tomwer 1.4.2__py3-none-any.whl → 1.4.4__py3-none-any.whl

tomwer/app/stitching/common.py

@@ -181,21 +181,8 @@ class _StitcherThread(qt.QThread):
             },
         )
 
-        if self._cluster_config in (None, {}):
-            self._runLocally(task)
-        else:
-            self._runRemotely(task)
-
-    def _runLocally(self, task):
-        task.run()
-
-    def _runRemotely(self, task):
         task.run()
-        # wait for processing to be finished
-        for future in task.outputs.future_tomo_obj.futures:
-            future.result()
-        # note: there is also a callback to aggregate result once all are finished.
-        # so at this stage the final "nxtomo" or "volume" might not exists yet
+        print("stitching finished")
 
 
 class MainWindow(qt.QDialog):

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

@@ -445,13 +445,47 @@ def interpret_tomwer_configuration(config: dict, scan: TomwerScanBase | None) ->
         return nabu_config
 
     if "tomwer_slices" in config and scan is not None:
+        reconstruction_axis = NabuPlane.from_value(
+            config.get("reconstruction", {}).get("slice_plane", "XY")
+        )
         slices = list(
             NabuSliceMode.getSlices(
                 config["tomwer_slices"],
                 scan=scan,
-                axis=config.get("reconstruction", {}).get("slice_plane", "XY"),
+                axis=reconstruction_axis,
+            )
+        )
+
+        def filter_slice(slice_index: int, axis: NabuPlane):
+            """remove slices that 'cannot' be reconstructed (out of bounds)"""
+            if axis is NabuPlane.XY:
+                index_max = scan.dim_2
+            elif axis in (NabuPlane.XZ, NabuPlane.YZ):
+                index_max = scan.dim_1
+            else:
+                raise ValueError
+
+            if index_max is None:
+                return True
+
+            index_max = index_max - 1
+
+            if slice_index > index_max:
+                _logger.error(
+                    f"slice index {slice_index} requested. But slice index must be in 0-{index_max} - ignore this request"
+                )
+                return False
+            return True
+
+        slices = list(
+            filter(
+                lambda slice_index: filter_slice(
+                    int(slice_index), axis=reconstruction_axis
+                ),
+                slices,
             )
         )
+
     else:
         slices = []
 
@@ -464,17 +498,6 @@ def interpret_tomwer_configuration(config: dict, scan: TomwerScanBase | None) ->
     else:
         pag_dbs = (None,)
 
-    # remove slices that 'cannot' be reconstructed (out of bounds)
-    def filter_slice(slice_index: int):
-        if scan.dim_2 is not None and slice_index > scan.dim_2:
-            _logger.error(
-                f"slice index {slice_index} requested. But slice index must be in 0-{scan.dim_2} - ignore this request"
-            )
-            return False
-        return True
-
-    slices = list(filter(lambda slice_index: filter_slice(int(slice_index)), slices))
-
     # by default add the slice 'None' which is the slice for the volume
     slices.append(None)
     nabu_config = get_nabu_config(config=config)

tomwer/core/process/stitching/nabustitcher.py

@@ -26,7 +26,6 @@ from processview.core.superviseprocess import SuperviseProcess
 from tomwer.core.process.task import Task
 from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanfactory import ScanFactory
-from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.volume.volumefactory import VolumeFactory
 
 
@@ -135,32 +134,24 @@ class StitcherTask(
                 stitching_config=config,
                 progress_bars=slurm_job_progress_bars,
             )
-            for future in futures.values():
-                # TODO: do we ned to make sure the processing is not finished yet ?
-                future.add_done_callback(data_aggregation.onePartFinished)
+            # will wait and provide feedback until the stitching is completed.
+            data_aggregation.process()
 
