tomwer 1.2.1__py3-none-any.whl → 1.3.12__py3-none-any.whl

tomwer/resources/gui/icons/ruler.svg

@@ -0,0 +1,273 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
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tomwer/resources/gui/icons/short_description.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="svg975"
+   inkscape:version="1.2.2 (b0a8486541, 2022-12-01)"
+   sodipodi:docname="short.svg"
+   inkscape:export-filename="short.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="namedview977"
+     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="6.7277216"
+     inkscape:cx="13.154528"
+     inkscape:cy="36.862405"
+     inkscape:window-width="1920"
+     inkscape:window-height="1131"
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+     inkscape:label="Layer 1"
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+    <text
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+       style="font-style:italic;font-size:5.95578px;font-family:'Nimbus Sans';-inkscape-font-specification:'Nimbus Sans Italic';opacity:0.907409;fill:#000000;stroke-width:0.759712;stroke-miterlimit:3.5"
+       x="-0.02063646"
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+       transform="scale(0.89694342,1.1148975)"><tspan
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+         id="tspan1148"
+         style="stroke-width:0.759713"
+         x="-0.02063646"
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+  </g>
+</svg>

tomwer/resources/gui/icons/url.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="url.svg"
+   inkscape:export-filename="url.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="3.3638608"
+     inkscape:cx="36.119211"
+     inkscape:cy="25.863139"
+     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">
+    <text
+       xml:space="preserve"
+       style="font-style:italic;font-size:9.97676px;font-family:'Nimbus Sans';-inkscape-font-specification:'Nimbus Sans Italic';opacity:0.907409;fill:#000000;fill-opacity:1;stroke:#000000;stroke-width:1.27262;stroke-miterlimit:3.5"
+       x="0.16326435"
+       y="9.5309248"
+       id="text236"
+       transform="scale(0.97072659,1.0301562)"><tspan
+         sodipodi:role="line"
+         id="tspan234"
+         style="fill:#000000;fill-opacity:1;stroke:none;stroke-width:1.27263"
+         x="0.16326435"
+         y="9.5309248">url</tspan></text>
+  </g>
+</svg>

tomwer/resources/gui/illustrations/no_rot.svg

@@ -14,7 +14,7 @@
    height="160"
    version="1.1"
    inkscape:version="0.48.5 r10040"
-   sodipodi:docname="lamino_beta_angle.svg">
+   sodipodi:docname="no_rot.svg">
   <sodipodi:namedview
      pagecolor="#ffffff"
      bordercolor="#666666"

tomwer/synctools/stacks/edit/darkflatpatch.py

@@ -38,7 +38,7 @@ from tomwer.core.process.edit import darkflatpatch
 from tomwer.core.scan.edfscan import EDFTomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import get_lbsram_path, isOnLbsram
-from tomwer.core.utils import isLowOnMemory
+from tomwer.core.utils.lbsram import is_low_on_memory
 
 from ..processingstack import FIFO, ProcessingThread
 
@@ -60,7 +60,7 @@ class DarkFlatPatchProcessStack(FIFO, qt.QObject):
         assert isinstance(data, TomwerScanBase)
         self._computationThread.finished.connect(self._end_threaded_computation)
 
-        if isOnLbsram(data) and isLowOnMemory(get_lbsram_path()) is True:
+        if isOnLbsram(data) and is_low_on_memory(get_lbsram_path()) is True:
             # if computer is running into low memory on lbsram skip it
             mess = "low memory, skip dark-flat-patch reconstruction for", data.path
             _logger.processSkipped(mess)
@@ -142,18 +142,23 @@ class _DarkFlatPatchProcessingThread(ProcessingThread, SuperviseProcess):
         for key in keys:
             if isinstance(configuration_to_dump[key], DataUrl):
                 configuration_to_dump[key] = configuration_to_dump[key].path()
-        try:
-            darkflatpatch.DarkFlatPatchTask._register_process(
-                process_file=self._scan.process_file,
-                entry=entry,
-                configuration=configuration_to_dump,
-                results={},
-                process=darkflatpatch.DarkFlatPatchTask,
-                process_index=index,
-                overwrite=True,
-            )
-        except Exception as e:
-            _logger.warning(f"Fail to register DarkFlatPatch process. Reason is {e}")
+
+        with self._scan.acquire_process_file_lock():
+
+            try:
+                darkflatpatch.DarkFlatPatchTask._register_process(
+                    process_file=self._scan.process_file,
+                    entry=entry,
+                    configuration=configuration_to_dump,
+                    results={},
+                    process=darkflatpatch.DarkFlatPatchTask,
+                    process_index=index,
+                    overwrite=True,
+                )
+            except Exception as e:
+                _logger.warning(
+                    f"Fail to register DarkFlatPatch process. Reason is {e}"
+                )
         info = f"Dark-flat patched for {self._scan}."
         _logger.processSucceed(info)
         ProcessManager().notify_dataset_state(

tomwer/synctools/stacks/edit/imagekeyeditor.py

@@ -36,7 +36,7 @@ from silx.gui import qt
 from tomwer.core.process.edit import imagekeyeditor
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import get_lbsram_path, isOnLbsram
-from tomwer.core.utils import isLowOnMemory
+from tomwer.core.utils.lbsram import is_low_on_memory
 
 from ..processingstack import FIFO, ProcessingThread
 
@@ -57,7 +57,7 @@ class ImageKeyEditorProcessStack(FIFO, qt.QObject):
         assert isinstance(data, TomwerScanBase)
         self._computationThread.finished.connect(self._end_threaded_computation)
 
