ptychodus 1.0__tar.gz

ptychodus-1.0/.git_archival.txt

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+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true)$
+ref-names: $Format:%D$

ptychodus-1.0/.gitattributes

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+.git_archival.txt  export-subst

ptychodus-1.0/.github/workflows/python-package.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install with minimal dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install .
+    - name: Test CLI with headless minimal install
+      run: |
+        ptychodus --version

ptychodus-1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+.aider*

ptychodus-1.0/Dockerfile

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+#FROM python:3.12-slim-bullseye
+FROM pytorch/pytorch:2.7.0-cuda12.6-cudnn9-runtime
+
+# Set the working directory in the container
+WORKDIR /app
+
+# Copy the sources
+COPY . /src
+
+# Install & upgrade software
+RUN apt-get update && \
+    apt-get install -y git libqt5gui5 && \
+    rm -rf /var/lib/apt/lists/* && \
+    python3 -m pip install --root-user-action=ignore --no-cache-dir --upgrade pip && \
+    python3 -m pip install --root-user-action=ignore --no-cache-dir /src[globus,gui,ptychi] && \
+    rm -rf /src
+
+# Run ptychodus when the container launches
+#ENV QT_DEBUG_PLUGINS=1
+CMD ["python3", "-m", "ptychodus"]

ptychodus-1.0/LICENSE

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+Copyright (c) 2024, UChicago Argonne, LLC. All rights reserved.
+
+Copyright 2024. UChicago Argonne, LLC. This software was produced
+under U.S. Government contract DE-AC02-06CH11357 for Argonne National
+Laboratory (ANL), which is operated by UChicago Argonne, LLC for the
+U.S. Department of Energy. The U.S. Government has rights to use,
+reproduce, and distribute this software.  NEITHER THE GOVERNMENT NOR
+UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR
+ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE.  If software is
+modified to produce derivative works, such modified software should
+be clearly marked, so as not to confuse it with the version available
+from ANL.
+
+Additionally, redistribution and use in source and binary forms, with
+or without modification, are permitted provided that the following
+conditions are met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+
+    * 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.
+
+    * Neither the name of UChicago Argonne, LLC, Argonne National
+      Laboratory, ANL, the U.S. Government, 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 UChicago Argonne, LLC 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 UChicago
+Argonne, LLC 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.

ptychodus-1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ptychodus
+Version: 1.0
+Summary: Ptychodus is a ptychography data analysis application.
+License: Copyright (c) 2024, UChicago Argonne, LLC. All rights reserved.
+        
+        Copyright 2024. UChicago Argonne, LLC. This software was produced
+        under U.S. Government contract DE-AC02-06CH11357 for Argonne National
+        Laboratory (ANL), which is operated by UChicago Argonne, LLC for the
+        U.S. Department of Energy. The U.S. Government has rights to use,
+        reproduce, and distribute this software.  NEITHER THE GOVERNMENT NOR
+        UChicago Argonne, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR
+        ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE.  If software is
+        modified to produce derivative works, such modified software should
+        be clearly marked, so as not to confuse it with the version available
+        from ANL.
+        
+        Additionally, redistribution and use in source and binary forms, with
+        or without modification, are permitted provided that the following
+        conditions are met:
+        
+            * Redistributions of source code must retain the above copyright
+              notice, this list of conditions and the following disclaimer.
+        
+            * 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.
+        
+            * Neither the name of UChicago Argonne, LLC, Argonne National
+              Laboratory, ANL, the U.S. Government, 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 UChicago Argonne, LLC 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 UChicago
+        Argonne, LLC 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.
+        
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: h5py>=3
+Requires-Dist: hdf5plugin
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: psutil
+Requires-Dist: requests
+Requires-Dist: scikit-image
+Requires-Dist: scipy
+Requires-Dist: tables
+Requires-Dist: tifffile
+Requires-Dist: watchdog
+Provides-Extra: globus
+Requires-Dist: gladier; extra == "globus"
+Requires-Dist: gladier-tools>=0.5.4; extra == "globus"
+Provides-Extra: gui
+Requires-Dist: PyQt5; extra == "gui"
+Provides-Extra: ptychonn
+Requires-Dist: ptychonn==0.3.*,>=0.3.7; extra == "ptychonn"
+Provides-Extra: tike
+Requires-Dist: tike==0.25.*,>=0.25.3; extra == "tike"
+Provides-Extra: ptychi
+Requires-Dist: ptychi==1.*; extra == "ptychi"
+Dynamic: license-file
+
+Ptychodus
+=========
+
+`ptychodus`_ is a ptychography analysis application that supports multiple reconstruction libraries.
+
+
+Standard Installation
+---------------------
+
+1. Install `miniforge <https://github.com/conda-forge/miniforge>`_.
+
+2. Install ptychodus.
+
+   * To install `ptychodus` with the GUI and all optional packages:
+
+     .. code-block:: shell
+
+           $ conda create -c conda-forge -n ptychodus ptychodus-all
+
+   * To install `ptychodus` with the GUI and no optional packages:
+
+     .. code-block:: shell
+
+           $ conda create -c conda-forge -n ptychodus ptychodus
+
+   * To install `ptychodus` without the GUI or optional packages:
+
+     .. code-block:: shell
+
+           $ conda create -c conda-forge -n ptychodus ptychodus-core
+
+3. Activate the `ptychodus` conda environment to run ptychodus.
+
+   .. code-block:: shell
+
+       $ conda activate ptychodus
+       $ ptychodus -h
+
+       usage: ptychodus [-h] [-b {reconstruct,train}] [-f FILE_PREFIX] [-s SETTINGS_FILE] [-v] [-w OUTPUT_DIR]
+
+       ptychodus is a ptychography analysis application
+
+       options:
+         -h, --help            show this help message and exit
+         -b {reconstruct,train}, --batch {reconstruct,train}
+                               run action non-interactively
+         -f FILE_PREFIX, --file-prefix FILE_PREFIX
+                               replace file path prefix in settings
+         -s SETTINGS_FILE, --settings SETTINGS_FILE
+                               use settings from file
+         -v, --version         show program's version number and exit
+         -w OUTPUT_DIR, --write OUTPUT_DIR
+                               stage reconstruction inputs to directory
+
+       $ ptychodus
+
+
+Developer Installation
+----------------------
+
+* For a developer installation:
+
+.. code-block:: shell
+
+   $ git clone https://github.com/AdvancedPhotonSource/ptychodus.git
+   $ conda create -c conda-forge -n ptychodus --file ptychodus/requirements-dev.txt
+   $ conda activate ptychodus
+   $ pip install -e ./ptychodus
+
+* To install the `pty-chi`_ backend:
+
+.. code-block:: shell
+
+   $ pip install ptychi
+
+* To install the `PtychoNN`_ backend:
+
+.. code-block:: shell
+
+   $ conda install -n ptychodus -c conda-forge ptychonn
+
+* Launch `ptychodus`:
+
+.. code-block:: shell
+
+   $ conda activate ptychodus
+   $ ptychodus
+
+
+Reporting Bugs
+--------------
+
+Open a bug at https://github.com/AdvancedPhotonSource/ptychodus/issues.
+
+.. _`ptychodus`: https://github.com/AdvancedPhotonSource/ptychodus
+.. _`pty-chi`: https://github.com/AdvancedPhotonSource/pty-chi
+.. _`PtychoNN`: https://github.com/mcherukara/PtychoNN
+.. _`PvaPy`: https://github.com/epics-base/pvaPy

