pumpia 0.1.0__tar.gz

pumpia-0.1.0/.github/workflows/main.yml

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+name: documentation
+
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v4
+        - uses: actions/setup-python@v5
+          with:
+            python-version: '3.12'
+        - name: Install pumpia dependencies
+          run: |
+            pip install -r requirements.txt
+        - name: Install dependencies
+          run: |
+            pip install sphinx sphinx_rtd_theme
+        - name: Sphinx build
+          run: |
+            sphinx-build docs/source docs/_build
+        - name: Deploy to GitHub Pages
+          uses: peaceiris/actions-gh-pages@v4
+          with:
+            publish_branch: gh-pages
+            github_token: ${{ secrets.GITHUB_TOKEN }}
+            publish_dir: docs/_build
+            force_orphan: true

pumpia-0.1.0/.github/workflows/publish.yml

@@ -0,0 +1,32 @@
+name: Upload Python Package
+
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

pumpia-0.1.0/.gitignore

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+# Editor temporary/working/backup files #
+#########################################
+.#*
+[#]*#
+*~
+*$
+*.bak
+*.diff
+.idea/
+*.iml
+*.ipr
+*.iws
+*.org
+.project
+pmip
+*.rej
+.settings/
+.*.sw[nop]
+.sw[nop]
+*.tmp
+*.vim
+.vscode
+tags
+cscope.out
+# gnu global
+GPATH
+GRTAGS
+GSYMS
+GTAGS
+.cache
+.mypy_cache/
+
+# Compiled source #
+###################
+*.a
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.o.d
+*.py[ocd]
+*.so
+*.mod
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.bz2
+*.bzip2
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.tbz2
+*.tgz
+*.zip
+
+# Python files #
+################
+# meson build/installation directories
+build
+build-install
+# meson python output
+.mesonpy-native-file.ini
+# sphinx build directory
+_build
+# dist directory is where sdist/wheel end up
+dist
+doc/build
+doc/docenv
+doc/cdoc/build
+# Egg metadata
+*.egg-info
+# The shelf plugin uses this dir
+./.shelf
+.cache
+pip-wheel-metadata
+.python-version
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# Patches #
+###########
+*.patch
+*.diff
+
+# OS generated files #
+######################
+.DS_Store*
+.VolumeIcon.icns
+.fseventsd
+Icon?
+.gdb_history
+ehthumbs.db
+Thumbs.db
+.directory
+
+# pytest generated files #
+##########################
+/.pytest_cache
+
+# doc build generated files #
+#############################
+doc/source/savefig/
+doc/source/**/generated/
+doc/source/release/notes-towncrier.rst
+doc/source/.jupyterlite.doit.db

pumpia-0.1.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2025, Zack Ravetz
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

pumpia-0.1.0/PKG-INFO

@@ -0,0 +1,52 @@
+Metadata-Version: 2.4
+Name: pumpia
+Version: 0.1.0
+Summary: A simple to use framework for making user interfaces for image analysis.
+Project-URL: Homepage, https://github.com/Principle-Five/PumpIA
+Project-URL: Source, https://github.com/Principle-Five/PumpIA
+Project-URL: Issues, https://github.com/Principle-Five/PumpIA/issues
+Author: Zack Ravetz et al.
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Software Development
+Requires-Python: >=3.12
+Requires-Dist: matplotlib==3.*
+Requires-Dist: numpy==2.*
+Requires-Dist: pillow==11.*
+Requires-Dist: pydicom==3.*
+Requires-Dist: scipy==1.*
+Description-Content-Type: text/markdown
+
+Introduction
+------------
+
+PumpIA is a python framework designed to allow users to visualise the analysis of images through a user interface.
+It does not do any image analysis itself, but rather provides a platform for users to write their own analysis code and view the results.
+This means that the full power of python and its libraries are available to the user.
+
+Requirements
+------------
+PumpIA has been designed to use the minimum number of dependencies, so the user interface relies on tkinter.
+PumpIA has the following dependencies:
+
+* numpy
+* scipy
+* pillow
+* pydicom
+* matplotlib
+
+Installation
+------------
+
+PumpIA requires python 3.12 or greater.
+To use PumpIA, install it using pip:
+
+    pip install pumpia

pumpia-0.1.0/README.md

@@ -0,0 +1,25 @@
+Introduction
+------------
+
+PumpIA is a python framework designed to allow users to visualise the analysis of images through a user interface.
+It does not do any image analysis itself, but rather provides a platform for users to write their own analysis code and view the results.
+This means that the full power of python and its libraries are available to the user.
+
+Requirements
+------------
+PumpIA has been designed to use the minimum number of dependencies, so the user interface relies on tkinter.
+PumpIA has the following dependencies:
+
+* numpy
+* scipy
+* pillow
+* pydicom
+* matplotlib
+
+Installation
+------------
+
+PumpIA requires python 3.12 or greater.
+To use PumpIA, install it using pip:
+
+    pip install pumpia

