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

tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py

@@ -1,45 +1,17 @@
-# 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 the SADeltaBetaProcess. Half automatic best delta / beta finder
 """
 
-__authors__ = [
-    "H.Payno",
-]
-__license__ = "MIT"
-__date__ = "28/10/2021"
-
+from __future__ import annotations
 
 import logging
 import os
 from copy import copy, deepcopy
-from typing import Optional, Union
 
 import h5py
 import numpy
 from multiprocessing import Pool
+from tqdm import tqdm
+
 from nabu.pipeline.config import get_default_nabu_config
 from nabu.pipeline.fullfield.nabu_config import (
     nabu_config as nabu_fullfield_default_config,
@@ -65,7 +37,6 @@ from tomwer.core.process.reconstruction.scores import (
 )
 from tomwer.core.utils.locker import FileLockerManager
 from tomwer.core.process.task import Task
-from tomwer.core.progress import Progress
 from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
 from tomwer.core.scan.scanfactory import ScanFactory
@@ -92,19 +63,18 @@ DEFAULT_RECONS_FOLDER = "multi_delta_beta_results"
 
 def one_slice_several_db(
     scan: TomwerScanBase,
-    configuration: Union[dict, SADeltaBetaParams],
-    process_id: Optional[int] = None,
+    configuration: dict | SADeltaBetaParams,
+    process_id: int | None = None,
 ) -> tuple:
     """
     Run a slice reconstruction using nabu per Center Of Rotation (cor) provided
     Then for each compute a score (quality) of the center of rotation
 
-    :param TomwerScanBase scan:
-    :param Union[dict,SADeltaBetaParams] configuration:
+    :param scan:
+    :param configuration:
     :return: cor_reconstructions, outs, errs
              cor_reconstructions is a dictionary of cor as key and a tuple
              (url, score) as value
-    :rtype: tuple
     """
     if isinstance(configuration, SADeltaBetaParams):
         configuration = configuration.to_dict()
@@ -208,7 +178,7 @@ class SADeltaBetaTask(
             )
 
     @staticmethod
-    def autofocus(scan) -> Optional[float]:
+    def autofocus(scan) -> float | None:
         scores = scan.sa_delta_beta_params.scores
         if scores is None:
             return
@@ -283,8 +253,8 @@ class SADeltaBetaTask(
             output_dir=params.output_dir,
         )
         # step 2: run reconstructions
-        advancement = Progress(
-            f"sa-delta-beta - slice {slice_index} of {scan.get_identifier().short_description()}"
+        advancement = tqdm(
+            desc=f"sa-delta-beta - slice {slice_index} of {scan.get_identifier().short_description()}"
         )
 
         dbs_res = {}
@@ -397,7 +367,9 @@ class SADeltaBetaTask(
         ):
             if "reconstruction" in config:
                 # move the cor value to the nabu reference
-                cor_nabu_ref = scan.axis_params.relative_cor_value + scan.dim_1 / 2.0
+                cor_nabu_ref = (
+                    scan.axis_params.relative_cor_value + (scan.dim_1 - 1) / 2.0
+                )
                 config["reconstruction"]["rotation_axis_position"] = str(cor_nabu_ref)
 
         _logger.info(f"set nabu reconstruction parameters to {scan}")
@@ -430,7 +402,7 @@ class SADeltaBetaTask(
         advancement,
         dry_run,
         axis,
-        cluster_config: Optional[dict],
+        cluster_config: dict | None,
     ):
         future_tomo_objs = {}
         success = True
@@ -452,7 +424,7 @@ class SADeltaBetaTask(
             advancement=advancement,
             cluster_config=cluster_config,
             process_id=self.process_id,
-            instanciate_classes_only=True,
+            instantiate_classes_only=True,
             output_file_prefix_pattern=None,
             axis=axis,
         )
@@ -493,7 +465,7 @@ class SADeltaBetaTask(
                         future_tomo_objs[db] = future_tomo_obj
 
             if advancement is not None:
-                advancement.increaseAdvancement(1)
+                advancement.update()
 
         return success, recons_urls, future_tomo_objs, std_outs, std_errs
 

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

@@ -1,34 +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__ = "04/05/2021"
-
-
-from typing import Optional, Union
+from __future__ import annotations
 
 from tomwer.core.cluster.cluster import SlurmClusterConfiguration
 from tomwer.core.process.reconstruction.scores.scores import ScoreMethod
@@ -71,11 +41,11 @@ class SABaseParams:
         self._n_reconstruction = n
 
