tomwer 1.4.9__py3-none-any.whl → 1.4.11__py3-none-any.whl

orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py

@@ -147,11 +147,13 @@ class FutureSupervisorOW(OWBaseWidget, openclass=True):
                         source_scan=tomo_obj,
                     )
 
-                self.Outputs.data_portal_processed_datasets = tuple(
-                    [
-                        build_drac_dataset(vol_id=vol_id)
-                        for vol_id in tomo_obj.latest_vol_reconstructions
-                    ]
+                self.Outputs.data_portal_processed_datasets.send(
+                    tuple(
+                        [
+                            build_drac_dataset(vol_id=vol_id)
+                            for vol_id in tomo_obj.latest_vol_reconstructions
+                        ]
+                    )
                 )
 
             elif isinstance(tomo_obj, TomwerVolumeBase):

orangecontrib/tomwer/widgets/control/DataListenerOW.py

@@ -139,9 +139,8 @@ class DataListenerOW(
 
         def create_default_config():
             configuration = HDF5Config()
-            # insure minimal bacward compatibility
-            if hasattr(configuration, "bam_single_file"):
-                configuration.bam_single_file = True
+            configuration.bam_single_file = True
+            configuration.no_master_file = True
             return configuration
 
         if cfg_file in (None, ""):
@@ -150,7 +149,7 @@ class DataListenerOW(
             try:
                 config = HDF5Config.from_cfg_file(cfg_file)
             except Exception as e:
-                logger.warning(f"Fail to load configuraiton file. Error is {e}")
+                logger.warning(f"Fail to load configuration file. Error is {e}")
                 config = create_default_config()
 
         return config

tomwer/core/process/control/nxtomomill.py

@@ -85,6 +85,7 @@ class H5ToNxProcess(
                 "h5_to_nx_configuration should be a dict or an instance of {HDF5Config}"
             )
         config.bam_single_file = True
+        config.no_master_file = True
         try:
             convs = nxtomomill_converter.from_h5_to_nx(
                 configuration=config, progress=self.progress

tomwer/core/process/edit/nxtomoeditor.py

@@ -139,7 +139,7 @@ class NXtomoEditorTask(
             _logger.debug(
                 "Old version of NXtomo found. No information about transformation will be saved"
             )
-            return
+            return None, None
 
         nx_transformations = NXtransformations()
         nx_transformations.add_transformation(DetYFlipTransformation(flip=y_flip))

tomwer/version.py

@@ -77,7 +77,7 @@ RELEASE_LEVEL_VALUE = {
 
 MAJOR = 1
 MINOR = 4
-MICRO = 9
+MICRO = 11
 RELEV = "final"  # <16
 SERIAL = 0  # <16
 

{tomwer-1.4.9.dist-info → tomwer-1.4.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: tomwer
-Version: 1.4.9
+Version: 1.4.11
 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-1.4.9.dist-info → tomwer-1.4.11.dist-info}/RECORD

