[refactoring] move tomwer.core.experiment.operation to tomwer.core.operation

- also remove one outdated unit test

id06workflow/core/experiment/__init__.py

@@ -28,18 +28,20 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "01/10/2018"
 
+import logging
+from collections import OrderedDict
+from silx.io import fabioh5
+from silx.io.fabioh5 import FabioReader
+
+import numpy
+from id06workflow.core.operation import _BaseOperation
+from id06workflow.core.operation.datareduction import DataReduction
+
 from id06workflow.core.Dataset import Dataset
 from id06workflow.core.geometry import GeometryBase
 from id06workflow.core.geometry.TwoThetaGeometry import TwoThetaGeometry
-from id06workflow.core.experiment.operation import _BaseOperation
-from id06workflow.core.experiment.operation.roi import RoiOperation
-from id06workflow.core.experiment.operation.datareduction import DataReduction
-from collections import OrderedDict
+from id06workflow.core.operation.roi import RoiOperation
 from id06workflow.core.utils import metadata as metadatautils
-from silx.io.fabioh5 import FabioReader
-from silx.io import fabioh5
-import numpy
-import logging
 
 _logger = logging.getLogger(__file__)
 

id06workflow/core/test/test_experiment.py

@@ -42,79 +42,6 @@ class TestDataset(unittest.TestCase):
     pass
 
 
-class TestExperiement(unittest.TestCase):
-    """Test behavior of :class:Experiment"""
-
-    def testApplyThreshod(self):
-        """
-        Make sure the :func:`apply_threshold` is correctly applied
-        """
-        dims = (100, 100)
-        pattern = numpy.arange(dims[0]*dims[1]).reshape(dims)
-        background = numpy.zeros(dims)
-        dataset = utils.createDataset(_dir=tempfile.mkdtemp(),
-                                      pattern=pattern,
-                                      background=background,
-                                      nb_data_files=10)
-        experiment = Experiment(dataset=dataset)
-        thRes = pattern.copy()
-        thRes[thRes < 20.0] = 0.0
-        back_sub_data = experiment.apply_threshold(threshold=20, lower=True,
-                                                   replacement_value=0.0)
-        self.assertTrue(numpy.array_equal(back_sub_data[0], thRes))
-        thRes[thRes > 70.0] = 0.0
-        back_sub_data = experiment.apply_threshold(threshold=70, lower=False,
-                                                   replacement_value=0.0)
-        self.assertTrue(numpy.array_equal(back_sub_data[0], thRes))
-
-    def testApplyBackgroundSubstraction(self):
-        """
-        Make sure the :func:`apply_background_subtraction` is correctly applied
-        """
-        dims = (100, 100)
-        pattern = numpy.zeros(dims)
-        background = numpy.random.random(dims)
-        dataset = utils.createDataset(_dir=tempfile.mkdtemp(),
-                                      pattern=pattern,
-                                      background=background,
-                                      nb_data_files=10,
-                                      nb_flat_field_files=1)
-        experiment = Experiment(dataset=dataset)
-        back_sub_data = experiment.apply_background_subtraction()
-        self.assertTrue(numpy.array_equal(back_sub_data[2], numpy.zeros(dims)))
-        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'), 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'
-        files = []
-        [files.append(os.path.join(_dir, _file)) for _file in os.listdir(_dir)]
-        dataset = Dataset(data_files_pattern=files)
-        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)
-        experiment = Experiment(dataset=dataset, geometry=geometry)
-        experiment.roi = (750, 750), (600, 600)
-        dim = experiment.compute_dx2d_map()
-        self.assertTrue(dim is not None)
-        self.assertTrue(len(dim) is 1)
-        self.assertTrue(dim[0].shape == (274, 274, 4))
-
-        from id06workflow.gui.mapping import MappingPlot
-        from silx.gui import qt
-        app = qt.QApplication([])
-        widget = MappingPlot()
-        widget.setExperiment(experiment)
-        widget.show()
-        app.exec_()
-
-
 class TestAcquisitionDims(unittest.TestCase):
     """
     Test the AcquisitionDims API
@@ -137,7 +64,7 @@ class TestAcquisitionDims(unittest.TestCase):
 
