[orangecontrib] move a few more utils to ewoks.bindings

est/core/io.py

@@ -217,7 +217,7 @@ class XASWriter(object):
 
         if not self._output_file:
             _logger.warning(
-                "no output file defined, please give path to the" "output file"
+                "no output file defined, please give path to the output file"
             )
             self._output_file = input()
 

est/core/process/energyroi.py

@@ -83,15 +83,16 @@ class EnergyROIProcess(
             xas_obj.spectra.energy >= roi.from_
         )
         xas_obj.spectra.energy = xas_obj.spectra.energy[mask]
-        for spectrum in xas_obj.spectra.data.flat:
+        n_s = len(xas_obj.spectra.data.flat)
+        for i_s, spectrum in enumerate(xas_obj.spectra.data.flat):
             spectrum.energy = spectrum.energy[mask]
             spectrum.mu = spectrum.mu[mask]
             for attached_key in ("I0", "I1", "I2", "mu_ref"):
                 if hasattr(spectrum, attached_key):
                     values = getattr(spectrum, attached_key)[mask]
                     setattr(spectrum, attached_key, values)
-        #     print(spectrum.__dict__)
-        # print(xas_obj.__dict__)
+            self.progress = i_s / n_s * 100.0
+
         return xas_obj
 
     def run(self):
@@ -109,8 +110,10 @@ class EnergyROIProcess(
 
         # existing roi is priority. This is the case if called from pushworkflow
         # for example.
+        self.progress = 0.0
         if self._roi is not None:
             xas_obj = self._apply_roi(xas_obj=_xas_obj, roi=self._roi)
+        self.progress = 100.0
 
         self.register_process(_xas_obj, data_keys=("Mu", "energy"))
         self.outputs.xas_obj = _xas_obj.to_dict()

est/core/process/io.py

@@ -31,22 +31,24 @@ __date__ = "06/11/2019"
 from .process import Process
 from est.core.types import XASObject
 from est.io.utils.information import InputInformation
+from typing import Optional
 import pkg_resources
 
 
 class DumpXasObject(
     Process, name="dump xas object", input_names=["xas_obj"], output_names=["result"]
 ):
-    def __init__(self, **kwargs):
+    def __init__(self, missing_file_callback: Optional[str] = None, **kwargs):
+        self._missing_file_callback = missing_file_callback
         super().__init__(**kwargs)
         self._output_file = kwargs.get("varinfo", dict()).get("output_file", None)
 
     @property
-    def output_file(self):
+    def output_file(self) -> Optional[str]:
         return self._output_file
 
     @output_file.setter
-    def output_file(self, output_file):
+    def output_file(self, output_file: Optional[str]):
         self._output_file = output_file
 
     def program_name(self):
@@ -72,6 +74,8 @@ class DumpXasObject(
                 "xas_object should be a convertable dict or an" "instance of XASObject"
             )
 
+        if self.output_file is None and self._missing_file_callback is not None:
+            self.output_file = self._missing_file_callback()
         if self.output_file is None:
             raise ValueError("output file not provided")
         else:

orangecontrib/est/process.py

@@ -51,8 +51,7 @@ class _ProcessForOrangeMixIn(OWEwoksWidgetOneThread):
 
     def outputsChanged(self):
         # TODO: maybe we would expect a task_outputs to match the task_inputs
-        if "xas_obj" in self.task_inputs:
-            print("xas_obj contains", self.task_inputs)
+        if "xas_obj" in self.output_variables:
             xas_obj = self.output_variables["xas_obj"].value
             if isinstance(xas_obj, MissingData):
                 _logger.warning("no output data set. Unable to update the GUI")
@@ -65,4 +64,3 @@ class _ProcessForOrangeMixIn(OWEwoksWidgetOneThread):
             elif hasattr(self, "_window") and hasattr(self._window, "xasObjViewer"):
                 if hasattr(self._window.xasObjViewer, "setXASObj"):
                     self._window.xasObjViewer.setXASObj(xas_obj=xas_obj)
-                # emit signal for the plot

orangecontrib/est/widgets/utils/e0calculator.py

@@ -33,7 +33,7 @@ from Orange.widgets import gui
 from Orange.widgets.widget import OWWidget
 from Orange.widgets.widget import Input, Output
 import Orange.data
-from orangecontrib.est.utils import Converter
+from orangecontrib.est.process import _ProcessForOrangeMixIn
 from silx.gui import qt
 import functools
 import est.core.process.ignoreprocess
@@ -45,7 +45,8 @@ _logger = logging.getLogger(__file__)
 