@@ -26,7 +26,7 @@ orangecontrib/tomwer/tutorials/id16b/ID16b_normalization.ows,sha256=kFGXGxc3eW7i
 orangecontrib/tomwer/tutorials/id16b/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 orangecontrib/tomwer/widgets/__init__.py,sha256=dX_TpkBh3mVsrj3EeGglEESsnZAEVq7V0Nb9bnBrb-8,1214
 orangecontrib/tomwer/widgets/utils.py,sha256=yq1wZfpfY3iVAhwMRBls57q02lhljO89WRKN7MxMMNg,983
-orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py,sha256=iFbgx5SeztXfxomL488rnR2MQJIS1OGSOTmsEKuEMa4,9865
+orangecontrib/tomwer/widgets/cluster/FutureSupervisorOW.py,sha256=zXjddYmkhyBnoRCstZ6AYN1mG84xiOKaIntg5tqe4jw,9927
 orangecontrib/tomwer/widgets/cluster/SlurmClusterOW.py,sha256=L_fX3EFyyx71Fg-FI8ab34ZPSUzrwKGJLcS2FnYCY_c,2565
 orangecontrib/tomwer/widgets/cluster/__init__.py,sha256=vOOJnIIaLWAj8tnxD9MRzWDyYgk-cyuBsN7QQ5FrIoQ,385
 orangecontrib/tomwer/widgets/cluster/icons/slurm.png,sha256=C-YBLwXCnh0oo4nvEt80WxX_jKYGUAFpWMUSlzt6ke0,1995
@@ -36,7 +36,7 @@ orangecontrib/tomwer/widgets/cluster/icons/slurmobserver.svg,sha256=N22gP4exnQP5
 orangecontrib/tomwer/widgets/cluster/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 orangecontrib/tomwer/widgets/control/AdvancementOW.py,sha256=XCZ3UEVNa_QneIBtcK03jbjmimszhs0_JiIcQAVS8y8,1108
 orangecontrib/tomwer/widgets/control/DataDiscoveryOW.py,sha256=kGzxJZMMw30ZaMm_cVv_a-99AvkWHVhHcZS7RRZvmJM,8039
-orangecontrib/tomwer/widgets/control/DataListenerOW.py,sha256=PV7AOW5dIEk88uMf39y_oR8DhJJvfy67MBA6zJGsxig,13902
+orangecontrib/tomwer/widgets/control/DataListenerOW.py,sha256=YEjPbDJCEi9O0YYxy9lIHiZ68jO_jQmPtbmNMyG9LuI,13837
 orangecontrib/tomwer/widgets/control/DataSelectorOW.py,sha256=zQNxYEJTxprjc83eyG6b9Ng0JVWmaZxhGb1T-jovMlU,4078
 orangecontrib/tomwer/widgets/control/DataTransfertOW.py,sha256=SKokOHQT-LPDB1hpnsaLyUzCw_GValyC-B9WyXMjxzM,5942
 orangecontrib/tomwer/widgets/control/DataValidatorOW.py,sha256=p19UYGoXtem_OxfQm_kEjQf3xKsqwyF_Ay5tQYDlVeY,5774
@@ -219,7 +219,7 @@ orangecontrib/tomwer/widgets/visualization/tests/__init__.py,sha256=47DEQpj8HBSa
 tomwer/__init__.py,sha256=cMIyH-uRxpa9WVnAuWjiBD7k9TK57WO21RzP_S-Mb8I,460
 tomwer/__main__.py,sha256=7tCADiS4u7k1PCxFhlRAcYSIOpxQTGUTx8sCEQ-hi1E,8707
 tomwer/utils.py,sha256=7h7dEgKAEUmQ43jkULvC1B9Adl55nkCty-SEKUKCl4U,7008
-tomwer/version.py,sha256=2tlKJNuy_7mdqerRMwrXUS210Pm2p0BxM-HwT3_tfsU,4386
+tomwer/version.py,sha256=n3CqDxj5kf_QPmQ3-LqwLdY1J9aJiQgW9_dN0vfGnJg,4387
 tomwer/app/__init__.py,sha256=h1FKED7Tw5f99yikygt7ruXsdrxQhcJxO7kagLGxhJg,84
 tomwer/app/axis.py,sha256=lB-IZx1o6KTWLIelITvYCIu2flFTB9NhuIfD2MhUZZA,5826
 tomwer/app/canvas.py,sha256=y8rYOiwmv6ug7JcjgkOzEiGQnNXjKWNNmKofT0n8TFg,1538
@@ -275,7 +275,7 @@ tomwer/core/process/control/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMp
 tomwer/core/process/control/datadiscovery.py,sha256=Rihr0KI0EhrgG9WTotx3r9gXKkIgRic5lu5jXPRSy-o,377
 tomwer/core/process/control/emailnotifier.py,sha256=N6tOQO2f0IBbIfUtSChl3XQCrkTJzNOiaRFDl3Ghbhk,4433
 tomwer/core/process/control/nxtomoconcatenate.py,sha256=fRa8XeLyc4ocQGQtwcHYX4dbN5vM2oHO-2_3fv3HtII,3866
-tomwer/core/process/control/nxtomomill.py,sha256=Wnkm1xCh4vuqdCvBKVpl_xfogynTe-NGpckgC-UB6hk,7753
+tomwer/core/process/control/nxtomomill.py,sha256=4G5AvsRRzUdl-OjNjb3G8RO9Mn5iNe1Ux0XednfbAHQ,7790
 tomwer/core/process/control/scanlist.py,sha256=bDUf7TDUslhCUPElUXTT_1fHAKRvhrDTzz3Gr1Wg640,697
 tomwer/core/process/control/scanselector.py,sha256=YD41hajIF4KdDEb6bkP2ZqMyCRmwvVNXzRyzqD5nSNQ,368
