tomwer 1.6.22__tar.gz → 2.0.0.dev0__tar.gz

tomwer-2.0.0.dev0/PKG-INFO

@@ -0,0 +1,200 @@
+Metadata-Version: 2.4
+Name: tomwer
+Version: 2.0.0.dev0
+Summary: Tomography workflow tools
+Author-email: Henri Payno <henri.payno@esrf.fr>, Pierre Paleo <pierre.paleo@esrf.fr>, Pierre-Olivier Autran <pierre-olivier.autran@esrf.fr>, Jérôme Lesaint <jerome.lesaint@esrf.fr>, Alessandro Mirone <mirone@esrf.fr>
+License: MIT
+Project-URL: Homepage, https://gitlab.esrf.fr/tomotools/tomwer
+Project-URL: Documentation, https://tomotools.gitlab-pages.esrf.fr/tomwer/
+Project-URL: Repository, https://gitlab.esrf.fr/tomotools/tomwer
+Project-URL: Issues, https://gitlab.esrf.fr/tomotools/tomwer/-/issues
+Project-URL: Changelog, https://gitlab.esrf.fr/tomotools/tomwer/-/blob/main/CHANGELOG.rst?ref_type=heads
+Keywords: orange3 add-on,ewoks
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Environment :: Console
+Classifier: Environment :: X11 Applications :: Qt
+Classifier: Operating System :: POSIX
+Classifier: Natural Language :: English
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: setuptools
+Requires-Dist: psutil
+Requires-Dist: silx[full_no_qt]>=3
+Requires-Dist: tomoscan>=2.4.0dev0
+Requires-Dist: nxtomo>2.0.0dev2
+Requires-Dist: nxtomomill>=2.0.0dev0
+Requires-Dist: processview>=1.5.2
+Requires-Dist: ewokscore
+Requires-Dist: sluurp>=0.4.1
+Requires-Dist: packaging
+Requires-Dist: pint
+Requires-Dist: tqdm
+Requires-Dist: eval_type_backport; python_version < "3.10"
+Requires-Dist: platformdirs
+Requires-Dist: esrf-pathlib
+Provides-Extra: full-base
+Requires-Dist: orange-canvas-core; extra == "full-base"
+Requires-Dist: orange-widget-base; extra == "full-base"
+Requires-Dist: ewokscore; extra == "full-base"
+Requires-Dist: ewoksorange>=3.3.0; extra == "full-base"
+Requires-Dist: fabio; extra == "full-base"
+Requires-Dist: h5py>=3; extra == "full-base"
+Requires-Dist: lxml; extra == "full-base"
+Requires-Dist: scipy; extra == "full-base"
+Requires-Dist: Pillow; extra == "full-base"
+Requires-Dist: glymur<0.14; extra == "full-base"
+Requires-Dist: resource; extra == "full-base"
+Requires-Dist: tifffile; extra == "full-base"
+Requires-Dist: hdf5plugin; extra == "full-base"
+Requires-Dist: pyicat_plus; extra == "full-base"
+Requires-Dist: ewoksnotify[base]; extra == "full-base"
+Requires-Dist: ewoksnotify[icat]; extra == "full-base"
+Requires-Dist: chime; extra == "full-base"
+Requires-Dist: pyicat_plus; extra == "full-base"
+Requires-Dist: blissdata; extra == "full-base"
+Provides-Extra: full-no-cuda
+Requires-Dist: tomwer[full_base]; extra == "full-no-cuda"
+Requires-Dist: nabu>=2024.2.0; extra == "full-no-cuda"
+Requires-Dist: PyQt6; extra == "full-no-cuda"
+Requires-Dist: qtawesome; extra == "full-no-cuda"
+Provides-Extra: full-no-qt
+Requires-Dist: tomwer[full_base]; extra == "full-no-qt"
+Requires-Dist: nabu[full]>=2024.2.0; extra == "full-no-qt"
+Requires-Dist: pycuda<2024.1.1; extra == "full-no-qt"
+Requires-Dist: scikit-cuda; extra == "full-no-qt"
+Requires-Dist: PyQt6; extra == "full-no-qt"
+Requires-Dist: qtawesome; extra == "full-no-qt"
+Provides-Extra: full
+Requires-Dist: tomwer[full_no_qt]; extra == "full"
+Requires-Dist: PyQt6; extra == "full"
+Provides-Extra: doc
+Requires-Dist: tomwer[full_no_cuda]; extra == "doc"
+Requires-Dist: Sphinx>=4.0.0; extra == "doc"
+Requires-Dist: nbsphinx; extra == "doc"
+Requires-Dist: pandoc; extra == "doc"
+Requires-Dist: jupyterlab; extra == "doc"
+Requires-Dist: pydata_sphinx_theme; extra == "doc"
+Requires-Dist: sphinx-design; extra == "doc"