 
 class E0calculatorOW(
-    OWWidget,
+    _ProcessForOrangeMixIn,
+    ewokstaskclass=est.core.process.ignoreprocess.IgnoreE0Calculation,
 ):
     """
     Widget used to make compute E0 from the dataset.
@@ -70,19 +71,6 @@ class E0calculatorOW(
 
     want_main_area = True
     resizing_enabled = True
-    compress_signal = False
-    ewokstaskclass = est.core.process.ignoreprocess.IgnoreE0Calculation
-
-    class Inputs:
-        xas_obj = Input("xas_obj", XASObject, default=True)
-        # simple compatibility for some Orange widget and especialy the
-        # 'spectroscopy add-on'
-        data_table = Input("Data", Orange.data.Table)
-
-    class Outputs:
-        xas_obj = Output("xas_obj", XASObject)
-        # by default we want to avoid sending 'Orange.data.Table' to avoid
-        # loosing the XASObject flow process and results.
 
     def __init__(self):
         super().__init__()
@@ -113,8 +101,6 @@ class E0calculatorOW(
         # set up
         self._buttons.hide()
 
-        # self.handleNewSignals()
-
     def validateMethodToUse(self, method):
         """Define the method to use and close the dialog"""
         method = E0ComputationMethod.from_value(method)
@@ -128,17 +114,8 @@ class E0calculatorOW(
         else:
             return self._widget.getE0(method=self._methodToUse)
 
-    @Inputs.data_table
-    def processFrmDataTable(self, data_table):
-        if data_table is None:
-            return
-        self.process(Converter.toXASObject(data_table=data_table))
-
-    @Inputs.xas_obj
-    def process(self, xas_obj):
-        if xas_obj is None:
-            return
-        self._widget.setXasObject(xas_obj=xas_obj)
+    def inputsChanged(self):
+        super(EnergyRoiOW, self).inputsChanged()
         self._buttons.show()
         self.show()
 

orangecontrib/est/widgets/utils/energyroi.py

@@ -34,6 +34,7 @@ from Orange.widgets.settings import Setting
 from Orange.widgets.widget import OWWidget
 from Orange.widgets.widget import Input, Output
 import Orange.data
+from orangecontrib.est.process import _ProcessForOrangeMixIn
 from orangecontrib.est.utils import Converter
 from silx.gui import qt
 import est.core.process.energyroi
@@ -44,7 +45,8 @@ _logger = logging.getLogger(__file__)
 
 
 class EnergyRoiOW(
-    OWWidget,
+    _ProcessForOrangeMixIn,
+    ewokstaskclass=est.core.process.energyroi.EnergyROIProcess,
 ):
     """
     Widget used to make the selection of a region of Interest to treat in a
@@ -55,7 +57,6 @@ class EnergyRoiOW(
     id = "orange.widgets.xas.utils.energyroi"
     description = "Select the energy ROI to analyse"
     icon = "icons/curveroi.svg"
-    ewokstaskclass = est.core.process.energyroi.EnergyROIProcess
 
     priority = 8
     category = "esrfWidgets"
@@ -71,23 +72,11 @@ class EnergyRoiOW(
 
     want_main_area = True
     resizing_enabled = True
-    compress_signal = False
 
     _energy_roi = Setting(dict())
     # kept for compatibility
     static_input = Setting({"xas_obj": None, "energy_roi": None})
 
-    class Inputs:
-        xas_obj = Input("xas_obj", XASObject, default=True)
-        # simple compatibility for some Orange widget and especially the
-        # 'spectroscopy add-on'
-        data_table = Input("Data", Orange.data.Table)
-
-    class Outputs:
-        xas_obj = Output("xas_obj", XASObject)
-        # by default we want to avoid sending 'Orange.data.Table' to avoid
-        # loosing the XASObject flow process and results.
-
     def __init__(self):
         super().__init__()
 
@@ -121,17 +110,8 @@ class EnergyRoiOW(
     def setROI(self, roi):
         self._widget.setROI(roi=roi)
 
