[metadata] use silx.io.fabioh5 module to get specific metadata values

id06workflow/core/experiment/__init__.py

@@ -34,13 +34,28 @@ 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 collections import OrderedDict, namedtuple
+from silx.io.fabioh5 import FabioReader
+from silx.io import fabioh5
 import numpy
 import logging
 
 _logger = logging.getLogger(__file__)
 
 
+_Dim = namedtuple('_Dim', ['name', 'size'])
+# TODO: define dimension of the Experiment, with a get dim...
+
+
+DEFAULT_METADATA = FabioReader.DEFAULT
+
+COUNTER_METADATA = FabioReader.COUNTER
+
+POSITIONER_METADATA = FabioReader.POSITIONER
+
+_METADATA_TYPES = (DEFAULT_METADATA, COUNTER_METADATA, POSITIONER_METADATA)
+
+
 class Experiment(object):
     """
     Define all component of an experiment:
@@ -95,6 +110,8 @@ class Experiment(object):
 
     @property
     def metadata(self):
+        if self.__metadata is None:
+            self.data
         return self.__metadata
 
     @property
@@ -139,13 +156,14 @@ class Experiment(object):
             return data_with_z_reduction[:, ::steps[1], ::steps[0]]
 
     def _loadFileSeries(self, fileseries, z_step):
+        """This will only deal with .edf file for now"""
         data = []
         headers = []
         for iFrame in numpy.arange(start=0, stop=fileseries.nframes, step=z_step):
             # TODO: deal with motors
             frame = fileseries.getframe(iFrame)
             data.append(frame.data)
-            headers.append(frame.header)
+            headers.append(fabioh5.EdfFabioReader(fabio_image=frame))
         return numpy.asarray(data), headers
 
     @property

id06workflow/core/test/test_operation.py

@@ -30,11 +30,13 @@ __date__ = "03/10/2018"
 
 import unittest
 from id06workflow.core.experiment.operation import OverwritingOperation, AdditiveOperation, shift
-from id06workflow.core.experiment import Experiment, Dataset
+from id06workflow.core.experiment import Experiment, Dataset, POSITIONER_METADATA
+from id06workflow.core.utils import metadata as metadatautils
 from id06workflow.test import utils
 import shutil
 import numpy
 import tempfile
+import os
 
 
 class TestOperation(unittest.TestCase):
@@ -123,7 +125,31 @@ class TestShift(unittest.TestCase):
 
 class TestOperationStream(unittest.TestCase):
     """Test some default operation streaming"""
-    pass
+    def setUp(self):
+        unittest.TestCase.setUp(self)
+
+        root_folder = '/nobackup/linazimov/payno/datasets/id06/strain_scan'
+        data_file_pattern = os.path.join(root_folder, 'reduced_strain/strain_0000.edf')
+        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)
+        self.experiment = Experiment(dataset=self.dataset, geometry=None)
+
+    def applyGeometry(self):
+        """Apply some geometry"""
+        pass
+
+    def testGeomtry(self):
+        """Make sure geometry is well applied"""
+        self.assertTrue(len(metadatautils.getUnique(self.experiment,
+                                                    kind=POSITIONER_METADATA,
+                                                    key='diffry')) is 30)
+        self.assertTrue(len(metadatautils.getUnique(self.experiment,
+                                                    kind=POSITIONER_METADATA,
+                                                    key='obpitch')) is 4)
 
 
 def suite():

id06workflow/core/utils/metadata.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__ = "21/11/2018"
+
+
+from id06workflow.core.experiment import Experiment
+import numpy
+import logging
+_logger = logging.getLogger(__file__)
+
+
+def getUnique(experiment, key, kind):
+    """Return the set of (unique) value in all the headers
+    
+    :param str key: the type of value we want
+    :param Dataset dataset: the dataset to treat
+    
+    :return set: set of value
+    """
+    assert isinstance(experiment, Experiment)
+    metadata = experiment.metadata
+    if metadata is None:
+        _logger.warning('no metadata found in the given experiment, unable to '
+                        'unique value of %s' % key)
+        return set()
+    res = set()
+    for metadata_slice in experiment.metadata:
+        try:
+            value = metadata_slice.get_value(kind=kind, name=key)
+            assert isinstance(value, numpy.ndarray)
+            assert value.size is 1
+            res.add(value[0])
+        except Exception as e:
+            _logger.error("fail to load %s, %s cause %s" % (kind, key, e))
+    return res

id06workflow/gui/datasetselection.py

@@ -77,8 +77,13 @@ class DatasetSelection(qt.QTabWidget):
 
