tomwer 1.3.26__py3-none-any.whl → 1.4.0__py3-none-any.whl

tomwer/core/process/reconstruction/axis/side.py

@@ -0,0 +1,8 @@
+from silx.utils.enum import Enum as _Enum
+
+
+class Side(_Enum):
+    LEFT = "left"
+    RIGHT = "right"
+    CENTER = "center"
+    ALL = "all"

tomwer/core/process/reconstruction/darkref/darkrefs.py

@@ -1,38 +1,12 @@
-# coding: utf-8
-# /*##########################################################################
-# Copyright (C) 2016 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.
-#
-#############################################################################*/
 """
 This module provides global definitions and functions to manage dark and flat fields
 especially for tomo experiments and workflows
 """
 
-__authors__ = ["C. Nemoz", "H.Payno"]
-__license__ = "MIT"
-__date__ = "06/09/2017"
+from __future__ import annotations
 
 import logging
 import os
-import typing
 from queue import Queue
 
 from processview.core.manager import DatasetState, ProcessManager
@@ -88,9 +62,8 @@ class DarkRefsTask(
     ):
         """
 
-        :param str file_ext:
+        :param file_ext:
         :param reconsparams: reconstruction parameters
-        :type reconsparams: Union[None, ReconsParams, DKRFRP]
         """
         Task.__init__(
             self,
@@ -230,12 +203,12 @@ class DarkRefsTask(
     @staticmethod
     def get_darks_frm_process_file(
         process_file, entry=None, as_url: bool = False
-    ) -> typing.Union[None, dict]:
+    ) -> dict | None:
         """
 
-        :param str process_file: path to the process file
+        :param process_file: path to the process file
         :param entry: entry to read in the process file if more than one
-        :param bool as_url: if true then an url will be used instead of a
+        :param as_url: if true then an url will be used instead of a
                             numpy.array
         :return: dictionary with index in the sequence as key and numpy array
                  as value (or url if as_url set to True)
@@ -251,12 +224,12 @@ class DarkRefsTask(
     @staticmethod
     def get_flats_frm_process_file(
         process_file, entry=None, as_url: bool = False
-    ) -> typing.Union[None, dict]:
+    ) -> dict | None:
         """
 
         :param process_file:
         :param entry: entry to read in the process file if more than one
-        :param bool as_url: if true then an url will be used instead of a
+        :param as_url: if true then an url will be used instead of a
                             numpy.array
         :return:
         """
@@ -478,18 +451,20 @@ class DarkRefsTask(
     @docstring(Task.definition)
     @staticmethod
     def definition():
-        return "Compute mean or median dark and refs per each serie"
+        return "Compute mean or median dark and refs per each series"
 
 
-def requires_reduced_dark_and_flat(scan: TomwerScanBase, logger_=None) -> tuple:
-    """helper function: If no dark / flat are computed yet then will pick the first
+def requires_reduced_dark_and_flat(
+    scan: TomwerScanBase, logger_: logging.Logger | None = None
+) -> tuple:
+    r"""helper function: If no dark / flat are computed yet then will pick the first
     dark and the first flat.
 
     Expected usage: for tomwer application which requires some time and flat and to avoid some warnings
     within standalones.
 
-    :params TomwerScanBase scan: scan for which we want to get quick dark and flat
-    :params Optional[Logger] logger_: if provided will add some warning when attempt to get reduced flat / dark.
+    :params scan: scan for which we want to get quick dark and flat
+    :params logger\_: if provided will add some warning when attempt to get reduced flat / dark.
     :returns: tuple of what was missing and has been computed
     """
     computed = []

tomwer/core/process/reconstruction/darkref/darkrefscopy.py

@@ -1,42 +1,14 @@
-# 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.
-#
-#############################################################################*/
-
 """
 This module is used to define the process of the reference creator.
 This is related to the issue #184
 """
 
-__authors__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "17/08/2021"
-
+from __future__ import annotations
 
 import logging
 import os
 import h5py
 import tempfile
-from typing import Union
 
 from silx.io.dictdump import dicttoh5, h5todict
 from silx.io.url import DataUrl
@@ -136,13 +108,12 @@ class DarkRefsCopy(DarkRefsTask):
         url: DataUrl, reduced_target: REDUCER_TARGET, check_for_reduced_key: bool = True
     ) -> tuple:
         """
-        :param Data url: url expected to contain the dict with one key per serie of reduced frame
-        :param REDUCER_TARGET reduced_target: what we are looking for (used when check_for_reduced_key is set to True)
-        :param bool check_for_reduced_key: if True then if the dict contains the given key then return the value of this key instead
+        :param url: url expected to contain the dict with one key per serie of reduced frame
+        :param reduced_target: what we are looking for (used when check_for_reduced_key is set to True)
+        :param check_for_reduced_key: if True then if the dict contains the given key then return the value of this key instead
                                            of the loaded dict. Used as a user friendly feature to be able to load dict when upper data path
                                            is provided instead of the 'darks' or 'flats' one.
-        :return: data, metadata
-        :rtype: tuple of two dicts
+        :return: tuple as (data, metadata)
         """
         reduced_target = REDUCER_TARGET.from_value(reduced_target)
 