     @property
-    def slice_indexes(self) -> Union[None, dict, str]:
+    def slice_indexes(self) -> dict | str | None:
         return self._slice_indexes
 
     @slice_indexes.setter
-    def slice_indexes(self, indexes: Union[None, dict, str]):
+    def slice_indexes(self, indexes: dict | str | None):
         if isinstance(indexes, str):
             if not indexes == "middle":
                 raise ValueError("the only valid indexes values is 'middle'")
@@ -116,12 +86,12 @@ class SABaseParams:
         self._dry_run = dry_run
 
     @property
-    def output_dir(self) -> Union[str, None]:
+    def output_dir(self) -> str | None:
         """nabu cfg_files output dir. If not provided will use nabu slice output with saaxis/cfg_files as postfix"""
         return self._output_dir
 
     @output_dir.setter
-    def output_dir(self, output_dir: Union[str, None]) -> None:
+    def output_dir(self, output_dir: str | None) -> None:
         if not isinstance(output_dir, (str, type(None))):
             raise TypeError("output_dir should be None or a str")
         self._output_dir = output_dir
@@ -135,11 +105,11 @@ class SABaseParams:
         self._score_method = ScoreMethod.from_value(method)
 
     @property
-    def scores(self) -> Union[dict, None]:
+    def scores(self) -> dict | None:
         return self._scores
 
     @scores.setter
-    def scores(self, scores: Union[None, dict]):
+    def scores(self, scores: dict | None):
         if not isinstance(scores, (type(None), dict)):
             raise TypeError("scores should be None or a dictionary")
         self._scores = scores
@@ -159,11 +129,11 @@ class SABaseParams:
         self._file_format = format_
 
     @property
-    def cluster_config(self) -> Optional[dict]:
+    def cluster_config(self) -> dict | None:
         return self._cluster_config
 
     @cluster_config.setter
-    def cluster_config(self, config: Optional[dict]):
+    def cluster_config(self, config: dict | None):
         if isinstance(config, SlurmClusterConfiguration):
             config = config.to_dict()
         if not isinstance(config, (dict, type(None))):

tomwer/core/process/reconstruction/scores/scores.py

@@ -1,36 +1,7 @@
-# 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__ = "18/02/2021"
-
+from __future__ import annotations
 
 import logging
 import sys
-from typing import Union
 
 import numpy
 from silx.utils.enum import Enum as _Enum
@@ -120,9 +91,8 @@ def compute_score_contrast_std(data: numpy.ndarray):
     """
     Compute a contrast score by simply computing the standard deviation of
     the frame
-    :param numpy.ndarray data: frame for which we should compute the score
+    :param data: frame for which we should compute the score
     :return: score of the frame
-    :rtype: float
     """
     if data is None:
         return None
@@ -134,9 +104,8 @@ def compute_tv_score(data: numpy.ndarray):
     """
     Compute the data score as image total variation
 
-    :param numpy.ndarray data: frame for which we should compute the score
+    :param data: frame for which we should compute the score
     :return: score of the frame
-    :rtype: float
     """
     tv = numpy.sum(
         numpy.sqrt(
@@ -155,17 +124,16 @@ _METHOD_TO_FCT = {
 def compute_score(
     data: numpy.ndarray,
     method: ScoreMethod,
-    angles: Union[None, list] = None,
-    original_sinogram: Union[None, numpy.array] = None,
-    original_axis_position: Union[float, None] = None,
-    detector_width: Union[float, None] = None,
-) -> Union[float, None]:
+    angles: list | None = None,
+    original_sinogram: numpy.array | None = None,
+    original_axis_position: float | None = None,
+    detector_width: float | None = None,
+) -> float | None:
     """
 