pumpia-0.1.0/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

pumpia-0.1.0/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

pumpia-0.1.0/docs/source/components/components.rst

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+Core Components
+===============
+
+Most people will want to use PumpIA through the :doc:`modules </usage/modules>` and :doc:`collections </usage/collections>` as described in :doc:`usage </usage/usage>`,
+however the core components and how they iteract are described for anyone who wants more control over them, or who wants to embed them in their own program.
+
+:doc:`manager`
+--------------
+This is the central piece of the program, it controls the loading of all images and links all the other components together.
+Use the manager to get the treeviews and widgets for the controls within the program.
+Users can right click on different entries in treeviews for different options.
+There is typically only one manager per program.
+
+:doc:`viewers`
+--------------
+These are the widgets which show the images.
+There are a few different kinds depending on if the image loaded should be limited.
+Viewers have multiple shortcuts to make it easier for the end user.
+
+:doc:`images`
+-------------
+Different classes which represent images and collections of images.
+Also see :doc:`file handling </file_handling/file_handling>`.
+
+:doc:`rois`
+-----------
+These represent regions of interest of different shapes.
+
+Contents
+--------
+.. toctree::
+    manager
+    viewers
+    images
+    rois

pumpia-0.1.0/docs/source/components/images.rst

@@ -0,0 +1,10 @@
+Images
+======
+
+.. autoclass:: pumpia.image_handling.image_structures.BaseImageSet
+
+.. autoclass:: pumpia.image_handling.image_structures.ArrayImage
+
+.. autoclass:: pumpia.image_handling.image_structures.FileImageSet
+
+.. autoclass:: pumpia.image_handling.image_structures.ImageCollection

pumpia-0.1.0/docs/source/components/manager.rst

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+The Manager
+===========
+
+.. autoclass:: pumpia.module_handling.manager.Manager

pumpia-0.1.0/docs/source/components/rois.rst

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+Regions of Interest
+-------------------
+
+.. autoclass:: pumpia.image_handling.roi_structures.BaseROI
+
+.. autoclass:: pumpia.image_handling.roi_structures.Angle
+
+.. autoclass:: pumpia.image_handling.roi_structures.PointROI
+
+.. autoclass:: pumpia.image_handling.roi_structures.EllipseROI
+
+.. autoclass:: pumpia.image_handling.roi_structures.RectangleROI
+
+.. autoclass:: pumpia.image_handling.roi_structures.LineROI

pumpia-0.1.0/docs/source/components/viewers.rst

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+Viewers
+=======
+
+.. autoclass:: pumpia.widgets.viewers.BaseViewer
+
+.. autoclass:: pumpia.widgets.viewers.Viewer
+
+.. autoclass:: pumpia.widgets.viewers.ArrayViewer
+
+.. autoclass:: pumpia.widgets.viewers.MonochromeViewer
+
+.. autoclass:: pumpia.widgets.viewers.DicomViewer
+
+.. autoclass:: pumpia.widgets.viewers.MonochromeDicomViewer

pumpia-0.1.0/docs/source/conf.py

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+import sys
+from pathlib import Path
+
+sys.path.insert(0, str(Path(__file__).resolve().parent.parent.parent))
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'PumpIA'
+copyright = '2025, Zack Ravetz'
+author = 'Zack Ravetz'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.coverage', 'sphinx.ext.napoleon', 'sphinx.ext.autosectionlabel']
+coverage_modules = ("pumpia",)
+templates_path = ['_templates']
+exclude_patterns = []
+autosectionlabel_prefix_document = True
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']

pumpia-0.1.0/docs/source/file_handling/dicom_tags.rst

@@ -0,0 +1,10 @@
+DICOM Tags
+==========
+
+.. autofunction:: pumpia.file_handling.dicom_tags.get_tag
+
+.. autoclass:: pumpia.file_handling.dicom_tags.Tag
+
+.. autoclass:: pumpia.file_handling.dicom_tags.DicomTags
+
+.. autoclass:: pumpia.file_handling.dicom_tags.MRTags

pumpia-0.1.0/docs/source/file_handling/dicoms.rst

@@ -0,0 +1,10 @@
+DICOM File Handling
+===================
+
+.. autoclass:: pumpia.file_handling.dicom_structures.Patient
+
+.. autoclass:: pumpia.file_handling.dicom_structures.Study
+
+.. autoclass:: pumpia.file_handling.dicom_structures.Series
+
+.. autoclass:: pumpia.file_handling.dicom_structures.Instance