-        if isOnLbsram(data) and isLowOnMemory(get_lbsram_path()) is True:
+        if isOnLbsram(data) and is_low_on_memory(get_lbsram_path()) is True:
             # if computer is running into low memory on lbsram skip it
             mess = f"low memory, skip image-key-edition for {data.path}"
             _logger.processSkipped(mess)

tomwer/synctools/stacks/reconstruction/axis.py

@@ -37,10 +37,10 @@ from silx.gui import qt
 from tomwer.core.process.reconstruction.axis import AxisTask
 from tomwer.core.process.reconstruction.axis.axis import NoAxisUrl
 from tomwer.core.process.reconstruction.axis.mode import AxisMode
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import get_lbsram_path, isOnLbsram
-from tomwer.core.utils import isLowOnMemory
+from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.synctools.axis import QAxisRP
 
 from ..processingstack import FIFO, ProcessingThread
@@ -70,7 +70,7 @@ class AxisProcessStack(FIFO, qt.QObject):
         self._data_currently_computed = data
         self._axis_params.frame_width = data.dim_1
         mode = self._axis_params.mode
-        if isOnLbsram(data) and isLowOnMemory(get_lbsram_path()) is True:
+        if isOnLbsram(data) and is_low_on_memory(get_lbsram_path()) is True:
             # if computer is running into low memory on lbsram skip it
             mess = "low memory, skip axis calculation", data.path
             ProcessManager().notify_dataset_state(
@@ -92,7 +92,7 @@ class AxisProcessStack(FIFO, qt.QObject):
                 cor = 0
             data._axis_params.set_relative_value(cor)
             cor = data._axis_params.relative_cor_value
-            if isinstance(data, HDF5TomoScan):
+            if isinstance(data, NXtomoScan):
                 entry = data.entry
             else:
                 entry = "entry"

tomwer/synctools/stacks/reconstruction/castvolume.py

@@ -38,7 +38,7 @@ from tomwer.core.process.reconstruction.nabu.castvolume import CastVolumeTask
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import get_lbsram_path, isOnLbsram
 from tomwer.core.tomwer_object import TomwerObject
-from tomwer.core.utils import isLowOnMemory
+from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.volume.volumebase import TomwerVolumeBase
 from tomwer.core.volume.volumefactory import VolumeFactory
 
@@ -81,7 +81,7 @@ class CastVolumeProcessStack(FIFO, qt.QObject):
         if (
             path is not None
             and isOnLbsram(path)
-            and isLowOnMemory(get_lbsram_path()) is True
+            and is_low_on_memory(get_lbsram_path()) is True
         ):
             # if computer is running into low memory on lbsram skip it
             mess = f"low memory, skip volume cast {data}"
@@ -94,11 +94,26 @@ class CastVolumeProcessStack(FIFO, qt.QObject):
             self.scan_ready(scan=data)
         else:
             self._data_currently_computed = data
-            self._computationThread.init(data=data, configuration=configuration)
-            # need to manage connect before starting it because
-            fct_callback = functools.partial(self._end_threaded_computation, callback)
-            self._computationThread.finished.connect(fct_callback)
-            self._computationThread.start()
+            try:
+                self._computationThread.init(data=data, configuration=configuration)
+            except ValueError as e:
+                # initialization can fail (for example for cast volume is there is no volume or be case this will raise an error)
+                # then we want to keep the thread active
+                self._data_currently_computed = None
+                ProcessManager().notify_dataset_state(
+                    dataset=data, process=self._process_id, state=DatasetState.SKIPPED
+                )
+                _logger.processSkipped(f"thread initialization failed. Error is {e}")
+                if callback is not None:
+                    callback()
+                self.scan_ready(scan=data)
+            else:
+                # need to manage connect before starting it because
+                fct_callback = functools.partial(
+                    self._end_threaded_computation, callback
+                )
+                self._computationThread.finished.connect(fct_callback)
+                self._computationThread.start()
 
     def _end_computation(self, data, future_tomo_obj, callback):
         """

tomwer/synctools/stacks/reconstruction/dkrefcopy.py

@@ -38,7 +38,7 @@ from silx.gui import qt
 from tomwer.core.process.reconstruction.darkref.darkrefscopy import DarkRefsCopy
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import get_lbsram_path, isOnLbsram
-from tomwer.core.utils import isLowOnMemory
+from tomwer.core.utils.lbsram import is_low_on_memory
 
 from ..processingstack import FIFO, ProcessingThread
 
@@ -53,7 +53,12 @@ class DarkRefCopyProcessStack(FIFO, qt.QObject):
     """Signal emit when dark or flat are set by a scan. str is the scan identifier"""
 
     def __init__(self, process_id=None):
-        self._save_dir = tempfile.mkdtemp()
+        try:
+            self._save_dir = tempfile.mkdtemp()
+        except Exception as e:
+            _logger.warning(
+                f"unable to create save dir. Error is {e}. Won't be able to copy any dark or flat"
+            )
         qt.QObject.__init__(self)
         FIFO.__init__(self, process_id=process_id)
 