-    :param numpy.ndarray data: frame for which we should compute the score
-    :param str method:
+    :param data: frame for which we should compute the score
+    :param method:
     :return: score of the frame
-    :rtype: float
     """
     method = ScoreMethod.from_value(method)
     if data.ndim == 3:

tomwer/core/process/reconstruction/tests/test_axis.py

@@ -0,0 +1,46 @@
+import h5py
+from nxtomo.paths.nxtomo import get_paths as get_nexus_paths
+from tomwer.core.process.reconstruction.axis import AxisTask
+from tomwer.tests.conftest import nxtomo_scan_360  # noqa F811
+from tomwer.core.process.reconstruction.axis import AxisRP
+
+
+def test_read_x_rotation_axis_pixel_position(nxtomo_scan_360):  # noqa F811
+    """
+    test reading of the estimated cor from the motor using scan metadata
+    """
+    nexus_paths = get_nexus_paths(None)
+
+    x_rotation_axis_pixel_position_path = "/".join(
+        [
+            nxtomo_scan_360.entry,
+            nexus_paths.INSTRUMENT_PATH,
+            nexus_paths.nx_instrument_paths.DETECTOR_PATH,
+            nexus_paths.nx_detector_paths.X_ROTATION_AXIS_PIXEL_POSITION
+            or nexus_paths.nx_detector_paths.ESTIMATED_COR_FRM_MOTOR_PATH,
+        ]
+    )
+    with h5py.File(nxtomo_scan_360.master_file, mode="r") as h5f:
+        assert x_rotation_axis_pixel_position_path not in h5f
+
+    axis_params = AxisRP()
+    axis_params.mode = "read"
+    task = AxisTask(
+        inputs={
+            "data": nxtomo_scan_360,
+            "axis_params": axis_params,
+        }
+    )
+    # test the task when there is no metadata
+    task.run()
+    assert nxtomo_scan_360.axis_params.absolute_cor_value is None
+    assert nxtomo_scan_360.axis_params.relative_cor_value is None
+
+    # test the task when there is metadata
+    with h5py.File(nxtomo_scan_360.master_file, mode="a") as h5f:
+        h5f[x_rotation_axis_pixel_position_path] = 12.5
+
+    nxtomo_scan_360.clear_caches()
+    task.run()
+    assert nxtomo_scan_360.axis_params.absolute_cor_value == 22.0
+    assert nxtomo_scan_360.axis_params.relative_cor_value == 12.5

tomwer/core/process/reconstruction/tests/test_darkref.py

@@ -0,0 +1,33 @@
+# coding: utf-8
+from __future__ import annotations
+
+from tomwer.core.process.reconstruction.darkref.darkrefs import (
+    requires_reduced_dark_and_flat,
+)
+from tomwer.core.utils.scanutils import MockEDF, MockNXtomo
+
+
+def test_quick_run_necessary_edf(tmpdir):
+    """test the `quick_run_necessary` function for EDFTomoScan"""
+    scan = MockEDF.mockScan(scanID=str(tmpdir), start_dark=True, start_flat=True)
+    assert scan.reduced_darks in (None, {})
+    assert scan.reduced_flats in (None, {})
+    requires_reduced_dark_and_flat(scan=scan)
+    assert len(scan.reduced_darks) == 1
+    assert len(scan.reduced_flats) == 1
+
+
+def test_quick_run_necessary_hdf5(tmpdir):
+    """test the `quick_run_necessary` function for NXtomoScan"""
+    scan = MockNXtomo(
+        scan_path=tmpdir,
+        n_proj=20,
+        n_ini_proj=20,
+        dim=10,
+    ).scan
+    assert scan.reduced_darks in (None, {})
+    assert scan.reduced_flats in (None, {})
+    computed = requires_reduced_dark_and_flat(scan=scan)
+    assert len(computed) == 2
+    assert len(scan.reduced_darks) == 1
+    assert len(scan.reduced_flats) == 1

