tomwer 1.4.4__py3-none-any.whl → 1.4.5__py3-none-any.whl

tomwer/core/process/reconstruction/nabu/nabucommon.py

@@ -15,6 +15,8 @@ import sys
 import numpy
 from silx.io.url import DataUrl
 from silx.io.utils import open as open_hdf5
+from silx.gui.utils import concurrent
+
 from sluurp.executor import submit as submit_to_slurm_cluster
 from sluurp.job import SBatchScriptJob
 from tomoscan.io import HDF5File
@@ -41,6 +43,8 @@ from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.utils.slurm import get_slurm_script_name, is_slurm_available
 from tomwer.core.volume.volumefactory import VolumeFactory
+from tomwer.core.resourcemanager import HDF5VolumeManager
+from tomwer.core.volume.hdf5volume import HDF5VolumeIdentifier
 
 from . import settings, utils
 
@@ -279,25 +283,43 @@ class _NabuBaseReconstructor:
                 success=True,
                 config=config_to_dump,
             )
-        elif self.target is Target.LOCAL:
-            _logger.info(f"run {info} for {self.scan} with {config_to_dump}")
-            return self._run_nabu_locally(
-                conf_file=config_file,
-                file_format=file_format,
-                config_to_dump=config_to_dump,
-                axis=config_to_dump["reconstruction"].get("slice_plane", "XY"),
-            )
-        elif self.target is Target.SLURM:
-            _logger.info(
-                f"run {info} on slurm for {self.scan.path} with {config_to_dump}"
-            )
-            return self._run_nabu_on_slurm(
-                conf_file=config_file,
-                config_to_dump=config_to_dump,
-                cluster_config=self.cluster_config.to_dict(),
-                process_name=process_name,
-                info=info,
-            )
+        elif self.target in (Target.LOCAL, Target.SLURM):
+            axis = config_to_dump["reconstruction"].get("slice_plane", "XY")
+            if file_format in ("hdf5", "h5", "hdf"):
+                vol_identifiers = utils.get_recons_volume_identifier(
+                    file_prefix=config_to_dump["output"]["file_prefix"],
+                    location=config_to_dump["output"]["location"],
+                    slice_index=None,
+                    scan=self.scan,
+                    file_format=file_format,
+                    axis=axis,
+                )
+                # release potential resource lockers (like the HDF5 volume viewer)
+                for vol_identifier in vol_identifiers:
+                    if isinstance(vol_identifier, HDF5VolumeIdentifier):
+                        concurrent.submitToQtMainThread(
+                            HDF5VolumeManager.release_resource,
+                            vol_identifier.file_path,
+                        )
+            if self.target is Target.LOCAL:
+                _logger.info(f"run {info} for {self.scan} with {config_to_dump}")
+                return self._run_nabu_locally(
+                    conf_file=config_file,
+                    file_format=file_format,
+                    config_to_dump=config_to_dump,
+                    axis=axis,
+                )
+            elif self.target is Target.SLURM:
+                _logger.info(
+                    f"run {info} on slurm for {self.scan.path} with {config_to_dump}"
+                )
+                return self._run_nabu_on_slurm(
+                    conf_file=config_file,
+                    config_to_dump=config_to_dump,
+                    cluster_config=self.cluster_config.to_dict(),
+                    process_name=process_name,
+                    info=info,
+                )
         else:
             raise ValueError(f"{self.target} is not recognized as a valid target")
 
@@ -362,7 +384,7 @@ class _NabuBaseReconstructor:
             self._process.kill()
             outs, errs = self._process.communicate()
 
-        recons_urls = utils.get_recons_volume_identifier(
+        recons_vol_identifiers = utils.get_recons_volume_identifier(
             file_prefix=config_to_dump["output"]["file_prefix"],
             location=config_to_dump["output"]["location"],
             slice_index=None,
@@ -372,7 +394,7 @@ class _NabuBaseReconstructor:
         )
         return ResultsLocalRun(
             success=not nabu_std_err_has_error(errs),
-            results_identifiers=recons_urls,
+            results_identifiers=recons_vol_identifiers,
             std_out=outs,
             std_err=errs,
             config=config_to_dump,  # config_slices,

tomwer/core/process/reconstruction/nabu/utils.py

@@ -12,6 +12,7 @@ from nabu.pipeline.fullfield.nabu_config import (
 )
 from silx.utils.enum import Enum as _Enum
 