ptychodus-1.0/README.rst

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+Ptychodus
+=========
+
+`ptychodus`_ is a ptychography analysis application that supports multiple reconstruction libraries.
+
+
+Standard Installation
+---------------------
+
+1. Install `miniforge <https://github.com/conda-forge/miniforge>`_.
+
+2. Install ptychodus.
+
+   * To install `ptychodus` with the GUI and all optional packages:
+
+     .. code-block:: shell
+
+           $ conda create -c conda-forge -n ptychodus ptychodus-all
+
+   * To install `ptychodus` with the GUI and no optional packages:
+
+     .. code-block:: shell
+
+           $ conda create -c conda-forge -n ptychodus ptychodus
+
+   * To install `ptychodus` without the GUI or optional packages:
+
+     .. code-block:: shell
+
+           $ conda create -c conda-forge -n ptychodus ptychodus-core
+
+3. Activate the `ptychodus` conda environment to run ptychodus.
+
+   .. code-block:: shell
+
+       $ conda activate ptychodus
+       $ ptychodus -h
+
+       usage: ptychodus [-h] [-b {reconstruct,train}] [-f FILE_PREFIX] [-s SETTINGS_FILE] [-v] [-w OUTPUT_DIR]
+
+       ptychodus is a ptychography analysis application
+
+       options:
+         -h, --help            show this help message and exit
+         -b {reconstruct,train}, --batch {reconstruct,train}
+                               run action non-interactively
+         -f FILE_PREFIX, --file-prefix FILE_PREFIX
+                               replace file path prefix in settings
+         -s SETTINGS_FILE, --settings SETTINGS_FILE
+                               use settings from file
+         -v, --version         show program's version number and exit
+         -w OUTPUT_DIR, --write OUTPUT_DIR
+                               stage reconstruction inputs to directory
+
+       $ ptychodus
+
+
+Developer Installation
+----------------------
+
+* For a developer installation:
+
+.. code-block:: shell
+
+   $ git clone https://github.com/AdvancedPhotonSource/ptychodus.git
+   $ conda create -c conda-forge -n ptychodus --file ptychodus/requirements-dev.txt
+   $ conda activate ptychodus
+   $ pip install -e ./ptychodus
+
+* To install the `pty-chi`_ backend:
+
+.. code-block:: shell
+
+   $ pip install ptychi
+
+* To install the `PtychoNN`_ backend:
+
+.. code-block:: shell
+
+   $ conda install -n ptychodus -c conda-forge ptychonn
+
+* Launch `ptychodus`:
+
+.. code-block:: shell
+
+   $ conda activate ptychodus
+   $ ptychodus
+
+
+Reporting Bugs
+--------------
+
+Open a bug at https://github.com/AdvancedPhotonSource/ptychodus/issues.
+
+.. _`ptychodus`: https://github.com/AdvancedPhotonSource/ptychodus
+.. _`pty-chi`: https://github.com/AdvancedPhotonSource/pty-chi
+.. _`PtychoNN`: https://github.com/mcherukara/PtychoNN
+.. _`PvaPy`: https://github.com/epics-base/pvaPy