@@ -162,7 +133,7 @@ class DarkRefsCopy(DarkRefsTask):
                     return reduced_info_dict
 
     @staticmethod
-    def save_flats_to_be_copied(save_dir, data: Union[DataUrl, dict]):
+    def save_flats_to_be_copied(save_dir, data: DataUrl | dict):
         if isinstance(data, DataUrl):
             data = DarkRefsCopy.get_reduced_frame_data(url=data, reduced_target="flats")
         if data is None:
@@ -181,7 +152,7 @@ class DarkRefsCopy(DarkRefsTask):
         )
 
     @staticmethod
-    def save_darks_to_be_copied(save_dir, data: Union[DataUrl, dict]):
+    def save_darks_to_be_copied(save_dir, data: DataUrl | dict):
         if isinstance(data, DataUrl):
             data = DarkRefsCopy.get_reduced_frame_data(url=data, reduced_target="darks")
         if data is None:
@@ -313,7 +284,6 @@ class DarkRefsCopy(DarkRefsTask):
 
         :return: True if the process has at least registered one flat or one
                  dark
-        :rtype: bool
         """
         return self.has_flat_stored() or self.has_dark_stored()
 
@@ -321,7 +291,6 @@ class DarkRefsCopy(DarkRefsTask):
         """
 
         :return: True if the process has registered at least one ref
-        :rtype: bool
         """
         if not os.path.exists(self._save_file):
             return False
@@ -333,7 +302,6 @@ class DarkRefsCopy(DarkRefsTask):
         """
 
         :return: True if the process has registered at least one dark
-        :rtype: bool
         """
         if not os.path.exists(self._save_file):
             return False

tomwer/core/process/reconstruction/darkref/params.py

@@ -1,32 +1,5 @@
 # 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__ = "07/03/2019"
-
+from __future__ import annotations
 
 import enum
 

tomwer/core/process/reconstruction/nabu/castvolume.py

@@ -1,34 +1,9 @@
 # coding: utf-8
-###########################################################################
-# Copyright (C) 2016 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.
-#
-#############################################################################
 
 """
 This module is dedicated to cast of volume from one file format to the other.
 """
-
-__authors__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "15/12/2021"
+from __future__ import annotations
 
 
 import logging
@@ -103,10 +78,12 @@ class CastVolumeTask(
         self._cluster_config = configuration.pop("cluster_config", None)
         if isinstance(self._cluster_config, SlurmClusterConfiguration):
             self._cluster_config = self._cluster_config.to_dict()
+
         if self.inputs.scan:
             scan = self.inputs.scan
         else:
             scan = None
+
         if self.inputs.output_volume:
             output_volume = self.inputs.output_volume
             if not isinstance(output_volume, TomwerVolumeBase):
@@ -114,15 +91,15 @@ class CastVolumeTask(
                     output_volume
                 )
         else:
-            output_data_type = configuration.get(
-                "output_type", None
+            output_file_format = configuration.get(
+                "output_file_format", None
             )  # expects values like hdf5, edf ...
             output_dir = configuration.get("output_dir", None)
-            if output_data_type is None or output_dir is None:
-                mess = "'output_volume' or ('output_type' and 'output_dir' from configuraiton) should be provided."
+            if output_file_format is None or output_dir is None:
+                mess = "'output_volume' or ('output_file_format' and 'output_dir' from configuration) should be provided."
                 _logger.processFailed(f"volume cast of {str(input_volume)} failed")
                 ProcessManager().notify_dataset_state(
-                    dataset=input_volume,
+                    dataset=scan or input_volume,
                     process=self,
                     state=DatasetState.FAILED,
                 )
@@ -135,7 +112,7 @@ class CastVolumeTask(
 
             output_volume = get_default_output_volume(
                 input_volume=input_volume,
-                output_type=NabuOutputFileFormat.from_value(output_data_type).value,
+                output_type=NabuOutputFileFormat.from_value(output_file_format).value,
                 output_dir=output_dir,
             )
             # convert from tomoscan volume to tomwer volume
@@ -188,7 +165,7 @@ class CastVolumeTask(
                 state = DatasetState.SUCCEED
 
