pymagnetos 0.1.0__tar.gz → 0.7.6__tar.gz

pymagnetos-0.7.6/PKG-INFO

@@ -0,0 +1,118 @@
+Metadata-Version: 2.3
+Name: pymagnetos
+Version: 0.7.6
+Summary: Applications for high magnetic field analysis
+Author: Guillaume Le Goc
+Author-email: Guillaume Le Goc <guillaume.le-goc@lncmi.cnrs.fr>
+License: MIT
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Dist: fftekwfm>=0.3.0.1
+Requires-Dist: matplotlib>=3.10.8
+Requires-Dist: nexusformat>=2.0.0
+Requires-Dist: numpy>=2.4.1
+Requires-Dist: pydantic>=2.12.5
+Requires-Dist: pyqt6>=6.10.2
+Requires-Dist: pyqtgraph>=0.14.0
+Requires-Dist: rich>=14.3.1
+Requires-Dist: scipy>=1.17.0
+Requires-Dist: tomlkit>=0.14.0
+Requires-Dist: mkdocstrings>=1.0.2 ; extra == 'docs'
+Requires-Dist: mkdocstrings-python>=2.0.1 ; extra == 'docs'
+Requires-Dist: zensical>=0.0.20 ; extra == 'docs'
+Requires-Python: >=3.11
+Project-URL: Source Code, https://gitlab.in2p3.fr/himagnetos/pymagnetos
+Project-URL: Docs, https://himagnetos.pages.in2p3.fr/pymagnetos/index.html
+Provides-Extra: docs
+Description-Content-Type: text/markdown
+
+# pymagnetos
+[![Latest Release](https://gitlab.in2p3.fr/himagnetos/pymagnetos/-/badges/release.svg)](https://gitlab.in2p3.fr/himagnetos/pymagnetos/-/releases) 
+[![PyPI](https://img.shields.io/pypi/v/pymagnetos.svg?label=PyPI)](https://pypi.org/project/pymagnetos/)
+[![Documentation](https://img.shields.io/website?label=Documentation&url=https%3A%2F%2Fhimagnetos.pages.in2p3.fr%2Fpymagnetos%2F)](https://himagnetos.pages.in2p3.fr/pymagnetos/)
+[![Pipeline](https://gitlab.in2p3.fr/himagnetos/pymagnetos/badges/main/pipeline.svg?key_text=Pipeline)](https://gitlab.in2p3.fr/himagnetos/pymagnetos/-/pipelines)
+![Coverage](https://gitlab.in2p3.fr/himagnetos/pymagnetos/badges/main/coverage.svg?job=test&key_text=Coverage)
+
+Collection of Python tools for high magnetic field experiments analysis.
+
+It provides libraries and apps to analyse data acquired at the LNCMI in Toulouse.
+
+Currently available apps :
+- `pyuson` : for ultra-sound experiments
+- `pytdo` : for TDO experiments
+
+Those are also available as a library that can be used within custom Python scripts. They use a common framework that can also be used to build other experiment-specific app.
+
+The documention is hosted [here](https://himagnetos.pages.in2p3.fr/pymagnetos/).
+
+## Installation
+For more detailed instructions, see the [installation instructions](https://himagnetos.pages.in2p3.fr/pymagnetos/installation.html).
+
+### Method 1 : as an app
+If you plan to just use the graphical user interfaces, consider installing `pymagnetos` as a tool managed by [uv](https://docs.astral.sh/uv/), a modern Python package manager, that will install the required Python version and dependencies.
+
+<details>
+<summary>Method 1 : Click to see instructions</summary>
+
+1. Install uv (see their official [installation instructions](https://docs.astral.sh/uv/getting-started/installation/)).
+    - On Windows, enter the following command in PowerShell :
+    ```powershell
+    powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
+    ```
+    - On Linux and MacOS, enter the following in a shell :
+    ```bash
+    curl -LsSf https://astral.sh/uv/install.sh | sh
+    ```
+2. From a shell (PowerShell in Windows), install `pymagnetos` globally :
+    ```bash
+    uv tool install pymagnetos
+    ```
+
+`pymagnetos` is now installed along its dependencies in an isolated environment with no risks to mess up with your current tools and Python versions. Its main command, `pymagnetos`, is made available from any shell.
+
+#### Update
+To upgrade to the latest version, run :
+```bash
+uv tool upgrade pymagnetos
+```
+</details>
+
+### Method 2 : as a library
+Installing `pymagnetos` as a library will allow you to use it from scripts and Jupyter notebooks (e.g. you will be able to import it with `import pymagnetos`).
+
+<details>
+<summary>Method 2 : Click to see instructions</summary>
+
+From a virtual environment with Python>=3.11, install `pymagnetos` from PyPI :
+```bash
+pip install pymagnetos
+```
+
+#### Update
+To upgrade to the latest version, run, from the virtual environment :
+```bash
+pip install --upgrade pymagnetos
+```
+</details>
+
+## Usage
+### Run an app
+Once installed, the `pymagnetos` command should be available from the shell (PowerShell in Windows).
+You can check its usage with :
+`pymagnetos --help`
+
+Which comes down to :
+- Run the app for ultra-sound experiments : `pymagnetos pyuson`
+- Run the app for TDO experiments : `pymagnetos pytdo`
+
+Tip : hit the top arrow on the keyboard to show previous commands you ran.
+
+Grab a configuration file template from the [`configs`](https://gitlab.in2p3.fr/himagnetos/pymagnetos/-/tree/main/configs) folder, edit it according to your settings (essentially the path to the data directory) and drag & drop in the app window.
+
+### Use in a script
+Subpackages (e.g. `pyuson` or `pytdo`) can be imported in Python scripts or Jupyter notebooks. There are some examples in the [`examples`](https://gitlab.in2p3.fr/himagnetos/pymagnetos/-/tree/main/examples) folder.
+
+## Acknowledgments
+`pymagnetos` is developed in the Laboratoire National des Champs Magnétiques Intenses ([LNCMI](https://lncmi.cnrs.fr/)) in Toulouse, France, with the support of the [OSCARS HiMagnetOS project](https://oscars-project.eu/projects/himagnetos-high-magnetic-field-open-science).

