tomwer 1.1.0rc7__py3-none-any.whl → 1.2.0a0__py3-none-any.whl

tomwer/core/scan/scanbase.py

@@ -28,29 +28,30 @@ __license__ = "MIT"
 __date__ = "09/08/2018"
 
 
-import numpy
-import logging
-import typing
-import json
 import io
+import json
+import logging
 import os
+import typing
 from glob import glob
+from typing import Optional
+
+import numpy
 from silx.io.url import DataUrl
-from tomwer.core.tomwer_object import TomwerObject
-from tomwer.core.utils.locker import FileLockerManager, FileLockerContext
-from tomwer.core.utils.ftseriesutils import orderFileByLastLastModification
-from tomoscan.normalization import IntensityNormalization
-from tomoscan.io import HDF5File
+from silx.utils.enum import Enum as _Enum
 from tomoscan.identifier import VolumeIdentifier
+from tomoscan.io import HDF5File
+from tomoscan.normalization import IntensityNormalization
 from tomoscan.volumebase import VolumeBase
-from typing import Optional
-from silx.utils.enum import Enum as _Enum
-from tomwer.core.volume.hdf5volume import HDF5Volume
+
+from tomwer.core.tomwer_object import TomwerObject
+from tomwer.core.utils.ftseriesutils import orderFileByLastLastModification
+from tomwer.core.utils.locker import FileLockerContext, FileLockerManager
 from tomwer.core.volume.edfvolume import EDFVolume
+from tomwer.core.volume.hdf5volume import HDF5Volume
 from tomwer.core.volume.jp2kvolume import JP2KVolume
 from tomwer.core.volume.tiffvolume import MultiTIFFVolume
 
-
 logger = logging.getLogger(__name__)
 
 
@@ -327,10 +328,10 @@ class TomwerScanBase(TomwerObject):
             del self._cache_radio_axis[(mode, nearest)]
 
         def compute():
+            from ..process.reconstruction.axis.anglemode import CorAngleMode
             from ..process.reconstruction.axis.params import (
                 AxisResource,
             )  # avoid cyclic import
-            from ..process.reconstruction.axis.anglemode import CorAngleMode
 
             _mode = CorAngleMode.from_value(mode)
             if self.path is None:  # pylint: disable=E1101
@@ -759,8 +760,7 @@ class TomwerScanBase(TomwerObject):
                     if len(indexes) > 0:
                         self._process_index = max(indexes) + 1
                         logger.debug(
-                            "set process_index from tomwer process file"
-                            "to {}".format(self._process_index)
+                            f"set process_index from tomwer process file to {self._process_index}"
                         )
 
     def get_nabu_dataset_info(self, binning=1, binning_z=1, proj_subsampling=1):
@@ -790,8 +790,8 @@ class _TomwerBaseDock(object):
         return self.__instance
 
 
-def _containsDigits(input):
-    return any(char.isdigit() for char in input)
+def _containsDigits(input_):
+    return any(char.isdigit() for char in input_)
 
 
 def _get_reconstructed_single_file_volume(

tomwer/core/scan/scanfactory.py

@@ -28,22 +28,25 @@ __license__ = "MIT"
 __date__ = "27/02/2019"
 
 
+import glob
+import logging
+import os
+from typing import Union
+from urllib.parse import urlparse
+
 import h5py
-from tomoscan.scanbase import TomoScanBase
-from tomoscan.factory import Factory as _oScanFactory
+from tomoscan.esrf.identifier.url_utils import split_path
 from tomoscan.esrf.scan.hdf5scan import HDF5TomoScan as _oHDF5TomoScan
+from tomoscan.factory import Factory as _oScanFactory
 from tomoscan.identifier import BaseIdentifier, ScanIdentifier, VolumeIdentifier
+from tomoscan.scanbase import TomoScanBase
 from tomoscan.tomoobject import TomoObject
+
 from tomwer.utils import docstring
-from typing import Union
+
+from .blissscan import BlissScan
 from .edfscan import EDFTomoScan, EDFTomoScanIdentifier
 from .hdf5scan import HDF5TomoScan, HDF5TomoScanIdentifier
-from .blissscan import BlissScan
-import os
-import glob
-import logging
-from urllib.parse import urlparse
-from tomoscan.esrf.identifier.url_utils import split_path
 
 _logger = logging.getLogger(__name__)
 