tomwer/core/process/reconstruction/{test → tests}/test_saaxis.py

@@ -1,31 +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__ = "27/02/2021"
+from __future__ import annotations
 
 
 import os

tomwer/core/process/reconstruction/tests/test_sadeltabeta.py

@@ -0,0 +1,48 @@
+# coding: utf-8
+from __future__ import annotations
+
+
+import os
+import shutil
+import tempfile
+import unittest
+
+from tomwer.core.process.reconstruction.sadeltabeta.sadeltabeta import (
+    SADeltaBetaParams,
+    SADeltaBetaTask,
+)
+from tomwer.core.utils.scanutils import MockNXtomo
+
+
+class TestSADeltaBetaProcess(unittest.TestCase):
+    """Test the SAAxisProcess class"""
+
+    def setUp(self) -> None:
+        super().setUp()
+        self.tempdir = tempfile.mkdtemp()
+        dim = 10
+        mock = MockNXtomo(
+            scan_path=self.tempdir, n_proj=10, n_ini_proj=10, scan_range=180, dim=dim
+        )
+        self.scan = mock.scan
+
+    def tearDown(self) -> None:
+        shutil.rmtree(self.tempdir)
+        super().tearDown()
+
+    def test(self):
+        process = SADeltaBetaTask(
+            inputs={
+                "data": self.scan,
+                "sa_delta_beta_params": SADeltaBetaParams().to_dict(),
+                "serialize_output_data": False,
+            }
+        )
+
+        default_sadelta_beta_params = SADeltaBetaParams()
+        default_sadelta_beta_params.output_dir = os.path.join(
+            self.tempdir, "output_dir"
+        )
+        default_sadelta_beta_params.dry_run = True
+
+        process.run()

tomwer/core/process/script/python.py

@@ -1,31 +1,5 @@
 # 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.
-#
-#############################################################################*/
-
-
-__authors__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "03/08/2020"
+from __future__ import annotations
 
 
 import code

tomwer/core/process/script/tests/test_script.py

@@ -0,0 +1,41 @@
+# coding: utf-8
+from __future__ import annotations
+
+import os
+import shutil
+import tempfile
+import unittest
+
+from tomwer.core.process.script.python import PythonScript
+from tomwer.core.utils.scanutils import MockNXtomo
+
+
+class TestPythonScript(unittest.TestCase):
+    def setUp(self):
+        self.tempdir = tempfile.mkdtemp()
+        dim = 10
+        mock = MockNXtomo(
+            scan_path=os.path.join(self.tempdir, "scan1"),
+            n_proj=10,
+            n_ini_proj=10,
+            scan_range=180,
+            dim=dim,
+        )
+        self.scan = mock.scan
+
+    def tearDown(self):
+        shutil.rmtree(self.tempdir)
+
+    def test(self):
+        process = PythonScript(inputs={"data": self.scan})
+        process.definition()
+        process.program_version()
+        process.program_name()
+        # TODO: configuration should be passed in inputs during construction
+        process.set_configuration(
+            {
+                "scriptText": "print('toto')",
+            }
+        )
+
+        process.run()

tomwer/core/process/stitching/metadataholder.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import weakref
 import logging
 import numpy
@@ -5,7 +7,6 @@ import numpy
 from tomoscan.tomoobject import TomoObject
 from tomoscan.scanbase import TomoScanBase
 from tomoscan.volumebase import VolumeBase
-from typing import Optional
 
 _logger = logging.getLogger(__name__)
 
@@ -61,10 +62,10 @@ class StitchingMetadata:
         bb = self.tomo_obj.get_bounding_box(axis)
         return (bb.max - bb.min) / 2 + bb.min
 
-    def get_abs_position_px(self, axis, warn=True) -> Optional[int]:
+    def get_abs_position_px(self, axis, warn=True) -> int | None:
         if axis not in (0, 1, 2):
             raise ValueError("axis is expected to be in (0, 1, 2)")
-        # if user registerd position as pixels
+        # if user registered position as pixels
         if self._pos_as_px[axis] is not None:
             return int(self._pos_as_px[axis])
         else:
@@ -100,7 +101,7 @@ class StitchingMetadata:
         self._pos_as_px = [None, None, None]
         self._pos_as_m = [None, None, None]
 