pymagnetos-0.7.6/README.md

@@ -0,0 +1,88 @@
+# pymagnetos
+[![Latest Release](https://gitlab.in2p3.fr/himagnetos/pymagnetos/-/badges/release.svg)](https://gitlab.in2p3.fr/himagnetos/pymagnetos/-/releases) 
+[![PyPI](https://img.shields.io/pypi/v/pymagnetos.svg?label=PyPI)](https://pypi.org/project/pymagnetos/)
+[![Documentation](https://img.shields.io/website?label=Documentation&url=https%3A%2F%2Fhimagnetos.pages.in2p3.fr%2Fpymagnetos%2F)](https://himagnetos.pages.in2p3.fr/pymagnetos/)
+[![Pipeline](https://gitlab.in2p3.fr/himagnetos/pymagnetos/badges/main/pipeline.svg?key_text=Pipeline)](https://gitlab.in2p3.fr/himagnetos/pymagnetos/-/pipelines)
+![Coverage](https://gitlab.in2p3.fr/himagnetos/pymagnetos/badges/main/coverage.svg?job=test&key_text=Coverage)
+
+Collection of Python tools for high magnetic field experiments analysis.
+
+It provides libraries and apps to analyse data acquired at the LNCMI in Toulouse.
+
+Currently available apps :
+- `pyuson` : for ultra-sound experiments
+- `pytdo` : for TDO experiments
+
+Those are also available as a library that can be used within custom Python scripts. They use a common framework that can also be used to build other experiment-specific app.
+
+The documention is hosted [here](https://himagnetos.pages.in2p3.fr/pymagnetos/).
+
+## Installation
+For more detailed instructions, see the [installation instructions](https://himagnetos.pages.in2p3.fr/pymagnetos/installation.html).
+
+### Method 1 : as an app
+If you plan to just use the graphical user interfaces, consider installing `pymagnetos` as a tool managed by [uv](https://docs.astral.sh/uv/), a modern Python package manager, that will install the required Python version and dependencies.
+
+<details>
+<summary>Method 1 : Click to see instructions</summary>
+
+1. Install uv (see their official [installation instructions](https://docs.astral.sh/uv/getting-started/installation/)).
+    - On Windows, enter the following command in PowerShell :
+    ```powershell
+    powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"
+    ```
+    - On Linux and MacOS, enter the following in a shell :
+    ```bash
+    curl -LsSf https://astral.sh/uv/install.sh | sh
+    ```
+2. From a shell (PowerShell in Windows), install `pymagnetos` globally :
+    ```bash
+    uv tool install pymagnetos
+    ```
+
+`pymagnetos` is now installed along its dependencies in an isolated environment with no risks to mess up with your current tools and Python versions. Its main command, `pymagnetos`, is made available from any shell.
+
+#### Update
+To upgrade to the latest version, run :
+```bash
+uv tool upgrade pymagnetos
+```
+</details>
+
+### Method 2 : as a library
+Installing `pymagnetos` as a library will allow you to use it from scripts and Jupyter notebooks (e.g. you will be able to import it with `import pymagnetos`).
+
+<details>
+<summary>Method 2 : Click to see instructions</summary>
+
+From a virtual environment with Python>=3.11, install `pymagnetos` from PyPI :
+```bash
+pip install pymagnetos
+```
+
+#### Update
+To upgrade to the latest version, run, from the virtual environment :
+```bash
+pip install --upgrade pymagnetos
+```
+</details>
+
+## Usage
+### Run an app
+Once installed, the `pymagnetos` command should be available from the shell (PowerShell in Windows).
+You can check its usage with :
+`pymagnetos --help`
+
+Which comes down to :
+- Run the app for ultra-sound experiments : `pymagnetos pyuson`
+- Run the app for TDO experiments : `pymagnetos pytdo`
+
+Tip : hit the top arrow on the keyboard to show previous commands you ran.
+
+Grab a configuration file template from the [`configs`](https://gitlab.in2p3.fr/himagnetos/pymagnetos/-/tree/main/configs) folder, edit it according to your settings (essentially the path to the data directory) and drag & drop in the app window.
+
+### Use in a script
+Subpackages (e.g. `pyuson` or `pytdo`) can be imported in Python scripts or Jupyter notebooks. There are some examples in the [`examples`](https://gitlab.in2p3.fr/himagnetos/pymagnetos/-/tree/main/examples) folder.
+
+## Acknowledgments
+`pymagnetos` is developed in the Laboratoire National des Champs Magnétiques Intenses ([LNCMI](https://lncmi.cnrs.fr/)) in Toulouse, France, with the support of the [OSCARS HiMagnetOS project](https://oscars-project.eu/projects/himagnetos-high-magnetic-field-open-science).