@@ -140,9 +143,8 @@ class ScanFactory(object):
                 entry = valid_entries[-1]
             elif entry not in valid_entries:
                 raise ValueError(
-                    "entry {} is invalid. Does it exists ? Is the "
-                    "file NXTomo compliant ?. Valid entry are {}"
-                    "".format(entry, valid_entries)
+                    f"entry {entry} is invalid. Does it exists ? Is the "
+                    f"file NXTomo compliant ?. Valid entry are {valid_entries}"
                 )
             return HDF5TomoScan(scan=scan_path, entry=entry)
         elif ScanFactory.is_edf_tomo(scan_path):
@@ -152,13 +154,12 @@ class ScanFactory(object):
                 valid_entries = BlissScan.get_valid_entries(scan_path)
                 if len(valid_entries) > 1:
                     _logger.warning(
-                        "more than one entry found for %s."
-                        "Pick the last entry" % scan_path
+                        f"more than one entry found for {scan_path}. Pick the last entry"
                     )
                 entry = valid_entries[-1]
             return BlissScan(master_file=scan_path, entry=entry, proposal_file=None)
 
-        raise ValueError("Unable to generate a scan object from %s" % scan_path)
+        raise ValueError(f"Unable to generate a scan object from {scan_path}")
 
     @docstring(_oScanFactory.create_scan_objects)
     @staticmethod
@@ -183,9 +184,9 @@ class ScanFactory(object):
         return tuple()
 
     @staticmethod
-    def mock_scan(type="edf"):
+    def mock_scan(type_="edf"):
         """Mock a scan structure which is not associated to any real acquistion"""
-        if type == "edf":
+        if type_ == "edf":
             return EDFTomoScan(scan=None)
         else:
             raise NotImplementedError("Other TomoScan are not defined yet")
@@ -194,9 +195,7 @@ class ScanFactory(object):
     def create_scan_object_frm_dict(_dict):
         if TomoScanBase.DICT_TYPE_KEY not in _dict:
             raise ValueError(
-                "given dict is not recognized. Cannot find {}".format(
-                    TomoScanBase.DICT_TYPE_KEY
-                )
+                f"given dict is not recognized. Cannot find {TomoScanBase.DICT_TYPE_KEY}"
             )
         elif _dict[TomoScanBase.DICT_TYPE_KEY] == EDFTomoScan._TYPE:
             return EDFTomoScan(scan=None).load_from_dict(_dict)
@@ -204,7 +203,7 @@ class ScanFactory(object):
             return HDF5TomoScan.from_dict(_dict)
         else:
             raise ValueError(
-                "Scan type {} is not managed".format(_dict[TomoScanBase.DICT_TYPE_KEY])
+                f"Scan type {_dict[TomoScanBase.DICT_TYPE_KEY]} is not managed"
             )
 
     @staticmethod

tomwer/core/scan/scantype.py

@@ -0,0 +1,7 @@
+from silx.utils.enum import Enum as _Enum
+
+
+class ScanType(_Enum):
+    BLISS = "bliss-hdf5"
+    SPEC = "spec-edf"
+    NX_TOMO = "NXtomo"

tomwer/core/scan/test/test_edf.py

@@ -29,9 +29,10 @@ __license__ = "MIT"
 __date__ = "23/11/2021"
 
 
+import os
+
 from tomwer.core.scan.edfscan import EDFTomoScan
 from tomwer.core.utils.scanutils import MockEDF
-import os
 
 
 def test_scan_dir(tmpdir):

tomwer/core/scan/test/test_future_scan.py

@@ -30,9 +30,10 @@ __date__ = "04/11/2021"
 
 
 import asyncio
+import os
+
 from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.utils.scanutils import MockHDF5
-import os
 
 
 def test_simple_future_tomo_obj(tmpdir):

tomwer/core/scan/test/test_h5.py

@@ -28,14 +28,15 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "16/09/2019"
 
-import unittest
-import shutil
 import os
+import shutil
 import tempfile
-from tomwer.tests.utils import UtilsTest
-from tomwer.core.scan.hdf5scan import HDF5TomoScan
+import unittest
+
 from tomwer.core.process.reconstruction.darkref.darkrefs import DarkRefs
+from tomwer.core.scan.hdf5scan import HDF5TomoScan
 from tomwer.core.utils.scanutils import MockHDF5
+from tomwer.tests.utils import UtilsTest
 
 
 class TestHDF5Scan(unittest.TestCase):

tomwer/core/scan/test/test_process_registration.py

@@ -28,12 +28,14 @@ __license__ = "MIT"
 __date__ = "02/09/2020"
 