+Requires-Dist: sphinx-autodoc-typehints; extra == "doc"
+Requires-Dist: sphinxcontrib-programoutput; extra == "doc"
+Requires-Dist: sphinxcontrib-youtube; extra == "doc"
+Requires-Dist: myst-parser; extra == "doc"
+Requires-Dist: nb_extension_tagstyler; extra == "doc"
+Requires-Dist: ewokssphinx; extra == "doc"
+Provides-Extra: dev-spec
+Requires-Dist: black; extra == "dev-spec"
+Requires-Dist: flake8; extra == "dev-spec"
+Requires-Dist: timeout-decorator; extra == "dev-spec"
+Requires-Dist: pyopencl; extra == "dev-spec"
+Provides-Extra: dev
+Requires-Dist: tomwer[full]; extra == "dev"
+Requires-Dist: tomwer[dev_spec]; extra == "dev"
+Provides-Extra: dev-no-cuda
+Requires-Dist: tomwer[full_no_cuda]; extra == "dev-no-cuda"
+Requires-Dist: tomwer[dev_spec]; extra == "dev-no-cuda"
+Provides-Extra: test
+Requires-Dist: tomwer[full_no_cuda]; extra == "test"
+Requires-Dist: pytest-asyncio; extra == "test"
+Requires-Dist: tomoscan[test]>=2.4.0dev0; extra == "test"
+Dynamic: license-file
+
+.. image:: doc/img/tomwer.png
+   :alt: Tomwer Logo
+   :align: left
+   :width: 400px
+
+Introduction
+------------
+
+**Tomwer** provides tools to automate acquisition and reconstruction processes for tomography. The package includes:
+
+- A library to individually access each acquisition process.
+- Graphical User Interface (GUI) applications to control key processes such as reconstruction and data transfer, which can be executed as standalone applications.
+- An Orange add-on to help users define custom workflows (`Orange3 <http://orange.biolab.si>`_).
+
+Tomwer relies on `Nabu <https://gitlab.esrf.fr/tomotools/nabu>`_ for tomographic reconstruction.
+
+**Note**: Currently, the software is only compatible with Linux.
+
+Documentation
+-------------
+
+The documentation is available here:
+
+`Stable Version <https://tomwer.readthedocs.io/en/stable/>`_
+
+`Latest Version <https://tomotools.gitlab-pages.esrf.fr/tomwer/>`_
+
+Installation
+------------
+
+To install Tomwer with all features:
+
+.. code-block:: bash
+
+    pip install tomwer[full]
+
+Alternatively, you can install the latest development branch from the repository:
+
+.. code-block:: bash
+
+    pip install git+https://gitlab.esrf.fr/tomotools/tomwer/#egg=tomwer[full]
+
+
+Launching Applications
+-----------------------
+
+After installation, Tomwer includes several applications. You can launch an application by running:
+
+.. code-block:: bash
+
+    tomwer <appName> [options]
+
+- If you run `tomwer` without arguments, a manual page will be displayed.
+- For application-specific help, run:
+
+.. code-block:: bash
+
+    tomwer <appName> --help
+
+
+Tomwer Canvas - Orange Canvas
+-----------------------------
+
+You can launch the Orange canvas to create workflows using the available building blocks:
+
+.. code-block:: bash
+
+    tomwer canvas
+
+- Alternatively, you can use `orange-canvas`.
+- If you're using a virtual environment, remember to activate it:
+
+.. code-block:: bash
+
+    source myvirtualenv/bin/activate
+
+
+Building Documentation
+-----------------------
+
+To build the documentation:
+
+.. code-block:: bash
+
+    sphinx-build doc build/html
+
+The documentation will be generated in `doc/build/html`, and the entry point is `index.html`. To view the documentation in a browser:
+
+.. code-block:: bash
+
+    firefox build/html/index.html
+
+**Note**: Building the documentation requires `sphinx` to be installed, which is not a hard dependency of Tomwer. If needed, install it separately.