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pymagnetos"
-version = "0.1.0"
+version = "0.7.6"
 description = "Applications for high magnetic field analysis"
 readme = "README.md"
 authors = [
@@ -8,10 +8,12 @@ authors = [
 ]
 license = {text = "MIT"}
 classifiers = [
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 	"Programming Language :: Python :: 3.13",
 	"Programming Language :: Python :: 3.14"
 ]
-requires-python = ">=3.13"
+requires-python = ">=3.11"
 dependencies = [
     "fftekwfm>=0.3.0.1",
     "matplotlib>=3.10.8",
@@ -27,6 +29,7 @@ dependencies = [
 
 [project.urls]
 "Source Code" = "https://gitlab.in2p3.fr/himagnetos/pymagnetos"
+"Docs" = "https://himagnetos.pages.in2p3.fr/pymagnetos/index.html"
 
 [project.scripts]
 pymagnetos = "pymagnetos.cli:main"
@@ -35,6 +38,13 @@ pymagnetos = "pymagnetos.cli:main"
 pytdo = "pymagnetos.pytdo.gui:run"
 pyuson = "pymagnetos.pyuson.gui:run"
 
+[project.optional-dependencies]
+docs = [
+    "mkdocstrings>=1.0.2",
+    "mkdocstrings-python>=2.0.1",
+    "zensical>=0.0.20",
+]
+
 
 [build-system]
 requires = ["uv_build>=0.9.26,<0.10.0"]
@@ -56,8 +66,8 @@ convention = "numpy"
 [dependency-groups]
 dev = [
     "ipython>=9.9.0",
-]
-docs = [
-    "mkdocstrings-python>=2.0.1",
-    "zensical>=0.0.19",
+    "pytest>=9.0.2",
+    "pytest-cov>=7.0.0",
+    "ruff>=0.14.14",
+    "ty>=0.0.14",
 ]

pymagnetos-0.7.6/src/pymagnetos/__init__.py

@@ -0,0 +1,53 @@
+"""
+The pymagnetos package.
+
+It provides analysis tools for high magnetic field experiments performed at LNCMI-T.
+
+Experiment-specific library are specialized implementations of the base classes found in
+the `core` subpackage. They should be generic enough to be used to build any pipeline
+relying on a 'configuration > analysis > store' workflow :
+
+1. Configuration : handled by the `Config` object, which uses `pydantic` models to read
+and validate TOML configuration files. One needs to define the `pydantic` models. The
+`BaseConfig` object provides the TOML parser and writer and interface with `pydantic`.
+2. Analysis : handled by the `Processor` objects. It is initialized with the path to a
+configuration file. The `BaseProcessor` object provides the base framework and some
+shared methods related to magnetic field computation.
+3. Store : the `Processor` objects uses the `nexusformat` library to store data
+in-memory. The whole data structure can be easily dumped to a NeXus-compliant HDF5 file,
+and can be consolidated (i.e. add sample- and experiment-related metadata) via the
+configuration file. The output NeXus file is self-contained : it has the raw and
+processed data, along with the analysis configuration. The `Processor` objects can be
+initialized with such a file instead of a configuration file.
+
+Graphical user interface
+------------------------
+pymagnetos provides graphical applications built with PyQt6. Each subpackages have a
+`gui` submodule (that are not imported by default). The `core.gui` module contains the
+base components to build an app with a configuration panel, a zone with graphs, action
+buttons and a log text box. It interfaces with a `Worker` object, which is a `Processor`
+instance set in its own thread. The components are Qt widgets that can be built upon and
+re-used.
+
+Available subpackages
+---------------------
+- `core` : base classes and components.
+- `pytdo` : a library for TDO experiments.
+- `pyuson` : a library for ultra-sound experiments.
+
+Available modules
+-----------------
+- `sp` : signal processing functions.
+- `utils` : utilities for dictionary manipulation.
+- `cli` : used to run the applications.
+"""
+
+import nexusformat.nexus as nx
+
+from . import core, pytdo, pyuson
+from .core import sp, utils
+
+__all__ = ["core", "pytdo", "pyuson", "sp", "utils"]
+
+# Configure NeXus globally
+nx.nxsetconfig(compression=None, encoding="utf-8", lock=0, memory=8000, recursive=True)

pymagnetos-0.7.6/src/pymagnetos/__main__.py

@@ -0,0 +1,5 @@
+"""Run the CLI when running as module."""
+
+if __name__ == "__main__":
+    from . import cli
+    cli.main()

pymagnetos-0.7.6/src/pymagnetos/core/__init__.py

@@ -0,0 +1,33 @@
+"""
+The core subpackage, containing base classes and components.
+
+Those are meant to be subclassed to build experiment-specific objects.
+
+Provides
+--------
+- `BaseConfig` : the base class for the `Config` object.
+- `BaseProcessor` : the base class for the `Processor` object.
+- `BaseData` : NeXus base interface.
+- `DataRaw` : NeXus interface for a raw data container.
+- `DataProcessed` : NeXus interface for a processed data container.
+- `config_models` : `pydantic` models to define the configuration.
+- `sp` : signal processing functions.
+- `utils` : dictionary manipulation utility functions.
+"""
+
+from . import config_models, utils
+from . import signal_processing as sp
+from ._baseprocessor import BaseProcessor
+from ._config import BaseConfig
+from ._data import BaseData, DataProcessed, DataRaw
+
+__all__ = [
+    "BaseConfig",
+    "BaseProcessor",
+    "BaseData",
+    "DataProcessed",
+    "DataRaw",
+    "config_models",
+    "sp",
+    "utils",
+]

pymagnetos-0.1.0/src/pymagnetos/core/_processor.py → pymagnetos-0.7.6/src/pymagnetos/core/_baseprocessor.py

@@ -255,7 +255,7 @@ class BaseProcessor:
 
         return data
 
-    def load_pickup(self):
+    def load_pickup(self) -> Self:
         """
         Load the pickup binary file, gathering metadata (if any) and the file.
 
@@ -674,7 +674,7 @@ class BaseProcessor:
             "magfield_time", checkonly=True
         ) or not self.get_data_processed("magfield", checkonly=True):
             logger.warning("The magnetic field was not computed yet.")
-            return None
+            return
 
         fig = plt.figure()
         plt.plot(

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/core/_data.py

@@ -5,7 +5,7 @@ import importlib.metadata
 import nexusformat.nexus as nx
 
 
-class DataBase(nx.NXgroup):
+class BaseData(nx.NXgroup):
     """Base Data class integrating NXgroup."""
 
     def __init__(self, attr: dict = {}, **kwargs) -> None:
@@ -30,7 +30,7 @@ class DataBase(nx.NXgroup):
             self.attrs[k] = v
 
 
-class DataRaw(DataBase):
+class DataRaw(BaseData):
     """Store raw data in a NeXus NXdata group."""
 
     def __init__(self, attr: dict = {}, **kwargs) -> None:
@@ -54,7 +54,7 @@ class DataRaw(DataBase):
         self.nxname = "data"
 
 
-class DataProcessed(DataBase):
+class DataProcessed(BaseData):
     """Store processed data in a NeXus NXprocess group."""
 
     def __init__(

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/core/config_models.py

@@ -6,7 +6,7 @@ Each model corresponds to a section in the configuration file.
 
 from typing import Any, Literal
 
-from pydantic import BaseModel, ValidationInfo, field_validator
+from pydantic import BaseModel
 
 
 class File(BaseModel):
@@ -23,17 +23,6 @@ class File(BaseModel):
     # For text file
     delimiter: str | None = None
 
-    @field_validator("precision", "endian", "order", "delimiter")
-    @classmethod
-    def disallow_none(
-        cls,
-        value: int | str | Literal["<", ">"] | Literal["C", "F"],
-        info: ValidationInfo,
-    ):
-        """Prevent setting None explicitely."""
-        assert value is not None, f"{info.field_name} can't be None"
-        return value
-
 
 class Parameters(BaseModel):
     """Parameters section, things related to the experiment itself."""

