tomwer 1.2.0a1__py3-none-any.whl → 1.2.0a3__py3-none-any.whl

orangecontrib/tomwer/widgets/control/EDF2NXTomomillOW.py

@@ -74,7 +74,6 @@ class EDF2NXOW(
     want_main_area = True
     want_control_area = False
     resizing_enabled = True
-    compress_signal = False
 
     CONFIG_CLS = EDFConfig
 
@@ -89,8 +88,9 @@ class EDF2NXOW(
         _layout = gui.vBox(self.mainArea, self.name).layout()
         self.widget = EDFDataListMainWindow(parent=self)
         _layout.addWidget(self.widget)
+        # for edf default output path is still the 'near to input file'
+        self.widget._dialog._nxTomomillOutputWidget._closeToBlissFileRB.setChecked(True)
         # add 'convert auto' check box
-
         self._convertAutoCB = qt.QCheckBox(
             "convert automatically when edf scan send through 'edf scan' channel", self
         )
@@ -181,6 +181,7 @@ class EDF2NXOW(
     def get_task_inputs(self):
         return {
             "edf_to_nx_configuration": self.__configuration_cache.to_dict(),
+            "serialize_output_data": False,
         }
 
     def handleNewSignals(self) -> None:

orangecontrib/tomwer/widgets/control/EmailOW.py

@@ -0,0 +1,82 @@
+from orangewidget import gui
+from orangewidget.settings import Setting
+
+from silx.gui import qt
+from ewoksorange.bindings.owwidgets import OWEwoksWidgetNoThread
+
+import tomwer.core.process.control.email
+from tomwer.gui.control.email import Emailwidget
+from tomwer.core.utils import concatenate_dict
+
+
+class EmailOW(
+    OWEwoksWidgetNoThread,
+    ewokstaskclass=tomwer.core.process.control.email.TomoEmailTask,
+):
+    """
+    This widget will browse a folder and sub folder to find valid tomo scan project.
+    Contrary to the scan watcher it will parse all folder / sub folders then stop.
+    """
+
+    name = "email notifier"
+    id = "orangecontrib.widgets.tomwer.control.EmailOW.EmailOW"
+    description = (
+        "This widget will send an email to receivers when the input is provided. \n"
+    )
+    icon = "icons/email.svg"
+    priority = 146
+    keywords = [
+        "tomography",
+        "tomwer",
+        "tomo_obj",
+        "email",
+        "notifier",
+        "notification",
+    ]
+
+    want_main_area = True
+    want_control_area = False
+    resizing_enabled = True
+
+    _ewoks_default_inputs = Setting({"configuration": {}, "tomo_obj": None})
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._widget = Emailwidget(parent=self)
+
+        self._box = gui.vBox(self.mainArea, self.name)
+        layout = self._box.layout()
+        layout.addWidget(self._widget)
+
+        # load settings
+        self._widget.setConfiguration(self._ewoks_default_inputs)
+
+        # connect signal / slot
+        self._widget.sigChanged.connect(self._updateSettings)
+
+    def _updateSettings(self):
+        self._ewoks_default_inputs = {
+            "configuration": self.getConfiguration(),
+            "tomo_obj": None,
+        }
+
+    # expose some API
+    def getConfiguration(self) -> dict:
+        return self._widget.getConfiguration()
+
+    def setConfiguration(self, config: dict):
+        self._widget.setConfiguration(config.get("configuration", {}))
+
+    def get_task_inputs(self):
+        return concatenate_dict(
+            super().get_task_inputs(),
+            {"configuration": self.getConfiguration()},
+        )
+
+    def sizeHint(self):
+        return qt.QSize(500, 200)
+
+    def _execute_ewoks_task(self, *args, **kwargs):
+        arguments = self._get_task_arguments()
+        if arguments.get("inputs", {}).get("tomo_obj", None) is not None:
+            super()._execute_ewoks_task(*args, **kwargs)

orangecontrib/tomwer/widgets/control/FilterOW.py

@@ -57,9 +57,8 @@ class NameFilterOW(SuperviseOW):
 
     want_main_area = True
     resizing_enabled = True
-    compress_signal = False
 
-    ewokstaskclass = tomwer.core.process.conditions.filters.FileNameFilter
+    ewokstaskclass = tomwer.core.process.conditions.filters.FileNameFilterTask
 
     class Inputs:
         data = Input(name="data", type=TomwerScanBase, multiple=True)
@@ -87,12 +86,13 @@ class NameFilterOW(SuperviseOW):
         if not isinstance(scan, TomwerScanBase):
             raise TypeError(f"{scan} is expected to be an instance of {TomwerScanBase}")
 
