sigima 0.0.1.dev0__py3-none-any.whl → 1.0.0__py3-none-any.whl

sigima/__init__.py

@@ -1,2 +1,142 @@
-"""Placeholder for future sigima package."""
-__version__ = "0.0.1.dev0"
+# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
+
+"""
+Sigima
+======
+
+Sigima is a scientific computing engine for 1D signals and 2D images.
+
+It provides a set of tools for image and signal processing, including
+denoising, segmentation, and restoration. It is designed to be used in
+scientific and research applications.
+
+It is a part of the DataLab Platform, which aims at providing a
+comprehensive set of tools for data analysis and visualization, around
+the DataLab application.
+"""
+
+# TODO: Use `numpy.typing.NDArray` for more precise type annotations once NumPy >= 1.21
+# can be safely required (e.g. after raising the minimum required version of
+# scikit-image to >= 0.19).
+
+__all__ = [
+    "NO_ROI",
+    "CircularROI",
+    "ExponentialParam",
+    "Gauss2DParam",
+    "GaussParam",
+    "GeometryResult",
+    "ImageDatatypes",
+    "ImageObj",
+    "ImageROI",
+    "ImageTypes",
+    "KindShape",
+    "LinearChirpParam",
+    "LogisticParam",
+    "LorentzParam",
+    "NormalDistribution1DParam",
+    "NormalDistribution2DParam",
+    "PlanckParam",
+    "PolygonalROI",
+    "ROI1DParam",
+    "ROI2DParam",
+    "Ramp2DParam",
+    "RectangularROI",
+    "SegmentROI",
+    "SignalObj",
+    "SignalROI",
+    "SignalTypes",
+    "SimpleBaseProxy",
+    "SimpleRemoteProxy",
+    "StepParam",
+    "TableResult",
+    "TypeObj",
+    "TypeROI",
+    "UniformDistribution1DParam",
+    "UniformDistribution2DParam",
+    "VoigtParam",
+    "calc_table_from_data",
+    "create_image",
+    "create_image_from_param",
+    "create_image_parameters",
+    "create_image_roi",
+    "create_signal",
+    "create_signal_from_param",
+    "create_signal_parameters",
+    "create_signal_roi",
+    "read_image",
+    "read_images",
+    "read_signal",
+    "read_signals",
+    "write_image",
+    "write_signal",
+]
+
+
+from guidata.config import ValidationMode, set_validation_mode
+
+from sigima.client import SimpleBaseProxy, SimpleRemoteProxy
+from sigima.io import (
+    read_image,
+    read_images,
+    read_signal,
+    read_signals,
+    write_image,
+    write_signal,
+)
+from sigima.objects import (
+    NO_ROI,
+    CircularROI,
+    ExponentialParam,
+    Gauss2DParam,
+    GaussParam,
+    GeometryResult,
+    ImageDatatypes,
+    ImageObj,
+    ImageROI,
+    ImageTypes,
+    KindShape,
+    LinearChirpParam,
+    LogisticParam,
+    LorentzParam,
+    NormalDistribution1DParam,
+    NormalDistribution2DParam,
+    PlanckParam,
+    PolygonalROI,
+    Ramp2DParam,
+    RectangularROI,
+    ROI1DParam,
+    ROI2DParam,
+    SegmentROI,
+    SignalObj,
+    SignalROI,
+    SignalTypes,
+    StepParam,
+    TableResult,
+    TypeObj,
+    TypeROI,
+    UniformDistribution1DParam,
+    UniformDistribution2DParam,
+    VoigtParam,
+    calc_table_from_data,
+    create_image,
+    create_image_from_param,
+    create_image_parameters,
+    create_image_roi,
+    create_signal,
+    create_signal_from_param,
+    create_signal_parameters,
+    create_signal_roi,
+)
+
+# Set validation mode to ENABLED by default (issue warnings for invalid inputs)
+set_validation_mode(ValidationMode.ENABLED)
+
+__version__ = "1.0.0"
+__docurl__ = "https://sigima.readthedocs.io/"
+__homeurl__ = "https://github.com/DataLab-Platform/Sigima"
+__supporturl__ = "https://github.com/DataLab-Platform/sigima/issues/new/choose"
+
+# Dear (Debian, RPM, ...) package makers, please feel free to customize the
+# following path to module's data (images) and translations:
+DATAPATH = LOCALEPATH = ""

sigima/client/__init__.py

@@ -0,0 +1,105 @@
+# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
+
+"""
+DataLab Client (:mod:`sigima.client`)
+-------------------------------------
+
+The `sigima.client` module provides a proxy to DataLab application through XML-RPC
+protocol.
+
+DataLab may be controlled remotely using the `XML-RPC`_ protocol which is
+natively supported by Python (and many other languages). Remote controlling
+allows to access DataLab main features from a separate process.
+
+From an IDE
+^^^^^^^^^^^
+
+DataLab may be controlled remotely from an IDE (e.g. `Spyder`_ or any other
+IDE, or even a Jupyter Notebook) that runs a Python script. It allows to
+connect to a running DataLab instance, adds a signal and an image, and then
+runs calculations. This feature is exposed by the `sigima.client.SimpleRemoteProxy`
+class.
+
+From a third-party application
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+DataLab may also be controlled remotely from a third-party application, for the
+same purpose.
+
+If the third-party application is written in Python 3, it may directly use
+:py:class:`cdlclient.SimpleRemoteProxy` as mentioned above. From another language,
+it is also achievable, but it requires to implement a XML-RPC client in this
+language using the same methods of proxy server as in the
+:py:class:`cdlclient.SimpleRemoteProxy` class.
+
+Data (signals and images) may also be exchanged between DataLab and the remote
+client application, in both directions.
+
+The remote client application may be run on the same computer as DataLab or on
+different computer. In the latter case, the remote client application must
+know the IP address of the computer running DataLab.
+
+The remote client application may be run before or after DataLab. In the latter
+case, the remote client application must try to connect to DataLab until it
+succeeds.
+
+Supported features
+^^^^^^^^^^^^^^^^^^
+
+Supported features are the following:
+  - Switch to signal or image panel
+  - Remove all signals and images
+  - Save current session to a HDF5 file
+  - Open HDF5 files into current session
+  - Browse HDF5 file
+  - Open a signal or an image from file
+  - Add a signal
+  - Add an image
+  - Get object list
+  - Run calculation with parameters
+
+Example
+^^^^^^^
+
+Here is an example in Python 3 of a script that connects to a running DataLab
+instance, adds a signal and an image, and then runs calculations (the cell
+structure of the script make it convenient to be used in `Spyder`_ IDE):
+
+.. literalinclude:: ../examples/features/datalab_client.py
+
+Additional features
+^^^^^^^^^^^^^^^^^^^
+
+For simple remote controlling, :py:class:`sigima.client.SimpleRemoteProxy` may be
+used. For more advanced remote controlling, the `datalab.control.proxy.RemoteProxy`
+class provided by the DataLab package may be used.
+
+See DataLab documentation for more details about the
+``datalab.control.proxy.RemoteProxy`` class (on the section "Remote control").
+
+.. _XML-RPC: https://docs.python.org/3/library/xmlrpc.html
+
+.. _Spyder: https://www.spyder-ide.org/
+
+API
+^^^
+
+Remote client
+~~~~~~~~~~~~~
+
+.. autoclass:: sigima.client.remote.SimpleRemoteProxy
+    :members:
+
+Base proxy
+~~~~~~~~~~
+
+.. autoclass:: sigima.client.base.SimpleBaseProxy
+    :members:
+"""
+
+from sigima.client.base import SimpleBaseProxy
+from sigima.client.remote import SimpleRemoteProxy
+
+__all__ = ["SimpleBaseProxy", "SimpleRemoteProxy"]
+
+# TODO: Refactor the `sigima.client` with `datalab.base` and `datalab.control.remote`