Merge pull request #149 from e10harvey/full_res_example

Full res example

.github/workflows/ubi8-nightly.yml

@@ -33,14 +33,14 @@ jobs:
         with:
           path: OpenCSP
 
-      - name: pytest-cov
+      - name: pytest-cov (OpenCSP/example)
         working-directory: OpenCSP/example
         run: |
           python3 -m pip install -r ../requirements.txt
           export PYTHONPATH=$PWD/../
           pytest --color=yes -rs -vv --cov=. --cov-report term --cov-config=.coveragerc
 
-      - name: Pip Upgrade pytest-cov
+      - name: Pip Upgrade pytest-cov (OpenCSP/example)
         working-directory: OpenCSP/example
         run: |
           python3 -m pip install -U -r ../requirements.txt

.github/workflows/ubi8-weekly.yml

@@ -0,0 +1,43 @@
+name: github-UBI8-WEEKLY
+
+# Runs every Sunday at midnight
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '00 00 * * 0'
+
+permissions:
+  contents: none
+
+# Cancels any in progress 'workflow' associated with this PR
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  ubi8-weekly:
+    runs-on: [opencsp-latest-ubi8]
+    permissions:
+      packages: read
+      contents: read
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+        with:
+          path: OpenCSP
+
+      - name: pytest-cov (OpenCSP/example - scene_reconstruction)
+        working-directory: OpenCSP/example
+        run: |
+          python3 -m pip install -r ../requirements.txt
+          export PYTHONPATH=$PWD/../
+          pytest \
+            --color=yes \
+            -rs \
+            -vv \
+            --cov=. --cov-report term \
+            --cov-config=.coveragerc \
+            --dir-input=/box_data/scene_reconstruction/data_measurement/ \
+            --dir-output=/box_data/scene_reconstruction/data_calculation/ \
+            scene_reconstruction/example_scene_reconstruction.py

.github/workflows/ubi8.yml

@@ -35,7 +35,7 @@ jobs:
         with:
           path: OpenCSP
 
-      - name: pytest-cov
+      - name: pytest-cov (OpenCSP/opencsp)
         working-directory: OpenCSP/opencsp
         run: |
           python3 -m pip install -r ../requirements.txt

example/conftest.py

@@ -0,0 +1,19 @@
+import pytest
+
+
+#
+# Ensure pytest adds root directory to the system path.
+#
+def pytest_addoption(parser):
+    parser.addoption('--dir-input', action='store', default='', help='Base directory with data input')
+    parser.addoption('--dir-output', action='store', default='', help='Base directory where output will be written')
+
+
+@pytest.fixture
+def dir_input_fixture(request):
+    return request.config.getoption('--dir-input')
+
+
+@pytest.fixture
+def dir_output_fixture(request):
+    return request.config.getoption('--dir-output')

example/scene_reconstruction/example_scene_reconstruction.py

@@ -10,10 +10,40 @@
 import opencsp.common.lib.tool.log_tools as lt
 
 
-def scene_reconstruction(save_dir):
-    """Example script that reconstructs the XYZ locations of Aruco markers in a scene."""
-    # Define input directory
-    dir_input = join(opencsp_code_dir(), 'app/scene_reconstruction/test/data/data_measurement')
+def scene_reconstruction(dir_output, dir_input):
+    """
+    Reconstructs the XYZ locations of Aruco markers in a scene.
+
+    Parameters
+    ----------
+    dir_output : str
+        The directory where the output files, including point locations and calibration figures, will be saved.
+    dir_input : str
+        The directory containing the input files needed for scene reconstruction. This includes:
+        - 'camera.h5': HDF5 file containing camera parameters.
+        - 'known_point_locations.csv': CSV file with known point locations.
+        - 'aruco_marker_images/NAME.JPG': Directory containing images of Aruco markers.
+        - 'point_pair_distances.csv': CSV file with distances between point pairs.
+        - 'alignment_points.csv': CSV file with alignment points.
+
+    Notes
+    -----
+    This function performs the following steps:
+    1. Loads the camera parameters from an HDF5 file.
+    2. Loads known point locations, point pair distances, and alignment points from CSV files.
+    3. Initializes the SceneReconstruction object with the camera parameters and known point locations.
+    4. Runs the calibration process to determine the marker positions.
+    5. Scales the points based on the provided point pair distances.
+    6. Aligns the points using the provided alignment points.
+    7. Saves the reconstructed point locations to a CSV file.
+    8. Saves calibration figures as PNG files in the output directory.
+
+    Examples
+    --------
+    >>> scene_reconstruction('/path/to/output', '/path/to/input')
+
+    """
+    # "ChatGPT 4o" assisted with generating this docstring.
 
