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

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

@@ -1,38 +1,10 @@
-# coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2020 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__ = "26/10/2021"
-
+from __future__ import annotations
 
 import copy
 import functools
 import logging
 import os
-from typing import Iterable, Optional
+from typing import Iterable
 
 from nabu import version as nabu_version
 from nabu.pipeline.config import generate_nabu_configfile
@@ -50,11 +22,7 @@ from tomwer.core.cluster.cluster import SlurmClusterConfiguration
 from tomwer.core.futureobject import FutureTomwerObject
 from tomwer.core.process.reconstruction.nabu.plane import NabuPlane
 from tomwer.core.process.task import Task
-from tomwer.core.process.icat.gallery import (
-    IcatScreenshots,
-    deduce_dataset_gallery_location,
-    select_screenshot_from_volume,
-)
+from tomwer.core.process.drac.processeddataset import DracReconstructedVolumeDataset
 from tomwer.core.scan.edfscan import EDFTomoScan
 from tomwer.core.scan.nxtomoscan import NXtomoScan
 from tomwer.core.scan.scanbase import TomwerScanBase
@@ -65,6 +33,9 @@ from tomwer.core.volume.volumefactory import VolumeFactory
 from tomwer.io.utils.h5pyutils import EntryReader
 from tomwer.utils import docstring
 from tomwer.io.utils import format_stderr_stdout
+from tomwer.core.process.reconstruction.output import (
+    PROCESS_FOLDER_RECONSTRUCTED_VOLUMES,
+)
 
 from . import settings, utils
 from .nabucommon import ResultsLocalRun, ResultSlurmRun, _NabuBaseReconstructor
@@ -77,17 +48,16 @@ def run_volume_reconstruction(
     scan: TomwerScanBase,
     config: dict,
     dry_run: bool,
-    process_id: Optional[int] = None,
+    process_id: int | None = None,
 ) -> tuple:
     """
     Run a volume reconstruction. Scan need to have reconstruction parameters for nabu.
 
     Behavior: will clear link to the last volume reconstructed
 
-    :param int process_id: optional process id
+    :param process_id: optional process id
 
     :return: succeed, stdouts, stderrs, configs, future_scan
-    :rtype: tuple
     """
 
     if scan.nabu_recons_params in ({}, None):
@@ -199,7 +169,7 @@ class VolumeRunner(_NabuBaseReconstructor):
         self,
         scan: TomwerScanBase,
         config_nabu,
-        cluster_config: Optional[dict],
+        cluster_config: dict | None,
         dry_run: bool,
         target: Target,
         process_name: str,
@@ -217,15 +187,20 @@ class VolumeRunner(_NabuBaseReconstructor):
     def configuration(self):
         return self._config
 
+    @property
+    def processed_data_folder_name(self):
+        """return the specific processed folder name associated to this type of reconstruction."""
+        return PROCESS_FOLDER_RECONSTRUCTED_VOLUMES
+
     @docstring(_NabuBaseReconstructor)
     def run(self) -> Iterable:
         dataset_params = self.scan.get_nabu_dataset_info()
         if "dataset" in self.configuration:
             dataset_params.update(self.configuration["dataset"])
         self.configuration["dataset"] = dataset_params
-        self.configuration["resources"] = utils.get_nabu_resources_desc(
-            scan=self.scan, workers=1, method="local"
-        )
+
+        self.configuration["resources"] = self.configuration.get("resources", {})
+        self.configuration["resources"]["method"] = "local"
 
         # force overwrite results
         if "output" not in self.configuration:
@@ -337,12 +312,8 @@ class VolumeRunner(_NabuBaseReconstructor):
     def _get_file_basename_reconstruction(self, pag, db, ctf, axis):
         """
 
