[process] update signature: remove xas_obj from the signature

est/core/process/energyroi.py

@@ -100,7 +100,7 @@ class EnergyROIProcess(Process):
         # print(xas_obj.__dict__)
         return xas_obj
 
-    def run(self, xas_obj: Union[dict, XASObject] = None):
+    def run(self):
         """
 
         :param xas_obj: object containing the configuration and spectra to process
@@ -108,8 +108,9 @@ class EnergyROIProcess(Process):
         :return: spectra dict
         :rtype: :class:`.XASObject`
         """
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
 
         # existing roi is priority. This is the case if called from pushworkflow

est/core/process/ignoreprocess.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__ = "22/07/2021"
+
 from ewokscore.task import Task
 
 
-class IgnoreTask(Task):
-    def process(self):
-        print("*** ignore task {}".format(self))
+class IgnoreOutput(Task):
+    """Simple Ignore task when an input is provided but no output. Used
+    in the case of pure display widget.
 
+    ..note: each OW should define it own task to insure a safe conversion to
+    ewoks
+    """
 
-class IgnoreInput(IgnoreTask):
-    _INPUT_NAMES = set([])
-    _OUTPUT_NAMES = set(["xas_obj"])
+    _INPUT_NAMES = set(["xas_obj"])
+    _OUTPUT_NAMES = set()
 
-    pass
-    # @staticmethod
-    # def registry_name():
-    #     return "orangecontrib.est.widgets.utils.xas_input.XASInputOW"
-    #
 
+class BlankTask(Task):
+    """Simple black task which will copy received xas_obj from inputs to
+    outputs.
 
-class IgnoreOrangeConversion(IgnoreTask):
-    pass
-    # @staticmethod
-    # def registry_name():
-    #     return "orangecontrib.est.widgets.utils.converter.ConverterOW"
+    ..note: each OW should define it own task to insure a safe conversion to
+    ewoks
+    """
+
+    _INPUT_NAMES = set(["xas_obj"])
+    _OUTPUT_NAMES = set(["xas_obj"])
+
+    def run(self):
+        self.outputs.xas_obj = self.inputs.xas_obj
 
 
-class IgnoreSavingPoint(IgnoreTask):
+class IgnoreSavingPoint(BlankTask):
     pass
-    # @staticmethod
-    # def registry_name():
-    #     return "orangecontrib.est.widgets.utils.saving_point.SavingPointOW"
 
 
-class IgnoreE0Calculation(IgnoreTask):
+class IgnoreE0Calculation(BlankTask):
     pass
-    # @staticmethod
-    # def registry_name():
-    #     return "orangecontrib.est.widgets.utils.e0calculator.E0calculatorOW"

est/core/process/io.py

@@ -104,6 +104,8 @@ class DumpXasObject(Process):
 
 class ReadXasObject(Process):
 
+    _INPUT_NAMES = set()
+
     _OUTPUT_NAMES = set(["xas_obj"])
 
     def __init__(self, varinfo=None, **inputs):

est/core/process/larch/autobk.py

@@ -147,9 +147,10 @@ class Larch_autobk(Process):
         if "_larchSettings" in properties:
             self._settings = properties["_larchSettings"]
 
-    def run(self, xas_obj=None):
+    def run(self):
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
         if self._settings:
             _xas_obj.configuration["autobk"] = self._settings

est/core/process/larch/mback.py

@@ -138,9 +138,10 @@ class Larch_mback(Process):
         if "_larchSettings" in properties:
             self._settings = properties["_larchSettings"]
 
-    def run(self, xas_obj=None):
+    def run(self):
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
         if self._settings:
             _xas_obj.configuration["mback"] = self._settings

est/core/process/larch/mback_norm.py

@@ -147,9 +147,10 @@ class Larch_mback_norm(Process):
         if "_larchSettings" in properties:
             self._settings = properties["_larchSettings"]
 
-    def run(self, xas_obj=None):
+    def run(self):
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            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

est/core/process/larch/pre_edge.py

@@ -98,6 +98,8 @@ def process_spectr_pre_edge(
     ):
         if opt_name in _conf:
             opts[opt_name] = _conf[opt_name]
+    print("{{{{{{{{{{{{{{{{{{{{{")
+    print("configuration is", configuration)
 
     if _DEBUG is True:
         assert isinstance(spectrum, Group)
@@ -143,9 +145,10 @@ class Larch_pre_edge(Process):
         if "_larchSettings" in properties:
             self._settings = properties["_larchSettings"]
 
