Merge branch 'ewoks_second_round' into 'master'

[ewoks integration] add static_input to OW

See merge request workflow/est!46

est/core/process/larch/autobk.py

@@ -133,7 +133,11 @@ _USE_MULTIPROCESSING_POOL = False
 
 
 class Larch_autobk(
-    Process, name="autobk", input_names=["xas_obj"], output_names=["xas_obj"]
+    Process,
+    name="autobk",
+    input_names=["xas_obj"],
+    output_names=["xas_obj"],
+    optional_input_names=["autobk"],
 ):
     def set_properties(self, properties):
         if "_larchSettings" in properties:
@@ -144,8 +148,9 @@ class Larch_autobk(
         if xas_obj is None:
             raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
-        if self._settings:
-            _xas_obj.configuration["autobk"] = self._settings
+        if self.inputs.autobk:
+            self.setConfiguration(self.inputs.autobk)
+            _xas_obj.configuration["autobk"] = self.inputs.autobk
 
         self._advancement.reset(max_=_xas_obj.n_spectrum)
         self._advancement.startProcess()

est/core/process/larch/mback.py

@@ -124,7 +124,11 @@ _USE_MULTIPROCESSING_POOL = False
 
 
 class Larch_mback(
-    Process, name="mback", input_names=["xas_obj"], output_names=["xas_obj"]
+    Process,
+    name="mback",
+    input_names=["xas_obj"],
+    output_names=["xas_obj"],
+    optional_input_names=["mback"],
 ):
     def set_properties(self, properties):
         if "_larchSettings" in properties:
@@ -135,8 +139,10 @@ class Larch_mback(
         if xas_obj is None:
             raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
-        if self._settings:
-            _xas_obj.configuration["mback"] = self._settings
+
+        if self.inputs.mback:
+            self.setConfiguration(self.inputs.mback)
+            _xas_obj.configuration["mback"] = self.inputs.mback
         elif "mback" not in _xas_obj.configuration:
             _xas_obj.configuration["mback"] = {}
 

est/core/process/larch/mback_norm.py

@@ -133,7 +133,11 @@ _USE_MULTIPROCESSING_POOL = False
 
 
 class Larch_mback_norm(
-    Process, name="mback_norm", input_names=["xas_obj"], output_names=["xas_obj"]
+    Process,
+    name="mback_norm",
+    input_names=["xas_obj"],
+    output_names=["xas_obj"],
+    optional_input_names=["mback_norm"],
 ):
     def set_properties(self, properties):
         if "_larchSettings" in properties:
@@ -144,8 +148,9 @@ class Larch_mback_norm(
         if xas_obj is None:
             raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
-        if self._settings:
-            _xas_obj.configuration["mback_norm"] = self._settings
+        if self.inputs.mback_norm:
+            self.setConfiguration(self.inputs.mback_norm)
+            _xas_obj.configuration["mback_norm"] = self.inputs.mback_norm
 
         self._advancement.reset(max_=_xas_obj.n_spectrum)
         self._advancement.startProcess()

est/core/process/larch/pre_edge.py

@@ -129,7 +129,11 @@ _USE_MULTIPROCESSING_POOL = False
 
 
 class Larch_pre_edge(
-    Process, name="pre_edge", input_names=["xas_obj"], output_names=["xas_obj"]
+    Process,
+    name="pre_edge",
+    input_names=["xas_obj"],
+    output_names=["xas_obj"],
+    optional_input_names=["pre_edge"],
 ):
     def set_properties(self, properties):
         if "_larchSettings" in properties:
@@ -141,8 +145,9 @@ class Larch_pre_edge(
             raise ValueError("xas_obj should be provided")
         self._xas_obj = self.getXasObject(xas_obj=xas_obj)
         _xas_obj = self._xas_obj
-        if self._settings:
-            _xas_obj.configuration["pre_edge"] = self._settings
+        if self.inputs.pre_edge:
+            self.setConfiguration(self.inputs.pre_edge)
+            _xas_obj.configuration["pre_edge"] = self.inputs.pre_edge
 
         self._advancement.reset(max_=_xas_obj.n_spectrum)
         self._advancement.startProcess()

