Merge branch 'orange_addon' into 'master'

Orange addon

See merge request !11

id06workflow/core/experiment/__init__.py

@@ -483,3 +483,38 @@ class Dim(object):
 
     def __str__(self):
         return " ".join((str(self.kind), str(self.name), 'size:', str(self.size)))
+
+    def to_dict(self):
+        """translate the current Dim to a dictionary"""
+        return {
+            'name': self.name,
+            'kind': self.kind,
+            'size': self.size,
+            'relative_prev_val': self.relative_prev_val,
+        }
+
+    @staticmethod
+    def from_dict(_dict):
+        """
+
+        :param dict _dict: dict defining the dimension. Should contains the
+                           following keys: name, kind, size, relative_prev_val
+                           unique values are not stored into it because it
+                           depends on the metadata and should be obtain from a
+                           fit / set_dims
+        :return: Dim corresponding to the dict given
+        :rtype: :class:`Dim`
+        """
+        assert type(_dict) is dict
+        missing_keys = []
+        for _key in ('name', 'kind', 'size', 'relative_prev_val'):
+            if _key not in _dict:
+                missing_keys.append(missing_keys)
+        if len(missing_keys) > 0:
+            raise ValueError('There is some missing keys (%s), unable to create'
+                             'a valid Dim')
+        else:
+            return Dim(name=_dict['name'],
+                       kind=_dict['kind'],
+                       size=_dict['size'],
+                       relative_prev_val=_dict['relative_prev_val'])

id06workflow/gui/dimensions.py

@@ -108,6 +108,7 @@ class DimensionMapping(qt.QWidget):
         :return: 
         """
         self.clear()
+        assert type(dims) is dict
         for axis, dim in dims.items():
             assert type(axis) is int
             assert isinstance(dim, Dim)

orangecontrib/id06workflow/widgets/dataselection.py

@@ -31,9 +31,9 @@ __date__ = "02/10/2018"
 from Orange.widgets import gui
 from Orange.widgets.widget import OWWidget
 from Orange.canvas.registry.description import OutputSignal
+from Orange.widgets.settings import Setting
 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
@@ -85,12 +85,18 @@ class DataSelectionOW(OWWidget):
 
         if os.path.isfile(self._data_file_pattern):
             self._widget.setDataFilesPattern(self._data_file_pattern)
+        elif self._data_file_pattern != '':
+            _logger.info('%s is not recognized as an existing file pattern' % self._data_file_pattern)
         for _file in self._flat_field_files:
             if os.path.isfile(_file):
                 self._widget.addFlatFieldFile(_file)
+            else:
+                _logger.info('%s is not a valid file path')
         for _file in self._dark_files:
             if os.path.isfile(_file):
                 self._widget.addDarkFile(_file)
+            else:
+                _logger.info('%s is not a valid file path')
 
     def _process(self):
         """
@@ -106,3 +112,8 @@ class DataSelectionOW(OWWidget):
 
     def sizeHint(self):
         return qt.QSize(400, 400)
+
+    def updateProperties(self):
+        self._data_file_pattern = self._widget.getDataFilesPattern()
+        self._flat_field_files = self._widget.getFlatFieldFiles()
+        self._dark_files = self._widget.getDarkFiles()

orangecontrib/id06workflow/widgets/dimensions.py

@@ -32,8 +32,9 @@ from silx.gui import qt
 from Orange.widgets import gui
 from Orange.widgets.widget import OWWidget
 from Orange.canvas.registry.description import InputSignal, OutputSignal
+from Orange.widgets.settings import Setting
 from id06workflow.gui.dimensions import DimensionWidget
-from id06workflow.core.experiment import Experiment
+from id06workflow.core.experiment import Experiment, Dim
 from functools import partial
 import logging
 
@@ -61,6 +62,8 @@ class DimensionOW(OWWidget):
     resizing_enabled = True
     compress_signal = False
 
