pty-chi

Dockerfile

@@ -0,0 +1,23 @@
+#FROM python:3.12-slim-bullseye
+FROM pytorch/pytorch:2.5.1-cuda12.4-cudnn9-runtime
+
+RUN apt-get update && \
+    apt-get install -y libqt5gui5 && \
+    rm -rf /var/lib/apt/lists/*
+#ENV QT_DEBUG_PLUGINS=1
+
+# Upgrade pip
+RUN python3 -m pip install --upgrade pip
+
+# Set the working directory in the container
+WORKDIR /app
+
+# Copy the wheel file into the container at /app
+COPY dist/ptychodus-*.whl dist/ptychi-*.whl .
+
+# Install the wheel
+RUN python3 -m pip install --no-cache-dir --find-links=. ptychodus[globus,gui] ptychi && \
+    rm ptychodus-*.whl ptychi-*.whl
+
+# Run ptychodus when the container launches
+CMD ["python3", "-m", "ptychodus"]

doc/dist.rst

@@ -0,0 +1,47 @@
+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
+
+   $ time docker build -t python-ptychodus .
+
+Run container
+
+.. code-block:: shell
+
+   $ xhost +local:docker
+   $ docker 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:docker
+
+Check container status
+
+.. code-block:: shell
+
+   $ docker ps -a
+
+Clean up images
+
+.. code-block:: shell
+
+   $ sudo docker system prune -a

polaris.yaml

@@ -0,0 +1,40 @@
+engine:
+    type: HighThroughputEngine
+    max_workers_per_node: 1
+
+    # Un-comment to give each worker exclusive access to a single GPU
+    # available_accelerators: 4
+
+    strategy:
+        type: SimpleStrategy
+        max_idletime: 3600
+
+    address:
+        type: address_by_interface
+        ifname: bond0
+
+    provider:
+        type: PBSProProvider
+
+        launcher:
+            type: MpiExecLauncher
+            # Ensures 1 manger per node, work on all 64 cores
+            bind_cmd: --cpu-bind
+            overrides: --depth=64 --ppn 1
+
+        account: APSDataAnalysis
+        queue: preemptable
+        cpus_per_node: 32
+        select_options: ngpus=4
+
+        # e.g., "#PBS -l filesystems=home:grand:eagle\n#PBS -k doe"
+        scheduler_options: "#PBS -l filesystems=home:grand:eagle"
+
+        # Node setup: activate necessary conda environment and such
+        worker_init: "source ~/miniconda3/etc/profile.d/conda.sh; conda activate ptychodus",
+
+        walltime: 01:00:00
+        nodes_per_block: 1
+        init_blocks: 0
+        min_blocks: 0
+        max_blocks: 2

pyproject.toml

@@ -1,20 +1,22 @@
 [build-system]
-requires = ["setuptools>=64", "setuptools_scm>=8"]
+requires = ["setuptools>=64", "setuptools_scm[toml]>=8"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "ptychodus"
 description = "Ptychodus is a ptychography data analysis application."
 readme = "README.rst"
 requires-python = ">=3.10"
-license = {file = "LICENSE.txt"}
+license = {file = "LICENSE"}
 dependencies = [
-    "h5py",
+    "h5py>=3",
+    "hdf5plugin",
     "matplotlib",
     "numpy",
     "psutil",
     "scikit-image",
     "scipy",
+    "tables",
     "tifffile",
     "watchdog",
 ]
@@ -24,11 +26,17 @@ dynamic = ["version"]
 ptychodus = "ptychodus.__main__:main"
 
 [project.optional-dependencies]
-globus = ["gladier", "gladier-tools"]
+globus = ["gladier", "gladier-tools>=0.5.4"]
 gui = ["PyQt5"]
 ptychonn = ["ptychonn==0.3.*,>=0.3.7"]
 tike = ["tike==0.25.*,>=0.25.3"]
 
+[tool.setuptools.package-data]
+"ptychodus" = ["py.typed"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
 [tool.setuptools_scm]
 
 [tool.mypy]
@@ -44,6 +52,7 @@ module = [
     "hdf5plugin",
     "lightning.*",
     "parsl.*",
+    "ptychi.*",
     "ptychonn.*",
     "pvaccess",
     "pvapy.*",
@@ -60,10 +69,3 @@ target-version = "py310"
 
 [tool.ruff.format]
 quote-style = "single"
-
-[tool.setuptools.package-data]
-"ptychodus" = ["py.typed"]
-
-[tool.setuptools.packages.find]
-where = ["src"]
-

requirements-dev.txt

@@ -1,11 +1,13 @@
-h5py
+build
+h5py>=3
 hdf5plugin
 matplotlib
 mypy
 numpy
 psutil
 pyqt
 pyqt-stubs
+pytables
 pytest
 python>=3.10
 ruff
@@ -16,4 +18,3 @@ setuptools_scm>=8
 tifffile
 toml
 watchdog
-wheel

src/ptychodus/__main__.py

@@ -2,11 +2,14 @@
 
 from pathlib import Path
 import argparse
+import logging
 import sys
 
 from ptychodus.model import ModelCore
 import ptychodus
 
+logger = logging.getLogger(__name__)
+
 
 def versionString() -> str:
     return f'{ptychodus.__name__.title()} ({ptychodus.__version__})'
@@ -120,6 +123,7 @@ def main() -> int:
         try:
             from PyQt5.QtWidgets import QApplication
         except ModuleNotFoundError:
+            logger.warning('PyQt5 not found.')
             return 0
 
         # QApplication expects the first argument to be the program name

src/ptychodus/api/geometry.py

@@ -11,6 +11,12 @@ class PixelGeometry:
     widthInMeters: float
     heightInMeters: float
 
+    def copy(self) -> PixelGeometry:
+        return PixelGeometry(
+            widthInMeters=float(self.widthInMeters),
+            heightInMeters=float(self.heightInMeters),
+        )
+
     def __repr__(self) -> str:
         return f'{type(self).__name__}({self.widthInMeters}, {self.heightInMeters})'