_TYPES = OrderedDict([
-        (_COM_VALUE, 0),
-        (_COM_VARIANCE, 1),
-        (_COM_GRADIENTS, 2)
-    ])
+class _ComControlWidget(qt.QWidget):
 
     sigSelectionChanged = qt.Signal()
     """Signal emitted when the selection of the com change"""
@@ -102,9 +93,9 @@ class _ComControlWidget(qt.QWidget):
         self._map = qt.QComboBox(parent=self)
         self.layout().addWidget(self._map)
         # TODO: are those name correct ?
-        for map_type in (_ComControlWidget._MAP_TYPES):
+        for map_type in (MEAN, VARIANCE, SKEWNESS, KURTOSIS):
             self._map.addItem(map_type)
-        index = self._map.findText(_ComControlWidget._COM_VALUE)
+        index = self._map.findText(MEAN)
         assert index >= 0
         self._map.setCurrentIndex(index)
 
@@ -124,14 +115,12 @@ class _ComControlWidget(qt.QWidget):
     def getDim(self):
         currentDim = self._dim.currentText()
         if currentDim == '':
-            return -1
+            return None
         else:
             return int(currentDim)
 
     def getMapType(self):
-        currentMapType = self._map.currentText()
-        assert currentMapType in _ComControlWidget._MAP_TYPES
-        return _ComControlWidget._MAP_TYPES[currentMapType]
+        return self._map.currentText()
 
     def __selectionChanged(self, *args, **kwargs):
         self.sigSelectionChanged.emit()