tomwer 1.3.27__py3-none-any.whl → 1.4.0rc0__py3-none-any.whl

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

@@ -1,48 +1,15 @@
-# 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__ = "04/03/2019"
-
+from __future__ import annotations
 
 import logging
-import os
 from collections import namedtuple
-from typing import Union
 
-import h5py
 import numpy
 from silx.io.url import DataUrl
 from silx.utils.deprecation import deprecated
 from silx.utils.enum import Enum as _Enum
 from tomoscan.esrf.scan.utils import get_data
 
-from tomwer.core.process.task import Task
 from tomwer.core.scan.scanbase import TomwerScanBase
-from tomwer.core.utils.spec import getParametersFromParOrInfo
 
 from .anglemode import CorAngleMode
 from .mode import AxisMode, AXIS_MODE_METADATAS
@@ -183,8 +150,7 @@ class AxisResource(object):
     def normalized_data_paganin(self):
         """
 
-        :return: data processed by the pagagnin phase retrieval
-        :rtype: 2D numpy.array
+        :return: data processed by the Pagagin phase retrieval
         """
         if self.__url is None:
             return None
@@ -342,7 +308,7 @@ class AxisRP:
         self.changed()
 
     @property
-    def frame_width(self) -> Union[None, float]:
+    def frame_width(self) -> float | None:
         return self.__frame_width
 
     @frame_width.setter
@@ -369,11 +335,6 @@ class AxisRP:
             self.__angle_mode = mode
             self.changed()
 
-    @property
-    @deprecated(replacement="relative_cor_value", since_version="0.7")
-    def value_ref_tomwer(self):
-        return self.relative_cor_value
-
     @property
     def relative_cor_value(self):
         return self.__relative_value
@@ -401,19 +362,10 @@ class AxisRP:
                 self.__relative_value = float(value)
                 if self.frame_width is not None:
                     self.__absolute_value = (
-                        self.__relative_value + self.frame_width / 2.0
+                        self.__relative_value + (self.frame_width - 1) / 2.0
                     )
             self.changed()
 
-    @deprecated(replacement="set_relative_value", since_version="0.7")
-    def set_value_ref_tomwer(self, value):
-        self.set_relative_value(value=value)
-
-    @property
-    @deprecated(replacement="absolute_cor_value", since_version="0.7")
-    def value_ref_nabu(self):
-        return self.__absolute_value
-
     @property
     def estimated_cor(self):
         return self.__estimated_cor
@@ -620,7 +572,7 @@ class AxisRP:
     @composite_options.setter
     def composite_options(self, opts: dict) -> None:
         """
-        :param dict opts: options to use for the composite COR search
+        :param opts: options to use for the composite COR search
         :raises:
             * KeyError if some provided keys are not handled
             * TypeError if opts is not an instance of dictionary
@@ -658,99 +610,6 @@ class AxisRP:
         """callback to overwrite when the paramter value changed"""
         pass
 
-    def set_position_frm_par_file(self, file_path, entry=None, force=False):
-        """Set position value from a file
-
-        :param str file_path: path to the par file
-        :param bool force: if True, force the mode to read and set
-                           `position_value` to None if failed to read the file.
-                           Otherwise only `mode` and `position_value` when the
-                           file read succeed.
-        """
-
-        def get_position_in_file():
-            if not os.path.isfile(file_path):
-                raise ValueError(file_path, "is not a valid file path")
-
-            if h5py.is_hdf5(file_path):
-                return self.get_cor_position_frm_tomwer_file(
-                    file_path=file_path, entry=entry
-                )
-            elif file_path.lower().endswith(".par") or file_path.lower().endswith(
-                ".info"
-            ):
-                _dict = getParametersFromParOrInfo(file_path)
-                if self.AXIS_POSITION_PAR_KEY.lower() not in _dict:
-                    err = f"fail to find `{self.AXIS_POSITION_PAR_KEY}` in {file_path}"
-                    _logger.info(err)
-                    raise KeyError(err)
-                else:
-                    return _dict[self.AXIS_POSITION_PAR_KEY.lower()]
-            else:
-                with open(file_path, mode="r") as fd:
-                    l1 = fd.readline()
-                    values = l1.split(" ")
-                    if len(values) > 0:
-                        try:
-                            res = float(values[0])
-                        except Exception:
-                            _logger.info(
-                                f"fail to load center of rotation from {file_path}"
-                            )
-                            return None
-                        else:
-                            return res
-
-        if force:
-            try:
-                position = get_position_in_file()
-            except (KeyError, ValueError) as e:
-                _logger.warning(e)
-                position = None
-        else:
-            position = get_position_in_file()
-
-        changed = self.mode != AxisMode.read or position != self.relative_cor_value
-        self.mode = AxisMode.read
-        if position is None:
-            self.set_relative_value(None)
-        else:
-            self.set_relative_value(float(position))
-
-        if changed:
-            self.changed()
-
-    @staticmethod
-    def get_cor_position_frm_tomwer_file(
-        file_path: str, entry=None
-    ) -> Union[None, float]:
-        """
-        Parse the given .h5 file, looking for axis processes. If found some
-        then return the first value discover
-
-        :param str file_path: tomwer processes file (.h5)
-        :return: center of rotation or none
-        :rtype: Union[None, float]
-        """
-        from .axis import AxisTask  # avoid cyclic import
-
-        processes = Task.get_processes_frm_type(
-            process_file=file_path, process_type=AxisTask, entry=entry
-        )
-        if len(processes) == 0:
-            _logger.warning("failed to find any information on center " "of rotation")
-            return None
-        elif len(processes) > 1:
-            _logger.info("found more than one value computed for " "center of rotation")
-        _logger.info(
-            f"load center of rotation from {file_path}: {processes[0].results['center_of_rotation']}"
-        )
-        cor = processes[0].results["center_of_rotation"]
-        if cor in [None, ""]:
-            return None
-        else:
-            return float(cor)
-
     def n_url(self):
         """
 

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

@@ -1,32 +1,4 @@
 # 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__ = "15/10/2019"
-
 
 from silx.utils.enum import Enum as _Enum
 

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",
+            )