[core mapping] rework Intensity mapping too fit several dimension

id06workflow/core/experiment/__init__.py

@@ -325,21 +325,21 @@ class Experiment(object):
         self.__dims.clear()
         _fail = False, None  # register fail status and latest reason
         for axis, dim in dims.items():
-            if dim.size is None:
-                assert isinstance(dim, _Dim)
-                # try to deduce dimension size
-                try:
-                    unique_dim_value = metadatautils.getUnique(self,
-                                                               kind=dim.kind,
-                                                               key=dim.name,
-                                                               relative_prev_val=dim.relative_prev_val,
-                                                               cycle_length=dim.size,
-                                                               axis=axis)
-                except Exception as e:
-                    if _fail[0] is False:
-                        _fail = True, e
-                else:
+            try:
+                unique_dim_value = metadatautils.getUnique(self,
+                                                           kind=dim.kind,
+                                                           key=dim.name,
+                                                           relative_prev_val=dim.relative_prev_val,
+                                                           cycle_length=dim.size,
+                                                           axis=axis)
+            except Exception as e:
+                if _fail[0] is False:
+                    _fail = True, e
+            else:
+                if dim.size is None:
                     dim._setSize(size=len(unique_dim_value))
+                dim._setUniqueValues(unique_dim_value)
+
             self.__dims.add_dim(axis=axis, dim=dim)
 
         if _fail[0] is True:
@@ -390,6 +390,10 @@ class AcquisitionDims(object):
                                      kind=self.__dims[axis].kind,
                                      size=size)
 
+    def __iter__(self):
+        for iAxis, dim in self.__dims.items():
+            yield (iAxis, dim)
+
 
 class _Dim(object):
     def __init__(self, kind, name, size=None, relative_prev_val=False):
@@ -418,6 +422,8 @@ class _Dim(object):
         self.__name = name
         self._size = size
         self.__relative_prev_val = relative_prev_val
+        self.__unique_values = []
+        """Ordered values through the dimension"""
 
     @property
     def kind(self):
@@ -450,3 +456,16 @@ class _Dim(object):
                 (see :class:`_DimensionItem`) 
         """
         self._size = size
+
+    @property
+    def unique_values(self):
+        return self.__unique_values
+
+    def _setUniqueValues(self, values):
+        if len(values) != self.size:
+            _logger.warning('Unique values set for %s, is incoherent with size' % self)
+            raise ValueError('Unique values set for %s, is incoherent with size' % self)
+        self.__unique_values = values
+
+    def __str__(self):
+        return " ".join((str(self.kind), str(self.name), 'size:', str(self.size)))

id06workflow/core/experiment/operation/com.py

@@ -62,7 +62,7 @@ class COM(AdditiveOperation):
         assert self._map.ndim is 1
         self.__maps = []
 
-        for dim in self._map.dim:
+        for dim in self._map.dims:
             _map1 = dim[:, :, 0]
             _map1 = _map1 - numpy.nan_to_num(_map1.mean())
 

id06workflow/core/experiment/operation/mapping.py

@@ -29,12 +29,17 @@ __license__ = "MIT"
 __date__ = "15/10/2018"
 
 from . import AdditiveOperation
+from collections import namedtuple
 import numpy
 import logging
 
 _logger = logging.getLogger(__file__)
 
 
+_IMap = namedtuple('_IMap', ['name', 'kind', 'mean', 'variance', 'skewness',
+                             'kurtosis'])
+
+
 class _MappingBase(AdditiveOperation):
     """
     Base class used for mapping
@@ -73,7 +78,8 @@ class IntensityMapping(_MappingBase):
             self._threshold = threshold
 
         self.__intensity_map = None
-        self.__dim = []
+        self.__dim = {}
+        """Associate to each dimension the _IMap"""
 
     def key(self):
         return self.KEY
@@ -85,18 +91,15 @@ class IntensityMapping(_MappingBase):
             _logger.warning('Experiment as no data defined, unable to apply'
                             'mapping')
             return None
-        elif self._experiment.geometry is None:
-            _logger.warning('No geometry defined to apply mapping')
-            return None
         else:
-            assert self.data.ndim is 3
+            assert self.data.ndim > 2
 