-        process = filters.FileNameFilter(
+        process = filters.FileNameFilterTask(
             inputs={
                 "data": scan,
                 "pattern": self.getPattern(),
                 "filter_type": self.getActiveFilter(),
                 "invert_result": self.invertFilterAction(),
+                "serialize_output_data": False,  # avoid spending time on scan serialization / deserialization when use orange
             }
         )
         process.run()

orangecontrib/tomwer/widgets/control/NXTomomillOW.py

@@ -79,7 +79,6 @@ class NXTomomillOW(
     want_main_area = True
     want_control_area = False
     resizing_enabled = True
-    compress_signal = False
 
     CONFIG_CLS = HDF5Config
 
@@ -144,6 +143,7 @@ class NXTomomillOW(
     def get_task_inputs(self):
         return {
             "h5_to_nx_configuration": self.__configuration_cache.to_dict(),
+            "serialize_output_data": False,
         }
 
     def handleNewSignals(self) -> None:

orangecontrib/tomwer/widgets/control/NotifierOW.py

@@ -48,7 +48,6 @@ class NotifierWidgetOW(widget.OWBaseWidget):
 
     want_main_area = True
     resizing_enabled = False
-    compress_signal = False
 
     _muted = settings.Setting(False)
 

orangecontrib/tomwer/widgets/control/ReduceDarkFlatSelectorOW.py

@@ -0,0 +1,93 @@
+import logging
+from typing import Optional
+
+from orangewidget import gui
+from orangewidget.settings import Setting
+from orangewidget.widget import Input, Output, OWBaseWidget
+
+from tomwer.gui.control.reducedarkflatselector import ReduceDarkFlatSelectorDialog
+
+logger = logging.getLogger(__name__)
+
+
+class ReduceDarkFlatSelectorOW(OWBaseWidget, openclass=True):
+    name = "reduce dark-flat selector"
+    id = "orangecontrib.widgets.tomwer.control.ReduceDarkFlatSelectorOW.ReduceDarkFlatSelectorOW"
+    description = "Allow user to select one or several reduced dark / flat"
+    icon = "icons/reduced_darkflat_selector.svg"
+    priority = 242
+    keywords = [
+        "tomography",
+        "selection",
+        "tomwer",
+        "scan",
+        "data",
+        "reduce",
+        "dark",
+        "flat",
+        "reduced",
+    ]
+
+    want_main_area = True
+    want_control_area = False
+    resizing_enabled = True
+
+    _configuration = Setting(tuple())
+
+    class Inputs:
+        in_reduced_frames = Input(
+            name="reduced frames",
+            type=dict,
+            doc="dict of containing reduced frames (either dark or flat)",
+            multiple=True,
+        )
+
+    class Outputs:
+        out_reduced_darks = Output(
+            name="reduced dark(s)",
+            doc="dict of containing reduced darks(s)",
+            type=dict,
+        )
+        out_reduced_flats = Output(
+            name="reduced flat(s)",
+            type=dict,
+            doc="dict of containing reduced flat(s)",
+        )
+
+    def __init__(self, parent=None):
+        """ """
+        super().__init__(parent)
+
+        self._dialog = ReduceDarkFlatSelectorDialog(parent=self)
+        self._layout = gui.vBox(self.mainArea, self.name).layout()
+        self._layout.addWidget(self._dialog)
+
+        self._dialog.setConfiguration(self._configuration)
+
+        # connect signal / slot
+        self._dialog.sigSelectActiveAsDarks.connect(self._sendDarks)
+        self._dialog.sigSelectActiveAsFlats.connect(self._sendFlats)
+        self._dialog.sigUpdated.connect(self._updateConfiguration)
+
+    def _updateConfiguration(self):
+        self._configuration = self.getConfiguration()
+
+    def _sendDarks(self, darks: dict):
+        self.Outputs.out_reduced_darks.send(darks)
+
+    def _sendFlats(self, flats: dict):
+        self.Outputs.out_reduced_flats.send(flats)
+
+    @Inputs.in_reduced_frames
+    def addReduceFrames(self, reduce_frames: Optional[dict], *args, **kwargs):
+        if reduce_frames is not None:
+            self._dialog.addReduceFrames(reduce_frames)
+
+    # expose API
+    def getConfiguration(self) -> tuple:
+        return self._dialog.getConfiguration()
+
+    def setConfiguration(self, configuration: tuple) -> None:
+        if configuration is None:
+            return
+        return self._dialog.setConfiguration(configuration)