-        :param TomwerScanBase scan: scan reconstructed
-        :param Union[None, int] slice_index: index of the slice reconstructed.
-                                            if None, we want to reconstruct the
-                                            entire volume
-        :param bool pag: is it a paganin reconstruction
-        :param int db: delta / beta parameter
+        :param pag: is it a Paganin reconstruction
+        :param db: delta / beta parameter
         :param axis: axis over which the reconstruction goes. For volume always expected to be z. So ignored in the function
         :return: basename of the file reconstructed (without any extension)
         """
@@ -373,7 +344,12 @@ class NabuVolumeTask(
     Task,
     SuperviseProcess,
     input_names=("data", "nabu_params"),
-    output_names=("data", "volumes", "future_tomo_obj", "screenshots"),
+    output_names=(
+        "data",
+        "volumes",
+        "future_tomo_obj",
+        "data_portal_processed_datasets",
+    ),
     optional_input_names=(
         "dry_run",
         "nabu_extra_params",  # some parameter that must update 'nabu_params' before launching the reconstruction. Such as z range...
@@ -530,29 +506,27 @@ class NabuVolumeTask(
         self.outputs.future_tomo_obj = future_tomo_obj
 
         # build screenshots
+        data_portal_processed_datasets = []
         if scan.latest_vol_reconstructions is not None:
-            try:
-                screenshots = {}
-                [
-                    screenshots.update(
-                        select_screenshot_from_volume(
-                            VolumeFactory.create_tomo_object_from_identifier(
-                                rec_identifier
-                            )
-                        )
+            for volume_id in scan.latest_vol_reconstructions:
+                try:
+                    volume = VolumeFactory.create_tomo_object_from_identifier(
+                        identifier=volume_id
                     )
-                    for rec_identifier in scan.latest_vol_reconstructions
-                ]
-            except Exception as e:
-                _logger.error(f"screenshot creation failed. Error is {e}")
-            else:
-                self.outputs.screenshots = IcatScreenshots(
-                    data_dir=deduce_dataset_gallery_location(scan),
-                    screenshots=screenshots,
-                    scan=scan,
-                )
-        else:
-            self.outputs.screenshots = tuple()
+                except Exception as e:
+                    _logger.error(
+                        f"Fail to build volume from {volume_id}. Error is {e}"
+                    )
+                else:
+                    icatReconstructedDataset = DracReconstructedVolumeDataset(
+                        tomo_obj=volume,
+                        source_scan=scan,
+                    )
+                    data_portal_processed_datasets.append(icatReconstructedDataset)
+
+        self.outputs.data_portal_processed_datasets = tuple(
+            data_portal_processed_datasets
+        )
 
     def set_configuration(self, configuration: dict) -> None:
         Task.set_configuration(self, configuration=configuration)

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

@@ -7,3 +7,13 @@ class NabuPlane(_Enum):
     YZ = "YZ"
     XZ = "XZ"
     XY = "XY"
+
+    @classmethod
+    def from_value(cls, value):
+        if value == 0:
+            return NabuPlane.XY
+        elif value == 1:
+            return NabuPlane.XZ
+        elif value == 2:
+            return NabuPlane.YZ
+        return super().from_value(value=value)

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

@@ -1,32 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2020 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__ = "06/08/2020"
-
+from __future__ import annotations
 
 import logging
 

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

@@ -1,32 +1,4 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2016-2020 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__ = "26/10/2021"
-
 