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/core/gui/__init__.py

@@ -1,6 +1,6 @@
 """Shared Graphical User Interface (GUI) components."""
 
 from . import widgets
-from ._base_mainwindow import BaseMainWindow
+from .main import BaseMainWindow
 
 __all__ = ["BaseMainWindow", "widgets"]

pymagnetos-0.1.0/src/pymagnetos/core/gui/_base_mainwindow.py → pymagnetos-0.7.6/src/pymagnetos/core/gui/main.py

@@ -795,7 +795,12 @@ class BaseMainWindow(QtWidgets.QMainWindow):
 
     def dragEnterEvent(self, a0: QtGui.QDropEvent | None = None) -> None:
         """Handle drag&drop configuration or data file."""
-        if a0.mimeData().hasText():
+        if a0 is None:
+            return
+        mime_data = a0.mimeData()
+        if mime_data is None:
+            return
+        if mime_data.hasText():
             a0.accept()
         else:
             a0.ignore()
@@ -806,7 +811,12 @@ class BaseMainWindow(QtWidgets.QMainWindow):
 
         This triggers the `load_file()` method.
         """
-        for url in a0.mimeData().urls():
+        if a0 is None:
+            return
+        mime_data = a0.mimeData()
+        if mime_data is None:
+            return
+        for url in mime_data.urls():
             file_path = url.toLocalFile()
             if file_path.endswith(ALLOWED_FORMAT):
                 self.wconfiguration.files_parameters["file"] = file_path

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/core/gui/widgets/_graphs.py

@@ -36,18 +36,20 @@ class BaseGraphsWidget(QtWidgets.QWidget):
         """Set and store QPen for styling of curves and ROIs."""
         raise NotImplementedError("Subclass must implement this method.")
 
-    def event(self, ev: QEvent) -> bool:
+    def event(self, a0: QEvent | None = None) -> bool:
         """Handle mouse selection while holding CTRL to make a ROI zoom in plots."""
         # Switch to rectangular zoom selection on the first Ctrl key press event
-        if ev.type() == QKeyEvent.Type.KeyPress and ev.key() == Qt.Key.Key_Control:
+        if a0 is None:
+            return False
+        if a0.type() == QKeyEvent.Type.KeyPress and a0.key() == Qt.Key.Key_Control:  # ty:ignore[unresolved-attribute]
             if self._mouse_pan_mode:
                 self.switch_mouse_pan_mode(False)
 
         # Switch back to pan mode on left click when releasing the Ctrl key
-        if ev.type() == QKeyEvent.Type.KeyRelease and ev.key() == Qt.Key.Key_Control:
+        if a0.type() == QKeyEvent.Type.KeyRelease and a0.key() == Qt.Key.Key_Control:  # ty:ignore[unresolved-attribute]
             self.switch_mouse_pan_mode(True)
 
-        return super().event(ev)
+        return super().event(a0)
 
     def switch_mouse_pan_mode(self, state: bool) -> None:
         """

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/core/signal_processing.py

@@ -1,4 +1,4 @@
-"""pyqtSignal processing module."""
+"""Signal processing module."""
 
 import warnings
 from collections.abc import Callable, Iterable
@@ -889,7 +889,7 @@ def fit_poly(
         Magnetic field vector (x).
     sig : np.ndarray
         pyqtSignal vector (y).
-    poly_boundary1, poly_boundary2 : float
+    boundary1, boundary2 : float
         Do the fit only in `field` comprised in `[poly_boundary1, poly_boundary2]`.
     poly_deg : int
         Polynome degree.

pymagnetos-0.7.6/src/pymagnetos/pytdo/__init__.py

@@ -0,0 +1,16 @@
+"""
+The `pytdo` subpackage, a library for TDO experiments.
+
+Provides
+--------
+- `TDOConfig` : The `Config` object specific to TDO experiments.
+- `TDOProcessor` : the `Processor` object specific to TDO experiments.
+- `config_models` : the `pydantic` models to define the configuration requirements.
+- `gui` : a graphical application. It needs to be imported explicitely.
+"""
+
+from . import config_models
+from ._config import TDOConfig
+from ._tdoprocessor import TDOProcessor
+
+__all__ = ["TDOConfig", "TDOProcessor", "config_models"]

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/pytdo/_config.py

@@ -1,8 +1,10 @@
+"""Config class for the TDOProcessor object."""
+
 from pathlib import Path
 from typing import Any
 
 from ..core import BaseConfig
-from ._config_models import TDOConfiguration
+from .config_models import TDOConfiguration
 
 CONFIG_DEFAULT = Path(__file__).parent / "assets" / "config_default.toml"
 

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/pytdo/_tdoprocessor.py

@@ -228,7 +228,7 @@ class TDOProcessor(BaseProcessor):
         where: Literal["raw", "processed"] = "raw",
         force: bool = False,
         append: str = "_full",
-    ):
+    ) -> None:
         """
         Crop a 1D vector from `start` to `stop`.
 
@@ -656,7 +656,7 @@ class TDOProcessor(BaseProcessor):
 
         return self
 
-    def _remove_data_changed(self):
+    def _remove_data_changed(self) -> None:
         """Remove data that was computed but the data it relied on changed."""
         self.remove_data_processed(self._tdo_name + "_fit_inc")
         self.remove_data_processed(self._tdo_name + "_fit_dec")
@@ -669,7 +669,7 @@ class TDOProcessor(BaseProcessor):
         self.remove_data_processed("fft_inc")
         self.remove_data_processed("fft_dec")
 
-    def _get_result_names_list(self, ud: Literal["inc", "dec"]):
+    def _get_result_names_list(self, ud: Literal["inc", "dec"]) -> list[str]:
         """
         Generate the list of things to save.
 