est/core/process/larch/xftf.py

@@ -156,7 +156,11 @@ _USE_MULTIPROCESSING_POOL = False
 
 
 class Larch_xftf(
-    Process, name="xftf", input_names=["xas_obj"], output_names=["xas_obj"]
+    Process,
+    name="xftf",
+    input_names=["xas_obj"],
+    output_names=["xas_obj"],
+    optional_input_names=["xftf"],
 ):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
@@ -173,9 +177,11 @@ class Larch_xftf(
         if xas_obj is None:
             raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
-        if self._settings:
-            _xas_obj.configuration["xftf"] = self._settings
+        if self.inputs.xftf:
+            self.setConfiguration(self.inputs.xftf)
+            _xas_obj.configuration["xftf"] = self.inputs.xftf
         elif "xftf" not in _xas_obj.configuration:
+            self.setConfiguration({})
             _xas_obj.configuration["xftf"] = {}
 
         self._advancement.reset(max_=_xas_obj.n_spectrum)

est/core/process/pymca/exafs.py

@@ -144,7 +144,11 @@ _USE_MULTIPROCESSING_POOL = False
 
 
 class PyMca_exafs(
-    Process, name="exafs", input_names=["xas_obj"], output_names=["xas_obj"]
+    Process,
+    name="exafs",
+    input_names=["xas_obj"],
+    output_names=["xas_obj"],
+    optional_input_names=["exafs"],
 ):
     """Process spectra for exafs and get information about the processing
     advancement"""
@@ -158,8 +162,9 @@ class PyMca_exafs(
         if xas_obj is None:
             raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
-        if self._settings:
-            _xas_obj.configuration["EXAFS"] = self._settings
+        if self.inputs.exafs:
+            self.setConfiguration(self.inputs.exafs)
+            _xas_obj.configuration["EXAFS"] = self.inputs.exafs
 
         self._advancement.reset(max_=_xas_obj.n_spectrum)
         self._advancement.startProcess()

est/core/process/pymca/ft.py

@@ -148,7 +148,13 @@ _USE_MULTIPROCESSING_POOL = False
 # note: we cannot use multiprocessing pool with pypushflow for now.
 
 
-class PyMca_ft(Process, name="ft", input_names=["xas_obj"], output_names=["xas_obj"]):
+class PyMca_ft(
+    Process,
+    name="ft",
+    input_names=["xas_obj"],
+    output_names=["xas_obj"],
+    optional_input_names=["ft"],
+):
     def set_properties(self, properties):
         if "_pymcaSettings" in properties:
             self._settings = properties["_pymcaSettings"]
@@ -165,8 +171,10 @@ class PyMca_ft(Process, name="ft", input_names=["xas_obj"], output_names=["xas_o
         if xas_obj is None:
             raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
-        if self._settings:
-            _xas_obj.configuration["FT"] = self._settings
+
+        if self.inputs.ft:
+            self.setConfiguration(self.inputs.ft)
+            _xas_obj.configuration["FT"] = self.inputs.ft
 
         self._advancement.reset(max_=_xas_obj.n_spectrum)
         self._advancement.startProcess()

est/core/process/pymca/k_weight.py

@@ -137,7 +137,11 @@ _USE_MULTIPROCESSING_POOL = False
 
 
 class PyMca_k_weight(
-    Process, name="k weight", input_names=["xas_obj"], output_names=["xas_obj"]
+    Process,
+    name="k weight",
+    input_names=["xas_obj"],
+    output_names=["xas_obj"],
+    optional_input_names=["k_weight"],
 ):
     def set_properties(self, properties):
         if "_kWeightSetting" in properties:
@@ -146,11 +150,6 @@ class PyMca_k_weight(
             del _properties["_kWeightSetting"]
             self.setConfiguration(_properties)
 
-    def _k_weight(self):
-        if "k_weight" in self._settings:
-            return self._settings["k_weight"]
-        return None
-
     def run(self):
         """
 
@@ -163,8 +162,10 @@ class PyMca_k_weight(
         if xas_obj is None:
             raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
-        if self._k_weight() is not None:
-            _xas_obj.configuration["SET_KWEIGHT"] = self._k_weight()
+
+        if self.inputs.k_weight:
+            self.setConfiguration({"k_weight": self.inputs.k_weight})
+            _xas_obj.configuration["SET_KWEIGHT"] = self.inputs.k_weight
 
         if "SET_KWEIGHT" not in _xas_obj.configuration:
             _logger.warning(

est/core/process/pymca/normalization.py

@@ -123,7 +123,11 @@ _USE_MULTIPROCESSING_POOL = False
 
 
 class PyMca_normalization(
-    Process, name="normalization", input_names=["xas_obj"], output_names=["xas_obj"]
+    Process,
+    name="normalization",
+    input_names=["xas_obj"],
+    output_names=["xas_obj"],
+    optional_input_names=["normalization"],
 ):
     def set_properties(self, properties):
         if "_pymcaSettings" in properties:
@@ -147,8 +151,9 @@ class PyMca_normalization(
             _logger.error("Energy not specified, unable to normalize spectra")
             return
 
