tomwer 1.3.0a5__tar.gz → 1.3.0a7__tar.gz

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.0a5
+Version: 1.3.0a7
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/orangecontrib/tomwer/widgets/control/NXTomomillOW.py

@@ -42,6 +42,7 @@ from tomwer.core.scan.blissscan import BlissScan
 from tomwer.core.scan.nxtomoscan import NXtomoScan, NXtomoScanIdentifier
 from tomwer.gui.control.datalist import BlissHDF5DataListMainWindow
 from tomwer.gui.control.nxtomomill import NXTomomillInput, OverwriteMessage
+from tomwer.core.process.output import ProcessDataOutputDirMode
 from ewoksorange.bindings.owwidgets import invalid_data
 
 
@@ -137,9 +138,10 @@ class NXTomomillOW(
                 self.add(nxtomo_scan)
             else:
                 self._scans.append(scan)
-        self._ewoks_default_inputs[  # pylint: disable=E1137
-            "output_dir"
-        ] = self.widget.getOutputFolder()
+        output_dir = self.widget.getOutputFolder()
+        if isinstance(output_dir, ProcessDataOutputDirMode):
+            output_dir = output_dir.value
+        self._ewoks_default_inputs["output_dir"] = output_dir  # pylint: disable=E1137
 
     @property
     def request_input(self):

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/orangecontrib/tomwer/widgets/debugtools/DatasetGeneratorOW.py

@@ -156,7 +156,7 @@ class _DatasetGeneratorThread(threading.Thread):
                 n_proj=self.n_proj,
                 n_ini_proj=self.n_proj,
                 create_ini_dark=self.create_ini_dark,
-                create_ini_ref=self.create_ini_flat,
+                create_ini_flat=self.create_ini_flat,
                 dim=self.dims[0],
             ).scan
         elif self.type_to_generate == BlissScan.__name__:

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/core/process/reconstruction/axis/axis.py

@@ -188,7 +188,7 @@ def compute_cor_nabu_growing_window_sinogram(
 
     corfinder = SinoCORFinder(
         dataset_info=adapt_tomwer_scan_to_nabu(scan),
-        method="growing-window",
+        method="sino-growing-window",
         slice_idx=scan.axis_params.sinogram_line or "middle",
         subsampling=scan.axis_params.sinogram_subsampling,
         do_flatfield=has_darks and has_flats,
@@ -389,7 +389,7 @@ def compute_cor_nabu_sliding_window_sinogram(
 
     corfinder = SinoCORFinder(
         dataset_info=adapt_tomwer_scan_to_nabu(scan),
-        method="sliding-window",
+        method="sino-sliding-window",
         slice_idx=scan.axis_params.sinogram_line or "middle",
         subsampling=scan.axis_params.sinogram_subsampling,
         do_flatfield=has_darks and has_flats,

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/core/process/reconstruction/nabu/utils.py

@@ -260,7 +260,6 @@ def get_multi_cor_recons_volume_identifiers(
         if file_format in ("hdf5", "h5", "hdf"):
             file_path = os.path.join(
                 location,
-                f"{file_prefix}_{cor:.3f}",  # this level is expected to be removed on the future nabu versions
                 f"{file_prefix}_{cor:.3f}_{str(slice_index).zfill(5)}.{file_format}",
             )
             volume = HDF5Volume(

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/core/process/reconstruction/saaxis/saaxis.py

@@ -520,7 +520,10 @@ class SAAxisTask(
                     cors_res, rois = self._post_processing(
                         scan=scan,
                         slice_index=slice_index,
-                        cor_reconstructions=cor_reconstructions,
+                        cor_reconstructions={
+                            cor: recons
+                            for cor, recons in zip(params.cors, cor_reconstructions)
+                        },
                     )
                 except Exception as e:
                     _logger.error(e)

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/core/process/reconstruction/test/test_darkref_copy.py

@@ -35,8 +35,8 @@ def test_register_and_copy_darks_and_flats(
     scan_with_raw = MockNXtomo(
         scan_path=scan_folder_with_raw,
         create_ini_dark=True,
-        create_ini_ref=True,
-        create_final_ref=False,
+        create_ini_flat=True,
+        create_final_flat=False,
         n_proj=10,
         n_ini_proj=10,
         dim=12,
@@ -44,8 +44,8 @@ def test_register_and_copy_darks_and_flats(
     scan_without_raw = MockNXtomo(
         scan_path=scan_folder_without_raw,
         create_ini_dark=False,
-        create_ini_ref=False,
-        create_final_ref=False,
+        create_ini_flat=False,
+        create_final_flat=False,
         n_proj=10,
         n_ini_proj=10,
         dim=12,

