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

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

@@ -17,8 +17,8 @@
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    sodipodi:docname="notification.svg"
    inkscape:export-filename="/media/payno/830add5c-f5d7-4db2-875e-03be4f0a67f0/dev/tomography/tomwer/orangecontrib/tomwer/widgets/control/icons/notification.png"
-   inkscape:export-xdpi="256"
-   inkscape:export-ydpi="256">
+   inkscape:export-xdpi="24.190001"
+   inkscape:export-ydpi="24.190001">
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@@ -29,7 +29,7 @@
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      inkscape:pageshadow="2"
      inkscape:zoom="2.8"
-     inkscape:cx="103.95999"
+     inkscape:cx="168.78142"
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      inkscape:document-units="mm"
      inkscape:current-layer="layer1"
@@ -48,7 +48,7 @@
         <dc:format>image/svg+xml</dc:format>
         <dc:type
            rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
-        <dc:title />
+        <dc:title></dc:title>
       </cc:Work>
     </rdf:RDF>
   </metadata>

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

@@ -15,7 +15,10 @@
    version="1.1"
    id="SVGRoot"
    sodipodi:docname="nxtomomill.svg"
-   inkscape:version="0.92.4 (5da689c313, 2019-01-14)">
+   inkscape:version="0.92.5 (2060ec1f9f, 2020-04-08)"
+   inkscape:export-filename="/media/payno/830add5c-f5d7-4db2-875e-03be4f0a67f0/dev/tomography/tomwer/orangecontrib/tomwer/widgets/control/icons/nxtomomill.png"
+   inkscape:export-xdpi="59.900002"
+   inkscape:export-ydpi="59.900002">
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      id="defs815">
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@@ -41,14 +44,14 @@
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      inkscape:pageshadow="2"
      inkscape:zoom="7.7781746"
-     inkscape:cx="26.605247"
-     inkscape:cy="25.624015"
+     inkscape:cx="3.527853"
+     inkscape:cy="25.109756"
      inkscape:document-units="px"
      inkscape:current-layer="layer1"
      showgrid="false"
-     inkscape:window-width="1920"
+     inkscape:window-width="1848"
      inkscape:window-height="1136"
-     inkscape:window-x="0"
+     inkscape:window-x="72"
      inkscape:window-y="27"
      inkscape:window-maximized="1"
      inkscape:grid-bbox="true" />

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

@@ -0,0 +1,138 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   width="48"
+   height="48"
+   viewBox="0 0 12.7 12.7"
+   version="1.1"
+   id="svg8"
+   inkscape:version="0.92.4 (5da689c313, 2019-01-14)"
+   sodipodi:docname="tomoobjserie.svg"
+   inkscape:export-filename="/home/payno/dev/tomo/tomwer/orangecontrib/tomwer/widgets/control/icons/tomoobjserie.png"
+   inkscape:export-xdpi="134.50999"
+   inkscape:export-ydpi="134.50999">
+  <defs
+     id="defs2">
+    <filter
+       id="filter3784">
+      <feGaussianBlur
+         id="feGaussianBlur3786"
+         stdDeviation="0.10012024" />
+    </filter>
+  </defs>
+  <sodipodi:namedview
+     id="base"
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1.0"
+     inkscape:pageopacity="0.0"
+     inkscape:pageshadow="2"
+     inkscape:zoom="5.6"
+     inkscape:cx="39.552424"
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+     inkscape:document-units="mm"
+     inkscape:current-layer="g824"
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+     units="px"
+     inkscape:window-width="1920"
+     inkscape:window-height="1043"
+     inkscape:window-x="1920"
+     inkscape:window-y="0"
+     inkscape:window-maximized="1" />
+  <metadata
+     id="metadata5">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+        <dc:title />
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+          <text
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+             id="text819-4-5"
+             y="273.65967"
+             x="-24.445742"
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orangecontrib/tomwer/widgets/edit/DarkFlatPatchOW.py

@@ -29,6 +29,8 @@ __license__ = "MIT"
 __date__ = "02/11/2020"
 
 
+from typing import Optional
+from silx.io.url import DataUrl
 from orangewidget.widget import Input, Output
 from orangewidget import gui
 from tomwer.gui.edit.dkrfpatch import DarkRefPatchWidget
@@ -116,11 +118,21 @@ class DarkFlatPatchOW(WidgetLongProcessing, SuperviseOW):
         self.process(dataset)
 
     def getConfiguration(self):
+        def cast_url_to_str(url: Optional[DataUrl]):
+            if url is None:
+                return None
+            elif not isinstance(url, DataUrl):
+                raise TypeError(
+                    f"url is expected to be an optional DataUrl. {type(url)} provided instead"
+                )
+            else:
+                return url.path()
+
         return {
-            "darks_start": self.widget.getStartDarkUrl(),
-            "flats_start": self.widget.getStartFlatUrl(),
-            "darks_end": self.widget.getEndDarkUrl(),
-            "flats_end": self.widget.getEndFlatUrl(),
+            "darks_start": cast_url_to_str(self.widget.getStartDarkUrl()),
+            "flats_start": cast_url_to_str(self.widget.getStartFlatUrl()),
+            "darks_end": cast_url_to_str(self.widget.getEndDarkUrl()),
+            "flats_end": cast_url_to_str(self.widget.getEndFlatUrl()),
         }
 
     @Inputs.config_in

orangecontrib/tomwer/widgets/edit/NXtomoEditorOW.py

@@ -0,0 +1,100 @@
+from orangewidget import gui
+from tomwer.gui.edit.nxtomoeditor import NXtomoEditorDialog as _NXtomoEditorDialog
+from orangewidget.widget import Input, Output
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.scanbase import TomwerScanBase
+from silx.gui import qt
+from ...orange.managedprocess import SuperviseOW
+import logging
+
+_logger = logging.getLogger(__name__)
+
+
+class NXtomoEditorDialog(_NXtomoEditorDialog):
+    def __init__(self, parent) -> None:
+        assert isinstance(parent, SuperviseOW)
+        self._ow = parent
+        # we need to save it become looks like orange is doing some stuff with parenting
+        super().__init__(parent)
+
+        # connect signal / slot
+        self._buttons.button(qt.QDialogButtonBox.Ok).released.connect(
+            self._overwriteNXtomo
+        )
+
+    def _overwriteNXtomo(self, *args, **kwargs):
+        scan = self.mainWidget.getScan()
+        if scan is not None:
+            assert isinstance(self._ow, SuperviseOW)
+            try:
+                self.overwriteNXtomo()
+            except Exception as e:
+                _logger.error(
+                    f"Fail to overwrite NXtomo ({scan.get_identifier().to_str()}). Error is {e}"
+                )
+                self._ow.notify_failed(scan=scan)
+            else:
+                self._ow.notify_succeed(scan=scan)
+                # self.validate()
+            self._ow._validateScan(scan)
+
+
+class NXtomoEditorOW(SuperviseOW):
+    """
+    Widget to edit manually an NXtomo
+    """
+
+    name = "nxtomo-editor"
+    id = "orange.widgets.tomwer.edit.NXtomoEditorOW.NXtomoEditorOW"
+    description = "Interface to edit manually a NXtomo"
+    icon = "icons/nx_tomo_editor.svg"
+    priority = 10
+    keywords = [
+        "hdf5",
+        "nexus",
+        "tomwer",
+        "file",
+        "edition",
+        "NXTomo",
+        "editor",
+        "energy",
+        "distance",
+        "pixel size",
+    ]
+
+    class Inputs:
+        data = Input(name="data", type=TomwerScanBase)
+
+    class Outputs:
+        data = Output(name="data", type=TomwerScanBase)
+
+    want_main_area = True
+    resizing_enabled = True
+    compress_signal = False
+
+    def __init__(self, parent=None, *args, **kwargs):
+        super().__init__(parent=parent, *args, **kwargs)
+
+        _layout = gui.vBox(self.mainArea, self.name).layout()
+        self.widget = NXtomoEditorDialog(parent=self)
+        _layout.addWidget(self.widget)
+
+    def _validateScan(self, scan):
+        self.Outputs.data.send(scan)
+        super().hide()
+
+    @Inputs.data
+    def setScan(self, scan):
+        if scan is None:
+            pass
+        elif not isinstance(scan, HDF5TomoScan):
+            raise TypeError(
+                f"expect to have an instance of {HDF5TomoScan}. {type(scan)} provided."
+            )
+        else:
+            self.widget.setScan(scan)
+            self.show()
+            self.raise_()
+
+    def sizeHint(self):
+        return qt.QSize(400, 500)