             # TODO: avoid recomputing several time the intensity map
             self._resetIntensityMap()
             self._resetDim()
-            for x in range(self.data.shape[2]):
+            for x in range(self.data.shape[-1]):
                 self.updateProgress(int(x / self.data.shape[2] * 100.0))
-                for y in range(self.data.shape[1]):
+                for y in range(self.data.shape[-2]):
                     # TODO: do this operation using a grid or something close
                     # but would have to find a way to write at the same position...
                     reciprocalVol = numpy.squeeze(self.data[:, y, x])
@@ -106,25 +109,21 @@ class IntensityMapping(_MappingBase):
                         self.__intensity_map[y, x] = maxIntensity
                         # Here: TODO, later when can have several dimension (motors scanned/rockers)
                         # do it for all dims
-                        for iDim in range(self._experiment.ndim):
+                        for axis, dim in self._experiment.dims:
                             intensity = numpy.squeeze(reciprocalVol.sum())
                             # TODO: move calculation of angle_mean, angle_variance,
-                            # angle_skewness, angle_kurtosis in :class:`Experiment`
-                            angles = self._experiment.angles
+                            dim_unique_values = self.expriment.get_unique_values(axis)
                             # TODO: why mean is obtained by the sum ?
                             # angles_mean = (intensity * angles).mean()
-                            angles_mean = (intensity * angles).sum()
-                            angles_variance = (
-                                intensity * (angles - angles_mean) ** 2).sum()
-                            angles_skewness = (
-                                intensity * (angles - angles_mean) ** 3).sum()
-                            angles_kurtosis = (
-                                intensity * (angles - angles_mean) ** 4).sum()
-                            # TODO: pb, this is overwritten at each image if maxIntensity > threshold ???
-                            self.dim[iDim][y, x, 0] = angles_mean
-                            self.dim[iDim][y, x, 1] = angles_variance
-                            self.dim[iDim][y, x, 2] = angles_skewness
-                            self.dim[iDim][y, x, 3] = angles_kurtosis
+                            _mean = (intensity * dim_unique_values).sum()
+                            diff = (dim_unique_values - _mean)
+                            _variance = (intensity * diff ** 2).sum()
+                            _skewness = (intensity * diff ** 3).sum()
+                            _kurtosis = (intensity * diff ** 4).sum()
+                            self.dim[axis].mean[y, x] = _mean
+                            self.dim[axis].variance[y, x] = _variance
+                            self.dim[axis].skewness[y, x] = _skewness
+                            self.dim[axis].kurtosis[y, x] = _kurtosis
 
             self.registerOperation()
             return self.dim
@@ -133,9 +132,16 @@ class IntensityMapping(_MappingBase):
         self.__intensity_map = numpy.zeros(self.data.shape[1:])
 
     def _resetDim(self):
-        self.__dim = []
-        for dim in range(self._experiment.ndim):
-            self.__dim.append(numpy.zeros((*(self.data.shape[1:]), 4)))
+        self.__dim = {}
+        for axis, dim in self._experiment.dims:
+            _map = _IMap(
+                    name=dim.name,
+                    kind=dim.kind,
+                    mean=numpy.zeros((self.data.shape[-2:])),
+                    variance=numpy.zeros((self.data.shape[-2:])),
+                    skewness=numpy.zeros((self.data.shape[-2:])),
+                    kurtosis=numpy.zeros((self.data.shape[-2:])))
+            self.__dim[axis] = _map
 
     @property
     def intensity_map(self):
@@ -192,7 +198,7 @@ class GradientRemoval(_MappingBase):
         # TODO: if necessary compute mean...
 
         for iDim in range(mapping.ndim):
-            gradient = mapping.dim[iDim][...]
+            gradient = mapping.dims[iDim][...]
 
             # TODO: for now gradient corrcetion is only apply on mean, why ?
             # TODO: this should be in enumerate(Mode) but intensity is stored

id06workflow/core/mapping.py

@@ -32,10 +32,10 @@ MEAN = 'mean'
 
 VARIANCE = 'variance'
 
-SKENESS = 'skeness'
+SKEWNESS = 'skewness'
 
 KURTOSIS = 'kurtosis'
 
 INTENSITY = 'intensity'
 