+from tomoscan.identifier import VolumeIdentifier
 import tomwer.version
 from tomwer.core.process.reconstruction.nabu.plane import NabuPlane
 from tomwer.core.scan.edfscan import EDFTomoScan
@@ -100,7 +101,7 @@ def get_recons_volume_identifier(
     scan: TomwerScanBase,
     slice_index: int | None,
     axis: NabuPlane,
-) -> tuple:
+) -> tuple[VolumeIdentifier]:
     """
     return tuple of DataUrl for existings slices
     """
@@ -160,19 +161,6 @@ def get_recons_volume_identifier(
             ),
         )
 
-    # case of the multitiff. Not handled by tomwer
-    # elif file_format == "tiff":
-    #     # for single frame tiff nabu uses another convention by saving it 'directly'.
-    #     volumes = (
-    #         MultiTIFFVolume(
-    #             file_path=os.path.join(
-    #                 location,
-    #                 file_prefix,
-    #                 ".".join([file_prefix, file_format]),
-    #             ),
-    #         ),
-    #     )
-
     else:
         raise ValueError(f"file format not managed: {file_format}")
 

tomwer/core/resourcemanager.py

@@ -0,0 +1,33 @@
+class BaseResourceObserver:
+    """base class of the resource observer"""
+
+    def release_resource(self, resource):
+        raise NotImplementedError("Base class")
+
+
+class _DummyResourceManager:
+    """
+    Simple resource manager. It holds a set of observer tha must release a resource when requested
+    Observers must implement the 'BaseResourceObserver'
+    """
+
+    def __init__(self):
+        self._observers = set()
+
+    def register(self, observer):
+        """Register a process to be notified when the resource should be released."""
+        if observer not in self._observers:
+            self._observers.add(observer)
+
+    def unregister(self, observer):
+        """Unregister a process so it won't be notified anymore."""
+        if observer in self._observers:
+            self._observers.remove(observer)
+
+    def release_resource(self, resource: str):
+        """Force all observer to release the given resource"""
+        for observer in self._observers:
+            observer.release_resource(resource)
+
+
+HDF5VolumeManager = _DummyResourceManager()

tomwer/gui/reconstruction/axis/ControlWidget.py

@@ -211,7 +211,7 @@ class _PositionInfoWidget(qt.QWidget):
         else:
             value = float(self._relativePositionQLE.text())
             # make sure we only emit the signal if the value changed (and when the Qline has been edited).
-            if self._axis_params.relative_cor_value is None or (
+            if isinstance(self._axis_params.relative_cor_value, (type(None), str)) or (
                 self._axis_params is not None
                 and not numpy.isclose(
                     value, self._axis_params.relative_cor_value, atol=1e-3

tomwer/gui/visualization/volumeviewer.py

@@ -6,6 +6,8 @@ import h5py
 
 import numpy
 import numpy.lib.npyio
+
+import os
 import silx
 from silx.gui import qt
 from silx.gui.colors import Colormap
@@ -18,6 +20,7 @@ from tomwer.core.volume.volumefactory import VolumeFactory
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.gui.visualization.reconstructionparameters import ReconstructionParameters
 from tomwer.core.volume.hdf5volume import HDF5Volume
+from tomwer.core.resourcemanager import BaseResourceObserver, HDF5VolumeManager
 from tomoscan.identifier import VolumeIdentifier
 
 from silx.gui.widgets.WaitingOverlay import WaitingOverlay
@@ -215,9 +218,9 @@ class _TomoApplicationContext(DataViewHooks):
         return self.__defaultColormapDialog
 