-    def get_pixel_or_voxel_size(self, axis) -> Optional[float]:
+    def get_pixel_or_voxel_size(self, axis) -> float | None:
         """
         return value provided by the user if any else return the value contained in metadata
         """

tomwer/core/process/stitching/nabustitcher.py

@@ -1,5 +1,6 @@
 import logging
 
+from tqdm import tqdm
 from ewokscore.missing_data import is_missing_data
 
 from sluurp.executor import submit as submit_to_slurm_cluster
@@ -12,8 +13,10 @@ from nabu.stitching.config import (
     StitchingConfiguration,
     StitchingType,
 )
-from nabu.stitching.z_stitching import (
-    z_stitching,
+from nabu.stitching.z_stitching import z_stitching
+from nabu.stitching.y_stitching import y_stitching
+
+from nabu.stitching.utils.post_processing import (
     StitchingPostProcAggregation as _StitchingPostProcAggregation,
 )
 from nabu.stitching.slurm_utils import split_stitching_configuration_to_slurm_job
@@ -64,8 +67,20 @@ class StitcherTask(
             progress = (
                 None if is_missing_data(self.inputs.progress) else self.inputs.progress
             )
-            stitched_identifier = z_stitching(configuration=config, progress=progress)
-            if config.stitching_type is StitchingType.Z_PREPROC:
+
+            if config.stitching_type in (
+                StitchingType.Z_PREPROC,
+                StitchingType.Y_PREPROC,
+            ):
+                if config.stitching_type is StitchingType.Z_PREPROC:
+                    stitched_identifier = z_stitching(
+                        configuration=config, progress=progress
+                    )
+                else:
+                    stitched_identifier = y_stitching(
+                        configuration=config, progress=progress
+                    )
+
                 nx_tomo = ScanFactory.create_tomo_object_from_identifier(
                     stitched_identifier.to_str()
                 )
@@ -76,6 +91,9 @@ class StitcherTask(
                 self.outputs.volume = None
                 self.outputs.future_tomo_obj = None
             elif config.stitching_type is StitchingType.Z_POSTPROC:
+                stitched_identifier = z_stitching(
+                    configuration=config, progress=progress
+                )
                 volume = VolumeFactory.create_tomo_object_from_identifier(
                     stitched_identifier.to_str()
                 )
@@ -85,10 +103,12 @@ class StitcherTask(
             else:
                 raise NotImplementedError()
         else:
-            # opt2: run remotly and aggregate locally
+            # opt2: run remotely and aggregate locally
             futures = {}
 
             # 2.1 launch jobs
+            # TODO: refactor: nabu.app.stitching could be called or something like that...
+            slurm_job_progress_bars: dict = {}
             for i_job, (job, sub_config) in enumerate(
                 split_stitching_configuration_to_slurm_job(
                     config, yield_configuration=True
@@ -99,11 +119,21 @@ class StitcherTask(
                     sub_config.get_output_object().get_identifier().to_str()
                 )
                 futures[output_tomo_obj] = submit_to_slurm_cluster(job, timeout=999999)
+                # note on total=100: we only consider percentage in this case (providing advancement from slurm jobs)
+                slurm_job_progress_bars[job] = tqdm(
+                    total=100,
+                    position=i_job + 1,
+                    desc=f"   part {str(i_job).ljust(3)}",
+                    delay=0.5,  # avoid to mess with terminal and (near) future logs
+                    bar_format="{l_bar}{bar}",  # avoid using 'r_bar' as 'total' is set to 100 (percentage)
+                    leave=False,
+                )
 
             # handle post processing
             data_aggregation = StitchingPostProcAggregation(
                 futures=futures,
                 stitching_config=config,
+                progress_bars=slurm_job_progress_bars,
             )
             for future in futures.values():
                 # TODO: do we ned to make sure the processing is not finished yet ?