-MODES = (MEAN, VARIANCE, SKENESS, KURTOSIS, INTENSITY)
+MODES = (MEAN, VARIANCE, SKEWNESS, KURTOSIS, INTENSITY)

id06workflow/core/test/test_geometry.py

@@ -34,13 +34,13 @@ from id06workflow.core.geometry.TwoThetaGeometry import TwoThetaGeometry
 
 class TestTwoThetaExpSetup(unittest.TestCase):
     """
-    Test that RefCopy process is correct
+    Test the :class:`TwoThetaGeometry`
     """
 
     def testCreation(self):
         """
         Some stupid test to make sur TwoThetaExpSetup is correctly
-        instanciated
+        instantiated
         """
         exp_setup = TwoThetaGeometry(orientation=TwoThetaGeometry.VERTICAL)
         self.assertTrue(exp_setup.orientation == TwoThetaGeometry.VERTICAL)

id06workflow/core/test/test_mapping.py

+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["H. Payno"]
+__license__ = "MIT"
+__date__ = "03/10/2018"
+
+
+import unittest
+import os
+from id06workflow.core.experiment.operation.mapping import IntensityMapping
+from id06workflow.core.experiment import Experiment, Dataset, POSITIONER_METADATA, _Dim
+from id06workflow.core.geometry.TwoThetaGeometry import TwoThetaGeometry
+
+
+@unittest.skipIf(os.path.exists('/nobackup/linazimov/payno/datasets/id06/strain_scan') is False, reason='data files not available')
+class TestMappingOperation(unittest.TestCase):
+    """
+    Test Mapping operation.
+    """
+
+    def setUp(self):
+        unittest.TestCase.setUp(self)
+        # define experiment data
+        root_folder = '/nobackup/linazimov/payno/datasets/id06/strain_scan'
+        data_file_pattern = os.path.join(root_folder, 'reduced_strain/strain_0000.edf')
+        assert os.path.exists(data_file_pattern)
+        data_bb_files = []
+        bb_folder = os.path.join(root_folder, 'bg_ff_5s_1x1')
+        for _file in os.listdir(bb_folder):
+            data_bb_files.append(os.path.join(bb_folder, _file))
+        self.dataset = Dataset(data_files_pattern=data_file_pattern,
+                               ff_files=data_bb_files)
+
+        # define geometry
+        geometry = TwoThetaGeometry(
+                twotheta=0.03, # for now those are defined in degree but should
+                # be defined in radians
+                xmag=1.0, # what is the unit of this ?
+                xpixelsize=1.0,
+                ypixelsize=1.0,
+                orientation=TwoThetaGeometry.VERTICAL)
+
+        # define experiment
+        self.experiment = Experiment(dataset=self.dataset, geometry=geometry)
+
+        # define dimensions
+        dim1 = _Dim(kind=POSITIONER_METADATA, name='diffry',
+                    relative_prev_val=True, size=31)
+        dim2 = _Dim(kind=POSITIONER_METADATA, name='obpitch')
+        self.experiment.set_dims(dims={0: dim1, 1: dim2})
+
+    def testIntensityMapping(self):
+        """
+        Test IntensityMapping operation
+        """
+        operation = IntensityMapping(experiment=self.experiment)
+        res = operation.compute()
+        self.assertTrue(len(res) is 2)
+        self.assertTrue(res[0].name == 'diffry')
+        self.assertTrue(res[0].kind == POSITIONER_METADATA)
+        self.assertTrue(res[1].name == 'obpitch')
+        self.assertTrue(res[1].kind == POSITIONER_METADATA)
+        self.assertTrue(res[0].mean.shape == (2048, 2048))
+        self.assertTrue(res[0].variance.shape == (2048, 2048))
+        self.assertTrue(res[0].skewness.shape == (2048, 2048))
+        self.assertTrue(res[0].kurtosis.shape == (2048, 2048))
+        self.assertTrue(res[1].mean.shape == (2048, 2048))
+
+
+def suite():
+    test_suite = unittest.TestSuite()
+    for ui in (TestMappingOperation, ):
+        test_suite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(ui))
+    return test_suite
+
+
+if __name__ == '__main__':
+    unittest.main(defaultTest="suite")

id06workflow/gui/com.py

@@ -65,7 +65,7 @@ class ComWidget(qt.QWidget):
         dim = self._control.getDim()
         _iMap = self._control.getMapType()
         if dim >= 0:
-            # TODO: maps[dim] should be also a list with key values: 'value',
+            # 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)
@@ -94,7 +94,7 @@ class _ComControlWidget(qt.QWidget):
     def __init__(self, parent=None):
         qt.QWidget.__init__(self, parent)
         self.setLayout(qt.QHBoxLayout())
-        self.layout().addWidget(qt.QLabel('dim:', parent=self))
+        self.layout().addWidget(qt.QLabel('dims:', parent=self))
         self._dim = qt.QComboBox(parent=self)
         self.layout().addWidget(self._dim)
         self.layout().addWidget(qt.QLabel('map type:', parent=self))

