tomwer 1.2.1__py3-none-any.whl → 1.3.12__py3-none-any.whl

tomwer/core/settings.py

@@ -92,6 +92,7 @@ class SlurmSettingsMode(_Enum):
     CAST_VOLUME = "cast_volume"
     SLICE_RECONSTRUCTION = "slice_reconstruction"
     VOLUME_RECONSTRUCTION = "volume_reconstruction"
+    STITCHING = "stitching"
 
     @staticmethod
     def get_settings_class(mode):
@@ -106,6 +107,8 @@ class SlurmSettingsMode(_Enum):
             return DefaultSlurmSettingsSliceReconstruction
         elif mode is SlurmSettingsMode.VOLUME_RECONSTRUCTION:
             return DefaultSlurmSettingsVolumeReconstruction
+        elif mode is SlurmSettingsMode.STITCHING:
+            return DefaultSlurmSettingsStitching
         else:
             raise ValueError(f"{mode} not handled")
 
@@ -122,7 +125,7 @@ class SlurmSettings:
     N_JOBS = 1
     """on how many job we want to split the EwoksTask"""
 
-    MEMORY_PER_WORKER = 64  # memory in GB
+    MEMORY_PER_WORKER = 128  # memory in GB
     """Amount of memory per worker"""
 
     PARTITION = "p9gpu"
@@ -133,7 +136,7 @@ class SlurmSettings:
     N_GPUS_PER_WORKER = 1
     """number of gpu per worker"""
 
-    PYTHON_VENV = "/scisoft/tomotools/activate stable"
+    PYTHON_VENV = None
     """Python executable to take. Useful if compute nodes have a different environment from the front end.
     """
 
@@ -141,6 +144,12 @@ class SlurmSettings:
     """Slurm cluster project name. `scan`, `process` and `info` will be format.
     """
 
+    MODULES_TO_LOAD = ("tomotools/stable", )
+
+    SBATCH_EXTRA_PARAMS = {
+        "export": "NONE",  # value to provide to sbatch --export={}
+    }
+
 
 class DefaultSlurmSettingsCastVolume(SlurmSettings):
     """
@@ -171,3 +180,14 @@ class DefaultSlurmSettingsVolumeReconstruction(SlurmSettings):
     MEMORY_PER_WORKER = 256  # memory in GB
 
     PARTITION = None
+
+
+class DefaultSlurmSettingsStitching(SlurmSettings):
+    """*
+    default proposed configuration for stitching
+    """
+    N_JOBS = 15
+
+    PARTITION = "nice-long"
+
+    N_GPUS_PER_WORKER = 0

tomwer/core/test/test_scanutils.py

@@ -31,22 +31,23 @@ import os
 import tempfile
 import unittest
 
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
-from tomwer.core.utils.scanutils import MockHDF5
+from nxtomo.application.nxtomo import NXtomo
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.utils.scanutils import MockNXtomo
 
 
-class TestMockHDF5(unittest.TestCase):
-    """Test the MockHDF5 file"""
+class TestMockNXtomo(unittest.TestCase):
+    """Test the MockNXtomo file"""
 
     def test_creation(self):
         folder = tempfile.mkdtemp()
-        mock = MockHDF5(scan_path=folder, n_proj=10, n_ini_proj=10)
+        mock = MockNXtomo(scan_path=folder, n_proj=10, n_ini_proj=10)
         self.assertEqual(
             mock.scan_master_file,
             os.path.join(folder, os.path.basename(folder) + ".h5"),
         )
-        tomoScan = HDF5TomoScan(mock.scan_path, entry=mock.scan_entry)
-        self.assertEqual(len(HDF5TomoScan.get_valid_entries(mock.scan_master_file)), 1)
+        tomoScan = NXtomoScan(mock.scan_path, entry=mock.scan_entry)
+        self.assertEqual(len(NXtomo.get_valid_entries(mock.scan_master_file)), 1)
         tomoScan.update()
         self.assertEqual(tomoScan.scan_range, 360)
         self.assertEqual(len(tomoScan.projections), 10)

tomwer/core/test/test_utils.py

@@ -35,22 +35,29 @@ import unittest
 
 import numpy
 
-from tomwer.core import utils
+from tomwer.core.utils import spec as spec_utils
 from tomwer.core.utils.normalization import flatFieldCorrection
-from tomwer.core.utils.scanutils import MockEDF, MockHDF5
-from tomwer.tests.utils import UtilsTest
+from tomwer.core.utils.scanutils import MockEDF, MockNXtomo
+from tomwer.tests.datasets import TomwerCIDatasets
 
 
 class TestGetClosestEnergy(unittest.TestCase):
     def setUp(self):
         self.topSrcFolder = tempfile.mkdtemp()
         self.dataSetID = "scan_3_"
-        self.dataDir = UtilsTest.getEDFDataset(self.dataSetID)
+        self.dataDir = TomwerCIDatasets.get_dataset(
+            f"edf_datasets/{self.dataSetID}",
+        )
         self.sourceS3 = os.path.join(self.topSrcFolder, self.dataSetID)
         shutil.copytree(src=os.path.join(self.dataDir), dst=self.sourceS3)
 