     # Load components
     camera = Camera.load_from_hdf(join(dir_input, 'camera.h5'))
@@ -38,22 +68,29 @@ def scene_reconstruction(save_dir):
     cal_scene_recon.align_points(marker_ids, alignment_values)
 
     # Save points as CSV
-    cal_scene_recon.save_data_as_csv(join(save_dir, 'point_locations.csv'))
+    cal_scene_recon.save_data_as_csv(join(dir_output, 'point_locations.csv'))
 
     # Save calibrtion figures
     for fig in cal_scene_recon.figures:
-        fig.savefig(join(save_dir, fig.get_label() + '.png'))
+        fig.savefig(join(dir_output, fig.get_label() + '.png'))
+
 
+def example_driver(dir_output_fixture, dir_input_fixture):
+
+    dir_input = join(opencsp_code_dir(), 'app/scene_reconstruction/test/data/data_measurement')
+    dir_output = join(dirname(__file__), 'data/output/scene_reconstruction')
+    if dir_input_fixture:
+        dir_input = dir_input_fixture
+    if dir_output_fixture:
+        dir_output = dir_input_fixture
 
-def example_driver():
     # Define output directory
-    save_path = join(dirname(__file__), 'data/output/scene_reconstruction')
-    ft.create_directories_if_necessary(save_path)
+    ft.create_directories_if_necessary(dir_input)
 
     # Set up logger
-    lt.logger(join(save_path, 'log.txt'), lt.log.INFO)
+    lt.logger(join(dir_output, 'log.txt'), lt.log.INFO)
 
-    scene_reconstruction(save_path)
+    scene_reconstruction(dir_output, dir_input)
 
 
 if __name__ == '__main__':

opencsp/__init__.py

@@ -15,6 +15,9 @@
 
 import configparser
 import os
+import copy
+import sys
+import argparse
 
 
 def _opencsp_settings_dirs() -> list[str]:
@@ -50,6 +53,57 @@ def _opencsp_settings_dirs() -> list[str]:
     return ret
 
 
+def apply_command_line_arguments(settings_from_ini: configparser.ConfigParser) -> configparser.ConfigParser:
+    settings_mixed = copy.copy(settings_from_ini)
+
+    # parse the command line
+    parser = argparse.ArgumentParser(
+        prog="OpenCSP/__init__.py", description='OpenCSP settings parser', add_help=False, exit_on_error=False
+    )
+    parser.add_argument(
+        '--dir-input',
+        dest="dir_input",
+        default="",
+        type=str,
+        help="Use the given directory value as the input directory instead of [opencsp_root_path]/[large_data_example_dir].",
+    )
+    parser.add_argument(
+        '--dir-output',
+        dest="dir_output",
+        default="",
+        type=str,
+        help="Use the given directory value as the output directory instead of [opencsp_root_path]/[scratch_dir]/[scratch_name].",
+    )
+    args, remaining = parser.parse_known_args(sys.argv[1:])
+    dir_input: str = args.dir_input
+    dir_output: str = args.dir_output
+    sys.argv = [sys.argv[0]] + remaining
+    overridden_values: list[tuple[str, str]] = []
+
+    # apply the command line arguments to the settings
+    if dir_input != "":
+        settings_mixed["opencsp_root_path"]["large_data_example_dir"] = dir_input
+        overridden_values.append(("opencsp_root_path/large_data_example_dir", dir_input))
+    if dir_output != "":
+        dir_output_path, dir_output_name = os.path.dirname(dir_output), os.path.basename(dir_output)
+        try:
+            os.makedirs(dir_output)
+        except FileExistsError:
+            pass
+        settings_mixed["opencsp_root_path"]["scratch_dir"] = dir_output_path
+        settings_mixed["opencsp_root_path"]["scratch_name"] = dir_output_name
+        overridden_values.append(("opencsp_root_path/scratch_dir", dir_output_path))
+        overridden_values.append(("opencsp_root_path/scratch_name", dir_output_name))
+
+    # let the user know if values have been overridden
+    if len(overridden_values) > 0:
+        print("Some settings have been overridden from the command line:")
+        for setting_name, command_line_value in overridden_values:
+            print(f"\t{setting_name}: {command_line_value}")
+
+    return settings_mixed
+
+
 _settings_files: list[str] = []
 
 # default settings file
@@ -66,4 +120,9 @@ def _opencsp_settings_dirs() -> list[str]:
 opencsp_settings = configparser.ConfigParser(allow_no_value=True)
 opencsp_settings.read(_settings_files)
 
+for section in opencsp_settings.sections():
+    for key in opencsp_settings[section]:
+        print(f"opencsp_settings[{section}][{key}]={opencsp_settings[section][key]}")
+
+opencsp_settings = apply_command_line_arguments(opencsp_settings)
 __all__ = ['opencsp_settings']