id06workflow/gui/mapping.py

@@ -31,7 +31,7 @@ __date__ = "10/10/2018"
 from silx.gui import qt
 from silx.gui.plot import Plot2D
 from id06workflow.gui import icons
-from id06workflow.core.mapping import MEAN, VARIANCE, SKENESS, KURTOSIS, MODES, INTENSITY
+from id06workflow.core.mapping import MEAN, VARIANCE, SKEWNESS, KURTOSIS, MODES, INTENSITY
 from id06workflow.core.experiment.operation.mapping import _MappingBase
 from id06workflow.gui.settings import DEFAULT_COLORMAP
 from collections import OrderedDict
@@ -48,6 +48,7 @@ class MappingPlot(qt.QMainWindow):
     """
     def __init__(self, parent=None):
         qt.QMainWindow.__init__(self, parent)
+        self._operation = None
         self.setWindowFlags(qt.Qt.Widget)
 
         self._plot = Plot2D(parent=self)
@@ -57,7 +58,7 @@ class MappingPlot(qt.QMainWindow):
         self._data = {
             MEAN: None,
             VARIANCE: None,
-            SKENESS: None,
+            SKEWNESS: None,
             KURTOSIS: None,
             INTENSITY: None
         }
@@ -65,6 +66,12 @@ class MappingPlot(qt.QMainWindow):
 
         # deal with toolbar
         self._modesToolbar = qt.QToolBar(parent=self)
+        _axis_widget = qt.QWidget(parent=self)
+        _axis_widget.setLayout(qt.QHBoxLayout())
+        self._dimCB = qt.QComboBox(parent=_axis_widget)
+        _axis_widget.layout().addWidget(qt.QLabel('dims:', self))
+        _axis_widget.layout().addWidget(self._dimCB)
+        # self._modesToolbar.addWidget(_axis_widget)
         self._intensityAction = None
         self._meanAction = None
         self._varianceAction = None
@@ -74,7 +81,7 @@ class MappingPlot(qt.QMainWindow):
             (INTENSITY, self._intensityAction),
             (MEAN, self._meanAction),
             (VARIANCE, self._varianceAction),
-            (SKENESS, self._skenessAction),
+            (SKEWNESS, self._skenessAction),
             (KURTOSIS, self._kurtosisAction),
         ])
 
@@ -86,10 +93,16 @@ class MappingPlot(qt.QMainWindow):
             action.changed.connect(callback)
             self._modesToolbar.addAction(action)
             self._actions[mode] = action
-        self._modesToolbar.setIconSize(qt.QSize(50, 50))
+            if mode == INTENSITY:
+                self._modesToolbar.addWidget(_axis_widget)
+
+        self._modesToolbar.setIconSize(qt.QSize(70, 70))
         self._plot.addToolBar(qt.Qt.LeftToolBarArea, self._modesToolbar)
         self.setMode(INTENSITY)
 
+        # connect signal / SLOT
+        self._dimCB.currentIndexChanged.connect(self._updatePlot)
+
     def setMode(self, mode):
         """
         Change the display mode
@@ -107,11 +120,18 @@ class MappingPlot(qt.QMainWindow):
 
     def _updatePlot(self):
         self._plot.clear()
+        if self._operation is None:
+            return
         mode = self._getMode()
-        if self._data[mode] is not None:
-            self._plot.addImage(self._data[mode])
+        dim = self._getDim()
+
+        assert dim in self._operation.dims
+        if mode == INTENSITY:
+            data = self._operation.intensity_map
         else:
-            self._plot.clear()
+            assert hasattr(self._operation.dims[dim], mode)
+            data = getattr(self._operation.dims[dim], mode)
+        self._plot.addImage(data)
 
     def _getMode(self):
         for action_mode, action in self._actions.items():
@@ -119,18 +139,38 @@ class MappingPlot(qt.QMainWindow):
                 return action_mode
         return None
 
+    def _getDim(self):
+        """
+
+        :return: dimension the user want to display
+        :rtype: int or None
+        """
+        if self._dimCB.size() is 0 or self._dimCB.currentText() == "":
+            return None
+        else:
+            return int(self._dimCB.currentText())
+
     def setOperation(self, operation):
-        self._data[MEAN] = self._data[VARIANCE] = None
-        self._data[SKENESS] = self._data[KURTOSIS] = None
+        self._operation = operation
 