tomwer-2.0.0.dev0/README.rst

@@ -0,0 +1,93 @@
+.. image:: doc/img/tomwer.png
+   :alt: Tomwer Logo
+   :align: left
+   :width: 400px
+
+Introduction
+------------
+
+**Tomwer** provides tools to automate acquisition and reconstruction processes for tomography. The package includes:
+
+- A library to individually access each acquisition process.
+- Graphical User Interface (GUI) applications to control key processes such as reconstruction and data transfer, which can be executed as standalone applications.
+- An Orange add-on to help users define custom workflows (`Orange3 <http://orange.biolab.si>`_).
+
+Tomwer relies on `Nabu <https://gitlab.esrf.fr/tomotools/nabu>`_ for tomographic reconstruction.
+
+**Note**: Currently, the software is only compatible with Linux.
+
+Documentation
+-------------
+
+The documentation is available here:
+
+`Stable Version <https://tomwer.readthedocs.io/en/stable/>`_
+
+`Latest Version <https://tomotools.gitlab-pages.esrf.fr/tomwer/>`_
+
+Installation
+------------
+
+To install Tomwer with all features:
+
+.. code-block:: bash
+
+    pip install tomwer[full]
+
+Alternatively, you can install the latest development branch from the repository:
+
+.. code-block:: bash
+
+    pip install git+https://gitlab.esrf.fr/tomotools/tomwer/#egg=tomwer[full]
+
+
+Launching Applications
+-----------------------
+
+After installation, Tomwer includes several applications. You can launch an application by running:
+
+.. code-block:: bash
+
+    tomwer <appName> [options]
+
+- If you run `tomwer` without arguments, a manual page will be displayed.
+- For application-specific help, run:
+
+.. code-block:: bash
+
+    tomwer <appName> --help
+
+
+Tomwer Canvas - Orange Canvas
+-----------------------------
+
+You can launch the Orange canvas to create workflows using the available building blocks:
+
+.. code-block:: bash
+
+    tomwer canvas
+
+- Alternatively, you can use `orange-canvas`.
+- If you're using a virtual environment, remember to activate it:
+
+.. code-block:: bash
+
+    source myvirtualenv/bin/activate
+
+
+Building Documentation
+-----------------------
+
+To build the documentation:
+
+.. code-block:: bash
+
+    sphinx-build doc build/html
+
+The documentation will be generated in `doc/build/html`, and the entry point is `index.html`. To view the documentation in a browser:
+
+.. code-block:: bash
+
+    firefox build/html/index.html
+
+**Note**: Building the documentation requires `sphinx` to be installed, which is not a hard dependency of Tomwer. If needed, install it separately.