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/core/process/test/test_axis.py

@@ -260,7 +260,7 @@ class TestSinogramAlgorithm(unittest.TestCase):
             n_proj=10,
             n_ini_proj=10,
             create_ini_dark=True,
-            create_final_ref=True,
+            create_final_flat=True,
             scan_range=360,
             dim=dim,
         ).scan

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/core/process/test/test_normalization.py

@@ -54,8 +54,8 @@ class TestNormalization(unittest.TestCase):
             scan_range=180,
             dim=dim,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
         ).scan
 
     def tearDown(self) -> None:

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/core/scan/test/test_future_scan.py

@@ -43,7 +43,7 @@ def test_simple_future_tomo_obj(tmpdir):
         n_proj=10,
         n_ini_proj=10,
         create_ini_dark=False,
-        create_ini_ref=False,
+        create_ini_flat=False,
         dim=10,
     ).scan
     future = asyncio.Future()

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/core/scan/test/test_h5.py

@@ -65,9 +65,9 @@ class TestHDF5Scan(unittest.TestCase):
             n_ini_proj=20,
             n_proj=20,
             n_alignement_proj=2,
-            create_final_ref=True,
+            create_final_flat=True,
             create_ini_dark=True,
-            create_ini_ref=True,
+            create_ini_flat=True,
             n_refs=5,
         ).scan
         self.assertEqual(scan_1.ff_interval, 20)
@@ -78,9 +78,9 @@ class TestHDF5Scan(unittest.TestCase):
             n_ini_proj=10,
             n_proj=10,
             n_alignement_proj=2,
-            create_final_ref=False,
+            create_final_flat=False,
             create_ini_dark=True,
-            create_ini_ref=True,
+            create_ini_flat=True,
             n_refs=1,
         ).scan
         self.assertEqual(scan_2.ff_interval, 0)

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/core/test/test_utils.py

@@ -279,8 +279,8 @@ class TestMockNXtomo(unittest.TestCase):
             n_ini_proj=20,
             n_alignement_proj=2,
             create_ini_dark=True,
-            create_ini_ref=True,
-            create_final_ref=True,
+            create_ini_flat=True,
+            create_final_flat=True,
             n_refs=10,
         )
         self.assertTrue(0 in mock.scan.darks.keys())

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/gui/cluster/test/test_supervisor.py

@@ -57,7 +57,7 @@ class TestSupervisor(TestCaseQt):
                 n_proj=10,
                 n_ini_proj=10,
                 create_ini_dark=False,
-                create_ini_ref=False,
+                create_ini_flat=False,
                 dim=10,
             ).scan
             self._scans.append(scan)

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/gui/control/test/test_single_tomo_obj.py

@@ -34,7 +34,7 @@ class TestSingletomoObj(TestCaseQt):
             n_proj=10,
             n_ini_proj=10,
             create_ini_dark=False,
-            create_ini_ref=False,
+            create_ini_flat=False,
             dim=10,
         ).scan
 

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/gui/edit/test/test_dkrf_patch.py

@@ -67,8 +67,8 @@ class TestDarkOrFlatUrl(TestCaseQt):
             n_ini_proj=20,
             n_proj=20,
             create_ini_dark=True,
-            create_ini_ref=True,
-            create_final_ref=True,
+            create_ini_flat=True,
+            create_final_flat=True,
         )
         self._scan = hdf5_mock.scan
         self.scan_url = DataUrl(
@@ -135,8 +135,8 @@ class TestDarkRefPatchWidget(TestCaseQt):
             n_ini_proj=20,
             n_proj=20,
             create_ini_dark=True,
-            create_ini_ref=True,
-            create_final_ref=True,
+            create_ini_flat=True,
+            create_final_flat=True,
         )
         self._scanWithDarkAndRef = hdf5_mock.scan
 
@@ -145,8 +145,8 @@ class TestDarkRefPatchWidget(TestCaseQt):
             n_ini_proj=20,
             n_proj=20,
             create_ini_dark=False,
-            create_ini_ref=False,
-            create_final_ref=False,
+            create_ini_flat=False,
+            create_final_flat=False,
         )
         self._scan = hdf5_mock.scan
         assert len(self._scan.darks) == 0

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer/version.py

@@ -79,7 +79,7 @@ MAJOR = 1
 MINOR = 3
 MICRO = 0
 RELEV = "alpha"  # <16
-SERIAL = 5  # <16
+SERIAL = 7  # <16
 
 date = __date__
 

{tomwer-1.3.0a5 → tomwer-1.3.0a7}/tomwer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.3.0a5
+Version: 1.3.0a7
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit