tomwer 1.0.4__py3-none-any.whl → 1.1.0__py3-none-any.whl

orangecontrib/tomwer/widgets/control/DataWatcherOW.py

@@ -35,16 +35,13 @@ from orangewidget.settings import Setting
 from orangewidget.widget import Output
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui.control.datawatcher import DataWatcherWidget
-from tomwer.web.client import OWClient
 import functools
 import logging
 
 logger = logging.getLogger(__name__)
 
 
-class DataWatcherOW(
-    widget.OWBaseWidget, OWClient, WidgetLongProcessing, openclass=True
-):
+class DataWatcherOW(widget.OWBaseWidget, WidgetLongProcessing, openclass=True):
     """
     This widget is used to observe a selected folder and his sub-folders to
     detect if they are containing valid-finished acquisitions.
@@ -78,7 +75,9 @@ class DataWatcherOW(
 
     DEFAULT_DIRECTORY = "/lbsram/data/visitor"
 
-    ewokstaskclass = tomwer.core.process.control.datawatcher.datawatcher.DataWatcher
+    ewokstaskclass = (
+        tomwer.core.process.control.datawatcher.datawatcher.DataWatcherEwoksTask
+    )
 
     class Outputs:
         data = Output(name="data", type=TomwerScanBase)
@@ -93,7 +92,6 @@ class DataWatcherOW(
         :param parent: the parent widget
         """
         widget.OWBaseWidget.__init__(self, parent)
-        OWClient.__init__(self)
         WidgetLongProcessing.__init__(self)
         self._widget = DataWatcherWidget(parent=self)
         self._widget.setFolderObserved(self.folderObserved)

orangecontrib/tomwer/widgets/control/EDF2NXTomomillOW.py

@@ -28,7 +28,6 @@ __license__ = "MIT"
 __date__ = "11/03/2020"
 
 from copy import copy
-import os
 from orangewidget import gui
 from tomwer.core.scan.edfscan import EDFTomoScan
 from orangecontrib.tomwer.orange.managedprocess import TomwerWithStackStack
@@ -37,8 +36,7 @@ from tomwer.gui.control.datalist import (
     EDFDataListMainWindow,
 )
 from nxtomomill.io.config import TomoEDFConfig as EDFConfig
-from .NXTomomillOW import _NXTomoMixIn
-from tomwer.gui.control.nxtomomill import NXTomomillInput
+from orangecontrib.tomwer.widgets.control.NXTomomillMixIn import NXTomomillMixIn
 from tomwer.core.process.control.nxtomomill import EDFToNxProcess
 from silx.gui import qt
 import logging
@@ -46,7 +44,11 @@ import logging
 logger = logging.getLogger(__name__)
 
 
-class EDF2NXOW(TomwerWithStackStack, _NXTomoMixIn, ewokstaskclass=EDFToNxProcess):
+class EDF2NXOW(
+    TomwerWithStackStack,
+    NXTomomillMixIn,
+    ewokstaskclass=EDFToNxProcess,
+):
     """
     Widget to allow user to pick some bliss files and that will convert them
     to HDF5scan.
@@ -74,12 +76,16 @@ class EDF2NXOW(TomwerWithStackStack, _NXTomoMixIn, ewokstaskclass=EDFToNxProcess
     resizing_enabled = True
     compress_signal = False
 
+    CONFIG_CLS = EDFConfig
+
+    LOGGER = logger
+
     def __init__(self, parent=None):
         self.__configuration_cache = None
         # cache updated for each folder in order to match `_execute_ewoks_task` design
 
         TomwerWithStackStack.__init__(self, parent=parent)
-        _NXTomoMixIn.__init__(self)
+        NXTomomillMixIn.__init__(self)
         _layout = gui.vBox(self.mainArea, self.name).layout()
         self.widget = EDFDataListMainWindow(parent=self)
         _layout.addWidget(self.widget)
@@ -109,8 +115,7 @@ class EDF2NXOW(TomwerWithStackStack, _NXTomoMixIn, ewokstaskclass=EDFToNxProcess
         self._loadSettings()
 
     def _updateSettings(self):
-        super()._updateSettings()
-        self._static_input[
+        self._ewoks_default_inputs[  # pylint: disable=E1137
             "convert_auto_edfscan_channel"
         ] = self.convertAutoEDFScanReceivedFromChannel()
 
@@ -120,59 +125,26 @@ class EDF2NXOW(TomwerWithStackStack, _NXTomoMixIn, ewokstaskclass=EDFToNxProcess
     def setConvertAutoEDFScanReceivedFromChannel(self, checked: bool):
         self._convertAutoCB.setChecked(checked)
 
