tomwer 1.2.9__py3-none-any.whl → 1.3.0a0__py3-none-any.whl

tomwer/core/process/control/test/test_concatenate_nxtomos.py

@@ -5,15 +5,15 @@ from tomwer.core.process.control.nxtomoconcatenate import (
     ConcatenateNXtomoTask,
     format_output_location,
 )
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
-from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.utils.scanutils import MockNXtomo
 
 
 def test_concatenate_nx_tomo_task(tmp_path):
     """
-    test execution of ConcatenateNXtomoTask with two HDF5TomoScan
+    test execution of ConcatenateNXtomoTask with two NXtomoScan
     """
-    scan_1 = MockHDF5(
+    scan_1 = MockNXtomo(
         scan_path=os.path.join(tmp_path, "scan1"),
         n_proj=10,
         n_ini_proj=10,
@@ -21,7 +21,7 @@ def test_concatenate_nx_tomo_task(tmp_path):
         dim=20,
         energy=12.3,
     ).scan
-    scan_2 = MockHDF5(
+    scan_2 = MockNXtomo(
         scan_path=os.path.join(tmp_path, "scan2"),
         n_proj=10,
         n_ini_proj=10,
@@ -42,18 +42,18 @@ def test_concatenate_nx_tomo_task(tmp_path):
         }
     )
     task.run()
-    assert isinstance(task.outputs.data, HDF5TomoScan)
+    assert isinstance(task.outputs.data, NXtomoScan)
     assert os.path.exists(output_scan_file)
     # note: correct processing of the concatenation is done at nxtomomill
 
 
 def test_format_output_location():
     """test behavior of format_output_location"""
-    scan1 = HDF5TomoScan(
+    scan1 = NXtomoScan(
         "/path/to/scan_1.nx",
         entry="entry0000",
     )
-    scan2 = HDF5TomoScan(
+    scan2 = NXtomoScan(
         "/path/to/scan_2.nx",
         entry="entry0001",
     )
@@ -65,7 +65,7 @@ def test_format_output_location():
     )
 
     assert format_output_location(
-        "concatenate.nx", Serie([scan1, scan2])
+        "concatenate.nx", Serie("my_serie", [scan1, scan2])
     ) == os.path.abspath("concatenate.nx")
 
     assert (

tomwer/core/process/control/test/test_email.py

@@ -1,7 +1,7 @@
 import os
 import numpy
-from tomwer.core.process.control.email import format_email_info, _ls_tomo_obj
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.process.control.emailnotifier import format_email_info, _ls_tomo_obj
+from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.volume.hdf5volume import HDF5Volume
 from tomwer.core.utils.scanutils import HDF5MockContext
 
@@ -11,11 +11,11 @@ def test__ls_tomo_obj(tmp_path):
     for i in range(2):
         open(os.path.join(tmp_path, f"{i}.nx"), "a").close()
 
-    scan = HDF5TomoScan(
+    scan = NXtomoScan(
         scan=os.path.join(tmp_path, "1.nx"),
         entry="entry0000",
     )
-    assert isinstance(scan, HDF5TomoScan)
+    assert isinstance(scan, NXtomoScan)
 
     assert len(_ls_tomo_obj(scan)) == 2
 

tomwer/core/process/control/test/test_h52nx_process.py

@@ -1,11 +1,12 @@
 import os
 from tomwer.core.scan.edfscan import EDFTomoScan
+from tomwer.core.process.output import ProcessDataOutputDirMode
 from tomwer.core.process.control.nxtomomill import (
     EDFToNxProcess,
     H5ToNxProcess,
-    NXtomomillNXDefaultOutput,
+    get_default_raw_data_output_file,
 )
-from tomwer.core.utils.scanutils import MockHDF5, MockEDF
+from tomwer.core.utils.scanutils import MockNXtomo, MockEDF
 from nxtomomill.converter.hdf5.utils import PROCESSED_DATA_DIR_NAME, RAW_DATA_DIR_NAME
 
 
@@ -14,14 +15,14 @@ def test_h52nx_process_deduce_output_file_path(tmp_path):
     scan_path = str(tmp_path / "path" / RAW_DATA_DIR_NAME / "my_scan")
     os.makedirs(scan_path)
 
-    scan = MockHDF5(scan_path=scan_path, n_proj=0).scan
+    scan = MockNXtomo(scan_path=scan_path, n_proj=0).scan
 