tomwer-2.0.0.dev0/pyproject.toml

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+[project]
+name = "tomwer"
+dynamic = ["version"]
+authors = [
+    { name = "Henri Payno", email = "henri.payno@esrf.fr" },
+    { name = "Pierre Paleo", email = "pierre.paleo@esrf.fr" },
+    { name = "Pierre-Olivier Autran", email = "pierre-olivier.autran@esrf.fr" },
+    { name = "Jérôme Lesaint", email = "jerome.lesaint@esrf.fr" },
+    { name = "Alessandro Mirone", email = "mirone@esrf.fr" }
+]
+description = "Tomography workflow tools"
+readme = { file = "README.rst", content-type = "text/x-rst" }
+license = { text = "MIT" }
+requires-python = ">=3.10"
+keywords = ["orange3 add-on", "ewoks"]
+classifiers = [
+    "Intended Audience :: Education",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Environment :: Console",
+    "Environment :: X11 Applications :: Qt",
+    "Operating System :: POSIX",
+    "Natural Language :: English",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Software Development :: Libraries :: Python Modules"
+]
+dependencies = [
+    "numpy",
+    "setuptools",
+    "psutil",
+    "silx[full_no_qt]>=3",
+    "tomoscan>=2.4.0dev0",
+    "nxtomo>2.0.0dev2",
+    "nxtomomill>=2.0.0dev0",
+    "processview>=1.5.2",
+    "ewokscore",
+    "sluurp>=0.4.1",
+    "packaging",
+    "pint",
+    "tqdm",
+    "eval_type_backport; python_version < '3.10'",
+    "platformdirs",
+    "esrf-pathlib",
+]
+
+[project.optional-dependencies]
+full_base = [
+    "orange-canvas-core",
+    "orange-widget-base",
+    "ewokscore",
+    "ewoksorange>=3.3.0",
+    "fabio",
+    "h5py>=3",
+    "lxml",
+    "scipy",
+    "Pillow",
+    "glymur<0.14",  # for python3.9 until https://github.com/quintusdias/glymur/issues/688 is fixed
+    "resource",
+    "tifffile",
+    "hdf5plugin",
+    "pyicat_plus",
+    "ewoksnotify[base]",  # note: avoid full to let silx determine which Qt binding to use.
+    "ewoksnotify[icat]",
+    "chime",  # to complete ewoksnotify
+    "pyicat_plus",
+    "blissdata",
+]
+full_no_cuda = [
+    "tomwer[full_base]",
+    "nabu>=2024.2.0",
+    "PyQt6",
+    'qtawesome',             # For icons
+]
+full_no_qt = [
+    "tomwer[full_base]",
+    "nabu[full]>=2024.2.0",
+    "pycuda<2024.1.1",
+    "scikit-cuda",
+    "PyQt6",
+    'qtawesome',             # For icons
+]
+full = [
+    "tomwer[full_no_qt]",
+    "PyQt6",
+]
+doc = [
+    "tomwer[full_no_cuda]",
+    "Sphinx>=4.0.0",
+    "nbsphinx",
+    "pandoc",
+    "jupyterlab",
+    "pydata_sphinx_theme",
+    "sphinx-design",
+    "sphinx-autodoc-typehints",
+    "sphinxcontrib-programoutput",
+    "sphinxcontrib-youtube",
+    "myst-parser",
+    "nb_extension_tagstyler",