orangecontrib/tomwer/widgets/edit/icons/nx_tomo_editor.svg

@@ -0,0 +1,123 @@
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+         d="m 15.108191,199.23424 q 0.119808,-0.21531 0.286497,-0.31775 0.166689,-0.10245 0.392414,-0.10245 0.303861,0 0.468814,0.21358 0.164953,0.21183 0.164953,0.60424 v 1.17377 h -0.321224 v -1.16335 q 0,-0.27955 -0.09897,-0.41499 -0.09897,-0.13543 -0.302124,-0.13543 -0.248298,0 -0.392414,0.16495 -0.144117,0.16496 -0.144117,0.44972 v 1.0991 h -0.321224 v -1.16335 q 0,-0.28129 -0.09897,-0.41499 -0.09897,-0.13543 -0.305597,-0.13543 -0.244825,0 -0.388941,0.16669 -0.144117,0.16495 -0.144117,0.44798 v 1.0991 h -0.321224 v -1.9447 h 0.321224 v 0.30212 q 0.10939,-0.17884 0.262188,-0.26392 0.152799,-0.0851 0.362897,-0.0851 0.211834,0 0.359423,0.10766 0.149326,0.10765 0.220516,0.31254 z"
+         style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:3.55603695px;font-family:'Noto Serif Gurmukhi';-inkscape-font-specification:'Noto Serif Gurmukhi';stroke-width:0.07525919"
+         id="path877" />
+      <path
+         inkscape:connector-curvature="0"
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+         id="path879" />
+    </g>
+  </g>
+</svg>

orangecontrib/tomwer/widgets/edit/test/test_dark_flat_patch.py

@@ -27,11 +27,18 @@ __license__ = "MIT"
 __date__ = "10/12/2021"
 
 
+import os
 import gc
+import h5py
 import pytest
+import pickle
+import tempfile
+import numpy
 from silx.gui import qt
-from tomwer.test.utils import skip_gui_test
+from silx.io.url import DataUrl
+from tomwer.tests.utils import skip_gui_test
 from silx.gui.utils.testutils import TestCaseQt
+from orangecanvas.scheme.readwrite import literal_dumps
 from orangecontrib.tomwer.widgets.edit.DarkFlatPatchOW import DarkFlatPatchOW
 
 
@@ -52,3 +59,16 @@ class TestDarkFlatPatch(TestCaseQt):
     def test(self):
         self._window.show()
         self.qWaitForWindowExposed(self._window)
+
+    def test_serialiazation(self):
+        with tempfile.TemporaryDirectory() as tmp_path:
+            file_path = os.path.join(tmp_path, "darks.hdf5")
+            with h5py.File(file_path, mode="w") as h5f:
+                h5f.require_group("darks")["0"] = numpy.ones((10, 10))
+            dark_url = DataUrl(file_path=file_path, data_path="darks/0")
+            self._window.widget.setStartDarkUrl(url=dark_url)
+            config = self._window.getConfiguration()
+            pickle.dumps(config)
+            literal_dumps(config)
+
+            self._window.setConfiguration(config)

orangecontrib/tomwer/widgets/edit/test/test_image_key_editor.py

@@ -30,7 +30,7 @@ __date__ = "10/12/2021"
 import gc
 import pytest
 from silx.gui import qt
-from tomwer.test.utils import skip_gui_test
+from tomwer.tests.utils import skip_gui_test
 from silx.gui.utils.testutils import TestCaseQt
 from orangecontrib.tomwer.widgets.edit.ImageKeyEditorOW import ImageKeyEditorOW
 

orangecontrib/tomwer/widgets/edit/test/test_image_key_upgrader.py

@@ -30,7 +30,7 @@ __date__ = "10/12/2021"
 import gc
 import pytest
 from silx.gui import qt
-from tomwer.test.utils import skip_gui_test
+from tomwer.tests.utils import skip_gui_test
 from silx.gui.utils.testutils import TestCaseQt
 from orangecontrib.tomwer.widgets.edit.ImageKeyUpgraderOW import ImageKeyUpgraderOW
 

orangecontrib/tomwer/widgets/edit/test/test_nxtomo_editor.py

@@ -0,0 +1,25 @@
+import gc
+import pytest
+from silx.gui import qt
+from tomwer.tests.utils import skip_gui_test
+from silx.gui.utils.testutils import TestCaseQt
+from orangecontrib.tomwer.widgets.edit.NXtomoEditorOW import NXtomoEditorOW
+
+
+@pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
+class TestNXtomoEditorOW(TestCaseQt):
+    """Test that the NXtomoEditorOW widget work correctly. Processing test are done in the core module. gui test are done in the tomwer.gui.edit module"""
+
+    def setUp(self):
+        super().setUp()
+        self._window = NXtomoEditorOW()
+
+    def tearDown(self):
+        self._window.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self._window.close()
+        self._window = None
+        gc.collect()
+
+    def test(self):
+        self._window.show()
+        self.qWaitForWindowExposed(self._window)