-        if self._settings:
-            _xas_obj.configuration["Normalization"] = self._settings
+        if self.inputs.normalization:
+            self.setConfiguration(self.inputs.normalization)
+            _xas_obj.configuration["Normalization"] = self.inputs.normalization
         self._advancement.reset(max_=_xas_obj.n_spectrum)
         self._advancement.startProcess()
         self._pool_process(xas_obj=_xas_obj)

est/core/reprocessing.py

-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2017-2019 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.
-#
-# ###########################################################################*/
-"""some utils function for executing reprocessing"""
-
-
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "07/18/2019"
-
-import importlib
-import logging
-from silx.io.utils import h5py_read_dataset
-
-_logger = logging.getLogger(__name__)
-
-
-def get_process_instance_frm_h5_desc(desc):
-    """
-
-    :param dict desc: description of the process to instanciate
-    :return: instance of the process to execute, configured from the description
-    """
-    assert "program" in desc
-    assert "class_instance" in desc
-    tmp = h5py_read_dataset(desc["class_instance"]).split(".")
-    module_name = ".".join(tmp[:-1])
-    class_name = tmp[-1]
-    try:
-        _module = importlib.import_module(module_name)
-        instance = getattr(_module, class_name)()
-    except Exception as e:
-        _logger.warning(
-            " ".join(("Fail to instanciate", module_name, class_name, "reason is", e))
-        )
-        instance = None
-    else:
-        if "configuration" in desc:
-            instance.setConfiguration(desc["configuration"])
-    return instance

orangecontrib/est/widgets/container.py

@@ -62,10 +62,6 @@ class _ParameterWindowContainer(qt.QWidget):
         # setup
         self._manualUpdatePB.setVisible(False)
 
-        # expose API
-        self.setParameters = self._mainwidget.setParameters
-        self.getParameters = self._mainwidget.getParameters
-
         # connect signal / slot
         self._autoCB.toggled.connect(self._manualUpdatePB.setVisible)
         self._manualUpdatePB.pressed.connect(self._update)
@@ -93,3 +89,9 @@ class _ParameterWindowContainer(qt.QWidget):
 
     def _update(self, *args, **kwargs):
         self.sigChanged.emit()
+
+    def getParameters(self):
+        return self._mainwidget.getParameters()
+
+    def setParameters(self, params):
+        self._mainwidget.setParameters(params=params)

orangecontrib/est/widgets/larch/autobk.py

@@ -158,7 +158,9 @@ class AutobkOW(_ProcessForOrangeMixIn, OWWidget):
     allows_cycle = False
 
     _larchSettings = Setting(dict())
-    """Store the configuration of the PyMca XASClass"""
+    # kept for compatibility
+    static_input = Setting({"xas_obj": None, "autobk": None})
+    """Store the configuration of the larch configuration"""
 
     ewokstaskclass = est.core.process.larch.autobk.Larch_autobk
 
@@ -182,8 +184,11 @@ class AutobkOW(_ProcessForOrangeMixIn, OWWidget):
         self._window.xasObjViewer.setWindowTitle("spectra")
 
         # manage settings
-        if self._larchSettings != dict():
-            self._window._parametersWindow.setParameters(self._larchSettings)
+        larch_settings = self.static_input.get("autobk", None)
+        if larch_settings is None:
+            larch_settings = self._larchSettings
+        if larch_settings != dict():
+            self._window._parametersWindow.setParameters(larch_settings)
 
         # connect signals / slots
         self._window._parametersWindow.sigChanged.connect(self._updateProcess)
@@ -206,6 +211,10 @@ class AutobkOW(_ProcessForOrangeMixIn, OWWidget):
 
     def _update_settings(self):
         self._larchSettings = self._window._parametersWindow.getParameters()
+        self.static_input = {
+            "autobk": self._window._parametersWindow.getParameters(),
+            "xas_obj": None,
+        }
 
     @Inputs.data_table
     def processFrmDataTable(self, data_table):

orangecontrib/est/widgets/larch/mback.py

@@ -134,6 +134,8 @@ class MbackOW(_ProcessForOrangeMixIn, OWWidget):
     allows_cycle = False
 
     _larchSettings = Setting(dict())
+    # kept for compatibility
+    static_input = Setting({"mback": None})
     """Store the configuration of the larch configuration"""
 
     ewokstaskclass = est.core.process.larch.mback.Larch_mback
@@ -158,8 +160,11 @@ class MbackOW(_ProcessForOrangeMixIn, OWWidget):
         self._window.xasObjViewer.setWindowTitle("spectra")
 