ptychodus-1.0/doc/api.rst

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+#!/usr/bin/env python
+
+from pathlib import Path
+from ptychodus.model import ModelCore
+
+def main() -> int:
+    settings_file = Path("path/to/settings.ini")
+
+    with ModelCore(settings_file) as model:
+        input_product_api = model.workflow_api.create_product("new_product_name")
+        output_product_api = input_product_api.reconstruct_local()
+        output_product_api.save_product("/path/to/file.h5", file_type="HDF5")

ptychodus-1.0/doc/dist.rst

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+Distribution Instructions
+=========================
+
+Python Package Index (PyPI)
+---------------------------
+
+From the ptychodus directory, create wheel in ./dist/
+
+.. code-block:: shell
+
+   $ python -m build .
+
+Upload to PyPI
+
+.. code-block:: shell
+
+   $ twine upload dist/*
+
+Docker
+------
+
+Build Docker image
+
+.. code-block:: shell
+
+   $ podman build -t ptychodus:latest .
+
+
+Run container
+
+.. code-block:: shell
+
+   $ xhost +local:podman
+   $ podman run -it --rm  -e "DISPLAY=$DISPLAY" -v "$HOME/.Xauthority:/root/.Xauthority:ro" --network host \
+         --gpus all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 python-ptychodus
+   $ xhost -local:podman

ptychodus-1.0/doc/globus.rst

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+Globus Compute Demonstration
+============================
+
+Perform steps 1-4 on the local and remote computers.
+
+1. Install Anaconda
+
+.. code-block:: shell
+
+   $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+   $ sh Miniconda3-latest-Linux-x86_64.sh
+
+2. Make conda available in your current bash environment
+
+.. code-block:: shell
+
+   $ eval "$(~/miniconda3/bin/conda shell.bash hook)"
+
+3. Create the "ptychodus" conda environment
+
+.. code-block:: shell
+   $ conda create -c conda-forge -n ptychodus ptychodus-all
+
+4. Activate the "ptychodus" conda environment
+
+.. code-block:: shell
+   $ conda activate ptychodus
+
+5. On the remote computer, install the funcX endpoint PyPI package into the "ptychodus" conda environment
+
+.. code-block:: shell
+   $ python -m pip install funcx-endpoint
+
+6. Configure and start the funcX endpoint
+
+.. code-block:: shell
+   $ cp ptychodus/ptychodusFuncXPolarisConfig.py ~/.funcx/default/config.py
+   $ vi ~/.funcx/default/config.py
+   $ funcx-endpoint configure
+   $ funcx-endpoint start
+
+7. For data transfer, use a guest collection on Globus Connect Server 5 (GCS5) or use Globus Connect Personal endpoint. See https://docs.globus.org/how-to/guest-collection-share-and-access/ for help setting up a guest collection on GCS5.
+8. On the local computer, launch the reconstruction tasks from the "Remote" view.
+9. On the remote computer, watch the queue (qstat) and funcX endpoint logs
+
+.. code-block:: shell
+   $ tail -f ~/.funcx/default/endpoint.log
+
+10. When the demo is done, stop the funcX endpoint on the remote computer
+
+.. code-block:: shell
+   $ funcx-endpoint stop

ptychodus-1.0/doc/streaming.rst

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+Streaming Demonstration
+=======================
+
+* To install the `PvaPy`_ backend:
+
+.. code-block:: shell
+
+   $ conda install -n ptychodus -c apsu pvapy
+
+* In terminal 1:
+
+.. code-block:: shell
+
+   $ pvapy-hpc-consumer \
+       --input-channel pvapy:image \
+       --control-channel consumer:*:control \
+       --status-channel consumer:*:status \
+       --output-channel consumer:*:output \
+       --processor-class ptychodus.PtychodusAdImageProcessor \
+       --processor-args '{ "settingsFilePath": "/path/to/ptychodus.ini", "reconstructFrameId": 1000 }' \
+       --report-period 10 \
+       --log-level debug
+
+* In terminal 2:
+
+.. code-block:: shell
+
+   # application status
+   $ pvget consumer:1:status
+
+   # configure application
+   $ pvput consumer:1:control '{"command" : "configure", "args" : "{\"nPatternsTotal\": 1000}"}'
+
+   # get last command status
+   $ pvget consumer:1:control
+
+   # start area detector sim server
+   $ pvapy-ad-sim-server -cn pvapy:image -if /path/to/fly001.npy -rt 120 -fps 1000
+
+* At the end of the demo,
+
+.. code-block:: shell
+
+   # shutdown consumer process
+   pvput consumer:1:control '{"command" : "stop"}'