 from silx.utils.enum import Enum as _Enum
 

tomwer/core/process/reconstruction/nabu/test/test_castvolume.py

@@ -0,0 +1,116 @@
+# coding: utf-8
+from __future__ import annotations
+
+import os
+
+import numpy
+import pytest
+
+from tomwer.core.process.reconstruction.nabu.castvolume import CastVolumeTask
+from tomwer.core.process.reconstruction.output import NabuOutputFileFormat
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.volume.edfvolume import EDFVolume
+from tomwer.core.volume.hdf5volume import HDF5Volume
+from tomwer.core.volume.tiffvolume import TIFFVolume
+
+
+def test_cast_volume_32bitstiff_to_16bits_tiff(tmp_path):
+    """test 32 bits tiffs to 16 bits works"""
+    dir_test = tmp_path / "test_dir"
+    dir_test.mkdir()
+    save_dir = tmp_path / "output_dir"
+    save_dir.mkdir()
+
+    vol_data = numpy.random.random(20 * 100 * 100) * 3600.4
+    vol_data = vol_data.reshape(20, 100, 100)
+    vol_data = vol_data.astype(numpy.float32)
+    volume = TIFFVolume(
+        folder=dir_test,
+        volume_basename="test_dir_vol_",
+        data=vol_data,
+    )
+    volume.save()
+
+    # test with output datadir as None
+    with pytest.raises(ValueError):
+        CastVolumeTask(
+            inputs={
+                "volume": volume,
+                "configuration": {
+                    "output_file_path": None,
+                    "output_file_format": NabuOutputFileFormat.EDF,
+                    "output_data_type": numpy.uint16,
+                },
+            },
+        ).run()
+
+    # test providing save dir and tiff
+    assert len(os.listdir(save_dir)) == 0
+    task = CastVolumeTask(
+        inputs={
+            "volume": volume,
+            "configuration": {
+                "output_dir": str(save_dir),
+                "output_file_format": NabuOutputFileFormat.EDF,
+                "output_data_type": numpy.uint16,
+            },
+        }
+    )
+    task.run()
+
+    assert len(os.listdir(save_dir)) == 20, "no files have been generated"
+    assert task.outputs.volume.load_data().shape == (20, 100, 100)
+    assert task.outputs.volume.load_data().dtype == numpy.uint16
+
+    # test providing save dir, a scan and hdf5
+    scan = NXtomoScan(scan=os.sep.join([str(tmp_path), "scan"]), entry="entry0000")
+    task = CastVolumeTask(
+        inputs={
+            "volume": volume,
+            "configuration": {
+                "output_dir": str(save_dir),
+                "output_file_format": NabuOutputFileFormat.HDF5,
+                "output_data_type": numpy.float32,
+            },
+            "scan": scan,
+        },
+    )
+    task.run()
+    assert task.outputs.volume.load_data().shape == (20, 100, 100)
+    assert task.outputs.volume.load_data().dtype == numpy.float32
+
+    # test providing a volume as output volume
+    output_volume = HDF5Volume(
+        file_path=os.path.join(str(tmp_path), "my_volume.hdf5"), data_path="entry0002"
+    )
+    task = CastVolumeTask(
+        inputs={
+            "volume": volume,
+            "configuration": {
+                "output_dir": str(save_dir),
+                "output_file_format": NabuOutputFileFormat.HDF5,
+                "output_data_type": numpy.uint8,
+            },
+            "output_volume": output_volume,
+        },
+    )
+    task.run()
+    assert task.outputs.volume.load_data().shape == (20, 100, 100)
+    assert task.outputs.volume.load_data().dtype == numpy.uint8
+
+    # test providing a volume us as output volume
+    output_volume = EDFVolume(folder=os.path.join(str(tmp_path), "my_edf_vol"))
+    task = CastVolumeTask(
+        inputs={
+            "volume": volume,
+            "configuration": {
+                "output_dir": str(save_dir),
+                "output_file_format": NabuOutputFileFormat.HDF5,
+                "output_data_type": numpy.int16,
+            },
+            "output_volume": output_volume.get_identifier().to_str(),
+        },
+    )
+    task.run()
+    assert task.outputs.volume.load_data().shape == (20, 100, 100)
+    assert task.outputs.volume.load_data().dtype == numpy.int16