 
+import shutil
+import tempfile
 import unittest
+
+from tomoscan.io import HDF5File
+
 from tomwer.core.process.task import Task
 from tomwer.core.utils.scanutils import MockHDF5
-import tempfile
-import shutil
-from tomoscan.io import HDF5File
 
 
 class TestProcessRegistration(unittest.TestCase):

tomwer/core/scan/test/test_scan.py

@@ -27,21 +27,23 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "24/01/2017"
 
-import unittest
+import contextlib
 import logging
+import os
+import shutil
 import tempfile
-import numpy
+import unittest
+from multiprocessing import Process
+
 import fabio.edfimage
-import contextlib
+import numpy
+
+from tomwer.core.process.reconstruction.nabu import nabuslices
+from tomwer.core.process.task import Task
 from tomwer.core.scan.edfscan import EDFTomoScan
 from tomwer.core.scan.scanfactory import ScanFactory
-from tomwer.core.process.task import Task
-from tomwer.tests.utils import UtilsTest
 from tomwer.core.utils.scanutils import MockEDF
-from tomwer.core.process.reconstruction.nabu import nabuslices
-import shutil
-import os
-from multiprocessing import Process
+from tomwer.tests.utils import UtilsTest
 
 logging.disable(logging.INFO)
 

tomwer/core/settings.py

@@ -30,7 +30,6 @@ __date__ = "02/06/2017"
 
 import os
 
-
 __LBSRAM_PATH = '/lbsram'
 
 __DEST_PATH = ''
@@ -104,7 +103,7 @@ class SlurmSettings:
     N_GPUS_PER_WORKER = 1
     """number of gpu per worker"""
 
-    PYTHON_VENV = "/scisoft/tomotools/activate.sh stable"
+    PYTHON_VENV = "/scisoft/tomotools/activate stable"
     """Python executable to take. Useful if compute nodes have a different environment from the front end.
     """
 

tomwer/core/test/test_lamino.py

@@ -27,9 +27,10 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "19/07/2018"
 
-import unittest
-import tempfile
 import shutil
+import tempfile
+import unittest
+
 from tomwer.core.process.reconstruction.lamino import tofu
 from tomwer.core.scan.edfscan import EDFTomoScan
 

tomwer/core/test/test_scanutils.py

@@ -27,11 +27,12 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "30/09/2019"
 
-import unittest
 import os
 import tempfile
-from tomwer.core.utils.scanutils import MockHDF5
+import unittest
+
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
+from tomwer.core.utils.scanutils import MockHDF5
 
 
 class TestMockHDF5(unittest.TestCase):

tomwer/core/test/test_utils.py

@@ -28,15 +28,17 @@ __license__ = "MIT"
 __date__ = "02/08/2017"
 
 
-import unittest
-import tempfile
 import os
 import shutil
+import tempfile
+import unittest
+
+import numpy
+
 from tomwer.core import 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.normalization import flatFieldCorrection
-import numpy
 
 
 class TestGetClosestEnergy(unittest.TestCase):

tomwer/core/utils/__init__.py

@@ -27,16 +27,18 @@ __authors__ = ["H. Payno"]
 __license__ = "MIT"
 __date__ = "17/05/2017"
 
-import fabio.edfimage
-import os
-import psutil
+import fileinput
 import logging
+import os
 import shutil
-from tomwer.core import settings
-from tomoscan.unitsystem import metricsystem
 from urllib.request import urlopen
-import fileinput
+
+import fabio.edfimage
+import psutil
 from lxml import etree
+from tomoscan.unitsystem import metricsystem
+
+from tomwer.core import settings
 
 logger = logging.getLogger(__name__)
 

tomwer/core/utils/deprecation.py

@@ -28,9 +28,9 @@ __authors__ = ["Jerome Kieffer", "H. Payno", "P. Knobel"]
 __license__ = "MIT"
 __date__ = "26/02/2018"
 
-import sys
-import logging
 import functools
+import logging
+import sys
 import traceback
 
 depreclog = logging.getLogger("silx.DEPRECATION")

tomwer/core/utils/image.py

@@ -28,9 +28,10 @@ __license__ = "MIT"
 __date__ = "25/02/2019"
 
 
-import numpy
-import logging
 import enum
+import logging
+
+import numpy
 from numpy.linalg import inv
 