-    def add(self, folder):
-        self.widget.add(folder)
-
-    def _saveNXTomoCfgFile(self, cfg_file):
-        """save the nxtomofile to the setttings"""
-        self._nxtomo_cfg_file = cfg_file
-        self._static_input["nxtomomill_cfg_file"] = cfg_file
-
-        if os.path.exists(cfg_file):
-            try:
-                configuration = EDFConfig.from_cfg_file(cfg_file)
-            except Exception as e:
-                logger.error(
-                    "Fail to use configuration file {}."
-                    "Error is {}. No conversion will be done."
-                    "".format(cfg_file, e)
-                )
-            else:
-                self.update_default_inputs(
-                    edf_to_nx_configuration=configuration.to_dict()
-                )
-        else:
-            self.update_default_inputs(edf_to_nx_configuration=EDFConfig().to_dict())
-
-    def _sendSelected(self):
-        self._inputGUI = NXTomomillInput()
-        # reset the GUI for input (reset all the cache for answers)
-        self._canOverwriteOutputs = False
-        for scan_id in self.widget.datalist._myitems:
-            tomo_obj = self.widget.datalist.getEDFTomoScan(scan_id, None)
-            if tomo_obj:
-                self._convertAndSend(tomo_obj)
-
-    def _sendAll(self):
-        self._inputGUI = NXTomomillInput()
-        # reset the GUI for input (reset all the cache for answers)
-        self._canOverwriteOutputs = False
-        for scan_id in self.widget.datalist._myitems:
-            tomo_obj = self.widget.datalist.getEDFTomoScan(scan_id, None)
-            if tomo_obj:
-                self._convertAndSend(tomo_obj)
-
     def _loadSettings(self):
-        for scan in self._scans:
+        for scan in self._scans:  # pylint: disable=E1133
             self.widget.add(scan)
-        if "nxtomomill_cfg_file" in self._static_input:
-            self._nxtomo_cfg_file = self._static_input["nxtomomill_cfg_file"]
+        if "nxtomomill_cfg_file" in self._ewoks_default_inputs:  # pylint: disable=E1135
+            self._nxtomo_cfg_file = self._ewoks_default_inputs[  # pylint: disable=E1136
+                "nxtomomill_cfg_file"
+            ]
             self.widget.setCFGFilePath(self._nxtomo_cfg_file)
-        if "output_dir" in self._static_input:
-            self.widget.setOutputFolder(self._static_input["output_dir"])
-        if "convert_auto_edfscan_channel" in self._static_input:
+        if "output_dir" in self._ewoks_default_inputs:  # pylint: disable=E1135
+            self.widget.setOutputFolder(
+                self._ewoks_default_inputs["output_dir"]  # pylint: disable=E1136
+            )
+        if (
+            "convert_auto_edfscan_channel"
+            in self._ewoks_default_inputs  # pylint: disable=E1135
+        ):
             self.setConvertAutoEDFScanReceivedFromChannel(
-                self._static_input["convert_auto_edfscan_channel"]
+                self._ewoks_default_inputs[  # pylint: disable=E1136
+                    "convert_auto_edfscan_channel"
+                ]
             )
 
     def _convertAndSend(self, edf_scan: EDFTomoScan):
@@ -192,7 +164,9 @@ class EDF2NXOW(TomwerWithStackStack, _NXTomoMixIn, ewokstaskclass=EDFToNxProcess
         self.__configuration_cache.dataset_basename = edf_scan.dataset_basename
 
         output_file = EDFToNxProcess.deduce_output_file_path(
-            folder_path=edf_scan.path, output_dir=self.widget.getOutputFolder()
+            folder_path=edf_scan.path,
+            output_dir=self.widget.getOutputFolder(),
+            scan=edf_scan,
         )
         output_entry = "entry"
         self.__configuration_cache.output_file = output_file
@@ -240,8 +214,21 @@ class EDF2NXOW(TomwerWithStackStack, _NXTomoMixIn, ewokstaskclass=EDFToNxProcess
         except Exception as e:
             logger.error(f"failed to handle task finished callback. Raiseon is {e}")
 
-    def _get_task_arguments(self):
-        adict = super()._get_task_arguments()
-        # pop progress as does not fully exists on the orange-widget-base
-        adict.pop("progress", None)
-        return adict
+    def _saveNXTomoCfgFile(self, cfg_file):
+        super()._saveNXTomoCfgFile(cfg_file, keyword="edf_to_nx_configuration")
+
+    def _sendSelected(self):
+        """send all selected items to be converted"""
+        self._canOverwriteOutputs = False
+        for scan_id in self.widget.datalist._myitems:
+            tomo_obj = self.widget.datalist.getEDFTomoScan(scan_id, None)
+            if tomo_obj:
+                self._convertAndSend(tomo_obj)
+
+    def _sendAll(self):
+        """send all items to be converted"""
+        self._canOverwriteOutputs = False
+        for scan_id in self.widget.datalist._myitems:
+            tomo_obj = self.widget.datalist.getEDFTomoScan(scan_id, None)
+            if tomo_obj:
+                self._convertAndSend(tomo_obj)