tomwer/core/process/reconstruction/nabu/test/test_nabu_utils.py

@@ -0,0 +1,277 @@
+import pytest
+
+from tomwer.core.process.reconstruction.nabu.utils import (
+    get_recons_volume_identifier,
+    get_multi_cor_recons_volume_identifiers,
+    nabu_std_err_has_error,
+)
+from tomwer.core.scan.edfscan import EDFTomoScan
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+
+_scans = (
+    NXtomoScan(
+        scan="/my_scan_file.nx",
+        entry="entry_test",
+    ),
+    EDFTomoScan("/my_scan_folder"),
+)
+
+
+@pytest.mark.parametrize("scan", _scans)
+@pytest.mark.parametrize("axis", ("YZ", "XZ", "XY"))
+def test_get_recons_volume_identifier(scan, axis):
+    """
+    test get_recons_volume_identifier behavior
+    """
+
+    entry = scan.entry if isinstance(scan, NXtomoScan) else "entry"
+    # check some exceptions
+    with pytest.raises(ValueError):
+        get_recons_volume_identifier(
+            file_prefix="volume_rec",
+            location="/this/is/a/test",
+            file_format="toto",
+            slice_index=1080,
+            scan=scan,
+            axis=axis,
+        )
+
+    # check hdf5 reconstructions
+    id_rec_vols = get_recons_volume_identifier(
+        file_prefix="volume_rec",
+        location="/this/is/a/test",
+        file_format="hdf5",
+        slice_index="1080",
+        scan=scan,
+        axis=axis,
+    )
+    assert len(id_rec_vols) == 1
+    assert (
+        id_rec_vols[0].to_str()
+        == f"hdf5:volume:/this/is/a/test/volume_rec_plane_{axis}_001080.hdf5?path={entry}/reconstruction"
+    )
+
+    # check edf and jp2k slice reconstructions (are expected to have the same behavior)
+    id_rec_vols = get_recons_volume_identifier(
+        file_prefix="volume_rec",
+        location="/this/is/a/test",
+        file_format="edf",
+        slice_index="1080",
+        scan=scan,
+        axis=axis,
+    )
+    assert len(id_rec_vols) == 1
+    assert (
+        id_rec_vols[0].to_str() == "edf:volume:/this/is/a/test?file_prefix=volume_rec"
+    )
+
+    id_rec_vols = get_recons_volume_identifier(
+        file_prefix="volume_recslice",
+        location="/this/is/a/test",
+        file_format="jp2k",
+        slice_index="1080",
+        scan=scan,
+        axis=axis,
+    )
+    assert len(id_rec_vols) == 1
+    assert (
+        id_rec_vols[0].to_str()
+        == "jp2k:volume:/this/is/a/test?file_prefix=volume_recslice"
+    )
+
+    # check tiff slice reconstructions
+    id_rec_vols = get_recons_volume_identifier(
+        file_prefix="volume_rec",
+        location="/this/is/a/test",
+        file_format="tiff",
+        slice_index="1080",
+        scan=scan,
+        axis=axis,
+    )
+    assert len(id_rec_vols) == 1
+    assert (
+        id_rec_vols[0].to_str() == "tiff:volume:/this/is/a/test?file_prefix=volume_rec"
+    )
+
+
+@pytest.mark.parametrize("scan", _scans)
+def test_get_multi_cor_recons_volume_identifier(scan):
+    """
+    test the get_multi_cor_recons_volume_identifier function
+    """
+    entry = scan.entry if isinstance(scan, NXtomoScan) else "entry"
+
+    # dummy test with hdf5
+    id_rec_vols = get_multi_cor_recons_volume_identifiers(
+        scan=scan,
+        slice_index="middle",
+        location="/this/is/a/test",
+        file_prefix="rec",
+        cors=(10, 12),
+        file_format="hdf5",
+    )
+    assert isinstance(id_rec_vols, dict)
+    assert len(id_rec_vols) == 2
+    assert 10 in id_rec_vols.keys()
+    assert 12 in id_rec_vols.keys()
+    assert (
+        id_rec_vols[10].to_str()
+        == f"hdf5:volume:/this/is/a/test/rec_10.000_01024.hdf5?path={entry}/reconstruction"
+    )
+
+    # dummy test with tiff
+    id_rec_vols = get_multi_cor_recons_volume_identifiers(
+        scan=scan,