-        if operation is not None:
+        if operation is not None and operation.ndim > 0:
             assert isinstance(operation, _MappingBase)
-            self._data[INTENSITY] = operation.intensity_map
-            self._data[MEAN] = operation.dim[0][:, :, 0]
-            self._data[VARIANCE] = operation.dim[0][:, :, 1]
-            self._data[SKENESS] = operation.dim[0][:, :, 2]
-            self._data[KURTOSIS] = operation.dim[0][:, :, 3]
-
+            self._updateAxis()
+            self._updatePlot()
+
+    def _updateAxis(self):
+        self._dimCB.blockSignals(True)
+        self._dimCB.clear()
+        if self._operation is None:
+            return
+        current_dim = self._getDim()
+        for dim in self._operation.dims:
+            self._dimCB.addItem(str(dim))
+
+        idx = self._dimCB.findText(current_dim)
+        if idx >= 0:
+            self._dimCB.setCurrentIndex(idx)
+        self._dimCB.blockSignals(False)
         self._updatePlot()
 
 

id06workflow/gui/shifcorrection.py

@@ -133,7 +133,7 @@ class ShiftCorrectionWidget(qt.QWidget):
         self._rawData = self._operation.data
         self._lastShift = (0, 0, 0)
         self._stack.setStack(self._operation.data_flatten)
-        self._sumPlot.addImage(self._operation.data.sum(axis=0))
+        self._sumPlot.addImage(self._operation.data_flatten.sum(axis=0))
         self._updateShift()
 
     def getOperation(self):

id06workflow/gui/test/__init__.py

@@ -30,6 +30,7 @@ __date__ = "29/05/2017"
 import unittest
 from . import test_geometry_gui
 from . import test_dimension_gui
+from . import test_mapping_gui
 
 
 def suite():
@@ -37,5 +38,6 @@ def suite():
     test_suite.addTests([
         test_geometry_gui.suite(),
         test_dimension_gui.suite(),
+        test_mapping_gui.suite(),
     ])
     return test_suite

id06workflow/gui/test/test_mapping_gui.py

+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+
+__authors__ = ["H. Payno"]
+__license__ = "MIT"
+__date__ = "03/10/2018"
+
+
+import unittest
+import os
+from id06workflow.core.experiment.operation.mapping import IntensityMapping
+from id06workflow.gui.mapping import MappingPlot
+from id06workflow.core.experiment import Experiment, Dataset, POSITIONER_METADATA, _Dim
+from id06workflow.core.geometry.TwoThetaGeometry import TwoThetaGeometry
+from silx.gui.utils.testutils import TestCaseQt
+from silx.gui import qt
+
+app = qt.QApplication.instance() or qt.QApplication([])
+
+# TODO: do it with TestCaseQt
+@unittest.skipIf(os.path.exists('/nobackup/linazimov/payno/datasets/id06/strain_scan') is False, reason='data files not available')
+class TestMappingOperation(unittest.TestCase):
+    """
+    Test Mapping operation.
+    """
+
+    def setUp(self):
+        unittest.TestCase.setUp(self)
+        # define experiment data
+        root_folder = '/nobackup/linazimov/payno/datasets/id06/strain_scan'
+        data_file_pattern = os.path.join(root_folder, 'reduced_strain/strain_0000.edf')
+        assert os.path.exists(data_file_pattern)
+        data_bb_files = []
+        bb_folder = os.path.join(root_folder, 'bg_ff_5s_1x1')
+        for _file in os.listdir(bb_folder):
+            data_bb_files.append(os.path.join(bb_folder, _file))
+        self.dataset = Dataset(data_files_pattern=data_file_pattern,
+                               ff_files=data_bb_files)
+
+        # define geometry
+        geometry = TwoThetaGeometry(
+                twotheta=0.03, # for now those are defined in degree but should
+                # be defined in radians
+                xmag=1.0, # what is the unit of this ?
+                xpixelsize=1.0,
+                ypixelsize=1.0,
+                orientation=TwoThetaGeometry.VERTICAL)
+
+        # define experiment
+        self.experiment = Experiment(dataset=self.dataset, geometry=geometry)
+
+        # define dimensions
+        dim1 = _Dim(kind=POSITIONER_METADATA, name='diffry',
+                    relative_prev_val=True, size=31)
+        dim2 = _Dim(kind=POSITIONER_METADATA, name='obpitch')
+        self.experiment.set_dims(dims={0: dim1, 1: dim2})
+
+        self._widget = MappingPlot(parent=None)
+
+    def tearDown(self):
+        self._widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self._widget.close()
+        unittest.TestCase.tearDown(self)
+
+    def testIntensityMapping(self):
+        """
+        Test IntensityMapping operation
+        """
+        operation = IntensityMapping(experiment=self.experiment)
+        operation.compute()
+        self._widget.setOperation(operation)
+
+
+def suite():
+    test_suite = unittest.TestSuite()
+    for ui in (TestMappingOperation, ):
+        test_suite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(ui))
+    return test_suite
+
+
+if __name__ == '__main__':
+    unittest.main(defaultTest="suite")

id06workflow/test/utils.py

@@ -79,7 +79,7 @@ def createDataset(pattern, background, dx=0, dy=0, dz=0, nb_data_files=10,
     """
     Create a dataset from a configuration
 