     # test H52NXDefaultOutput.PROCESSED_DATA
     assert H5ToNxProcess.deduce_output_file_path(
         master_file_name=scan.master_file,
         scan=scan,
         entry=scan.entry,
-        outputdir=NXtomomillNXDefaultOutput.PROCESSED_DATA.value,
+        outputdir=ProcessDataOutputDirMode.PROCESSED_DATA_FOLDER.value,
     ) == str(
         tmp_path
         / "path"
@@ -35,7 +36,7 @@ def test_h52nx_process_deduce_output_file_path(tmp_path):
         master_file_name=scan.master_file,
         scan=scan,
         entry=scan.entry,
-        outputdir=NXtomomillNXDefaultOutput.NEAR_INPUT_FILE.value,
+        outputdir=ProcessDataOutputDirMode.IN_SCAN_FOLDER.value,
     ) == str(
         tmp_path / "path" / RAW_DATA_DIR_NAME / "my_scan" / f"my_scan_{scan.entry}.nx"
     )
@@ -77,14 +78,14 @@ def test_edf2nx_process_deduce_output_file_path(tmp_path):
     # test NEAR_INPUT_FILE
     assert EDFToNxProcess.deduce_output_file_path(
         folder_path=scan_path,
-        output_dir=NXtomomillNXDefaultOutput.NEAR_INPUT_FILE.value,
+        output_dir=ProcessDataOutputDirMode.IN_SCAN_FOLDER.value,
         scan=scan,
     ) == os.path.join(tmp_path, "path", RAW_DATA_DIR_NAME, "my_edf_scan.nx")
 
     # test PROCESSED_DATA
     assert EDFToNxProcess.deduce_output_file_path(
         folder_path=scan_path,
-        output_dir=NXtomomillNXDefaultOutput.PROCESSED_DATA.value,
+        output_dir=ProcessDataOutputDirMode.PROCESSED_DATA_FOLDER.value,
         scan=scan,
     ) == os.path.join(tmp_path, "path", PROCESSED_DATA_DIR_NAME, "my_edf_scan.nx")
 
@@ -104,3 +105,54 @@ def test_edf2nx_process_deduce_output_file_path(tmp_path):
         )
         == "/tmp/output/my_edf_scan.nx"
     )
+
+
+def test_get_default_raw_data_output_file():
+    """test 'get_default_raw_data_output_file' function"""
+    assert get_default_raw_data_output_file("/tmp/path/file.h5") == "/tmp/path/file.nx"
+    assert (
+        get_default_raw_data_output_file(f"/tmp/{PROCESSED_DATA_DIR_NAME}/file.h5")
+        == f"/tmp/{RAW_DATA_DIR_NAME}/file.nx"
+    )
+
+    assert (
+        get_default_raw_data_output_file(
+            f"/tmp/path/{PROCESSED_DATA_DIR_NAME}/toto/file.h5"
+        )
+        == f"/tmp/path/{RAW_DATA_DIR_NAME}/toto/file.nx"
+    )
+    # note: _RAW_DATA_DIR_NAME part of the path but not a folder
+    assert (
+        get_default_raw_data_output_file(f"/tmp/path_{RAW_DATA_DIR_NAME}/toto/file.h5")
+        == f"/tmp/path_{RAW_DATA_DIR_NAME}/toto/file.nx"
+    )
+
+    # 2. advance test
+    # 2.1 use case: '_RAW_DATA_DIR_NAME' is present twice in the path -> replace the deeper one
+    assert (
+        get_default_raw_data_output_file(
+            f"/tmp/{PROCESSED_DATA_DIR_NAME}/path/{RAW_DATA_DIR_NAME}/toto/file.h5"
+        )
+        == f"/tmp/{PROCESSED_DATA_DIR_NAME}/path/{RAW_DATA_DIR_NAME}/toto/file.nx"
+    )
+
+    # 2.2 use case: contains both '_RAW_DATA_DIR_NAME' and '_PROCESSED_DATA_DIR_NAME' in the path
+    assert (
+        get_default_raw_data_output_file(
+            f"/tmp/{PROCESSED_DATA_DIR_NAME}/path/{RAW_DATA_DIR_NAME}/toto/file.h5"
+        )
+        == f"/tmp/{PROCESSED_DATA_DIR_NAME}/path/{RAW_DATA_DIR_NAME}/toto/file.nx"
+    )
+
+    assert (
+        get_default_raw_data_output_file(
+            f"/tmp/{RAW_DATA_DIR_NAME}/path/{PROCESSED_DATA_DIR_NAME}/toto/file.h5"
+        )
+        == f"/tmp/{RAW_DATA_DIR_NAME}/path/{RAW_DATA_DIR_NAME}/toto/file.nx"
+    )
+
+    # 2.3 use case: expected output file is the input file. Make sure append '_nxtomo'
+    assert (
+        get_default_raw_data_output_file("/tmp/path/file.nx")
+        == "/tmp/path/file_nxtomo.nx"
+    )

tomwer/core/process/control/test/test_volume_link.py

@@ -1,74 +1,74 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2017 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-# ###########################################################################*/
+# # coding: utf-8
+# # /*##########################################################################
+# #
+# # Copyright (c) 2016-2017 European Synchrotron Radiation Facility
+# #
+# # Permission is hereby granted, free of charge, to any person obtaining a copy
+# # of this software and associated documentation files (the "Software"), to deal
+# # in the Software without restriction, including without limitation the rights
+# # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# # copies of the Software, and to permit persons to whom the Software is
+# # furnished to do so, subject to the following conditions:
+# #
+# # The above copyright notice and this permission notice shall be included in
+# # all copies or substantial portions of the Software.
+# #
+# # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# # THE SOFTWARE.
+# #
+# # ###########################################################################*/
 