         # expose API
         self.getDataFilesPattern = self._dataFiles.getPattern
+        self.setDataFilesPattern = self._dataFiles.setPattern
         self.getDarkFiles = self._darkFiles.getFiles
+        self.setDarkFiles = self._darkFiles.setFiles
+        self.addDarkFile = self._darkFiles.addFile
         self.getFlatFieldFiles = self._ffFiles.getFiles
+        self.setFlatFieldFiles = self._ffFiles.setFiles
+        self.addFlatFieldFile = self._ffFiles.addFile
 
     def getDataset(self):
         """
@@ -144,6 +149,7 @@ class DataListWidget(qt.QWidget):
         # expose API
         self.getFiles = self.datalist.getFiles
         self.setFiles = self.datalist.setFiles
+        self.addFile = self.datalist.add
 
     def __getAddAndRmButtons(self):
         lLayout = qt.QHBoxLayout()

id06workflow/gui/geometry.py

@@ -32,6 +32,9 @@ from silx.gui import qt
 from id06workflow.core.geometry.TwoThetaGeometry import TwoThetaGeometry
 from id06workflow.gui.utils import _IllustrationWidget
 from id06workflow.core.utils.char import THETA_CHAR
+import logging
+
+_logger = logging.getLogger(__file__)
 
 
 class GeometryMainWidget(qt.QWidget):
@@ -81,6 +84,19 @@ class TwoThetaGeometryWidget(TwoThetaGeometry, qt.QWidget):
     """
     Widget used to defined a TwoTheta experimental setup
     """
+    class DimensionComboBox(qt.QComboBox):
+        def __init__(self, parent, default=None, locked=None):
+            qt.QComboBox.__init__(self, parent)
+            for itemName in ('diffry', 'obpitch'):
+                self.addItem(itemName)
+            if default is not None:
+                idx = self.findText(default)
+                if idx >= 0:
+                    self.setCurrentIndex(idx)
+                else:
+                    _logger.warning('requested default value %s is not recognized' % default)
+            self.setEnabled(not locked)
+
     def __init__(self, parent):
         qt.QWidget.__init__(self, parent)
         self.setLayout(qt.QGridLayout())
@@ -113,6 +129,15 @@ class TwoThetaGeometryWidget(TwoThetaGeometry, qt.QWidget):
         self.layout().addWidget(self._orientationCB, 4, 1)
         # TODO: user should be able to save the configuration of the geometry
 
+        self.layout().addWidget(qt.QLabel('dim 1'), 5, 0)
+        self._dim1 = self.DimensionComboBox(parent=self, default='diffry',
+                                            locked=True)
+        self.layout().addWidget(self._dim1, 5, 1)
+        self.layout().addWidget(qt.QLabel('dim 2'), 6, 0)
+        self._dim2 = self.DimensionComboBox(parent=self, default='obpitch',
+                                            locked=True)
+        self.layout().addWidget(self._dim2, 6, 1)
+
     def getSetupGeometry(self):
         orientation = self._orientationCB.currentText()
         assert orientation in TwoThetaGeometry.ORIENTATIONS

orangecontrib/id06workflow/widgets/dataselection.py

@@ -33,7 +33,9 @@ from Orange.widgets.widget import OWWidget
 from Orange.canvas.registry.description import OutputSignal
 from id06workflow.gui.datasetselection import DatasetSelection
 from id06workflow.core.experiment import Experiment
+from Orange.widgets.settings import Setting
 from silx.gui import qt
+import os
 import logging
 _logger = logging.getLogger(__file__)
 
@@ -56,6 +58,10 @@ class DataSelectionOW(OWWidget):
     resizing_enabled = True
     compress_signal = False
 
+    _data_file_pattern = Setting(str())
+    _flat_field_files = Setting(list())
+    _dark_files = Setting(list())
+
     def __init__(self):
         # TODO: add drag and drop stuff on it
         super().__init__()
@@ -77,6 +83,15 @@ class DataSelectionOW(OWWidget):
         # expose API
         self.setDataset = self._widget.setDataset
 
+        if os.path.isfile(self._data_file_pattern):
+            self._widget.setDataFilesPattern(self._data_file_pattern)
+        for _file in self._flat_field_files:
+            if os.path.isfile(_file):
+                self._widget.addFlatFieldFile(_file)
+        for _file in self._dark_files:
+            if os.path.isfile(_file):
+                self._widget.addDarkFile(_file)
+
     def _process(self):
         """
         Code executed when the dataset has been validated