 _logger = logging.getLogger(__file__)
@@ -67,7 +68,7 @@ def shift_img(
     assert data.ndim == 2
     assert dx is not None
     assert dy is not None
-    _logger.debug("apply shift dx=%s, dy=%s " % (dx, dy))
+    _logger.debug(f"apply shift dx={dx}, dy={dy} ")
 
     if use_scipy and has_scipy_shift:
         return shift_scipy(

tomwer/core/utils/laminoutils.py

@@ -0,0 +1,80 @@
+# coding: utf-8
+# /*##########################################################################
+#
+# Copyright (c) 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__ = "22/06/2018"
+
+
+import fabio
+import os
+import logging
+
+logger = logging.getLogger(__name__)
+
+
+def getMotorInformationFromEDfFile(_file):
+    """
+
+    :param _file: file to the edf file containing header with information
+    :return: dictionary with motor name as key and motor position as value
+    :rtype: dict
+    """
+    assert type(_file) is str
+    assert _file.endswith(".edf")
+    if not os.path.isfile(_file):
+        warn = "%s is not a valid file. Cannot retrieve motor information" % _file
+        logger.warning(warn)
+        return None
+    else:
+        with fabio.open(_file) as dsc:
+            header = dsc.header
+
+        if "motor_mne" not in header:
+            logger.warning(
+                'key "motor_mne" not found in the file header.'
+                "Cannot retrieve motor information"
+            )
+            return None
+
+        if "motor_pos" not in header:
+            logger.warning(
+                'key "motor_pos" not found in the file header.'
+                "Cannot retrieve motor information"
+            )
+            return None
+
+        motor_mne_lst = header["motor_mne"].split(" ")
+        motor_pos_lst = header["motor_pos"].split(" ")
+        if len(motor_mne_lst) != len(motor_pos_lst):
+            logger.warning(
+                "Incoherent number of motor_mne and motor_pos."
+                "Cannot retrieve motor information"
+            )
+            return None
+        res = {}
+        for mne, pos in zip(motor_mne_lst, motor_pos_lst):
+            res[mne] = pos
+        return res

tomwer/core/utils/locker.py

@@ -30,8 +30,8 @@ __date__ = "20/04/2020"
 
 import os
 import threading
-
 from contextlib import AbstractContextManager
+
 from tomwer.core.utils.Singleton import singleton
 
 

tomwer/core/utils/normalization.py

@@ -29,6 +29,7 @@ __date__ = "30/05/2018"
 
 
 import logging
+
 import fabio
 
 _logger = logging.getLogger(__name__)

tomwer/core/utils/nxtomoutils.py

@@ -29,8 +29,9 @@ __date__ = "02/12/2021"
 
 
 from typing import Union
-from tomoscan.esrf.scan.hdf5scan import ImageKey
+
 import numpy
+from tomoscan.esrf.scan.hdf5scan import ImageKey
 
 
 def get_n_series(image_key_values: Union[tuple, list], image_key_type: ImageKey) -> int:

tomwer/core/utils/scanutils.py

@@ -30,18 +30,21 @@ __license__ = "MIT"
 __date__ = "11/08/2022"
 
 import logging
-import h5py
-import numpy
-import time
 import os
+import time
 from typing import Any
+
+import h5py
+import numpy
+from silx.io.utils import h5py_read_dataset
+from tomoscan.esrf.scan.mock import MockEDF as _MockEDF
+from tomoscan.esrf.scan.mock import MockHDF5 as _MockHDF5
 from tomoscan.io import HDF5File
-from tomoscan.esrf.scan.mock import MockEDF as _MockEDF, MockHDF5 as _MockHDF5
 from tomoscan.test.utils import MockContext
+
 from tomwer.core.scan.blissscan import BlissScan
 from tomwer.core.scan.hdf5scan import HDF5TomoScan
 from tomwer.core.scan.scanfactory import ScanFactory
-from silx.io.utils import h5py_read_dataset
 
 _logger = logging.getLogger(__name__)
 
@@ -273,7 +276,7 @@ class _BlissSample:
             h5f["/".join((str(seq_ini_index) + ".1", "end_time"))] = str(time.ctime())
 
         if self.__with_nx:
-            nx_file = "sample_{}.nx".format(str(seq_ini_index).zfill(4))
+            nx_file = f"sample_{seq_ini_index:04}.nx"
             nx_file = os.path.join(self.path, nx_file)
             with h5py.File(nx_file, "a") as h5f:
                 pass

tomwer/core/utils/slurm.py

@@ -30,8 +30,9 @@ __license__ = "MIT"
 __date__ = "11/10/2021"
 