-    @Inputs.data_table
-    def processFrmDataTable(self, data_table):
-        if data_table is None:
-            return
-        self.process(Converter.toXASObject(data_table=data_table))
-
-    @Inputs.xas_obj
-    def process(self, xas_obj):
-        if xas_obj is None:
-            return
-        self._widget.setXasObject(xas_obj=xas_obj)
+    def inputsChanged(self):
+        super(EnergyRoiOW, self).inputsChanged()
         self._buttons.show()
         self.show()
 

orangecontrib/est/widgets/utils/roi.py

@@ -39,12 +39,14 @@ from silx.gui import qt
 import est.core.process.roi
 from est.core.types import XASObject
 from est.gui.roiselector import ROISelector
+from orangecontrib.est.process import _ProcessForOrangeMixIn
 
 _logger = logging.getLogger(__file__)
 
 
 class RoiSelectionOW(
-    OWWidget,
+    _ProcessForOrangeMixIn,
+    ewokstaskclass=est.core.process.roi.ROIProcess,
 ):
     """
     Widget used to make the selection of a region of Interest to treat in a
@@ -62,25 +64,12 @@ class RoiSelectionOW(
 
     want_main_area = True
     resizing_enabled = True
-    compress_signal = False
-    ewokstaskclass = est.core.process.roi.ROIProcess
 
     _roi_origin = Setting(tuple())
     _roi_size = Setting(tuple())
 
     static_input = Setting({"xas_obj": None, "roi": None})
 
-    class Inputs:
-        xas_obj = Input("xas_obj", XASObject, default=True)
-        # simple compatibility for some Orange widget and especialy the
-        # 'spectroscopy add-on'
-        data_table = Input("Data", Orange.data.Table)
-
-    class Outputs:
-        xas_obj = Output("xas_obj", XASObject)
-        # by default we want to avoid sending 'Orange.data.Table' to avoid
-        # loosing the XASObject flow process and results.
-
     def __init__(self):
         super().__init__()
 
@@ -103,19 +92,8 @@ class RoiSelectionOW(
         self.setROI = self._widget.setROI
         self.getROI = self._widget.getROI
 
-        # self.handleNewSignals()
-
-    @Inputs.data_table
-    def processFrmDataTable(self, data_table):
-        if data_table is None:
-            return
-        self.process(Converter.toXASObject(data_table=data_table))
-
-    @Inputs.xas_obj
-    def process(self, xas_obj):
-        if xas_obj is None:
-            return
-        self._widget.setXasObject(xas_obj=xas_obj)
+    def inputsChanged(self):
+        super(EnergyRoiOW, self).inputsChanged()
         self._buttons.show()
         self.show()
 

orangecontrib/est/widgets/utils/xas_input.py

@@ -31,7 +31,6 @@ __date__ = "06/11/2019"
 import logging
 from Orange.widgets import gui
 from Orange.widgets.settings import Setting
-from Orange.widgets.widget import OWWidget
 from Orange.widgets.widget import Output
 from silx.gui import qt
 from silx.io.url import DataUrl
@@ -39,13 +38,15 @@ import est.core.io
 import est.core.process.ignoreprocess
 import est.core.process.io
 from est.gui.xas_object_definition import XASObjectWindow
+from ewoksorange.bindings.owwidgets import OWEwoksWidgetNoThread
 from est.core.types import XASObject
 
 _logger = logging.getLogger(__file__)
 
 
 class XASInputOW(
-    OWWidget,
+    OWEwoksWidgetNoThread,
+    ewokstaskclass=est.core.process.io.ReadXasObject,
 ):
     """
     Widget used for signal extraction
@@ -61,7 +62,6 @@ class XASInputOW(
 
     want_main_area = True
     resizing_enabled = True
-    ewokstaskclass = est.core.process.io.ReadXasObject
 
     _spec_file_setting = Setting(tuple())
     _spectra_url_setting = Setting(str())
@@ -74,11 +74,6 @@ class XASInputOW(
     _I2_url_setting = Setting(str())
     _mu_ref_url_setting = Setting(str())
 
-    class Outputs:
-        xas_obj = Output("xas_obj", XASObject)
-        # by default we want to avoid sending 'Orange.data.Table' to avoid
-        # loosing the XASObject flow process and results.
-
     def __init__(self):
         super().__init__()
         self._inputWindow = qt.QWidget(parent=self)
@@ -114,8 +109,6 @@ class XASInputOW(
         self._inputDialog.getMainWindow().editingFinished.connect(self._storeSettings)
         self.setFileSelected = self._inputDialog.setDatFile
 