 def suite():
     test_suite = unittest.TestSuite()
-    for ui in (TestDataset, TestAcquisitionDims):
+    for ui in (TestDataset, TestAcquisitionDims,):
         test_suite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(ui))
     return test_suite
 

id06workflow/core/test/test_mapping.py

@@ -28,11 +28,13 @@ __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
+import unittest
+
+from id06workflow.core.experiment import Experiment, Dataset, \
+    POSITIONER_METADATA, _Dim
 from id06workflow.core.geometry.TwoThetaGeometry import TwoThetaGeometry
+from id06workflow.core.operation.mapping import IntensityMapping
 
 
 @unittest.skipIf(os.path.exists('/nobackup/linazimov/payno/datasets/id06/strain_scan') is False, reason='data files not available')

id06workflow/core/test/test_mask.py

@@ -29,9 +29,11 @@ __date__ = "08/10/2018"
 
 
 import unittest
-from id06workflow.core.experiment.operation.noisereduction import MaskSubstraction
+
 import numpy
 
+from id06workflow.core.operation.noisereduction import MaskSubstraction
+
 
 class TestMask(unittest.TestCase):
     """

id06workflow/core/test/test_operation.py

@@ -28,13 +28,17 @@ __license__ = "MIT"
 __date__ = "03/10/2018"
 
 
+import shutil
+import tempfile
 import unittest
-from id06workflow.core.experiment.operation import OverwritingOperation, AdditiveOperation, shift
+
+import numpy
+from id06workflow.core.operation import OverwritingOperation, \
+    AdditiveOperation
+
 from id06workflow.core.experiment import Experiment
+from id06workflow.core.operation import shift
 from id06workflow.test import utils
-import shutil
-import numpy
-import tempfile
 
 
 class TestOperation(unittest.TestCase):
@@ -115,6 +119,7 @@ class TestShift(unittest.TestCase):
     def testPracticalResult(self):
         original_data = self.experiment.data.copy()
         operation = shift.Shift(self.experiment, dx=1.0, dy=-1.0, dz=0)
+
         shifted_data = operation.compute()
 
         self.assertTrue(numpy.allclose(original_data[1, :-1, 1:],

id06workflow/core/test/test_stream_operations.py

@@ -28,14 +28,17 @@ __license__ = "MIT"
 __date__ = "21/11/2018"
 
 
+import os
 import unittest
-from id06workflow.core.experiment import Experiment, Dataset, POSITIONER_METADATA
+
+from id06workflow.core.operation.mapping import IntensityMapping, \
+    GradientRemoval
+
+from id06workflow.core.experiment import Dataset, POSITIONER_METADATA
+from id06workflow.core.experiment import Experiment, _Dim
 from id06workflow.core.geometry.TwoThetaGeometry import TwoThetaGeometry
+from id06workflow.core.operation import noisereduction
 from id06workflow.core.utils import metadata as metadatautils
-from id06workflow.core.experiment.operation.mapping import IntensityMapping, GradientRemoval
-from id06workflow.core.experiment.operation import noisereduction
-from id06workflow.core.experiment import Experiment, _Dim
-import os
 
 
 @unittest.skipIf(os.path.exists('/nobackup/linazimov/payno/datasets/id06/strain_scan') is False, reason='data files not available')
@@ -105,7 +108,7 @@ class TestOperationStream(unittest.TestCase):
                                                             lower=True, threshold=0.2)
         ope_low_threshold.compute()
         ope_high_threshold = noisereduction.ThresholdRemoval(self.experiment,
-                                                            lower=False, threshold=10000.0)
+                                                             lower=False, threshold=10000.0)
         ope_high_threshold.compute()
         ope_intensity_map = IntensityMapping(experiment=self.experiment)
         ope_intensity_map.compute()

id06workflow/gui/com.py

@@ -28,11 +28,12 @@ __license__ = "MIT"
 __date__ = "04/10/2018"
 