         # manage settings
-        if self._larchSettings != dict():
-            self._window._parametersWindow.setParameters(self._larchSettings)
+        larch_settings = self.static_input.get("mback", None)
+        if larch_settings is None:
+            larch_settings = self._larchSettings
+        if larch_settings != dict():
+            self._window._parametersWindow.setParameters(larch_settings)
 
         # connect signals / slots
         self._window._parametersWindow.sigChanged.connect(self._updateProcess)
@@ -180,6 +185,10 @@ class MbackOW(_ProcessForOrangeMixIn, OWWidget):
 
     def _update_settings(self):
         self._larchSettings = self._window._parametersWindow.getParameters()
+        self.static_input = {
+            "mback": self._window._parametersWindow.getParameters(),
+            "xas_obj": None,
+        }
 
     @Inputs.data_table
     def processFrmDataTable(self, data_table):

orangecontrib/est/widgets/larch/mback_norm.py

@@ -138,6 +138,8 @@ class Mback_normOW(
     ewokstaskclass = est.core.process.larch.mback_norm.Larch_mback_norm
 
     _larchSettings = Setting(dict())
+    """Kept for compatiblity"""
+    static_input = Setting({"mback_norm": None})
     """Store the configuration of the larch configuration"""
 
     class Inputs:
@@ -160,8 +162,11 @@ class Mback_normOW(
         self._window.xasObjViewer.setWindowTitle("spectra")
 
         # manage settings
-        if self._larchSettings != dict():
-            self._window._parametersWindow.setParameters(self._larchSettings)
+        larch_settings = self.static_input.get("mback_norm", None)
+        if larch_settings is None:
+            larch_settings = self._larchSettings
+        if larch_settings != dict():
+            self._window._parametersWindow.setParameters(larch_settings)
 
         # connect signals / slots
         self._window._parametersWindow.sigChanged.connect(self._updateProcess)
@@ -182,6 +187,10 @@ class Mback_normOW(
 
     def _update_settings(self):
         self._larchSettings = self._window._parametersWindow.getParameters()
+        self.static_input = {
+            "mback_norm": self._window._parametersWindow.getParameters(),
+            "xas_obj": None,
+        }
 
     @Inputs.data_table
     def processFrmDataTable(self, data_table):

orangecontrib/est/widgets/larch/pre_edge.py

@@ -157,6 +157,8 @@ class PreEdgeOW(
     ewokstaskclass = est.core.process.larch.pre_edge.Larch_pre_edge
 
     _larchSettings = Setting(dict())
+    # kept for compatibility
+    static_input = Setting({"pre_edge": None})
     """Store the configuration of the larch configuration"""
 
     class Inputs:
@@ -179,8 +181,11 @@ class PreEdgeOW(
         self._window.xasObjViewer.setWindowTitle("spectra")
 
         # manage settings
-        if self._larchSettings != dict():
-            self._window._parametersWindow.setParameters(self._larchSettings)
+        larch_settings = self.static_input.get("pre_edge", None)
+        if larch_settings is None:
+            larch_settings = self._larchSettings
+        if larch_settings != dict():
+            self._window._parametersWindow.setParameters(larch_settings)
 
         # connect signals / slots
         self._window._parametersWindow.sigChanged.connect(self._updateProcess)
@@ -201,6 +206,10 @@ class PreEdgeOW(
 
     def _update_settings(self):
         self._larchSettings = self._window._parametersWindow.getParameters()
+        self.static_input = {
+            "pre_edge": self._window._parametersWindow.getParameters(),
+            "xas_obj": None,
+        }
 
     @Inputs.data_table
     def processFrmDataTable(self, data_table):

orangecontrib/est/widgets/larch/xftf.py

@@ -174,6 +174,8 @@ class XFTFOW(
     ewokstaskclass = est.core.process.larch.xftf.Larch_xftf
 
     _larchSettings = Setting(dict())
+    # kept for compatibility
+    static_input = Setting({"xftf": None, "xas_obj": None})
     """Store the configuration of the larch configuration"""
 
     class Inputs:
@@ -196,8 +198,11 @@ class XFTFOW(
         self._window.xasObjViewer.setWindowTitle("spectra")
 
         # manage settings
-        if self._larchSettings != dict():
-            self._window._parametersWindow.setParameters(self._larchSettings)
+        larch_settings = self.static_input.get("xftf", None)
+        if larch_settings is None:
+            larch_settings = self._larchSettings
+        if larch_settings != dict():
+            self._window._parametersWindow.setParameters(larch_settings)
 
