tomwer 1.2.9__py3-none-any.whl → 1.3.0a0__py3-none-any.whl

tomwer/io/utils/tomoobj.py

@@ -36,7 +36,7 @@ def get_tomo_objs_instances(tomo_objs: tuple) -> tuple:
     """
     instances = []
     has_scans = False
-    has_vols = True
+    has_vols = False
     for tomo_obj in tomo_objs:
 
         def get_scans():
@@ -45,9 +45,7 @@ def get_tomo_objs_instances(tomo_objs: tuple) -> tuple:
             except Exception:
                 try:
                     return ScanFactory.create_scan_objects(tomo_obj)
-                except Exception as e:
-                    raise e
-                    print("error is", e)
+                except Exception:
                     return tuple()
 
         def get_volumes():
@@ -68,12 +66,12 @@ def get_tomo_objs_instances(tomo_objs: tuple) -> tuple:
             # we start by scan because they have a 'definition' as NXtomo available.
             # otherwise we might get some entries defined as scan AND volume...
             # for stitching we expect users to ask of for one or the other.
-            volumes = get_volumes()
+            volumes = get_volumes() or ()
             if len(volumes) > 0:
                 has_vols = True
                 instances.extend(volumes)
         else:
-            has_scans = True
+            has_scans = len(scans_found) > 0
             instances.extend(scans_found)
 
     return tuple(instances), (has_scans, has_vols)

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/) -->
+
+<svg
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+   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="ruler.svg"
+   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"
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+     borderopacity="0.25"
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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"
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+   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"
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+     inkscape:window-height="1131"
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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
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+   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"
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+     inkscape:cy="25.863139"
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+     inkscape:window-height="1131"
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+     inkscape:window-y="32"
+     inkscape:window-maximized="1"
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+       id="text236"
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+         sodipodi:role="line"
+         id="tspan234"
+         style="fill:#000000;fill-opacity:1;stroke:none;stroke-width:1.27263"
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+</svg>

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)

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}"

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
 
@@ -85,7 +85,7 @@ class DarkRefCopyProcessStack(FIFO, qt.QObject):
         _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-flat-copy", data.path
             try:
@@ -107,7 +107,7 @@ class DarkRefCopyProcessStack(FIFO, qt.QObject):
             # 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):
@@ -132,9 +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):
     """
@@ -167,15 +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)

tomwer/synctools/stacks/reconstruction/normalization.py

@@ -37,7 +37,7 @@ from silx.gui import qt
 from tomwer.core.process.reconstruction.normalization import SinoNormalizationTask
 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 INormalizationProcessStack(FIFO, qt.QObject):
         )
         _logger.processStarted(f"start intensity normalization {data}")
         assert isinstance(data, TomwerScanBase)
-        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 intensity normalization", data.path
             ProcessManager().notify_dataset_state(

tomwer/synctools/stacks/reconstruction/saaxis.py

@@ -37,7 +37,7 @@ from silx.gui import qt
 from tomwer.core.process.reconstruction.saaxis import SAAxisTask
 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 tomwer.synctools.saaxis import QSAAxisParams
 
@@ -78,7 +78,7 @@ class SAAxisProcessStack(FIFO, qt.QObject):
         self._data_currently_computed = data
         saaxis_params = QSAAxisParams.from_dict(configuration)
         saaxis_params.frame_width = data.dim_1
-        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 saaxis calculation {data.path}"
             ProcessManager().notify_dataset_state(

tomwer/synctools/stacks/reconstruction/sadeltabeta.py

@@ -39,7 +39,7 @@ from tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta import (
 )
 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 tomwer.synctools.sadeltabeta import QSADeltaBetaParams
 
@@ -79,7 +79,7 @@ class SADeltaBetaProcessStack(FIFO, qt.QObject):
             data.sa_delta_beta_params = QSADeltaBetaParams()
         self._data_currently_computed = data
         sa_delta_beta_params = QSADeltaBetaParams.from_dict(configuration)
-        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 sa-delta-beta-axis calculation {data.path}"
             ProcessManager().notify_dataset_state(