orangecontrib/tomwer/widgets/control/SingleTomoObjOW.py

@@ -55,7 +55,6 @@ class SingleTomoObjOW(OWBaseWidget, openclass=True):
     want_main_area = True
     want_control_area = False
     resizing_enabled = True
-    compress_signal = False
 
     ewokstaskclass = tomwer.core.process.control.singletomoobj.SingleTomoObjProcess
 
@@ -71,12 +70,22 @@ class SingleTomoObjOW(OWBaseWidget, openclass=True):
         reduced_darks = Output(
             name="reduced dark(s)",
             type=dict,
-            doc="DataUrl of the reduced dark. Key is the relative position, value is the reduced dark",
+            doc="Reduced darks as a dict",
         )
         reduced_flats = Output(
             name="reduced flat(s)",
             type=dict,
-            doc="DataUrl of the reduced flat. Key is the relative position, value is the reduced flat",
+            doc="Reduced flats as a dict",
+        )
+        relative_reduced_darks = Output(
+            name="relative reduced dark(s)",
+            type=dict,
+            doc="Reduced darks as a dict. Indexes are provided as relative so in [0.0, 1.0[",
+        )
+        relative_reduced_flats = Output(
+            name="relative reduced flat(s)",
+            type=dict,
+            doc="Reduced flats as a dict. Indexes are provided as relative so in [0.0, 1.0[",
         )
 
     def __init__(self, parent=None):
@@ -129,16 +138,31 @@ class SingleTomoObjOW(OWBaseWidget, openclass=True):
         # if the data is a scan then provide also access to the reduced frames. Can be convenient
         if isinstance(data, TomwerScanBase):
             if data.reduced_darks not in (None, {}):
+                reduced_darks = data.reduced_darks
+                self.Outputs.reduced_darks.send(reduced_darks)
+
                 # we want to send those in relative position to have something generic. This is a convention for now
-                self.Outputs.reduced_darks.send(
+                reduced_darks = (
                     tomoscan.esrf.scan.utils.from_absolute_reduced_frames_to_relative(
                         reduced_frames=data.reduced_darks, scan=data
                     )
                 )
+                reduced_darks[
+                    "reduce_frames_name"
+                ] = f"darks from {data.get_identifier().short_description()}"
+                self.Outputs.relative_reduced_darks.send(reduced_darks)
+
             if data.reduced_flats not in (None, {}):
+                reduced_flats = data.reduced_flats
+                self.Outputs.reduced_flats.send(reduced_flats)
+
                 # we want to send those in relative position to have something generic. This is a convention for now
-                self.Outputs.reduced_flats.send(
+                reduced_flats = (
                     tomoscan.esrf.scan.utils.from_absolute_reduced_frames_to_relative(
                         reduced_frames=data.reduced_flats, scan=data
                     )
                 )
+                reduced_flats[
+                    "reduce_frames_name"
+                ] = f"flats from {data.get_identifier().short_description()}"
+                self.Outputs.relative_reduced_flats.send(reduced_flats)

orangecontrib/tomwer/widgets/control/TimerOW.py

@@ -77,10 +77,9 @@ class TimerOW(SuperviseOW):
 
     want_main_area = True
     resizing_enabled = True
-    compress_signal = False
     _waiting_time = Setting(int(1))
 