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "16/06/2021"
+# __authors__ = ["H. Payno"]
+# __license__ = "MIT"
+# __date__ = "16/06/2021"
 
 
-import os
-import shutil
-import tempfile
-import unittest
+# import os
+# import shutil
+# import tempfile
+# import unittest
 
-from tomwer.core.process.control.volumesymlink import VolumeSymbolicLinkTask
-from tomwer.core.scan.edfscan import EDFTomoScan
-from tomwer.core.utils.scanutils import MockEDF
+# from tomwer.core.process.control.volumesymlink import VolumeSymbolicLinkTask
+# from tomwer.core.scan.edfscan import EDFTomoScan
+# from tomwer.core.utils.scanutils import MockEDF
 
 
-class TestVolumeSymbolicLink(unittest.TestCase):
-    """Simple test of the VolumeSymbolicLink"""
+# class TestVolumeSymbolicLink(unittest.TestCase):
+#     """Simple test of the VolumeSymbolicLink"""
 
-    def setUp(self) -> None:
-        self._scan_folder = tempfile.mkdtemp()
-        self._output_folder = tempfile.mkdtemp()
-        MockEDF.fastMockAcquisition(self._scan_folder)
-        MockEDF.mockReconstruction(self._scan_folder, nRecons=2, nPagRecons=2)
-        self._scan = EDFTomoScan(self._scan_folder)
-        # here we simply estimate that the slice reconstruction will be
-        # volume reconstruction but the mechanism is the same.
-        self._scan.set_latest_vol_reconstructions(self._scan.get_reconstructions_urls())
+#     def setUp(self) -> None:
+#         self._scan_folder = tempfile.mkdtemp()
+#         self._output_folder = tempfile.mkdtemp()
+#         MockEDF.fastMockAcquisition(self._scan_folder)
+#         MockEDF.mockReconstruction(self._scan_folder, nRecons=2, nPagRecons=2)
+#         self._scan = EDFTomoScan(self._scan_folder)
+#         # here we simply estimate that the slice reconstruction will be
+#         # volume reconstruction but the mechanism is the same.
+#         self._scan.set_latest_vol_reconstructions(self._scan.get_reconstructions_urls())
 
-    def tearDown(self) -> None:
-        for folder in (self._scan_folder, self._output_folder):
-            shutil.rmtree(folder)
+#     def tearDown(self) -> None:
+#         for folder in (self._scan_folder, self._output_folder):
+#             shutil.rmtree(folder)
 
-    def test(self):
-        """simple test that the creation of a symbolic link works"""
-        vlink_process = VolumeSymbolicLinkTask(
-            inputs={
-                "data": self._scan,
-                "serialize_output_data": False,
-                "output_type": "static",
-                "output_folder": self._output_folder,
-            }
-        )
-        self.assertEqual(len(os.listdir(self._output_folder)), 0)
-        vlink_process.run()
-        self.assertEqual(len(os.listdir(self._output_folder)), 4)
+#     def test(self):
+#         """simple test that the creation of a symbolic link works"""
+#         vlink_process = VolumeSymbolicLinkTask(
+#             inputs={
+#                 "data": self._scan,
+#                 "serialize_output_data": False,
+#                 "output_type": "static",
+#                 "output_folder": self._output_folder,
+#             }
+#         )
+#         self.assertEqual(len(os.listdir(self._output_folder)), 0)
+#         vlink_process.run()
+#         self.assertEqual(len(os.listdir(self._output_folder)), 4)
 
-        self.assertTrue(isinstance(vlink_process.program_name(), str))
-        self.assertTrue(isinstance(vlink_process.program_version(), str))
-        self.assertTrue(isinstance(vlink_process.definition(), str))
+#         self.assertTrue(isinstance(vlink_process.program_name(), str))
+#         self.assertTrue(isinstance(vlink_process.program_version(), str))
+#         self.assertTrue(isinstance(vlink_process.definition(), str))

tomwer/core/process/control/timer.py

@@ -35,7 +35,7 @@ from tomwer.core.process.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 silx.utils.deprecation import deprecated_warning, deprecated
+from tomwer.core.utils.deprecation import deprecated_warning, deprecated
 
 _logger = logging.getLogger(__name__)