+    "ewokssphinx",
+]
+dev_spec = [
+    "black",
+    "flake8",
+    "timeout-decorator",
+    "pyopencl",
+]
+dev = [
+    "tomwer[full]",
+    "tomwer[dev_spec]"
+]
+dev_no_cuda = [
+    "tomwer[full_no_cuda]",
+    "tomwer[dev_spec]"
+]
+test = [
+    "tomwer[full_no_cuda]",
+    "pytest-asyncio",
+    "tomoscan[test]>=2.4.0dev0",
+]
+
+[project.urls]
+Homepage = "https://gitlab.esrf.fr/tomotools/tomwer"
+Documentation = "https://tomotools.gitlab-pages.esrf.fr/tomwer/"
+Repository = "https://gitlab.esrf.fr/tomotools/tomwer"
+Issues = "https://gitlab.esrf.fr/tomotools/tomwer/-/issues"
+Changelog = "https://gitlab.esrf.fr/tomotools/tomwer/-/blob/main/CHANGELOG.rst?ref_type=heads"
+
+[build-system]
+requires = ["setuptools>=61.0", "wheel", "numpy>=1.12"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.dynamic]
+version = { attr = "tomwer.__version__" }
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[project.scripts]
+tomwer = "tomwer.__main__:main"
+
+[project.entry-points."orange3.addon"]
+tomwer-add-on = "orangecontrib.tomwer:addon"
+
+[project.entry-points."orange.widgets"]
+tomwer = "orangecontrib.tomwer.widgets"
+
+[project.entry-points."orangecanvas.examples"]
+tomo_examples = "orangecontrib.tomwer.examples"
+
+[project.entry-points."orange.widgets.tutorials"]
+tomo_tutorials = "orangecontrib.tomwer.tutorials"
+tomo_tutorials_id16b = "orangecontrib.tomwer.tutorials.id16b"
+
+[project.entry-points."orange.canvas.help"]
+html-index = "orangecontrib.tomwer.widgets:WIDGET_HELP_PATH"
+
+[project.entry-points."ewoks.tasks.class"]
+"tomwer.tasks.*.*" = "tomwer"
+
+[tool.setuptools.package-data]
+"tomwer.resources" = [
+    "gui/icons/*.png",
+    "gui/icons/*.svg",
+    "gui/icons/*.npy",
+    "gui/illustrations/*.svg",
+    "gui/illustrations/*.png"
+]
+"orangecontrib.tomwer" = [
+    "tutorials/*.ows",
+    "tutorials/id16b/*.ows",
+    "widgets/icons/*.png",
+    "widgets/icons/*.svg",
+    "widgets/cluster/icons/*.png",
+    "widgets/cluster/icons/*.svg",
+    "widgets/control/icons/*.png",
+    "widgets/control/icons/*.svg",
+    "widgets/debugtools/icons/*.png",
+    "widgets/debugtools/icons/*.svg",
+    "widgets/deprecated/icons/*.png",
+    "widgets/deprecated/icons/*.svg",
+    "widgets/edit/icons/*.png",
+    "widgets/edit/icons/*.svg",
+    "widgets/dataportal/icons/*.png",
+    "widgets/dataportal/icons/*.svg",
+    "widgets/reconstruction/icons/*.png",
+    "widgets/reconstruction/icons/*.svg",
+    "widgets/visualization/icons/*.png",
+    "widgets/visualization/icons/*.svg",
+    "widgets/other/icons/*.png",
+    "widgets/other/icons/*.svg"
+]
+
+[tool.sphinx]
+source-dir = "./doc"
+
+[tool.coverage.run]
+omit = ["setup.py", "*/test/*"]