orangecontrib/tomwer/widgets/control/FilterOW.py

@@ -33,7 +33,6 @@ from orangewidget import gui
 import tomwer.core.process.conditions.filters
 from orangecontrib.tomwer.orange.managedprocess import SuperviseOW
 from orangewidget.widget import Input, Output
-from tomwer.web.client import OWClient
 from tomwer.gui.conditions.filter import FileNameFilterWidget
 from tomwer.core.scan.scanbase import TomwerScanBase
 from processview.core.manager import DatasetState
@@ -44,7 +43,7 @@ import logging
 logger = logging.getLogger(__name__)
 
 
-class NameFilterOW(SuperviseOW, OWClient):
+class NameFilterOW(SuperviseOW):
     name = "scan filter"
     id = "orange.widgets.tomwer.filterow"
     description = (
@@ -69,8 +68,7 @@ class NameFilterOW(SuperviseOW, OWClient):
 
     def __init__(self, parent=None):
         """ """
-        SuperviseOW.__init__(self, parent)
-        OWClient.__init__(self)
+        super().__init__(parent)
 
         self.widget = FileNameFilterWidget(parent=self)
         self.widget.setContentsMargins(0, 0, 0, 0)

orangecontrib/tomwer/widgets/control/NXTomomillMixIn.py

@@ -0,0 +1,93 @@
+import os
+import logging
+from orangewidget.settings import Setting
+
+_logger = logging.getLogger(__name__)
+
+
+class NXTomomillMixIn:
+    """
+    MixIn class for nxtomomill + ewoks
+    """
+
+    _scans = Setting(list())
+
+    _ewoks_default_inputs = Setting(dict())
+
+    CONFIG_CLS = None
+    # logger to be used. Expected to be redefine by child class
+
+    LOGGER = None
+    # logger to be used. Expected to be redefine by child class
+
+    def __init__(self, *args, **kwargs) -> None:
+        self.__configuration_cache = None
+        # cache updated for each folder in order to match `_execute_ewoks_task` design
+
+    def add(self, *args, **kwargs):
+        self.widget.add(*args, **kwargs)
+
+    def _updateSettings(self):
+        raise NotImplementedError("Base class")
+
+    def _saveNXTomoCfgFile(self, cfg_file, keyword: str):
+        """save the nxtomofile to the setttings"""
+        assert (
+            self.CONFIG_CLS is not None
+        ), "inheriting classes are expected to redefine CONFIG_CLS"
+        self._ewoks_default_inputs[
+            "nxtomomill_cfg_file"
+        ] = cfg_file  # pylint: disable=E1137
+
+        if os.path.exists(cfg_file):
+            try:
+                configuration = self.CONFIG_CLS.from_cfg_file(
+                    cfg_file
+                )  # pylint: disable=E1102
+            except Exception as e:
+                self._logger.error(
+                    "Fail to use configuration file {}."
+                    "Error is {}. No conversion will be done."
+                    "".format(cfg_file, e)
+                )
+            else:
+                default_inputs = {
+                    keyword: configuration.to_dict(),
+                }
+        else:
+            default_inputs = {
+                keyword: self.CONFIG_CLS().to_dict(),  # pylint: disable=E1102
+            }
+
+        # hack: try to upgrade x_pixel_keys and y_pixels keys to list.
+        # otherwise has they have the same values and are tuples they have the same id and orange raises an
+        # dump_literals raise a ValueError - check_relaxed - is a recursive structure
+        try:
+            default_inputs[keyword]["KEYS_SECTION"]["x_pixel_keys"] = list(
+                default_inputs[keyword]["KEYS_SECTION"]["x_pixel_keys"]
+            )
+            default_inputs[keyword]["KEYS_SECTION"]["y_pixel_keys"] = list(
+                default_inputs[keyword]["KEYS_SECTION"]["y_pixel_keys"]
+            )
+        except KeyError:
+            pass
+
+        self.update_default_inputs(
+            **default_inputs,
+        )
+
+    def _get_task_arguments(self):
+        adict = super()._get_task_arguments()
+        # pop progress as does not fully exists on the orange-widget-base
+        adict.pop("progress", None)
+        return adict
+
+    def __new__(cls, *args, **kwargs):
+        # ensure backward compatibility with 'static_input'
+        static_input = kwargs.get("stored_settings", {}).get("static_input", None)
+        if static_input not in (None, {}):
+            _logger.warning(
+                "static_input has been deprecated. Will be replaced by _ewoks_default_inputs in the workflow file. Please save the workflow to apply modifications"
+            )
+            kwargs["stored_settings"]["_ewoks_default_inputs"] = static_input
+        return super().__new__(cls, *args, **kwargs)