@@ -755,31 +755,53 @@ class TDOProcessor(BaseProcessor):
 
         return self
 
-    def load_csv(self, filepath: Path | str, sep: str | None = None):
+    def load_csv(self, filepath: Path | str, sep: str | None = None) -> Self:
         """Load data from a CSV file."""
         filepath = Path(filepath)
         if not filepath.is_file():
             logger.error("File does not exist")
-            return
+            return self
 
         reader, delimiter = self._determine_file_format(filepath, sep=sep)
 
         if isinstance(reader, str) and reader == "unknown":
             logger.error(f"Could not load input file ({filepath})")
-            return
+            return self
 
         logger.info(f"Reading data from {filepath.name}...")
         self._reinit()
         status = reader(filepath, delimiter)
         if not status:
             logger.error(f"Failed to read {filepath.name}, check messages above")
-            return
+            return self
 
         # Get the up / down indices
         self.get_up_down_indices()
 
         logger.info(f"Read data from {filepath.name}.")
 
+        return self
+
+    def load(self, filename: str | Path | None) -> Self:
+        """
+        Load a previously saved NeXus file.
+
+        Use `BaseProcessor.save()` method, with additionnal steps : guess the internal
+        flags and add convenience attributes. The returned `TDOProcessor` object can be
+        used to resume analysis where it was left off.
+
+        Parameters
+        ----------
+        filename : str
+            Full path to the file to load.
+        """
+        super().load(filename)
+
+        # Find increasing/decreasing magnetic field indices
+        self.get_up_down_indices()
+
+        return self
+
     def _determine_file_format(
         self, filepath: Path, sep: str | None = None
     ) -> tuple[Callable[[Path, str], bool] | str, str]:
@@ -991,7 +1013,7 @@ class TDOProcessor(BaseProcessor):
             "fft_" + kw: extract_col(10),
         }
 
-    def _set_map_in_data_processed(self, data: dict[str, np.ndarray]):
+    def _set_map_in_data_processed(self, data: dict[str, np.ndarray]) -> None:
         """Set data in `data_processed`."""
         for key, value in data.items():
             self.set_data_processed(key, value)
@@ -1044,7 +1066,7 @@ class TDOProcessor(BaseProcessor):
             self._tdo_inv_inc_name, checkonly=True
         ) and self.get_data_processed(self._tdo_inv_dec_name, checkonly=True)
 
-    def _reinit(self):
+    def _reinit(self) -> None:
         """Clear data and initialize objects."""
         super()._reinit()
 

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/pytdo/gui/__init__.py

@@ -2,8 +2,11 @@
 
 from PyQt6 import QtWidgets
 
+from . import widgets
 from .main import MainWindow
 
+__all__ = ["MainWindow", "run", "widgets"]
+
 
 def run(exec: bool = True) -> None | MainWindow:
     """
@@ -23,4 +26,4 @@ def run(exec: bool = True) -> None | MainWindow:
     if exec:
         app.exec()
     else:
-        return win
+        return win

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/pytdo/gui/main.py

@@ -9,8 +9,8 @@ from PyQt6.QtCore import pyqtSignal, pyqtSlot
 from pymagnetos.core.gui import BaseMainWindow
 from pymagnetos.core.gui.widgets import BatchProcessingWidget, FileBrowserWidget
 
-from . import widgets
-from ._worker import DataWorker
+from .widgets import ButtonsWidget, ConfigurationWidget, GraphsWidget, ParamContent
+from .worker import DataWorker
 
 ICON_PATH = str(Path(__file__).parent / "assets" / "icon.png")
 REGEXP_EXPID_SEPARATORS = r"[_-]"
@@ -46,11 +46,11 @@ class MainWindow(BaseMainWindow):
     def __init__(self):
         # Register the widgets
         self._type_wbatch = BatchProcessingWidget
-        self._type_wbuttons = widgets.ButtonsWidget
-        self._type_wconfiguration = widgets.ConfigurationWidget
+        self._type_wbuttons = ButtonsWidget
+        self._type_wconfiguration = ConfigurationWidget
         self._type_wfiles = FileBrowserWidget
-        self._type_wgraphs = widgets.GraphsWidget
-        self._param_content = widgets.ParamContent
+        self._type_wgraphs = GraphsWidget
+        self._param_content = ParamContent
         self._type_worker = DataWorker
 
         super().__init__()
@@ -608,7 +608,12 @@ class MainWindow(BaseMainWindow):
 
     def dropEvent(self, a0: QtGui.QDropEvent | None = None) -> None:
         """Load a file when it is dropped in the main window."""
-        for url in a0.mimeData().urls():
+        if a0 is None:
+            return
+        mime_data = a0.mimeData()
+        if mime_data is None:
+            return
+        for url in mime_data.urls():
             file_path = url.toLocalFile()
             if file_path.endswith(OUT_FORMAT):
                 self.load_csv_file(file_path)

pymagnetos-0.1.0/src/pymagnetos/pytdo/gui/_worker.py → pymagnetos-0.7.6/src/pymagnetos/pytdo/gui/worker.py