tomwer-2.0.0.dev0/src/orangecontrib/tomwer/__init__.py

@@ -0,0 +1,10 @@
+"""
+(Ewoksorange) Orange add-on for tomography
+"""
+
+import logging
+
+from . import state_summary  # noqa F401
+
+fabio_logger = logging.getLogger("fabio.edfimage")
+fabio_logger.setLevel(logging.WARNING)

tomwer-2.0.0.dev0/src/orangecontrib/tomwer/orange/ewoks_compatibility.py

@@ -0,0 +1,9 @@
+from __future__ import annotations
+
+from ewokscore.variable import Variable
+
+
+def unpack_variable(obj: Variable):
+    if isinstance(obj, Variable):
+        return obj.value
+    return obj

tomwer-2.0.0.dev0/src/orangecontrib/tomwer/orange/managedprocess.py

@@ -0,0 +1,79 @@
+from __future__ import annotations
+
+import functools
+import logging
+
+from orangewidget.widget import OWBaseWidget
+from processview.core.manager import DatasetState, ProcessManager
+from processview.core.superviseprocess import SuperviseProcess
+
+_logger = logging.getLogger(__name__)
+
+
+class _SuperviseBase(SuperviseProcess):
+    """
+    MIxIn class for orange widgets that are doing some processing.
+    It provides API to:
+    * notify the ProcessManager a modification of a dataset / processing state.
+    * signal start and stop of a processing.
+
+    """
+
+    def __init__(self, process_id=None):
+        super().__init__(process_id=process_id)
+        self.destroyed.connect(functools.partial(ProcessManager().unregister, self))
+
+    def setCaption(self, caption):
+        self.name = caption
+        try:
+            ProcessManager().process_renamed(process=self)
+        except Exception as e:
+            _logger.warning(f"Fail to update process name. Error is {e}")
+
+    def notify_skip(self, scan, details=None):
+        ProcessManager().notify_dataset_state(
+            dataset=scan, process=self, state=DatasetState.SKIPPED, details=details
+        )
+
+    def notify_pending(self, scan, details=None):
+        ProcessManager().notify_dataset_state(
+            dataset=scan, process=self, state=DatasetState.PENDING, details=details
+        )
+
+    def notify_succeed(self, scan, details=None):
+        ProcessManager().notify_dataset_state(
+            dataset=scan, process=self, state=DatasetState.SUCCEED, details=details
+        )
+
+    def notify_failed(self, scan, details=None):
+        ProcessManager().notify_dataset_state(
+            dataset=scan, process=self, state=DatasetState.FAILED, details=details
+        )
+
+    def notify_on_going(self, scan, details=None):
+        ProcessManager().notify_dataset_state(
+            dataset=scan, process=self, state=DatasetState.ON_GOING, details=details
+        )
+
+    def _startProcessing(self, *args, **kwargs):
+        self.progressBarInit()
+        self.progressBarSet(-1)
+
+    def _endProcessing(self, *args, **kwargs):
+        self.progressBarFinished()
+
+
+class SuperviseOW(OWBaseWidget, _SuperviseBase, openclass=True):
+    """
+    A basic OWWidget but registered on the process manager and that can notify processing state to the orange-canvas
+    """
+
+    want_control_area = False
+
+    def __init__(self, parent, process_id=None):
+        OWBaseWidget.__init__(self, parent, process_id=process_id)
+        _SuperviseBase.__init__(self, process_id=process_id)
+
+    def setCaption(self, caption):
+        OWBaseWidget.setCaption(self, caption)
+        _SuperviseBase.setCaption(self, caption=caption)

tomwer-2.0.0.dev0/src/orangecontrib/tomwer/orange/task_widgets/TomwerWidgetNoThread.py

@@ -0,0 +1,8 @@
+from ewoksorange.gui.owwidgets.nothread import OWEwoksWidgetNoThread
+from ...orange.managedprocess import _SuperviseBase
+
+
+class TomwerWidgetNoThread(OWEwoksWidgetNoThread, _SuperviseBase, openclass=True):
+    want_main_area = True
+    want_control_area = False
+    resizing_enabled = True

tomwer-2.0.0.dev0/src/orangecontrib/tomwer/orange/task_widgets/TomwerWidgetOneThreadPerRun.py

@@ -0,0 +1,22 @@
+from ewoksorange.gui.owwidgets.threaded import OWEwoksWidgetOneThreadPerRun
+from ...orange.managedprocess import _SuperviseBase
+
+
+class TomwerWidgetOneThreadPerRun(
+    OWEwoksWidgetOneThreadPerRun, _SuperviseBase, openclass=True
+):
+    """
+    This widget make sure all input on "data" are triggering the workflow.
+
+    This is a work around for https://gitlab.esrf.fr/workflow/ewoks/ewoksorange/-/issues/60
+
+    Task are expected to have "data" as input and define the outputs from the pydantic model.
+    """
+
+    want_main_area = True
+    want_control_area = False
+    resizing_enabled = True
+
+    def __init__(self, *args, **kwargs):
+        OWEwoksWidgetOneThreadPerRun.__init__(self, *args, **kwargs)
+        _SuperviseBase.__init__(self)

tomwer-2.0.0.dev0/src/orangecontrib/tomwer/orange/task_widgets/TomwerWidgetWithStack.py

@@ -0,0 +1,20 @@
+from ewoksorange.gui.owwidgets.threaded import OWEwoksWidgetWithTaskStack
+from ...orange.managedprocess import _SuperviseBase
+
+
+class TomwerWidgetWithStack(OWEwoksWidgetWithTaskStack, _SuperviseBase, openclass=True):
+
+    want_main_area = True
+    want_control_area = False
+    resizing_enabled = True
+
+    def __init__(self, parent, process_id=None, *args, **kwargs):
+        OWEwoksWidgetWithTaskStack.__init__(self, parent, args, kwargs)
+        _SuperviseBase.__init__(self, process_id=process_id)
+
+        self.task_executor_queue.sigComputationStarted.connect(self._startProcessing)
+        self.task_executor_queue.sigComputationEnded.connect(self._endProcessing)
+
+    def setCaption(self, caption):
+        OWEwoksWidgetWithTaskStack.setCaption(self, caption)
+        _SuperviseBase.setCaption(self, caption=caption)