             if config.stitching_type is StitchingType.Z_PREPROC:
                 output_nx_tomo_file = config.output_file_path
                 output_nx_tomo_entry = config.output_data_path
-                tomwer_scan = NXtomoScan(
+                self.outputs.data = NXtomoScan(
                     scan=output_nx_tomo_file, entry=output_nx_tomo_entry
                 )
-                self.outputs.future_tomo_obj = FutureTomwerObject(
-                    tomo_obj=tomwer_scan,
-                    futures=tuple(futures.values()),
-                )
-                self.outputs.data = None
+                self.outputs.future_tomo_obj = None
                 self.outputs.volume = None
 
             elif config.stitching_type is StitchingType.Z_POSTPROC:
                 tomwer_volume = VolumeFactory.create_tomo_object_from_identifier(
                     config.output_volume.get_identifier().to_str()
                 )
-                self.outputs.future_tomo_obj = FutureTomwerObject(
-                    tomo_obj=tomwer_volume,
-                    futures=tuple(futures.values()),
-                )
-                self.outputs.volume = None
+                self.outputs.future_tomo_obj = None
+                self.outputs.volume = tomwer_volume
                 self.outputs.data = None
 
 
@@ -171,7 +162,7 @@ class StitchingPostProcAggregation(_StitchingPostProcAggregation):
 
     def __init__(self, *args, **kwargs) -> None:
         super().__init__(*args, **kwargs)
-        self._n_finished = 0
+        print("creates StitchingPostProcAggregation")
 
         if isinstance(self.stitching_config, dict):
             stitching_type = StitchingType.from_value(
@@ -192,10 +183,6 @@ class StitchingPostProcAggregation(_StitchingPostProcAggregation):
                 f"stitching_config is expected to be an instance of {StitchingConfiguration}. {type(self.stitching_config)} provided instead"
             )
 
-    def onePartFinished(self, *args, **kwargs):
-        self._n_finished += 1
-        # note: for now we only consider the user of the futures.
-        # if users want to only run post-processing agregation then they will use the nabu CLI for it.
-        if self._n_finished == len(self._futures):
-            _logger.info("All slurm job finished. Will aggregate results")
-            self.process()
+    def process(self):
+        super().process()
+        _logger.info("Stitching finished.")

tomwer/gui/reconstruction/nabu/nabuconfig/phase.py

@@ -95,6 +95,7 @@ class _NabuPhaseConfig(qt.QWidget, base._NabuStageConfigBase):
         self._unsharpOpts.setDiscourageUnsharpMask(
             self.getMethod() is _NabuPhaseMethod.NONE
         )
+        self._unsharpOpts._updateUnsharpMaskWarning()
         self.sigConfChanged.emit("method")
 
     def _signalConfChanged(self, param):

tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 4
-MICRO = 2
+MICRO = 4
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.4.2.dist-info → tomwer-1.4.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.4.2
+Version: 1.4.4
 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-1.4.2.dist-info → tomwer-1.4.4.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=Ut5Y5Pzhf7aqEi5CMCIwsyq_OqFINJdLxd0lcDcQ7js,4386
+tomwer/version.py,sha256=cQn0hp7H0RGoblTK9Od0_A4QCnVaVE5G-t2RThewbMg,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
@@ -253,7 +253,7 @@ tomwer/app/canvas_launcher/splash.py,sha256=cpUuZVKwlQbeAWfAqjpjP4q1v1MmkfxU6WWl
 tomwer/app/canvas_launcher/utils.py,sha256=4zWaao2EW5OcKomAw38YUIUgOLfkUPGdPCqLsfD1NMI,1031
 tomwer/app/canvas_launcher/widgetsscheme.py,sha256=9Or1KMmSxIs_dJmJGV0Xhjg9HH4m8aPGbtiEuK2i6q0,2744
 tomwer/app/stitching/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tomwer/app/stitching/common.py,sha256=-CztPRSwIAHocNIDksBdbRWALsy9G5aRFiG9b78vtlg,15203
+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/settings.py,sha256=57qD44LU_3eB50rD7RHdg5nBweiHerzWbXHcBUna6gY,4089
@@ -336,7 +336,7 @@ tomwer/core/process/reconstruction/nabu/castvolume.py,sha256=4VEVnJxWfG8_Ku2uhUS
 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/nabuscores.py,sha256=e5tRG1QtmVAdXb8KHMTMtBXA3KQXqKKcqipY2HzMURg,25275
-tomwer/core/process/reconstruction/nabu/nabuslices.py,sha256=sUpU1f6_qWbuKVUDNattFVvFE88By29f3CtTCtuKT-k,31517
+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
@@ -374,7 +374,7 @@ tomwer/core/process/script/python.py,sha256=NScx6DtRA6m71jciiN6a7QIr3ICWmo3rXJY1
 tomwer/core/process/script/tests/test_script.py,sha256=1uku23G5_6JEjohI53FZyLpTjkmfsdGrwX__5Mr3DBg,1024
 tomwer/core/process/stitching/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/core/process/stitching/metadataholder.py,sha256=QWo04TRsGFg1MdydLvuuK1C2ICRXNwL1oK32JXB1dE8,6530
-tomwer/core/process/stitching/nabustitcher.py,sha256=DQTmCqOvcei9S9eu-H9NoVXBcBQf6DRxYOJO2Nn50QY,8129
+tomwer/core/process/stitching/nabustitcher.py,sha256=wJGCpPIcBQXv-g6F6kxchEtcMEiqMGsq-r0Nq36aKmo,7422
 tomwer/core/process/stitching/tests/test_metadataholder.py,sha256=E9jgvtwdbcF9tgWS3uqHppHf8ff0aCvjROrLAFVZSpQ,631
 tomwer/core/process/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/core/process/tests/test_conditions.py,sha256=FBmBn3fvMW2H27ZLVnyYyS1bnfCb9v86WnWDw46WbMo,2140
@@ -568,7 +568,7 @@ tomwer/gui/reconstruction/nabu/nabuconfig/base.py,sha256=ZsfZORtztbZRIGmcX5bJGlV
 tomwer/gui/reconstruction/nabu/nabuconfig/ctf.py,sha256=z7mqBt77Y81gO7GO1OsXG3iGxcgSKNYLAjxlG-uC0K8,13142
 tomwer/gui/reconstruction/nabu/nabuconfig/nabuconfig.py,sha256=rJXFMr_dlTekd0mCbzzg7b7L2QJrLthDHX6JK1zkZTc,9059
 tomwer/gui/reconstruction/nabu/nabuconfig/output.py,sha256=0SShYqvFj-motxTw20e3I1Z0WiierSqgOsN15qwe-TY,11907
-tomwer/gui/reconstruction/nabu/nabuconfig/phase.py,sha256=3SPSokMuE4wvoKTn-aFStln__sjewcpG7H9oJY4x5qs,16239
+tomwer/gui/reconstruction/nabu/nabuconfig/phase.py,sha256=h4F0qtKXOeligVuqKa-pBAvP2ol2EgfSRHjxvsQkvAQ,16293
 tomwer/gui/reconstruction/nabu/nabuconfig/preprocessing.py,sha256=lmL2UTL7gt20nbDv921SFIAnVoJkumafSCjqTE4zGlY,32608
 tomwer/gui/reconstruction/nabu/nabuconfig/reconstruction.py,sha256=bGCF7bJBfnh0xh4zcWpqhLrzqHuG32F-Tn4xHVQny3M,41151
 tomwer/gui/reconstruction/nabu/test/test_cast_volume.py,sha256=kup5JVKNN4QZOXYGco1ZRb_4TWrXAQOtfuQcqTpraA0,2764
@@ -903,9 +903,9 @@ 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-1.4.2.dist-info/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
-tomwer-1.4.2.dist-info/METADATA,sha256=0YX0nYm5b6VVBEgnLOx-vDB7Hermd6Q0lDpus2rD-tc,13377
-tomwer-1.4.2.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-tomwer-1.4.2.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
-tomwer-1.4.2.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
-tomwer-1.4.2.dist-info/RECORD,,
+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,,