 tomwer/core/process/control/scantransfer.py,sha256=WoXwalXem7G3baP1cH4czpq1DqlTX614TilT6ojsNOs,24366
@@ -312,7 +312,7 @@ tomwer/core/process/drac/tests/test_icat_raw_dataset.py,sha256=2ufJs_1BBjrK8aVxV
 tomwer/core/process/edit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/core/process/edit/darkflatpatch.py,sha256=ONMoe2RqXddR7roNWjFUizjPPJKZPmKu3M10kZ0DLl4,3642
 tomwer/core/process/edit/imagekeyeditor.py,sha256=S44xxXXAbB1jmLe-O2wCabDeTCtF6vojv-80n9cCbeI,7403
-tomwer/core/process/edit/nxtomoeditor.py,sha256=HUYInTVIUbqVtFXQKMCOpQ-tvgFz5w3UrU-QSuCKd0c,11202
+tomwer/core/process/edit/nxtomoeditor.py,sha256=dNq6ZkhatIVHU7_kYeZnUYd4iwxYje7JVQW-s5Rww1w,11213
 tomwer/core/process/edit/tests/test_darkflatpatch.py,sha256=0QOjUgiYkjuWDZvI5pkuiViK4HUJA5E2sXF5LXtf_vY,9366
 tomwer/core/process/edit/tests/test_imagekey_editor.py,sha256=ft-xDMRk6CRs7DehNEnh1uJ9gLKJ-SxZAb0GmsLek0w,2345
 tomwer/core/process/reconstruction/__init__.py,sha256=G_vePtIyh1WlXtcmOyQI3nRsP-F0bsaDSdLWHC0bVzo,159
@@ -416,7 +416,6 @@ tomwer/core/scan/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
 tomwer/core/scan/tests/test_edf.py,sha256=JI7wH5emdjlYl08OhmjIO_8mui7rHa-aRCUwmkCRyys,830
 tomwer/core/scan/tests/test_future_scan.py,sha256=tsF9p57dCOmW0fPyl6BP2lLSo0rRYRF6hSF-kryLMDM,848
 tomwer/core/scan/tests/test_nxtomoscan.py,sha256=w2mNuCsfWMl1b9jP_-vkTDkCD_z9oM02yx42f6-DzY8,4751
-tomwer/core/scan/tests/test_process_registration.py,sha256=g4Toef92SjxCBUE82MTbjonFJpc3PQqfpF6FSCarN5U,1988
 tomwer/core/scan/tests/test_scan.py,sha256=mHFPi2Tc7Z2_5rWvAp3YmObVSTB5yi-sTkHm1iOJlDo,12228
 tomwer/core/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/core/tests/test_scanutils.py,sha256=xWwd1nycVDWmFaIaL2gQ_xxrUMhVCARaNHI2SxT9NOI,844
@@ -848,7 +847,6 @@ tomwer/synctools/tests/test_darkRefs.py,sha256=1OgWaV-hgDmi4rkh0hxjCW_codBAnxNhp
 tomwer/synctools/tests/test_foldertransfer.py,sha256=ZFIJWSjgYAWw3ktzamid5DJZNnMkAV6Pj72dKG69cJc,12024
 tomwer/synctools/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tomwer/synctools/utils/scanstages.py,sha256=vIUKVDSfM2UwPjjmZTiIN1tNg4antnGcSPv1aYapJCY,7830
-tomwer/tasks/reconstruction/cleardarkflat.py,sha256=_V_x7W8vp1_AqqtQ9xk2VRgwlivn4IPTLEpWySjSZRE,1353
 tomwer/tests/__init__.py,sha256=dPPaIvpzHssjwxsMzYJM_gxQ2e0cnRyQHXxi9ux6ZOY,19
 tomwer/tests/conftest.py,sha256=0XlKfOrVtPg8VmyQn4BoK_mzcliFUtacDGLlZ5wD_PM,1912
 tomwer/tests/datasets.py,sha256=QXQ3jSwgWzfq4CaELOSrk9kHg5GmrP7kGHsdOlNSEIE,336
@@ -905,9 +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-1.4.9.dist-info/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
-tomwer-1.4.9.dist-info/METADATA,sha256=NPzI78ud1GOKO6eFvOqUWdAr3uUtZ7h0VdJdWAVFy3c,13415
-tomwer-1.4.9.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-tomwer-1.4.9.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
-tomwer-1.4.9.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
-tomwer-1.4.9.dist-info/RECORD,,
+tomwer-1.4.11.dist-info/LICENSE,sha256=62p1wL0n9WMTu8x2YDv0odYgTqeSvTd9mQ0v6Mq7lzE,1876
+tomwer-1.4.11.dist-info/METADATA,sha256=M84LcLUCPsi1bQDUkRE6EOZww_25wETf53Gff3lwUhI,13416
+tomwer-1.4.11.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+tomwer-1.4.11.dist-info/entry_points.txt,sha256=py3ZUWvGnWGc5c7Yhw_uBTm8Fmew0BDw3aQZnWMBNZI,500
+tomwer-1.4.11.dist-info/top_level.txt,sha256=Yz5zKh0FPiImtzHYcPuztG1AO8-6KEpUWgoChGbA0Ys,21
+tomwer-1.4.11.dist-info/RECORD,,