 
+import logging
+from collections import OrderedDict
 from silx.gui import qt
 from silx.gui.plot import Plot2D
-from collections import OrderedDict
-from id06workflow.core.experiment.operation.com import COM as COMOperation
-import logging
+
+from id06workflow.core.operation.com import COM as COMOperation
 
 _logger = logging.getLogger(__file__)
 

id06workflow/gui/mapping.py

@@ -28,15 +28,17 @@ __license__ = "MIT"
 __date__ = "10/10/2018"
 
 
+import functools
+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, MODES, \
+    INTENSITY
+from id06workflow.core.operation.mapping import _MappingBase
 from id06workflow.gui import icons
-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
-import functools
-import logging
 
 _logger = logging.getLogger(__file__)
 

id06workflow/gui/noisereduction.py

@@ -28,15 +28,14 @@ __license__ = "MIT"
 __date__ = "05/10/2018"
 
 
+from collections import namedtuple
 from silx.gui import qt
 from silx.gui.plot.StackView import StackViewMainWindow
-from id06workflow.core.experiment.operation import noisereduction
-from id06workflow.gui.utils import _IllustrationWidget
-from collections import namedtuple
+
 from id06workflow.core.experiment import Experiment
+from id06workflow.core.operation import noisereduction
 from id06workflow.gui.settings import DEFAULT_COLORMAP
-import copy
-
+from id06workflow.gui.utils import _IllustrationWidget
 
 _ReconsParams = namedtuple('_ReconsParam', ['scale'])
 

id06workflow/gui/shifcorrection.py

@@ -28,15 +28,18 @@ __license__ = "MIT"
 __date__ = "08/10/2018"
 
 
+import logging
+from functools import partial
 from silx.gui import qt
 from silx.gui.plot import Plot2D
-from id06workflow.core.experiment.operation.shift import Shift as ShiftOperation
-from id06workflow.core.experiment.operation.ThreadedOperation import ThreadedOperation
-from id06workflow.core.image import guess_shift
 from silx.gui.plot.StackView import StackViewMainWindow
+
+from id06workflow.core.operation.ThreadedOperation import \
+    ThreadedOperation
+
+from id06workflow.core.image import guess_shift
+from id06workflow.core.operation.shift import Shift as ShiftOperation
 from id06workflow.gui.settings import DEFAULT_COLORMAP
-from functools import partial
-import logging
 
 _logger = logging.getLogger(__file__)
 

id06workflow/gui/test/test_mapping_gui.py

@@ -28,15 +28,16 @@ __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
+import unittest
 from silx.gui import qt
 
+from id06workflow.core.experiment import Experiment, Dataset, \
+    POSITIONER_METADATA, _Dim
+from id06workflow.core.geometry.TwoThetaGeometry import TwoThetaGeometry
+from id06workflow.core.operation.mapping import IntensityMapping
+from id06workflow.gui.mapping import MappingPlot
+
 app = qt.QApplication.instance() or qt.QApplication([])
 
 # TODO: do it with TestCaseQt

id06workflow/test/utils.py

@@ -27,12 +27,14 @@ __authors__ = ["H.Payno"]
 __license__ = "MIT"
 __date__ = "15/05/2017"
 
-import numpy
-import fabio
+import os
 import tempfile
+
+import fabio
+import numpy
+
 from id06workflow.core.experiment import Dataset
-from id06workflow.core.experiment.operation.mapping import _MappingBase
-import os
+from id06workflow.core.operation.mapping import _MappingBase
 
 
 def createRandomDataset(dims, nb_data_files=10, nb_dark_files=2,

orangecontrib/id06workflow/widgets/com.py

@@ -28,14 +28,17 @@ __license__ = "MIT"
 __date__ = "18/10/2018"
 
 
+import logging
+
+from Orange.canvas.registry.description import OutputSignal, InputSignal
 from Orange.widgets import gui
 from Orange.widgets.widget import OWWidget
-from Orange.canvas.registry.description import OutputSignal, InputSignal
+from id06workflow.core.operation.mapping import _MappingBase
+
 from id06workflow.core.experiment import Experiment
-from id06workflow.core.experiment.operation.mapping import _MappingBase
-from id06workflow.core.experiment.operation.com import COM as COMOperation
+from id06workflow.core.operation.com import COM as COMOperation
 from id06workflow.gui.com import ComWidget
-import logging
+
 _logger = logging.getLogger(__file__)
 