-    :param tuple of int dims: image dim
+    :param tuple of int dims: image dims
     :param numpy.ndarray pattern: pattern of the image
     :param numpy.ndarray background: noise to add to the image (detector noise)
     :param float dx: x translation between each image

orangecontrib/id06workflow/widgets/dimensions.py

@@ -101,8 +101,8 @@ class DimensionOW(OWWidget):
     def validate(self):
         succeed, msg = self._widget.fit()
         if succeed is False:
-            qt.QMessageBox.warning('Fail dataset dimension definition',
-                                   'Fail to define coherent diemnsion values. Reason is %s' % msg)
+            qt.QMessageBox.warning(self, 'Fail dataset dimension definition',
+                                   ''.join(('Fail to define coherent dimension values. Reason is ', str(msg))))
         else:
             self.send("data", self._widget.experiment)
             OWWidget.accept(self)

orangecontrib/id06workflow/widgets/mapping.py

@@ -96,13 +96,13 @@ class MappingOW(OWWidget):
         self.send("image",
                   _Image(img=operation.intensity_map, name='intensity_map'))
         self.send("image",
-                  _Image(img=operation.dim[0][:, :, 0], name='mean'))
+                  _Image(img=operation.dims[0][:, :, 0], name='mean'))
         self.send("image",
-                  _Image(img=operation.dim[0][:, :, 1], name='variance'))
+                  _Image(img=operation.dims[0][:, :, 1], name='variance'))
         self.send("image",
-                  _Image(img=operation.dim[0][:, :, 2], name='skeness'))
+                  _Image(img=operation.dims[0][:, :, 2], name='skeness'))
         self.send("image",
-                  _Image(img=operation.dim[0][:, :, 3], name='kurtosis'))
+                  _Image(img=operation.dims[0][:, :, 3], name='kurtosis'))
         self._plot.setOperation(operation)
 
         self.send("data", experiment)

test_real_dataset.py

@@ -42,7 +42,7 @@ logging.disable(logging.INFO)
 app = qt.QApplication.instance() or qt.QApplication([])
 
 
-@unittest.skipIf(os.path.exists('/users/payno/datasets/id06/strain_scan'))
+@unittest.skipIf(os.path.exists('/nobackup/linazimov/payno/datasets/id06/strain_scan') is False, reason='Data files not available')
 class TestTrueData(OrangeWorflowTest):
     """
     Create dummy workflow just to make sure all the widget can interact together
@@ -103,19 +103,22 @@ class TestTrueData(OrangeWorflowTest):
         OrangeWorflowTest.tearDown(self)
 
     def createDataset(self):
-        data_file_pattern = '/users/payno/datasets/id06/strain_scan/reduced_strain/strain_0000.edf'
+        root_folder = '/nobackup/linazimov/payno/datasets/id06/strain_scan'
+        data_file_pattern = os.path.join(root_folder, 'reduced_strain/strain_0000.edf')
         assert os.path.exists(data_file_pattern)
-
-        ff_files = []
-        dir_ff = "/users/payno/datasets/id06/strain_scan/bg_ff_5s_1x1/"
-        [ff_files.append(os.path.join(dir_ff, _file)) for _file in os.listdir(dir_ff)]
+        data_bb_files = []
+        bb_folder = os.path.join(root_folder, 'bg_ff_5s_1x1')
+        for _file in os.listdir(bb_folder):
+            data_bb_files.append(os.path.join(bb_folder, _file))
+        self.dataset = Dataset(data_files_pattern=data_file_pattern,
+                               ff_files=data_bb_files)
 
         dim1 = _Dim(kind=POSITIONER_METADATA, name='diffry',
                     relative_prev_val=True, size=31)
         dim2 = _Dim(kind=POSITIONER_METADATA, name='obpitch')
         self._dims = {0: dim1, 1: dim2}
 
-        return Dataset(data_files_pattern=data_file_pattern, ff_files=ff_files)
+        return self.dataset