@@ -77,26 +82,32 @@ class DarkRefCopyProcessStack(FIFO, qt.QObject):
             process=self,
             state=DatasetState.ON_GOING,
         )
-        _logger.processStarted(f"dk-ref-copy {data}")
+        _logger.processStarted(f"dk-flat-copy {data}")
         assert isinstance(data, TomwerScanBase)
         self._data_currently_computed = data
-        if isOnLbsram(data) and isLowOnMemory(get_lbsram_path()) is True:
+        if isOnLbsram(data) and is_low_on_memory(get_lbsram_path()) is True:
             # if computer is running into low memory on lbsram skip it
-            mess = "low memory, skip dk-ref-copy", data.path
-            ProcessManager().notify_dataset_state(
-                dataset=data, process=self._process_id, state=DatasetState.SKIPPED
-            )
-            _logger.processSkipped(mess)
-            if callback is not None:
-                callback()
-            self.scan_ready(scan=data)
+            mess = "low memory, skip dk-flat-copy", data.path
+            try:
+                ProcessManager().notify_dataset_state(
+                    dataset=data, process=self, state=DatasetState.SKIPPED
+                )
+                _logger.processSkipped(mess)
+                if callback is not None:
+                    callback()
+            except Exception as e:
+                _logger.error(e)
+            try:
+                FIFO._end_threaded_computation(self)
+            except Exception as e:
+                _logger.error(e)
         else:
             self._data_currently_computed = data
             self._computationThread.init(data=data, inputs=configuration)
             # need to manage connect before starting it because
             fct_callback = functools.partial(self._end_threaded_computation, callback)
             self._computationThread.finished.connect(fct_callback)
-            self._computationThread.sigRefSetted.connect(self._repeatSigRefSetted)
+            self._computationThread.sigRefSetted.connect(self.sigRefSetted)
             self._computationThread.start()
 
     def _end_computation(self, data, future_tomo_obj, callback):
@@ -121,9 +132,6 @@ class DarkRefCopyProcessStack(FIFO, qt.QObject):
     def _create_processing_thread(self, process_id=None) -> qt.QThread:
         return _ProcessingThread(process_id=process_id, save_dir=self._save_dir)
 
-    def _repeatSigRefSetted(self, *args, **kwargs):
-        self.sigRefSetted.emit(*args, **kwargs)
-
 
 class _ProcessingThread(ProcessingThread, SuperviseProcess):
     """
@@ -156,15 +164,12 @@ class _ProcessingThread(ProcessingThread, SuperviseProcess):
         process = DarkRefsCopyWithSig(
             parent=self.parent(), inputs=inputs, process_id=self.process_id
         )
-        process.sigRefSetted.connect(self._repeatSigRefSetted)
+        process.sigRefSetted.connect(self.sigRefSetted)
         try:
             process.run()
         except Exception as e:
             _logger.warning(e)
 
-    def _repeatSigRefSetted(self, *args, **kwargs):
-        self.sigRefSetted.emit(*args, **kwargs)
-
 
 class DarkRefsCopyWithSig(qt.QObject, DarkRefsCopy):
     sigRefSetted = qt.Signal(str)

tomwer/synctools/stacks/reconstruction/nabu.py

@@ -36,7 +36,7 @@ from silx.gui.utils import blockSignals
 
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.settings import get_lbsram_path, isOnLbsram
-from tomwer.core.utils import isLowOnMemory
+from tomwer.core.utils.lbsram import is_low_on_memory
 from tomwer.core.process.reconstruction.nabu.nabuslices import NabuSlicesTask
 from tomwer.core.process.reconstruction.nabu.nabuvolume import NabuVolumeTask
 
@@ -66,7 +66,7 @@ class NabuSliceProcessStack(FIFO, qt.QObject):
         assert isinstance(data, TomwerScanBase)
         self._computationThread.finished.connect(self._end_threaded_computation)
 
-        if isOnLbsram(data) and isLowOnMemory(get_lbsram_path()) is True:
+        if isOnLbsram(data) and is_low_on_memory(get_lbsram_path()) is True:
             # if computer is running into low memory on lbsram skip it
             mess = f"low memory, skip nabu reconstruction for {data.path}"
             _logger.processSkipped(mess)