[unit test] fix unit test for guessing shift

- now OverwritingOperation can set data_flatten but not data. Might evolve, it depends how we saw things.

id06workflow/app/test_.py

@@ -151,7 +151,7 @@ def main(argv):
     test_suite = unittest.TestSuite()
     test_suite.addTest(id06workflow.test.suite())
     import orangecontrib.id06workflow.test
-    test_suite.addTest(orangecontrib.id06workflow.test)
+    test_suite.addTest(orangecontrib.id06workflow.test.suite())
     result = runner.run(test_suite)
 
     if result.wasSuccessful():

id06workflow/core/experiment/__init__.py

@@ -193,8 +193,8 @@ class Experiment(object):
             self.__data = self.getRawData()
         return self.__data
 
-    @data.setter
-    def data(self, data):
+    @data_flatten.setter
+    def data_flatten(self, data):
         assert data.ndim > 2
         self.__data = data.reshape(-1, data.shape[-2], data.shape[-1])
 

id06workflow/core/experiment/operation/__init__.py

@@ -63,6 +63,12 @@ class _BaseOperation(qt.QObject):
         data.setflags(write=self._can_overwrite_data)
         return data
 
+    @property
+    def data_flatten(self):
+        data_flatten = self._experiment.data_flatten.view()
+        data_flatten.setflags(write=self._can_overwrite_data)
+        return data_flatten
+
     @property
     def experiment(self):
         return self._experiment
@@ -97,9 +103,9 @@ class OverwritingOperation(_BaseOperation):
     def __init__(self, experiment, name):
         _BaseOperation.__init__(self, experiment, name, can_overwrite_data=True)
 
-    @_BaseOperation.data.setter
-    def data(self, data):
-        self._experiment.data = data
+    @_BaseOperation.data_flatten.setter
+    def data_flatten(self, data):
+        self._experiment.data_flatten = data
 
     def dry_run(self, cache_data=None):
         """

id06workflow/core/experiment/operation/roi.py

@@ -49,7 +49,7 @@ class RoiOperation(OverwritingOperation):
                          str(self._size)))
 
     def compute(self):
-        self.data = self._compute(self.data)
+        self.data_flatten = self._compute(self.data)
         self.registerOperation()
         return self.data
 
@@ -64,7 +64,7 @@ class RoiOperation(OverwritingOperation):
     def apply(self):
         if self._cache_data is None:
             raise ValueError('No data in cache')
-        self.data = self._cache_data
+        self.data_flatten = self._cache_data
         self.clear_cache()
         self.registerOperation()
         return self.data

id06workflow/core/experiment/operation/shift.py

@@ -55,7 +55,6 @@ class Shift(OverwritingOperation):
         OverwritingOperation.__init__(self, experiment, name='shift')
         if dz != 0:
             raise NotImplementedError('z shift not taken into account yet')
-        assert self.data_flatten.ndim is 3
         self.dx = dx
         self.dy = dy
         self.dz = dz
@@ -110,9 +109,10 @@ class Shift(OverwritingOperation):
         self._cache_data = None
 
     def _compute(self, data):
+        assert data.ndim is 3
         res = []
         nImg = data.shape[0]
-        for iImg, img in enumerate(self.data_flatten[:]):
+        for iImg, img in enumerate(data[:]):
             self.updateProgress(int(iImg / nImg * 100.0))
             _dx = self.dx * iImg
             _dy = self.dy * iImg

id06workflow/core/test/test_experiment.py

@@ -85,7 +85,7 @@ class TestExperiement(unittest.TestCase):
         back_sub_data = experiment.apply_background_subtraction()
         self.assertTrue(numpy.array_equal(back_sub_data[3], numpy.zeros(dims)))
 
-    @unittest.skipUnless(os.path.exists('/nobackup/linazimov/payno/dev/esrf/ID06/dataset/for_mapping'))
+    @unittest.skipUnless(os.path.exists('/nobackup/linazimov/payno/dev/esrf/ID06/dataset/for_mapping'), reason='Data files not available')
     def testMapping(self):
         # TODO: store datasets on the web and retrieve them using utils.getDataset()
         _dir = '/nobackup/linazimov/payno/dev/esrf/ID06/dataset/for_mapping'

id06workflow/core/test/test_image.py

@@ -76,13 +76,12 @@ class TestShift(unittest.TestCase):
 
         dataset = createDataset()
         _experiment = experiment.Experiment(dataset=dataset)
-        # print(image.guess_shift(data=_experiment.data_flatten, axis=0))
         res = (image.guess_shift(data=_experiment.data_flatten, axis=1,
                                  start=-0.0005, stop=0.0005, step=0.0001))
-        self.assertTrue(numpy.isclose(
-                image.guess_shift(data=_experiment.data_flatten, axis=0), res))
-        self.assertTrue(numpy.isclose(
-                image.guess_shift(data=_experiment.data_flatten, axis=1), 0.0))
+        self.assertTrue(numpy.isclose(res, -2.0e-04))
+        res = image.guess_shift(data=_experiment.data_flatten, axis=0,
+                                start=-1.0, stop=1.0, step=0.5)
+        self.assertTrue(numpy.isclose(res, 0.0))
 
 
 

id06workflow/gui/shifcorrection.py

@@ -91,6 +91,12 @@ class ShiftCorrectionWidget(qt.QWidget):
         # and show some information on advancement
         if self._operation_thread.isRunning() is True:
             _logger.error('Cannot process shift until the current one is finished')
+            return
+
+        if self._experiment is None:
+            _logger.error(
+                'Cannot process shift because no experiment has been set')
+            return
 
         _shift = self.getShift()
         if _shift == self._lastShift:

orangecontrib/id06workflow/test/test_workflows.py

@@ -134,6 +134,13 @@ class TestFirstSetup(OrangeWorflowTest):
         # manage shift correction
         self.assertTrue(self._shiftCorrectionWidget._editedExperiment is not None)
         self._shiftCorrectionWidget.setShift(dx=1.0, dy=-1.0, dz=0.0)
+        timeout = 10*1000 # timeout in millisec
+        waiting_time = 0
+        # wait for shift to be processed
+        while (self._shiftCorrectionWidget._widget._operation_thread.isRunning() and
+                       waiting_time < timeout):
+            self.qWait(200)
+            waiting_time += 200
         self._shiftCorrectionWidget.validate()
         self._moveToNextStep()
 
@@ -141,7 +148,6 @@ class TestFirstSetup(OrangeWorflowTest):
         self.assertTrue(self._noiseReductionWidget._editedExperiment is not None)
         self._noiseReductionWidget.validate()
         self._moveToNextStep()
-        # TODO: check value of the next input
 
         noise_reducted_data = self._saveWidget._editedExperiment.data
         self.assertTrue(noise_reducted_data.min() >= 0.2)