 
-from datetime import datetime
 import uuid
+from datetime import datetime
+
 from sluurp.utils import has_sbatch_available
 
 

tomwer/core/utils/time.py

@@ -44,7 +44,5 @@ class Timer:
         self._start_time = time()
 
     def __exit__(self, type, value, traceback):
-        print(
-            "{title} exec time: {exec_time} s"
-            "".format(title=self.title, exec_time=(time() - self._start_time))
-        )
+        exec_time = time() - self._start_time
+        print(f"{self.title} exec time: {exec_time} s")

tomwer/core/utils/volumeutils.py

@@ -1,6 +1,7 @@
-from tomwer.core.volume.volumefactory import VolumeFactory
 from typing import Any
 
+from tomwer.core.volume.volumefactory import VolumeFactory
+
 
 def volume_identifier_to_volume(volume_identifier: Any):
     """

tomwer/core/volume/__init__.py

@@ -1,5 +1,5 @@
 from .edfvolume import EDFVolume  # noqa F401
 from .hdf5volume import HDF5Volume  # noqa F401
 from .jp2kvolume import JP2KVolume  # noqa F401
-from .tiffvolume import TIFFVolume, MultiTIFFVolume  # noqa F401
 from .rawvolume import RawVolume  # noqa F401
+from .tiffvolume import MultiTIFFVolume, TIFFVolume  # noqa F401

tomwer/core/volume/edfvolume.py

@@ -28,12 +28,13 @@ __license__ = "MIT"
 __date__ = "05/07/2022"
 
 
-from tomoscan.esrf.volume.edfvolume import EDFVolume as _EDFVolume
-from tomwer.core.volume.volumebase import TomwerVolumeBase
+from processview.core.dataset import Dataset, DatasetIdentifier
 from tomoscan.esrf.identifier.edfidentifier import (
     EDFVolumeIdentifier as _EDFVolumeIdentifier,
 )
-from processview.core.dataset import DatasetIdentifier, Dataset
+from tomoscan.esrf.volume.edfvolume import EDFVolume as _EDFVolume
+
+from tomwer.core.volume.volumebase import TomwerVolumeBase
 
 
 class EDFVolumeIdentifier(_EDFVolumeIdentifier, DatasetIdentifier):

tomwer/core/volume/hdf5volume.py

@@ -28,18 +28,16 @@ __license__ = "MIT"
 __date__ = "05/07/2022"
 
 
-from tomoscan.esrf.volume.hdf5volume import HDF5Volume as _HDF5Volume
+from urllib.parse import urlparse
+
+from processview.core.dataset import Dataset, DatasetIdentifier
 from tomoscan.esrf.identifier.hdf5Identifier import (
     HDF5VolumeIdentifier as _HDF5VolumeIdentifier,
 )
+from tomoscan.esrf.identifier.url_utils import UrlSettings, split_path, split_query
+from tomoscan.esrf.volume.hdf5volume import HDF5Volume as _HDF5Volume
+
 from tomwer.core.volume.volumebase import TomwerVolumeBase
-from processview.core.dataset import DatasetIdentifier, Dataset
-from urllib.parse import urlparse
-from tomoscan.esrf.identifier.url_utils import (
-    UrlSettings,
-    split_path,
-    split_query,
-)
 
 
 class HDF5VolumeIdentifier(_HDF5VolumeIdentifier, DatasetIdentifier):

tomwer/core/volume/jp2kvolume.py

@@ -28,12 +28,13 @@ __license__ = "MIT"
 __date__ = "05/07/2022"
 
 
-from tomoscan.esrf.volume.jp2kvolume import JP2KVolume as _JP2KVolume
-from tomwer.core.volume.volumebase import TomwerVolumeBase
+from processview.core.dataset import Dataset, DatasetIdentifier
 from tomoscan.esrf.identifier.jp2kidentifier import (
     JP2KVolumeIdentifier as _JP2KVolumeIdentifier,
 )
-from processview.core.dataset import DatasetIdentifier, Dataset
+from tomoscan.esrf.volume.jp2kvolume import JP2KVolume as _JP2KVolume
+
+from tomwer.core.volume.volumebase import TomwerVolumeBase
 
 
 class JP2KVolumeIdentifier(_JP2KVolumeIdentifier, DatasetIdentifier):