 

orangecontrib/id06workflow/widgets/gradientremoval.py

@@ -28,15 +28,16 @@ __license__ = "MIT"
 __date__ = "16/10/2018"
 
 
+from Orange.canvas.registry.description import InputSignal, OutputSignal
 from Orange.widgets import gui
 from Orange.widgets.widget import OWWidget
-from Orange.canvas.registry.description import InputSignal, OutputSignal
+
+from id06workflow.core.experiment import Experiment
 from id06workflow.core.experiment import _METADATA_TYPES_I
 from id06workflow.core.mapping import MEAN, VARIANCE, SKEWNESS, KURTOSIS
-from id06workflow.gui.mapping import MappingPlot
-from id06workflow.core.experiment import Experiment
-from id06workflow.core.experiment.operation.mapping import GradientRemoval, _MappingBase
+from id06workflow.core.operation.mapping import GradientRemoval, _MappingBase
 from id06workflow.core.types import _Image
+from id06workflow.gui.mapping import MappingPlot
 
 
 class GradientRemovalOW(OWWidget):

orangecontrib/id06workflow/widgets/mapping.py

@@ -27,18 +27,21 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "01/10/2018"
 
+import logging
+from functools import partial
+
+from Orange.canvas.registry.description import InputSignal, OutputSignal
 from Orange.widgets import gui
 from Orange.widgets.widget import OWWidget
-from Orange.canvas.registry.description import InputSignal, OutputSignal
+from id06workflow.core.operation.mapping import IntensityMapping, \
+    _MappingBase
+
 from id06workflow.core.experiment import Experiment
-from id06workflow.core.experiment.operation.mapping import IntensityMapping, _MappingBase
-from id06workflow.core.experiment.operation.ThreadedOperation import ThreadedOperation
-from id06workflow.core.mapping import MEAN, VARIANCE, SKEWNESS, KURTOSIS
 from id06workflow.core.experiment import _METADATA_TYPES_I
+from id06workflow.core.mapping import MEAN, VARIANCE, SKEWNESS, KURTOSIS
+from id06workflow.core.operation.ThreadedOperation import ThreadedOperation
 from id06workflow.core.types import _Image
 from id06workflow.gui.mapping import MappingPlot
-from functools import partial
-import logging
 
 _logger = logging.getLogger(__file__)
 

orangecontrib/id06workflow/widgets/roiselection.py

@@ -27,14 +27,17 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "02/10/2018"
 
+import logging
+from silx.gui import qt
+
+from Orange.canvas.registry.description import InputSignal, OutputSignal
 from Orange.widgets import gui
 from Orange.widgets.widget import OWWidget
-from Orange.canvas.registry.description import InputSignal, OutputSignal
+
 from id06workflow.core.experiment import Experiment
-from id06workflow.core.experiment.operation.roi import RoiOperation
-from silx.gui import qt
+from id06workflow.core.operation.roi import RoiOperation
 from id06workflow.gui.roiselection import ROIOnStackView
-import logging
+
 _logger = logging.getLogger(__file__)
 
 

orangecontrib/id06workflow/widgets/shiftcorrection.py

@@ -27,15 +27,16 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "02/10/2018"
 
-from Orange.widgets import gui
+import logging
 from silx.gui import qt
-from Orange.widgets.widget import OWWidget
+
 from Orange.canvas.registry.description import InputSignal, OutputSignal
+from Orange.widgets import gui
+from Orange.widgets.widget import OWWidget
+
 from id06workflow.core.experiment import Experiment
 from id06workflow.core.types import _Image
 from id06workflow.gui.shifcorrection import ShiftCorrectionWidget
-from id06workflow.core.experiment.operation.shift import Shift
-import logging
 
 _logger = logging.getLogger(__file__)