             ProcessManager().notify_dataset_state(
-                dataset=input_volume,
+                dataset=scan or input_volume,
                 process=self,
                 state=state,
                 details=mess,
@@ -199,7 +176,7 @@ class CastVolumeTask(
                 scan.cast_volume = output_volume.get_identifier()
             else:
                 input_volume.cast_volume = output_volume.get_identifier()
-        # run volume cast remotly
+        # run volume cast remotely
         else:
 
             def get_command():
@@ -252,3 +229,11 @@ class CastVolumeTask(
                 process_requester_id=self.process_id,
             )
             self.outputs.volume = output_volume
+
+            # for now at the task level we consider this is succeed if it has been submitted
+            ProcessManager().notify_dataset_state(
+                dataset=scan or input_volume,
+                process=self,
+                state=DatasetState.SUCCEED,
+                details="cast has been correctly submitted to slurm",
+            )

tomwer/core/process/reconstruction/nabu/nabucommon.py

@@ -1,42 +1,13 @@
-# coding: utf-8
-###########################################################################
-# Copyright (C) 2016 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.
-#
-#############################################################################
-
 """contain utils for score process
 """
 
-__authors__ = [
-    "H.Payno",
-]
-__license__ = "MIT"
-__date__ = "27/10/2021"
-
+from __future__ import annotations
 
 import logging
 import os
 import subprocess
 import uuid
-from typing import Iterable, Optional, Union
+from typing import Iterable
 import signal
 import psutil
 import sys
@@ -189,7 +160,7 @@ class ResultSlurmRun(ResultsWithStd):
     def __init__(
         self,
         future_slurm_jobs: tuple,
-        job_id: Optional[int],
+        job_id: int | None,
         *args,
         **kwargs,
     ) -> None:
@@ -202,7 +173,7 @@ class ResultSlurmRun(ResultsWithStd):
         return self.__future_slurm_jobs
 
     @property
-    def job_id(self) -> Optional[int]:
+    def job_id(self) -> int | None:
         return self.__job_id
 
     def __str__(self) -> str:
@@ -226,7 +197,7 @@ class _NabuBaseReconstructor:
         scan: TomwerScanBase,
         dry_run: bool,
         target: Target,
-        cluster_config: Optional[Union[dict, SlurmClusterConfiguration]],
+        cluster_config: dict | SlurmClusterConfiguration | None,
         process_name: str,
         axis: NabuPlane = NabuPlane.XY,
     ) -> None:
@@ -273,6 +244,11 @@ class _NabuBaseReconstructor:
     def axis(self) -> NabuPlane:
         return self._axis
 
+    @property
+    def processed_data_folder_name(self) -> str:
+        """return the specific processed folder name associated to this type of reconstruction."""
+        raise NotImplementedError("Base class")
+
     def only_create_config_file(self):
         """Should we run the reconstruction or only create the configuration file"""
         return False
@@ -290,13 +266,13 @@ class _NabuBaseReconstructor:
         config_to_dump: dict,
         config_file: str,
         file_format: str,
-        info: Optional[str],
+        info: str | None,
         process_name: str,
     ):
         """
         process provided configuration
 
-        :param str info:
+        :param info:
         """
         if self.dry_run is True or self.only_create_config_file():
             return ResultsRun(
@@ -347,11 +323,10 @@ class _NabuBaseReconstructor:
         """
         run locally nabu for a single configuration file.
 
-        :param str conf_file: path to the nabu .cfg file
-        :param str file_format: format of the generated file
-        :param dict config_to_dump: configuration saved in the .cfg as a dictionary
+        :param conf_file: path to the nabu .cfg file
+        :param file_format: format of the generated file
+        :param config_to_dump: configuration saved in the .cfg as a dictionary
         :return: results of the local run
-        :rtype: ResultsLocalRun
         """
         if not has_nabu:
             raise ImportError("Fail to import nabu")
@@ -365,7 +340,7 @@ class _NabuBaseReconstructor:
                 sys.executable,
                 "-m",
                 settings.NABU_FULL_FIELD_APP_PATH,
-                conf_file,
+                f"'{conf_file}'",  # adding ' around file name allows to handle config file with spaces
                 "--gpu_mem_fraction",
                 str(gpu_mem_fraction),
                 "--cpu_mem_fraction",
@@ -415,7 +390,6 @@ class _NabuBaseReconstructor:
         Run a nabu reconstruction on slurm of a single configuration
 
         :return: results of the slurm run
-        :rtype: ResultSlurmRun
         """
         if not isinstance(conf_file, str):
             raise TypeError(f"conf_file is expected to be a strg not {type(conf_file)}")
@@ -535,6 +509,7 @@ class _NabuBaseReconstructor:
                 file_format=config["output"].get(
                     "file_format", NabuOutputFileFormat.HDF5
                 ),
+                processed_data_folder_name=self.processed_data_folder_name,
             )
             # add reconstruction path to the list. scan `reconstruction_paths` register all the existing path where
             # reconstruction are saved in order to be able to browse them all
@@ -647,7 +622,7 @@ class _NabuBaseReconstructor:
 
 
 def dump_normalization_array_for_nabu(
-    scan: TomwerScanBase, output_file: str, array: Union[numpy.ndarray, float, int]
+    scan: TomwerScanBase, output_file: str, array: numpy.ndarray | float | int
 ) -> DataUrl:
     if not isinstance(array, (numpy.ndarray, float, int)):
         raise TypeError(