+    _dims = Setting(dict())
+
     def __init__(self):
         super().__init__()
         layout = gui.vBox(self.mainArea, 'dimensions').layout()
@@ -85,6 +88,10 @@ class DimensionOW(OWWidget):
         # expose API
         self.setDims = self._widget.setDims
 
+        # load properties
+        _dims = self._convertDictToDim(self._dims)
+        self._widget.setDims(_dims)
+
     @property
     def _ndim(self):
         return self._widget.ndim
@@ -112,3 +119,24 @@ class DimensionOW(OWWidget):
         else:
             self.send("data", self._widget.experiment)
             OWWidget.accept(self)
+
+    def updateProperties(self):
+        # as dim are named tuple we have to cast them to dict
+        self._dims = {}
+        if self._widget.ndim is 0:
+            return
+        else:
+            for _axis, _dim in  self._widget.dims.items():
+                assert isinstance(_dim, Dim)
+                self._dims[_axis] = _dim.to_dict()
+
+    def _convertDictToDim(self, _dict):
+        if len(_dict) > 0:
+            _dims = {}
+            for _axis, _dim in _dict.items():
+                assert type(_dim) is dict
+                _dims[_axis] = Dim.from_dict(_dim)
+            return _dims
+
+        else:
+            return {}

orangecontrib/id06workflow/widgets/roiselection.py

@@ -33,7 +33,7 @@ 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.widgets.settings import Setting
 from id06workflow.core.experiment import Experiment
 from id06workflow.core.operation.roi import RoiOperation
 from id06workflow.gui.roiselection import ROIOnStackView
@@ -63,6 +63,9 @@ class RoiSelectionOW(OWWidget):
     resizing_enabled = True
     compress_signal = False
 
+    _roi_origin = Setting(tuple())
+    _roi_size = Setting(tuple())
+
     def __init__(self):
         super().__init__()
 
@@ -83,6 +86,11 @@ class RoiSelectionOW(OWWidget):
         # expose API
         self.setROI = self._widget.setROI
 
+        if len(self._roi_size) is 2:
+            self._widget.getROI().setSize(size=self._roi_size)
+        if len(self._roi_origin) is 2:
+            self._widget.getROI().setOrigin(self._roi_origin)
+
     def _process(self, experiment):
         if experiment.dataset is None or experiment.dataset.is_valid() is False:
             _logger.warning('cannot process roi selection, need a valid dataset for this')
@@ -116,3 +124,11 @@ class RoiSelectionOW(OWWidget):
         else:
             OWWidget.accept(self)
         # TODO: what can be the image to send to show roi selection (z sum ?)
+
+    def updateProperties(self):
+        # as dim are named tuple we have to cast them to dict
+        self._roi_origin = tuple(self._widget.getROI().getOrigin())
+        self._roi_size = tuple(self._widget.getROI().getSize())
+
+        print(self._roi_origin)
+        print(self._roi_size)

orangecontrib/id06workflow/widgets/shiftcorrection.py

@@ -33,7 +33,7 @@ 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.widgets.settings import Setting
 from id06workflow.core.experiment import Experiment
 from id06workflow.core.types import _Image
 from id06workflow.gui.shifcorrection import ShiftCorrectionWidget
@@ -64,6 +64,10 @@ class ShiftCorrectionOW(OWWidget):
     resizing_enabled = True
     compress_signal = False
 
+    _dx = Setting(int())
+    _dy = Setting(int())
+    _dz = Setting(int())
+
     def __init__(self):
         super().__init__()
         self._editedExperiment = None
@@ -90,6 +94,8 @@ class ShiftCorrectionOW(OWWidget):
         # expose API
         self.setShift = self._widget.setShift
 
+        self._widget.setShift(dx=self._dx, dy=self._dy, dz=self._dz)
+
     def _setProgressValue(self, value):
         self._progress.widget.progressBarSet(value)
 
@@ -122,3 +128,6 @@ class ShiftCorrectionOW(OWWidget):
                       image)
             # TODO: clear widget to avoid reprocessing ?
             OWWidget.accept(self)
+
+    def updateProperties(self):
+        self._dx, self._dy, self._dz = self._widget.getShift()