 
-class VolumeViewer(qt.QMainWindow):
+class VolumeViewer(qt.QMainWindow, BaseResourceObserver):
     def __init__(self, parent):
-        qt.QMainWindow.__init__(self, parent)
+        super().__init__(parent)
 
         self._volume_loaded_in_background = (None, None)
         # store the volume loaded in the background and the thread used for it as (volume_identifier, thread)
@@ -259,6 +262,8 @@ class VolumeViewer(qt.QMainWindow):
         loading data on the fly and avoid loading everything into memory for
         hdf5."""
         self.__last_mode = None
+        # register the viewer as observer of the HDF5 volume (handle resource conflict)
+        HDF5VolumeManager.register(self)
 
     def _close_h5_file(self):
         if self._h5_file is not None:
@@ -266,9 +271,21 @@ class VolumeViewer(qt.QMainWindow):
         self._h5_file = None
 
     def close(self):
+        HDF5VolumeManager.unregister(self)
         self._close_h5_file()
         super().close()
 
+    def release_resource(self, resource: str):
+        if self._h5_file is not None and resource in (
+            self._h5_file.filename,
+            os.path.abspath(self._h5_file.filename),
+        ):
+            _logger.warning(
+                f"{resource} about to be overwrite. Closing resource and cleaning plot."
+            )
+            self._close_h5_file()
+            self.clear()
+
     def setScan(self, scan):
         self.clear()
         if scan is None:
@@ -276,7 +293,6 @@ class VolumeViewer(qt.QMainWindow):
 
         elif len(scan.latest_vol_reconstructions) == 0:
             _logger.warning(f"No reconstructed volume for {scan}")
-            self.clear()
             self._infoWidget.setScan(scan)
         else:
             self._set_volumes(volumes=scan.latest_vol_reconstructions)

tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 4
-MICRO = 4
+MICRO = 5
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.4.4.dist-info → tomwer-1.4.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.4.4
+Version: 1.4.5
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: Henri Payno, Pierre Paleo, Pierre-Olivier Autran, Jérôme Lesaint, Alessandro Mirone