+        slice_index="middle",
+        location="/this/is/a/test",
+        file_prefix="rec",
+        cors=(10, 12),
+        file_format="tiff",
+    )
+    assert isinstance(id_rec_vols, dict)
+    assert len(id_rec_vols) == 2
+    assert 10 in id_rec_vols.keys()
+    assert 12 in id_rec_vols.keys()
+    assert id_rec_vols[10].to_str() == "tiff:volume:/this/is/a?file_prefix=test"
+
+
+def test_nabu_std_err_has_error():
+    assert nabu_std_err_has_error(None) is False
+    assert nabu_std_err_has_error(b"") is False
+    assert nabu_std_err_has_error(b"this is an error") is True
+    assert (
+        nabu_std_err_has_error(
+            b"warnings.warn('creating CUBLAS context to get version num"
+        )
+        is False
+    )
+    assert (
+        nabu_std_err_has_error(
+            b"warnings.warn('creating CUBLAS context to get version num\n this is an error"
+        )
+        is True
+    )
+
+    assert (
+        nabu_std_err_has_error(
+            b"""/nobackup/lbs0511/tomotools/venvs/2023_10_04/lib/python3.8/site-packages/skcuda/cublas.py:284: UserWarning: creating CUBLAS context to get version number
+            warnings.warn('creating CUBLAS context to get version number')
+            /nobackup/lbs0511/tomotools/venvs/2023_10_04/lib/python3.8/site-packages/nabu/cuda/kernel.py:49: UserWarning: The CUDA compiler succeeded, but said the following:
+            nvcc warning : The 'compute_35', 'compute_37', 'sm_35', and 'sm_37' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
+            self.module = SourceModule(self.src, **self.sourcemodule_kwargs)
+            /nobackup/lbs0511/tomotools/venvs/2023_10_04/lib/python3.8/site-packages/pycuda/elementwise.py:47: UserWarning: The CUDA compiler succeeded, but said the following:
+            nvcc warning : The 'compute_35', 'compute_37', 'sm_35', and 'sm_37' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
+            return SourceModule(
+            /nobackup/lbs0511/tomotools/venvs/2023_10_04/lib/python3.8/site-packages/nabu/cuda/kernel.py:49: UserWarning: The CUDA compiler succeeded, but said the following:
+            nvcc warning : The 'compute_35', 'compute_37', 'sm_35', and 'sm_37' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
+            self.module = SourceModule(self.src, **self.sourcemodule_kwargs)
+            /nobackup/lbs0511/tomotools/venvs/2023_10_04/lib/python3.8/site-packages/pycuda/elementwise.py:47: UserWarning: The CUDA compiler succeeded, but said the following:
+            nvcc warning : The 'compute_35', 'compute_37', 'sm_35', and 'sm_37' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
+            return SourceModule(
+            /nobackup/lbs0511/tomotools/venvs/2023_10_04/lib/python3.8/site-packages/nabu/cuda/kernel.py:49: UserWarning: The CUDA compiler succeeded, but said the following:
+            nvcc warning : The 'compute_35', 'compute_37', 'sm_35', and 'sm_37' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
+            self.module = SourceModule(self.src, **self.sourcemodule_kwargs)
+            /nobackup/lbs0511/tomotools/venvs/2023_10_04/lib/python3.8/site-packages/nabu/cuda/kernel.py:49: UserWarning: The CUDA compiler succeeded, but said the following:
+            nvcc warning : The 'compute_35', 'compute_37', 'sm_35', and 'sm_37' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
+            self.module = SourceModule(self.src, **self.sourcemodule_kwargs)
+            /nobackup/lbs0511/tomotools/venvs/2023_10_04/lib/python3.8/site-packages/nabu/cuda/kernel.py:49: UserWarning: The CUDA compiler succeeded, but said the following:
+            nvcc warning : The 'compute_35', 'compute_37', 'sm_35', and 'sm_37' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