pumpia-0.1.0/docs/source/file_handling/file_handling.rst

@@ -0,0 +1,29 @@
+File Handling
+=============
+
+The :doc:`manager </components/manager>` is used to handle files and make sure all components have access to the loaded ones.
+
+:doc:`dicoms`
+-------------
+Loaded DICOMS can be accessed through the ``patients`` attribute of the manager.
+This provides a set of all patients loaded from DICOM files.
+
+Four classes are used to group and handle DICOM files:
+
+    * Patient
+    * Study
+    * Series
+    * Instance
+
+The DICOM file path and pydicom Dataset can be accessed through either `Series` or `Instance`.
+For `Series` these will be for the current instance defined by the ``current_slice`` attribute.
+
+:doc:`dicom_tags`
+-----------------
+DICOM tag handling is different to pydicom to allow for the handling of classic and enhanced DICOM files.
+
+Contents
+--------
+.. toctree::
+    dicoms
+    dicom_tags

pumpia-0.1.0/docs/source/index.rst

@@ -0,0 +1,46 @@
+PumpIA documentation
+====================
+
+Introduction
+------------
+
+PumpIA is a python framework designed to allow users to visualise the analysis of images through a user interface.
+It does not do any image analysis itself, but rather provides a platform for users to write their own analysis code and view the results.
+This means that the full power of python and its libraries are available to the user.
+
+Requirements
+------------
+PumpIA has been designed to use the minimum number of dependencies, so the user interface relies on `tkinter <https://docs.python.org/3/library/tkinter.html>`_.
+PumpIA has the following dependencies:
+
+* `numpy <https://numpy.org/>`_
+* `scipy <https://scipy.org/>`_
+* `pillow <https://pillow.readthedocs.io/en/stable/>`_
+* `pydicom <https://pydicom.github.io/pydicom/stable/>`_
+* `matplotlib <https://matplotlib.org/>`_
+
+See `pydicom: Compression of Pixel Data <https://pydicom.github.io/pydicom/stable/tutorials/pixel_data/compressing.html#compression-of-pixel-data>`_ for information on how to install the required libraries for reading compressed dicom files.
+
+Installation
+------------
+
+PumpIA requires `python <https://www.python.org>`_ 3.12 or greater.
+To use PumpIA, install it using pip:
+
+.. code-block:: console
+
+   (.venv) $ pip install pumpia
+
+Contents
+--------
+
+.. toctree::
+   :includehidden:
+   :titlesonly:
+   :maxdepth: 2
+
+   components/components
+   usage/usage
+   file_handling/file_handling
+   utilities/utilities
+   widgets/widgets

pumpia-0.1.0/docs/source/usage/collections.rst

@@ -0,0 +1,7 @@
+Collections
+===========
+.. autoclass:: pumpia.module_handling.module_collections.OutputFrame
+
+.. autoclass:: pumpia.module_handling.module_collections.WindowGroup
+
+.. autoclass:: pumpia.module_handling.module_collections.BaseCollection

pumpia-0.1.0/docs/source/usage/context.rst

@@ -0,0 +1,35 @@
+Context
+=======
+.. autoclass:: pumpia.module_handling.context.BaseContext
+
+.. autoclass:: pumpia.module_handling.context.PhantomContext
+
+.. autoclass:: pumpia.module_handling.context.BoundBoxContext
+
+.. autoclass:: pumpia.module_handling.context.SimpleContext
+
+Context Managers
+----------------
+
+.. autoclass:: pumpia.widgets.context_managers.BaseContextManager
+
+.. autoclass:: pumpia.widgets.context_managers.SimpleContextManager
+
+.. autoclass:: pumpia.widgets.context_managers.PhantomContextManager
+
+.. autoclass:: pumpia.widgets.context_managers.ManualPhantomManager
+
+.. autoclass:: pumpia.widgets.context_managers.AutoPhantomManager
+
+Context Manager Generators
+--------------------------
+
+.. autoclass:: pumpia.widgets.context_managers.BaseContextManagerGenerator
+
+.. autoclass:: pumpia.widgets.context_managers.SimpleContextManagerGenerator
+
+.. autoclass:: pumpia.widgets.context_managers.PhantomContextManagerGenerator
+
+.. autoclass:: pumpia.widgets.context_managers.ManualPhantomManagerGenerator
+
+.. autoclass:: pumpia.widgets.context_managers.AutoPhantomManagerGenerator