{tomwer-1.4.4.dist-info → tomwer-1.4.5.dist-info}/RECORD

@@ -220,7 +220,7 @@ orangecontrib/tomwer/widgets/visualization/tests/__init__.py,sha256=47DEQpj8HBSa
 tomwer/__init__.py,sha256=GeLSeY4__z-HQZu1y4ptZ5Y1OeXFvG8kuEwWXhkeaMA,360
 tomwer/__main__.py,sha256=7tCADiS4u7k1PCxFhlRAcYSIOpxQTGUTx8sCEQ-hi1E,8707
 tomwer/utils.py,sha256=7h7dEgKAEUmQ43jkULvC1B9Adl55nkCty-SEKUKCl4U,7008
-tomwer/version.py,sha256=cQn0hp7H0RGoblTK9Od0_A4QCnVaVE5G-t2RThewbMg,4386
+tomwer/version.py,sha256=YCgU5UeQQFVVtrqoIyPtoYMjDfnF7xbfD1Fop0kLlSA,4386
 tomwer/app/__init__.py,sha256=RYMB2YhbQaoMXC8W-oOyfZ_Y1vmHD7L13YkKeAMuShM,85
 tomwer/app/axis.py,sha256=OhDgMj_gS-45PnjKBTyOCOkmZ1Iy-Tb6Dj66mzQg0sU,5827
 tomwer/app/canvas.py,sha256=sM368nniUwbQXLA-oNCg1iNwMMol_ZGTKbiw8WsC4yw,1539
@@ -256,6 +256,7 @@ tomwer/app/stitching/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hS
 tomwer/app/stitching/common.py,sha256=TCXNnAz2MSJrrogB5iWptktxq-g5ED2FUt_jMnDXpnQ,14723
 tomwer/core/__init__.py,sha256=ry3BZxaZzsbjymW1wqPcKROzJO9ePkiiqWp1JRVOrS8,72
 tomwer/core/futureobject.py,sha256=YQE6zROyDFu2PYBI7hxZKpn-K_FqZQ9xGSIyqMErK5U,5114
+tomwer/core/resourcemanager.py,sha256=VLNnVodMa-HOMZhN2qpUR_L6phJ8IHPUEPYMxuW6VHg,1067
 tomwer/core/settings.py,sha256=57qD44LU_3eB50rD7RHdg5nBweiHerzWbXHcBUna6gY,4089
 tomwer/core/signal.py,sha256=I5TUcyeBZzrEh1SFGs-ylJSL1aBs41ZFb3IJo3O_55c,6115
 tomwer/core/tomwer_object.py,sha256=rIaD1QlN3Q0cR5h9Sap1Whn4lawu5z9zZ1KspdhYbg0,2023
@@ -334,14 +335,14 @@ tomwer/core/process/reconstruction/darkref/settings.py,sha256=35jliuOIjMKTOJjgn4
 tomwer/core/process/reconstruction/nabu/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/core/process/reconstruction/nabu/castvolume.py,sha256=4VEVnJxWfG8_Ku2uhUSQAgGfvP_08mXswmC3bHU7E4M,9317
 tomwer/core/process/reconstruction/nabu/helical.py,sha256=gauUkoPiShvnvMQrCQXv28g0yLe-GceML5kYMSXmNIg,1997
-tomwer/core/process/reconstruction/nabu/nabucommon.py,sha256=s1KxEzHQJ09JEWP3_EvKFe51k1boi_a8YRlbs3TppdE,23338
+tomwer/core/process/reconstruction/nabu/nabucommon.py,sha256=-rXMJmLL3e7BCF4keT7JcKmC5SuJQsCrvIDCYcbum48,24519
 tomwer/core/process/reconstruction/nabu/nabuscores.py,sha256=e5tRG1QtmVAdXb8KHMTMtBXA3KQXqKKcqipY2HzMURg,25275
 tomwer/core/process/reconstruction/nabu/nabuslices.py,sha256=WAmNlfyRWL0zhEE8jMjMg7WyzPM4BcBA6bWpaH8O53A,32101
 tomwer/core/process/reconstruction/nabu/nabuvolume.py,sha256=Fn0tkPDTDJQaMEJA4LzpPp0ZtG4MIu9YN82-jesxRKo,20052
 tomwer/core/process/reconstruction/nabu/plane.py,sha256=366gWprWw8Rlob8jsMn753CqgudruvvVauU0ihH2lU4,400
 tomwer/core/process/reconstruction/nabu/settings.py,sha256=3AJpxVQbJziw4v6F26Ppz8Q9vc9ZNepTWygqpCAbIEM,955
 tomwer/core/process/reconstruction/nabu/target.py,sha256=59BbpzpBRVKEpZowcZVgdAj1GLKZGVJ52s3XA7ouLPs,122
-tomwer/core/process/reconstruction/nabu/utils.py,sha256=MvGMeAKrpSzScvRowe2ZbyQyNLj80vxm3jk-ldMMPEU,16519
+tomwer/core/process/reconstruction/nabu/utils.py,sha256=ymORZjJR7YkQ0VBujDyptF0xXzkj1dCwo29NjXvhA2E,16140
 tomwer/core/process/reconstruction/nabu/test/test_castvolume.py,sha256=v7USCU3z0zeW4TPs-slNJJei6t6B_UeqeJG5MV9qRII,3881
 tomwer/core/process/reconstruction/nabu/test/test_nabu_utils.py,sha256=8HpR_1iLkE32GYYaOyS84SR7_5nh1e48E3W4N34666g,15347
 tomwer/core/process/reconstruction/nabu/test/test_nabunormalization.py,sha256=5rHDwUROEBlsEFsZoy8mmcdRpziEetF9g_oFyxlvS6k,6010