-    def run(self, xas_obj=None):
+    def run(self):
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            raise ValueError("xas_obj should be provided")
         self._xas_obj = self.getXasObject(xas_obj=xas_obj)
         _xas_obj = self._xas_obj
         if self._settings:

est/core/process/larch/xftf.py

@@ -173,9 +173,10 @@ class Larch_xftf(Process):
         if "plot_settings" in properties:
             self._plot_settings = properties["plot_settings"]
 
-    def run(self, xas_obj=None):
+    def run(self):
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
         if self._settings:
             _xas_obj.configuration["xftf"] = self._settings

est/core/process/noise.py

@@ -169,7 +169,7 @@ class NoiseProcess(Process):
         if "polynomial_order" in properties:
             self._polynomial_order = properties["polynomial_order"]
 
-    def run(self, xas_obj: Union[dict, XASObject] = None):
+    def run(self, xas_obj):
         """
 
         :param xas_obj: object containing the configuration and spectra to process
@@ -177,10 +177,10 @@ class NoiseProcess(Process):
         :return: spectra dict
         :rtype: :class:`.XASObject`
         """
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
-
         if self._settings:
             _xas_obj.configuration["noise"] = self._settings
 

est/core/process/pymca/exafs.py

@@ -160,9 +160,10 @@ class PyMca_exafs(Process):
         if "_pymcaSettings" in properties:
             self.setConfiguration(properties["_pymcaSettings"])
 
-    def run(self, xas_obj=None):
+    def run(self):
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
         if self._settings:
             _xas_obj.configuration["EXAFS"] = self._settings

est/core/process/pymca/ft.py

@@ -163,7 +163,7 @@ class PyMca_ft(Process):
         if "_pymcaSettings" in properties:
             self._settings = properties["_pymcaSettings"]
 
-    def run(self, xas_obj=None):
+    def run(self):
         """
 
         :param xas_obj: object containing the configuration and spectra to process
@@ -171,8 +171,9 @@ class PyMca_ft(Process):
         :return: spectra dict
         :rtype: dict
         """
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
         if self._settings:
             _xas_obj.configuration["FT"] = self._settings

est/core/process/pymca/k_weight.py

@@ -158,7 +158,7 @@ class PyMca_k_weight(Process):
             return self._settings["k_weight"]
         return None
 
-    def run(self, xas_obj=None):
+    def run(self):
         """
 
         :param xas_obj: object containing the configuration and spectra to process
@@ -166,8 +166,9 @@ class PyMca_k_weight(Process):
         :return: spectra dict
         :rtype: :class:`.XASObject`
         """
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            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()

est/core/process/pymca/normalization.py

@@ -138,7 +138,7 @@ class PyMca_normalization(Process):
         if "_pymcaSettings" in properties:
             self._settings = properties["_pymcaSettings"]
 
-    def run(self, xas_obj=None):
+    def run(self):
         """
 
         :param xas_obj: object containing the configuration and spectra to process
@@ -147,8 +147,9 @@ class PyMca_normalization(Process):
         :return: updated XASObject
         :rtype: :class:`.XASObject`
         """
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj)
 
         if _xas_obj.energy is None:

est/core/process/roi.py

@@ -174,7 +174,7 @@ class ROIProcess(Process):
         xas_obj.spectra.reshape((roi.size[1], roi.size[0]))
         return xas_obj
 
-    def run(self, xas_obj: Union[dict, XASObject] = None):
+    def run(self, xas_obj):
         """
 
         :param xas_obj: object containing the configuration and spectra to process
@@ -182,8 +182,9 @@ class ROIProcess(Process):
         :return: spectra dict
         :rtype: :class:`.XASObject`
         """
+        xas_obj = self.inputs.xas_obj
         if xas_obj is None:
-            xas_obj = self.inputs.xas_obj
+            raise ValueError("xas_obj should be provided")
         _xas_obj = self.getXasObject(xas_obj=xas_obj)
 
         # existing roi is priority. This is the case if called from pushworkflow

orangecontrib/est/process.py

@@ -147,4 +147,5 @@ class ProcessQThread(qt.QThread):
         self._process_obj = process_obj
 
     def run(self):
-        self._xas_obj = self._process_obj.run(self._xas_obj)
+        return
+        # self._xas_obj = self._process_obj({"xas_obj": self._xas_obj}).run()