-    ewokstaskclass = tomwer.core.process.control.timer.Timer
+    ewokstaskclass = tomwer.core.process.control.timer.TimerTask
 
     class Inputs:
         data = Input(name="data", type=TomwerScanBase, multiple=True)

orangecontrib/tomwer/widgets/control/TomoObjSerieOW.py

@@ -55,7 +55,6 @@ class TomoObjSerieOW(OWBaseWidget, openclass=True):
     want_main_area = True
     want_control_area = False
     resizing_enabled = True
-    compress_signal = False
 
     class Inputs:
         tomo_obj = Input(name="tomo obj", type=TomwerObject, multiple=True)

orangecontrib/tomwer/widgets/control/VolumeSelector.py

@@ -62,7 +62,6 @@ class VolumeSelectorOW(OWBaseWidget, openclass=True):
     want_main_area = True
     want_control_area = False
     resizing_enabled = True
-    compress_signal = False
 
     _scanIDs = Setting(list())
 

orangecontrib/tomwer/widgets/control/VolumeSymLinkOW.py

@@ -40,7 +40,7 @@ import tomwer.core.process.control.volumesymlink
 from orangecontrib.tomwer.orange.managedprocess import SuperviseOW
 from tomwer.core.process.control.volumesymlink import (
     OutputType,
-    VolumeSymbolicLinkProcess,
+    VolumeSymbolicLinkTask,
 )
 from tomwer.core.scan.scanbase import TomwerScanBase
 
@@ -73,9 +73,8 @@ class VolumeSymLinkOW(SuperviseOW):
 
     want_main_area = True
     resizing_enabled = True
-    compress_signal = False
 
-    ewokstaskclass = tomwer.core.process.control.volumesymlink.VolumeSymbolicLinkProcess
+    ewokstaskclass = tomwer.core.process.control.volumesymlink.VolumeSymbolicLinkTask
 
     _scans = Setting(list())
 
@@ -95,17 +94,12 @@ class VolumeSymLinkOW(SuperviseOW):
     def process(self, scan):
         if scan is None:
             return
-        symlink_process = VolumeSymbolicLinkProcess(
+        symlink_process = VolumeSymbolicLinkTask(
             inputs={
                 "data": scan,
                 "output_type": self._mainWidget.getOutputType(),
                 "output_folder": self._mainWidget.getOutputFolder(),
-            }
-        )
-        symlink_process.set_configuration(
-            {
-                "output_type": self._mainWidget.getOutputType(),
-                "output_folder": self._mainWidget.getOutputFolder(),
+                "serialize_output_data": False,
             }
         )
         ProcessManager().notify_dataset_state(

orangecontrib/tomwer/widgets/control/icons/email.svg

@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   width="48"
+   height="48"
+   viewBox="0 0 12.7 12.7"
+   version="1.1"
+   id="svg5"
+   inkscape:version="1.2.2 (b0a8486541, 2022-12-01)"
+   sodipodi:docname="email.svg"
+   inkscape:export-filename="email.png"
+   inkscape:export-xdpi="96"
+   inkscape:export-ydpi="96"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg">
+  <sodipodi:namedview
+     id="namedview7"
+     pagecolor="#ffffff"
+     bordercolor="#000000"
+     borderopacity="0.25"
+     inkscape:showpageshadow="2"
+     inkscape:pageopacity="0.0"
+     inkscape:pagecheckerboard="0"
+     inkscape:deskcolor="#d1d1d1"
+     inkscape:document-units="mm"
+     showgrid="false"
+     inkscape:zoom="9.5144352"
+     inkscape:cx="8.8812419"
+     inkscape:cy="18.813518"
+     inkscape:window-width="1920"
+     inkscape:window-height="1131"
+     inkscape:window-x="0"
+     inkscape:window-y="32"
+     inkscape:window-maximized="1"
+     inkscape:current-layer="layer1" />
+  <defs
+     id="defs2" />
+  <g
+     inkscape:label="Layer 1"
+     inkscape:groupmode="layer"
+     id="layer1">
+    <rect
+       style="fill:none;stroke-width:0.265;stroke:#000000;stroke-opacity:1;stroke-dasharray:none;stroke-linejoin:round"
+       id="rect111"
+       width="10.505496"
+       height="7.0666666"
+       x="1.1707107"
+       y="2.9006319" />
+    <path
+       style="fill:none;stroke:#000000;stroke-width:0.264999;stroke-linejoin:round;stroke-dasharray:none;stroke-opacity:1"
+       d="M 1.1442134,2.8768056 6.3157073,6.9139034 11.578496,2.9283596"
+       id="path908"
+       sodipodi:nodetypes="ccc" />
+  </g>
+</svg>