@@ -545,7 +546,7 @@ tomwer/gui/reconstruction/axis/AxisSettingsWidget.py,sha256=7GpHteE2j9RUo-jUQoJd
 tomwer/gui/reconstruction/axis/AxisWidget.py,sha256=nkORZHLo8D3Sk8j-8QVr9l3Qse66s-Nv-tB6kCkSMTY,19794
 tomwer/gui/reconstruction/axis/CalculationWidget.py,sha256=E9zwJ2dNnc7KGH1QHRZE2eElIzj_r4GbPCIG_hn2yhw,8628
 tomwer/gui/reconstruction/axis/CompareImages.py,sha256=jqzlMBU_tfIdR1yHuZa8Avt8Te0EPBkjI6R4TY6kIlw,11425
-tomwer/gui/reconstruction/axis/ControlWidget.py,sha256=DsBPFIEZCva-JPUFxORjkAnoYfgb5udfJ71W-fCwgRY,10686
+tomwer/gui/reconstruction/axis/ControlWidget.py,sha256=w2kNLuIhQhGT3KpEYWWq4XJks3Kr7R2aOPCTKz4je4U,10709
 tomwer/gui/reconstruction/axis/EstimatedCORWidget.py,sha256=dL9SCjPEZ7MQLGZP0gZARb-rxD8YYSl-gcFyuN14jwg,17081
 tomwer/gui/reconstruction/axis/EstimatedCorComboBox.py,sha256=Hq8o6X5-iVMqltGcpy2E5OpCP5nNV353Mepsf_R7zVY,4434
 tomwer/gui/reconstruction/axis/InputWidget.py,sha256=UhEWL3aJG56PfkI7DKw-sBd6hDsRJ2NnQ0XN0nBmM6g,13052
@@ -668,7 +669,7 @@ tomwer/gui/visualization/scanoverview.py,sha256=boXasH759jc8p9v43nFqq6oxFGDMn8gg
 tomwer/gui/visualization/sinogramviewer.py,sha256=M91xw63ptfG1erPt6jvFH5uqmV6KUm1B4xreco6Ixto,8380
 tomwer/gui/visualization/tomoobjoverview.py,sha256=8tsVhTZw0upDSYzE1W8VXCWMBmSFcEP7SlcGA6Nl6ig,1995
 tomwer/gui/visualization/volumeoverview.py,sha256=k0OLdw5dvbDlWFnk6I8TlrJu03dmKToCZVEtmAh_U9M,2496
-tomwer/gui/visualization/volumeviewer.py,sha256=nT9GXMFZ86Hy6ppCJB_HnE8jFgIyvEmUnPPY1JZau1A,17007
+tomwer/gui/visualization/volumeviewer.py,sha256=CVfRj_azmrfoSztjX3l6nnQ9Yoyk9yhNbREoXRRq7eY,17648
 tomwer/gui/visualization/diffviewer/__init__.py,sha256=rZ7qOTfAChU3FouCdkZllXT9ZZqTdo1XhLZMfmOqUAE,39
 tomwer/gui/visualization/diffviewer/diffviewer.py,sha256=_MOApAnImO7cYg0-Oz8EKfJt0hWeDqusYLZ_gBrRRdk,20556
 tomwer/gui/visualization/diffviewer/shiftwidget.py,sha256=7gD_mo9P7HXklD416BScUnrQNDDqXkItgkzehqBam00,19608
@@ -903,9 +904,9 @@ tomwer/tests/orangecontrib/tomwer/widgets/visualization/tests/test_volume_viewer
 tomwer/tests/test_ewoks/test_conversion.py,sha256=a8cEWbErXiFCAkaapi0jeEoRKYxcFQCoa-Jr_u77_OM,3656
 tomwer/tests/test_ewoks/test_single_node_execution.py,sha256=YBUHfiAnkciv_kjj7biC5fOs7c7ofNImM_azGMn4LZM,2813
 tomwer/tests/test_ewoks/test_workflows.py,sha256=Eq80eexf5NVL7SzvwctLOaUeuQ8V3vDiFiHgbJA4Yb8,4871
-tomwer-1.4.4.dist-info/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
-tomwer-1.4.4.dist-info/METADATA,sha256=rX-5hSdlbZ--HdznnGl7KCiDSBycJgqfzwxurDQeYFU,13377
-tomwer-1.4.4.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-tomwer-1.4.4.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
-tomwer-1.4.4.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
-tomwer-1.4.4.dist-info/RECORD,,
+tomwer-1.4.5.dist-info/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
+tomwer-1.4.5.dist-info/METADATA,sha256=0NdM0A0KYCcrCLxW5E546hD9VL2otACgkkf8UvJH6ao,13377
+tomwer-1.4.5.dist-info/WHEEL,sha256=A3WOREP4zgxI0fKrHUG8DC8013e3dK3n7a6HDbcEIwE,91
+tomwer-1.4.5.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
+tomwer-1.4.5.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
+tomwer-1.4.5.dist-info/RECORD,,

{tomwer-1.4.4.dist-info → tomwer-1.4.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (75.7.0)
 Root-Is-Purelib: true
 Tag: py3-none-any