         # connect signals / slots
         self._window._parametersWindow.sigChanged.connect(self._updateProcess)
@@ -219,6 +224,10 @@ class XFTFOW(
 
     def _update_settings(self):
         self._larchSettings = self._window._parametersWindow.getParameters()
+        self.static_input = {
+            "xftf": self._window._parametersWindow.getParameters(),
+            "xas_obj": None,
+        }
 
     @Inputs.data_table
     def processFrmDataTable(self, data_table):

orangecontrib/est/widgets/pymca/exafs.py

@@ -138,6 +138,8 @@ class ExafsOW(
     ewokstaskclass = est.core.process.pymca.exafs.PyMca_exafs
 
     _larchSettings = Setting(dict())
+    # kept for compatibility
+    static_input = Setting({"xas_obj": None, "exafs": None})
     """Store the configuration of the PyMca XASClass"""
 
     class Inputs:
@@ -164,8 +166,11 @@ class ExafsOW(
         )
 
         # manage settings
-        if self._larchSettings != dict():
-            self._window._pymcaWindow.setParameters(self._larchSettings)
+        pymca_settings = self.static_input.get("exafs", None)
+        if pymca_settings is None:
+            pymca_settings = self._larchSettings
+        if pymca_settings != dict():
+            self._window._pymcaWindow.setParameters(pymca_settings)
 
         # signal / slot connection
         self._window._pymcaWindow.sigChanged.connect(self._updateProcess)
@@ -179,6 +184,10 @@ class ExafsOW(
 
     def _update_settings(self):
         self._larchSettings = self._window._pymcaWindow.getParameters()
+        self.static_input = {
+            "xas_obj": None,
+            "exafs": self._window._pymcaWindow.getParameters(),
+        }
 
     @Inputs.data_table
     def processFrmDataTable(self, data_table):

orangecontrib/est/widgets/pymca/ft.py

@@ -157,6 +157,8 @@ class FTOW(
     ewokstaskclass = est.core.process.pymca.ft.PyMca_ft
 
     _pymcaSettings = Setting(dict())
+    # kept for compatibility
+    static_input = dict({"ft": None, "xas_obj": None})
     """Store the configuration of the PyMca XASClass"""
 
     class Inputs:
@@ -181,8 +183,11 @@ class FTOW(
         self._progress = gui.ProgressBar(self, 100)
 
         # manage settings
-        if self._pymcaSettings != dict():
-            self._window._pymcaWindow.setParameters(self._pymcaSettings)
+        pymca_settings = self.static_input.get("ft", None)
+        if pymca_settings is None:
+            pymca_settings = self._pymcaSettings
+        if pymca_settings != dict():
+            self._window._pymcaWindow.setParameters(pymca_settings)
 
         # signal / slot connection
         # connect signals / slots
@@ -235,6 +240,10 @@ class FTOW(
 
     def _update_settings(self):
         self._pymcaSettings = self._window._pymcaWindow.getParameters()
+        self.static_input = {
+            "xas_obj": None,
+            "ft": self._window._pymcaWindow.getParameters(),
+        }
 
     def _setProgressValue(self, value):
         self._progress.widget.progressBarSet(value)

orangecontrib/est/widgets/pymca/k_weight.py

@@ -87,6 +87,8 @@ class KWeightOW(
     ewokstaskclass = est.core.process.pymca.k_weight.PyMca_k_weight
 
     _kWeightSetting = Setting(int(3))
+    # kept for compatibility
+    static_input = Setting({"xas_obj": None, "k_weight": 3})
     """Store the configuration of the PyMca XASClass"""
 
     class Inputs:
@@ -111,8 +113,11 @@ class KWeightOW(
         self._progress = gui.ProgressBar(self, 100)
 
         # manage settings
-        if self._kWeightSetting != 3:
-            self._window._k_spin_box.setValue(self._kWeightSetting)
+        k_weight = self.static_input.get("k_weight")
+        if k_weight == 3:
+            k_weight = self._kWeightSetting
+        if k_weight != 3:
+            self._window._k_spin_box.setValue(k_weight)
 
         # signal / slot connection
         self._window._k_spin_box.valueChanged.connect(self._updateProcess)
@@ -163,6 +168,10 @@ class KWeightOW(
 
     def _update_settings(self):
         self._kWeightSetting = self._window._k_spin_box.value()
+        self.static_input = {
+            "xas_obj": None,
+            "k_weight": self._window._k_spin_box.value(),