+            kernel.cu(111): warning #1215-D: function "tex2D(texture<T, 2, cudaReadModeElementType>, float, float) [with T=float]"
+            /cvmfs/hpc.esrf.fr/software/packages/ubuntu20.04/x86_64/cuda/11.8.0//bin/../targets/x86_64-linux/include/texture_fetch_functions.h(198): here was declared deprecated
+            kernel.cu(112): warning #1215-D: function "tex2D(texture<T, 2, cudaReadModeElementType>, float, float) [with T=float]"
+            /cvmfs/hpc.esrf.fr/software/packages/ubuntu20.04/x86_64/cuda/11.8.0//bin/../targets/x86_64-linux/include/texture_fetch_functions.h(198): here was declared deprecated
+            kernel.cu(113): warning #1215-D: function "tex2D(texture<T, 2, cudaReadModeElementType>, float, float) [with T=float]"
+            /cvmfs/hpc.esrf.fr/software/packages/ubuntu20.04/x86_64/cuda/11.8.0//bin/../targets/x86_64-linux/include/texture_fetch_functions.h(198): here was declared deprecated
+            kernel.cu(114): warning #1215-D: function "tex2D(texture<T, 2, cudaReadModeElementType>, float, float) [with T=float]"
+            /cvmfs/hpc.esrf.fr/software/packages/ubuntu20.04/x86_64/cuda/11.8.0//bin/../targets/x86_64-linux/include/texture_fetch_functions.h(198): here was declared deprecated
+            self.module = SourceModule(self.src, **self.sourcemodule_kwargs)
+            /nobackup/lbs0511/tomotools/venvs/2023_10_04/lib/python3.8/site-packages/pycuda/elementwise.py:47: UserWarning: The CUDA compiler succeeded, but said the following:
+            nvcc warning : The 'compute_35', 'compute_37', 'sm_35', and 'sm_37' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
+            return SourceModule("""
+        )
+        is False
+    )
+
+    assert (
+        nabu_std_err_has_error(
+            b"""/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2024_02_26/lib/python3.11/site-packages/cupyx/jit/_interface.py:173: FutureWarning: cupyx.jit.rawkernel is experimental. The interface can change in the future.
+        cupy._util.experimental('cupyx.jit.rawkernel')
+        /cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2024_02_26/lib/python3.11/site-packages/skcuda/cublas.py:284: UserWarning: creating CUBLAS context to get version number
+        warnings.warn('creating CUBLAS context to get version number')"""
+        )
+        is False
+    )
+
+    assert (
+        nabu_std_err_has_error(
+            b"""/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2024_04_09/lib/python3.11/site-packages/cupyx/jit/_interface.py:173: FutureWarning: cupyx.jit.rawkernel is experimental. The interface can change in the future.
+        cupy._util.experimental('cupyx.jit.rawkernel')
+        z_translation Not supported for EDF
+        y_translation Not supported for EDF
+        x_translation Not supported for EDF
+        /cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2024_04_09/lib/python3.11/site-packages/skcuda/cublas.py:284: UserWarning: creating CUBLAS context to get version number
+        warnings.warn('creating CUBLAS context to get version number')
+        unable to load metadata from /lbsram/data/id16b/inhouse1/comm_24apr/tomwerUpdate/testTomwer04/reconstructed_volumes/testTomwer04slice_pag_001080_db0500_plane_XY.vol.info"""
+        )
+        is False
+    )
+
+    assert (
+        nabu_std_err_has_error(
+            b"""/cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2024_04_19/lib/python3.11/site-packages/cupyx/jit/_interface.py:173: FutureWarning: cupyx.jit.rawkernel is experimental. The interface can change in the future.
+        cupy._util.experimental('cupyx.jit.rawkernel')
+        /cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2024_04_19/lib/python3.11/site-packages/nabu/cuda/kernel.py:49: UserWarning: The CUDA compiler succeeded, but said the following:
+        kernel.cu(228): warning #177-D: variable "x_stop_other" was declared but never referenced
+
+        kernel.cu(230): warning #177-D: variable "y_stop_other" was declared but never referenced
+
+
+        self.module = SourceModule(self.src, **self.sourcemodule_kwargs)
+        /cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2024_04_19/lib/python3.11/site-packages/skcuda/cublas.py:284: UserWarning: creating CUBLAS context to get version number
+        warnings.warn('creating CUBLAS context to get version number')
+        /cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2024_04_19/lib/python3.11/site-packages/nabu/cuda/kernel.py:49: UserWarning: The CUDA compiler succeeded, but said the following:
+        kernel.cu(228): warning #177-D: variable "x_stop_other" was declared but never referenced
+
+        kernel.cu(230): warning #177-D: variable "y_stop_other" was declared but never referenced
+
+
+        self.module = SourceModule(self.src, **self.sourcemodule_kwargs)
+        /cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2024_04_19/lib/python3.11/site-packages/nabu/cuda/kernel.py:49: UserWarning: The CUDA compiler succeeded, but said the following:
+        kernel.cu(131): warning #1215-D: function "tex2D(texture<T, 2, cudaReadModeElementType>, float, float) [with T=float]"
+        /cvmfs/hpc.esrf.fr/software/packages/ubuntu20.04/x86_64/cuda/11.7.1/bin/../targets/x86_64-linux/include/texture_fetch_functions.h(198): here was declared deprecated
+
+        kernel.cu(132): warning #1215-D: function "tex2D(texture<T, 2, cudaReadModeElementType>, float, float) [with T=float]"
+        /cvmfs/hpc.esrf.fr/software/packages/ubuntu20.04/x86_64/cuda/11.7.1/bin/../targets/x86_64-linux/include/texture_fetch_functions.h(198): here was declared deprecated
+
+        kernel.cu(133): warning #1215-D: function "tex2D(texture<T, 2, cudaReadModeElementType>, float, float) [with T=float]"
+        /cvmfs/hpc.esrf.fr/software/packages/ubuntu20.04/x86_64/cuda/11.7.1/bin/../targets/x86_64-linux/include/texture_fetch_functions.h(198): here was declared deprecated
+
+        kernel.cu(134): warning #1215-D: function "tex2D(texture<T, 2, cudaReadModeElementType>, float, float) [with T=float]"
+        /cvmfs/hpc.esrf.fr/software/packages/ubuntu20.04/x86_64/cuda/11.7.1/bin/../targets/x86_64-linux/include/texture_fetch_functions.h(198): here was declared deprecated
+
+        kernel.cu(21): warning #177-D: function "linear_interpolation" was declared but never referenced
+
+
+        self.module = SourceModule(self.src, **self.sourcemodule_kwargs)
+        /cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2024_04_19/lib/python3.11/site-packages/cupy/cuda/compiler.py:233: PerformanceWarning: Jitify is performing a one-time only warm-up to populate the persistent cache, this may take a few seconds and will be improved in a future release...
+        jitify._init_module()"""
+        )
+        is False
+    )
+
+    assert (
+        nabu_std_err_has_error(
+            b"""pytools.persistent_dict: unable to import 'siphash24.siphash13', """
+        )
+        is False
+    )
+
+    assert (
+        nabu_std_err_has_error(
+            b"""CompilerWarning: Non-empty compiler output encountered. Set the environment variable PYOPENCL_COMPILER_OUTPUT=1 to see more.
+        _create_built_program_from_source_cached(
+        /cvmfs/tomo.esrf.fr/software/packages/linux/x86_64/tomotools/2024_09_06/lib/python3.11/site-packages/pyopencl/cache.py:499: CompilerWarning: Non-empty compiler output encountered. Set the environment variable PYOPENCL_COMPILER_OUTPUT=1 to see more.
+        prg.build(options_bytes, devices)"""
+        )
+        is False
+    )