{tomwer-1.4.9.dist-info → tomwer-1.4.11.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (76.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

tomwer/core/scan/tests/test_process_registration.py

@@ -1,64 +0,0 @@
-# coding: utf-8
-from __future__ import annotations
-
-import shutil
-import tempfile
-import unittest
-
-from tomoscan.io import HDF5File, get_swmr_mode
-
-from tomwer.core.process.task import Task
-from tomwer.core.utils.scanutils import MockNXtomo
-
-
-class TestProcessRegistration(unittest.TestCase):
-    """
-    Make sure utils link to the process registration are
-    correctly working
-    """
-
-    class DummyProcess(Task):
-        @staticmethod
-        def program_name():
-            """Name of the program used for this processing"""
-            return "dummy program"
-
-        @staticmethod
-        def program_version():
-            """version of the program used for this processing"""
-            return "0.0.0"
-
-        @staticmethod
-        def definition():
-            """definition of the process"""
-            return "no definition"
-
-    def setUp(self):
-        self.tmp_dir = tempfile.mkdtemp()
-        self.scan = MockNXtomo(scan_path=self.tmp_dir, n_proj=2).scan
-
-    def tearDown(self):
-        shutil.rmtree(self.tmp_dir)
-
-    def testGetProcessNodes(self):
-        """insure it return the last dark process based on the processing index"""
-
-        for i in range(20):
-            Task._register_process(
-                self.scan.process_file,
-                process=self.DummyProcess,
-                entry=self.scan.entry,
-                configuration=None,
-                results={"output": i},
-                process_index=i,
-            )
-
-        with HDF5File(self.scan.process_file, "r", swmr=get_swmr_mode()) as h5f:
-            nodes = Task._get_process_nodes(
-                root_node=h5f[self.scan.entry], process=self.DummyProcess
-            )
-            self.assertEqual(len(nodes), 20)
-            self.assertTrue("/entry/tomwer_process_16" in nodes)
-            self.assertEqual(nodes["/entry/tomwer_process_16"], 16)
-            self.assertTrue("/entry/tomwer_process_1" in nodes)
-            self.assertEqual(nodes["/entry/tomwer_process_1"], 1)

tomwer/tasks/reconstruction/cleardarkflat.py

@@ -1,42 +0,0 @@
-"""
-Contains task to clear reduced dark and flat frames
-"""
-
-from __future__ import annotations
-
-from tomoscan.scanbase import TomoScanBase as TomoscanScanBase
-
-from processview.core.manager import DatasetState, ProcessManager
-from processview.core.superviseprocess import SuperviseProcess
-
-from tomwer.tasks.task import Task
-from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.core.scan.scanfactory import ScanFactory
-from tomwer.core.utils.scanutils import data_identifier_to_scan
-from tomwer.core.reconstruction.darkflat import params as dkrf_reconsparams
-from tomwer.utils import docstring
-
-
-class ClearReducedDarkAndFlat(
-    Task,
-    SuperviseProcess,
-    input_names=("data",),
-    output_names=("data",),
-):
-    """
-    Task to clear reduced darks and flats. Both on disk and on the object cache.
-    th goal of this task is to make sure the scan is cleared of any reduced frames to reprocess it later.
-    """
-
-    def run(self):
-        scan = self.inputs.data
-        if not isinstance(scan, TomoscanScanBase):
-            raise TypeError(
-                f"scan should be an instance of {TomoscanScanBase}. Got {type(scan)}"
-            )
-        scan.set_reduced_flats(None)
-        scan.reduced_flats_infos = None
-        scan.set_reduced_darks(None)
-        scan.reduced_darks_infos = None
-
-        self.outputs.data = scan