@@ -69,6 +69,7 @@ class DataWorker(QObject):
         self.sig_offset_finished.emit()
 
     def align_field(self):
+        """Align magnetic field on signal."""
         self.proc.align_field()
         self.sig_align_finished.emit()
 
@@ -80,6 +81,7 @@ class DataWorker(QObject):
 
     @pyqtSlot()
     def batch_process(self):
+        """Not implemented, for compatiblity."""
         return
 
     @pyqtSlot(str)
@@ -102,5 +104,6 @@ class DataWorker(QObject):
 
     @pyqtSlot(str)
     def load_csv_file(self, fname: str):
+        """Save data as CSV file."""
         self.proc.load_csv(fname)
         self.sig_load_csv_finished.emit()

pymagnetos-0.7.6/src/pymagnetos/pyuson/__init__.py

@@ -0,0 +1,16 @@
+"""
+The `pyuson` subpackage, a library for ultra-sound echoes experiments.
+
+Provides
+--------
+- `EchoConfig` : The `Config` object specific to ultra-sound experiments.
+- `EchoProcessor` : the `Processor` object specific to ultra-sound experiments.
+- `config_models` : the `pydantic` models to define the configuration requirements.
+- `gui` : a graphical application. It needs to be imported explicitely.
+"""
+
+from . import config_models
+from ._config import EchoConfig
+from ._echoprocessor import EchoProcessor
+
+__all__ = ["EchoConfig", "EchoProcessor", "config_models"]

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/pyuson/_config.py

@@ -4,7 +4,7 @@ from pathlib import Path
 from typing import Any
 
 from ..core import BaseConfig
-from ._config_models import EchoConfigurationModel
+from .config_models import EchoConfigurationModel
 
 CONFIG_DEFAULT = Path(__file__).parent / "assets" / "config_default.toml"
 

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/pyuson/_echoprocessor.py

@@ -183,7 +183,7 @@ class EchoProcessor(BaseProcessor):
         """
         self.cfg.settings.analysis_window = value
 
-    def _init_flags(self):
+    def _init_flags(self) -> None:
         """Set up flags."""
         # Tektronix WFM files or LabVIEW binary file
         self.is_wfm = False
@@ -204,7 +204,7 @@ class EchoProcessor(BaseProcessor):
         # Moving mean was performed, if it was, use the smoothed data in data_processed
         self.is_rollmean = {m: False for m in self.measurements}
 
-    def _guess_flags(self):
+    def _guess_flags(self) -> None:
         """Attempt to guess flags from data after loading a NeXus file."""
         self.is_wfm = None  # no files so irrelevant
         self.is_us = self._check_measurement_time_us()
@@ -223,7 +223,7 @@ class EchoProcessor(BaseProcessor):
         self.is_decimated = self._check_time_subsampled()
         self.is_rollmean = self._check_rollmean()
 
-    def _init_digital(self):
+    def _init_digital(self) -> None:
         """Additional initializations for digital mode."""
         # Prepare internal names
         self._ref_name = REFNAME
@@ -249,7 +249,7 @@ class EchoProcessor(BaseProcessor):
         self.is_rollmean = {m: False for m in self.measurements}  # the keys changed
         self.is_meas_processed = True
 
-    def _reinit(self):
+    def _reinit(self) -> None:
         """Re-initialize data objects."""
         super()._reinit()
         if self.is_digital:
@@ -534,7 +534,7 @@ class EchoProcessor(BaseProcessor):
 
         return self
 
-    def _update_time_subsampled(self, new_npoints: int):
+    def _update_time_subsampled(self, new_npoints: int) -> None:
         """
         Update time vector if subsampling was used.
 
@@ -1158,7 +1158,7 @@ class EchoProcessor(BaseProcessor):
         """Alias for the `average_frame_range()` method."""
         return self.average_frame_range(**kwargs)
 
-    def _compute_amplitude_avg(self):
+    def _compute_amplitude_avg(self) -> None:
         """
         Compute amplitude from averaged I and Q.
 
@@ -1239,7 +1239,7 @@ class EchoProcessor(BaseProcessor):
             self.is_averaged = True
         return
 
-    def compute_phase_avg(self):
+    def compute_phase_avg(self) -> Self:
         """Compute phase from I and Q and correct for pi jumps."""
         # Get names
         iname = self._i_name + "_avg"
@@ -1264,6 +1264,8 @@ class EchoProcessor(BaseProcessor):
         # Mark for success
         self.is_averaged = True
 
+        return self
+
     def compute_attenuation(self) -> Self:
         """
         Compute attenuation from amplitude average for the current echo.
@@ -1305,7 +1307,7 @@ class EchoProcessor(BaseProcessor):
 
         return self
 
-    def compute_phase_shift(self):
+    def compute_phase_shift(self) -> Self:
         """
         Compute relative phase shift given the phase average for the current echo.
 