         self.sourceT01 = os.path.join(self.topSrcFolder, "test01")
-        shutil.copytree(src=UtilsTest.getEDFDataset("test01"), dst=self.sourceT01)
+        shutil.copytree(
+            src=TomwerCIDatasets.get_dataset(
+                "edf_datasets/test01",
+            ),
+            dst=self.sourceT01,
+        )
         self.S3XMLFile = os.path.join(self.sourceS3, "scan_3_.xml")
         self.S3Ref0000 = os.path.join(self.sourceS3, "ref0000_0000.edf")
         self.S3Ref0010 = os.path.join(self.sourceS3, "ref0000_0010.edf")
@@ -61,34 +68,42 @@ class TestGetClosestEnergy(unittest.TestCase):
     def testEnergyFromEDF(self):
         os.remove(self.S3XMLFile)
         self.assertTrue(
-            utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0000) == 61
+            spec_utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0000)
+            == 61
         )
         self.assertTrue(
-            utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0010) == 61
+            spec_utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0010)
+            == 61
         )
 
     def testEnergyFromXML(self):
         os.remove(self.S3Ref0000)
         os.remove(self.S3Ref0010)
         self.assertTrue(
-            utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0000) == 10
+            spec_utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0000)
+            == 10
         )
         self.assertTrue(
-            utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0010) == 10
+            spec_utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0010)
+            == 10
         )
 
     def testEnergyFromInfo(self):
-        self.assertTrue(utils.getClosestEnergy(scan=self.sourceT01, refFile=None) == 19)
+        self.assertTrue(
+            spec_utils.getClosestEnergy(scan=self.sourceT01, refFile=None) == 19
+        )
 
     def testDefaultEnergy(self):
         os.remove(self.S3XMLFile)
         os.remove(self.S3Ref0000)
         os.remove(self.S3Ref0010)
         self.assertTrue(
-            utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0000) is None
+            spec_utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0000)
+            is None
         )
         self.assertTrue(
-            utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0010) is None
+            spec_utils.getClosestEnergy(scan=self.sourceS3, refFile=self.S3Ref0010)
+            is None
         )
 
 
@@ -96,7 +111,9 @@ class TestGetClosestSREnergy(unittest.TestCase):
     def setUp(self):
         self.topSrcFolder = tempfile.mkdtemp()
         self.dataSetID = "test10"
-        self.dataDir = UtilsTest.getEDFDataset(self.dataSetID)
+        self.dataDir = TomwerCIDatasets.get_dataset(
+            f"edf_datasets/{self.dataSetID}",
+        )
         self.sourceT10 = os.path.join(self.topSrcFolder, self.dataSetID)
         shutil.copytree(src=os.path.join(self.dataDir), dst=self.sourceT10)
         self.T10XMLFile = os.path.join(self.sourceT10, "test10.xml")
@@ -106,16 +123,6 @@ class TestGetClosestSREnergy(unittest.TestCase):
     def tearDown(self):
         shutil.rmtree(self.topSrcFolder)
 
-    def testIntenistyFromInfo(self):
-        self.assertTrue(
-            utils.getClosestSRCurrent(scan_dir=self.sourceT10, refFile=None) == 101.3
-        )
-
-    def testDefaultIntensity(self):
-        os.remove(self.T10XMLFile)
-        os.remove(self.T10InfoFile)
-        self.assertTrue(utils.getClosestSRCurrent(scan_dir=self.sourceT10) is None)
-
 
 class TestMockEDFScan(unittest.TestCase):
     """Test that mock scan are adapted to other unit test"""
@@ -254,8 +261,8 @@ class TestMockEDFScan(unittest.TestCase):
             self.assertEqual(scan_dynamic[angle_id].file_path(), file_name)
 
 
-class TestMockHDF5(unittest.TestCase):
-    """Test MockHDF5 to check that the file produced is valid"""
+class TestMockNXtomo(unittest.TestCase):
+    """Test MockNXtomo to check that the file produced is valid"""
 
     def setUp(self) -> None:
         self._folder = tempfile.mkdtemp()
@@ -266,14 +273,14 @@ class TestMockHDF5(unittest.TestCase):
     def testSimpleMockCreationOneCall(self):
         """Test mock of an acquisition starting by one dark, then 10 ref,
         then 20 radios, then 10 'final' ref and 2 alignment radio"""
-        mock = MockHDF5(
+        mock = MockNXtomo(
             scan_path=self._folder,
             n_proj=20,
             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/core/tomwer_object.py

@@ -28,7 +28,7 @@ class TomwerObject(Dataset):
     def cast_volume(self, volume):
         from tomwer.core.volume.volumebase import TomwerVolumeBase
 
-        if not isinstance(volume, TomwerVolumeBase):
+        if not (volume is None or isinstance(volume, TomwerVolumeBase)):
             from tomwer.core.volume.volumefactory import (
                 VolumeFactory,
             )  # avoid cyclic import