-        # self.handleNewSignals()
-
     def _emitNewFile(self, *args, **kwargs):
         try:
             xas_obj = self._inputDialog.buildXASObject()

orangecontrib/est/widgets/utils/xas_output.py

@@ -29,11 +29,11 @@ __date__ = "06/11/2019"
 
 
 from Orange.widgets import gui
-from Orange.widgets.widget import OWWidget
 from Orange.widgets.settings import Setting
 from Orange.widgets.widget import Input
 from silx.gui import qt
 from est.core.types import XASObject
+from ewoksorange.bindings.owwidgets import OWEwoksWidgetNoThread
 import est.core.process.io
 import logging
 import h5py
@@ -42,7 +42,8 @@ _logger = logging.getLogger(__file__)
 
 
 class XASOutputOW(
-    OWWidget,
+    OWEwoksWidgetNoThread,
+    ewokstaskclass=est.core.process.io.DumpXasObject,
 ):
     """
     Widget used for signal extraction
@@ -58,13 +59,9 @@ class XASOutputOW(
 
     want_main_area = True
     resizing_enabled = True
-    ewokstaskclass = est.core.process.io.DumpXasObject
 
     _output_file_setting = Setting(str())
 
-    class Inputs:
-        xas_obj = Input("xas_obj", XASObject, default=True)
-
     def __init__(self):
         super().__init__()
         self._outputWindow = qt.QWidget(parent=self)
@@ -89,31 +86,28 @@ class XASOutputOW(
         # signal / slot connection
         self._selectPB.pressed.connect(self._selectFile)
 
-        # self.handleNewSignals()
-
     def _selectFile(self, *args, **kwargs):
-        old = self.blockSignals(True)
         dialog = qt.QFileDialog(self)
-        # dialog.setFileMode(qt.QFileDialog.AnyFile)
         dialog.setAcceptMode(qt.QFileDialog.AcceptSave)
+        dialog.setFileMode(qt.QFileDialog.AnyFile)
         dialog.setNameFilters(["hdf5 files (*.hdf5, *.hdf, *.h5)"])
 
-        if not dialog.exec_():
+        if dialog.exec_() is qt.QDialog.Rejected:
             dialog.close()
-            return False
-
+            return None
         fileSelected = dialog.selectedFiles()
         if len(fileSelected) == 0:
-            return False
+            return None
         else:
             assert len(fileSelected) == 1
             file_ = fileSelected[0]
             if not h5py.is_hdf5(file_):
-                file_ += ".h5"
+                if not file_.lower().endswith((".h5", ".hdf5", ".nx", ".nexus")):
+                    file_ += ".h5"
+            old = self.blockSignals(True)
             self.setFileSelected(file_)
-
-        self.blockSignals(old)
-        return True
+            self.blockSignals(old)
+            return str(file_)
 
     def setFileSelected(self, file_path):
         self._output_file_setting = file_path
@@ -122,23 +116,14 @@ class XASOutputOW(
     def _getFileSelected(self):
         return self._inputLe.text()
 
-    @Inputs.xas_obj
-    def process(self, xas_obj):
-        if xas_obj is None:
-            return
-        if isinstance(xas_obj, dict):
-            _xas_obj = XASObject.from_dict(xas_obj)
-        else:
-            _xas_obj = xas_obj
-
-        has_file = self._getFileSelected() != ""
-        if not has_file:
-            mess = qt.QMessageBox(parent=self)
-            mess.setIcon(qt.QMessageBox.Warning)
-            mess.setText("No output file defined, please give a file path")
-            mess.exec_()
-            has_file = self._selectFile()
-        if not has_file:
-            _logger.error("no valid output file given, skip save")
-        else:
-            _xas_obj.dump(self._getFileSelected())
+    def _missing_file_getter(self):
+        mess = qt.QMessageBox(self)
+        mess.setIcon(qt.QMessageBox.Warning)
+        mess.setText("No output file defined, please give a file path")
+        mess.exec_()
+        return self._selectFile()
+
+    def _getTaskArguments(self):
+        adict = super()._getTaskArguments()
+        adict["missing_file_callback"] = self._missing_file_getter
+        return adict