@@ -1602,7 +1604,7 @@ class EchoProcessor(BaseProcessor):
 
     def to_csv(
         self, fname: None | str | Path = None, sep: str = "\t", to_cm: bool = False
-    ):
+    ) -> None:
         r"""
         Export attenuation and phase shift data as a CSV file.
 
@@ -1780,7 +1782,7 @@ class EchoProcessor(BaseProcessor):
                 is_rollmean[meas] = False
         return is_rollmean
 
-    def _check_time_subsampled(self):
+    def _check_time_subsampled(self) -> bool:
         """
         Check if measurement time vector was subsampled.
 

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/pyuson/gui/__init__.py

@@ -2,8 +2,11 @@
 
 from PyQt6 import QtWidgets
 
+from . import widgets
 from .main import MainWindow
 
+__all__ = ["MainWindow", "run", "widgets"]
+
 
 def run(exec: bool = True) -> None | MainWindow:
     """

{pymagnetos-0.1.0 → pymagnetos-0.7.6}/src/pymagnetos/pyuson/gui/main.py

@@ -15,8 +15,8 @@ from PyQt6.QtCore import pyqtSignal, pyqtSlot
 from pymagnetos import sp
 from pymagnetos.core.gui import BaseMainWindow, widgets
 
-from ._worker import ProcessorWorker
 from .widgets import ButtonsWidget, ConfigurationWidget, GraphsWidget, ParamContent
+from .worker import ProcessorWorker
 
 ICON_PATH = str(Path(__file__).parent / "assets" / "icon.png")
 REGEXP_EXPID_SEPARATORS = r"[_-]"

pymagnetos-0.1.0/PKG-INFO

@@ -1,23 +0,0 @@
-Metadata-Version: 2.3
-Name: pymagnetos
-Version: 0.1.0
-Summary: Applications for high magnetic field analysis
-Author: Guillaume Le Goc
-Author-email: Guillaume Le Goc <guillaume.le-goc@lncmi.cnrs.fr>
-License: MIT
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Programming Language :: Python :: 3.14
-Requires-Dist: fftekwfm>=0.3.0.1
-Requires-Dist: matplotlib>=3.10.8
-Requires-Dist: nexusformat>=2.0.0
-Requires-Dist: numpy>=2.4.1
-Requires-Dist: pydantic>=2.12.5
-Requires-Dist: pyqt6>=6.10.2
-Requires-Dist: pyqtgraph>=0.14.0
-Requires-Dist: rich>=14.3.1
-Requires-Dist: scipy>=1.17.0
-Requires-Dist: tomlkit>=0.14.0
-Requires-Python: >=3.13
-Project-URL: Source Code, https://gitlab.in2p3.fr/himagnetos/pymagnetos
-Description-Content-Type: text/markdown
-

pymagnetos-0.1.0/src/pymagnetos/__init__.py

@@ -1,15 +0,0 @@
-"""
-The pymagnetos package.
-
-It provides analysis tools for high magnetic field experiments.
-"""
-
-import nexusformat.nexus as nx
-
-from . import core, pytdo, pyuson
-from .core import sp, utils
-
-__all__ = ["core", "pytdo", "pyuson", "sp", "utils"]
-
-# Configure NeXus globally
-nx.nxsetconfig(compression=None, encoding="utf-8", lock=0, memory=8000, recursive=True)

pymagnetos-0.1.0/src/pymagnetos/core/__init__.py

@@ -1,19 +0,0 @@
-"""The core module, containing base classes and components."""
-
-from . import config_models, gui, utils
-from . import signal_processing as sp
-from ._config import BaseConfig
-from ._data import DataBase, DataProcessed, DataRaw
-from ._processor import BaseProcessor
-
-__all__ = [
-    "BaseConfig",
-    "BaseProcessor",
-    "DataBase",
-    "DataProcessed",
-    "DataRaw",
-    "config_models",
-    "gui",
-    "sp",
-    "utils",
-]

pymagnetos-0.1.0/src/pymagnetos/pytdo/__init__.py

@@ -1,6 +0,0 @@
-"""The `pytdo` module, an app for TDO experiments."""
-
-from ._config import TDOConfig
-from ._tdoprocessor import TDOProcessor
-
-__all__ = ["TDOConfig", "TDOProcessor"]

pymagnetos-0.1.0/src/pymagnetos/pyuson/__init__.py

@@ -1,7 +0,0 @@
-"""The `pyuson` module, an app for ultra-sound echoes experiments."""
-
-from .. import core as core
-from ._config import EchoConfig
-from ._echoprocessor import EchoProcessor
-
-__all__ = ["EchoConfig", "EchoProcessor"]