orangecontrib/tomwer/widgets/other/PythonScriptOW.py

@@ -13,13 +13,13 @@ from silx.gui import qt
 from orangewidget import widget, gui
 from orangewidget.utils import itemmodels
 from orangewidget.settings import Setting, SettingsHandler
-from orangewidget.utils.widgetpreview import WidgetPreview
 from orangewidget.widget import OWBaseWidget, Input, Output
 import tomwer.core.process.script.python
 from tomwer.core.cluster.cluster import SlurmClusterConfiguration
 from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.volume.volumebase import TomwerVolumeBase
+from tomoscan.serie import Serie
 
 __all__ = ["OWPythonScript"]
 
@@ -413,6 +413,13 @@ class OWPythonScript(widget.OWBaseWidget, openclass=True):
             default=True,
             multiple=True,
         )
+        serie = Input(
+            "serie",
+            Serie,
+            replaces=["in_serie"],
+            default=True,
+            multiple=True,
+        )
 
     class Outputs:
         data = Output("data", TomwerScanBase, replaces=["out_data"])
@@ -425,6 +432,7 @@ class OWPythonScript(widget.OWBaseWidget, openclass=True):
         cluster_config = Output(
             "cluster_config", SlurmClusterConfiguration, replaces=["out_cluster_config"]
         )
+        serie = Output("serie", dict, replaces=["out_serie"])
 
     signal_names = (
         "data",
@@ -433,6 +441,7 @@ class OWPythonScript(widget.OWBaseWidget, openclass=True):
         "object",
         "configuration",
         "cluster_config",
+        "serie",
     )
 
     settingsHandler = PrepareSavingSettingsHandler()
@@ -453,7 +462,7 @@ class OWPythonScript(widget.OWBaseWidget, openclass=True):
         for name in self.signal_names:
             setattr(self, name, {})
 
-        for s in self.libraryListSource:
+        for s in self.libraryListSource:  # pylint: disable=E1133
             s.flags = 0
 
         self._cachedDocuments = {}
@@ -619,13 +628,17 @@ class OWPythonScript(widget.OWBaseWidget, openclass=True):
         self.handle_input(data, id, "configuration")
 
     @Inputs.future_tomo_obj  # noqa F811
-    def set_object(self, data, id):  # noqa F811
+    def set_future_tomo_object(self, data, id):  # noqa F811 pylint: disable=E0102
         self.handle_input(data, id, "future_tomo_obj")
 
     @Inputs.cluster_config  # noqa F811
-    def set_object(self, data, id):  # noqa F811
+    def set_cluster_config(self, data, id):  # noqa F811 pylint: disable=E0102
         self.handle_input(data, id, "cluster_config")
 
+    @Inputs.serie  # noqa F811
+    def set_serie(self, data, id):
+        self.handle_input(data, id, "serie")
+
     def handleNewSignals(self):
         self.commit()
 
@@ -643,7 +656,7 @@ class OWPythonScript(widget.OWBaseWidget, openclass=True):
         self.libraryList.append(Script("New script", self.text.toPlainText(), 0))
         self.setSelectedScript(len(self.libraryList) - 1)
 
-    def onAddScriptFromFile(self, *args):
+    def onAddScriptFromFile(self, *args):  # pragma: no cover
         filename, _ = qt.QFileDialog.getOpenFileName(
             self,
             "Open Python Script",
@@ -716,7 +729,7 @@ class OWPythonScript(widget.OWBaseWidget, openclass=True):
             self.text.document().setPlainText(self.libraryList[index].script)
             self.text.document().setModified(False)
 
-    def saveScript(self):
+    def saveScript(self):  # pragma: no cover
         index = self.selectedScriptIndex()
         if index is not None:
             script = self.libraryList[index]
@@ -772,7 +785,3 @@ class OWPythonScript(widget.OWBaseWidget, openclass=True):
                 getattr(self.Error, signal)()
                 out_var = None
             getattr(self.Outputs, signal).send(out_var)
-
-
-if __name__ == "__main__":  # pragma: no cover
-    WidgetPreview(OWPythonScript).run()