Merge pull request #56 from ECCCO-mission/add-weightless-runs

Add weightless runs, Bumps to Python 3.10

.github/workflows/CI.yml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3

README.md

@@ -6,10 +6,6 @@
 
 ![overlappogram example](https://raw.githubusercontent.com/ECCCO-mission/overlappogram/main/overlappogram.png)
 
-🚧🚧🚧 **UNDER DEVELOPMENT** 🚧🚧🚧
-
-**The package is still being developed. Expect breaking changes.**
-
 Overlappogram is a Python package for inverting overlappogram observations of the Sun,
 for examples MaGIXS, CubIXSS, or ECCCO observations.
 

overlappogram/cli.py

@@ -31,7 +31,8 @@ def unfold(config):
 
     os.makedirs(config["output"]["directory"], exist_ok=True)  # make sure output directory exists
 
-    overlappogram = load_overlappogram(config["paths"]["overlappogram"], config["paths"]["weights"])
+    overlappogram = load_overlappogram(config["paths"]["overlappogram"],
+                                       config["paths"]["weights"] if 'weights' in config['paths'] else None)
     response_cube = load_response_cube(config["paths"]["response"])
 
     inversion = Inverter(

overlappogram/error.py

@@ -0,0 +1,6 @@
+class OverlappogramWarning(Warning):
+    pass
+
+
+class NoWeightsWarnings(OverlappogramWarning):
+    """There are no weights passed to unfold."""

overlappogram/inversion.py

@@ -11,6 +11,7 @@
 from sklearn.linear_model import ElasticNet
 from tqdm import tqdm
 
+from overlappogram.error import NoWeightsWarnings
 from overlappogram.response import prepare_response_function
 
 __all__ = ["Inverter"]
@@ -226,6 +227,9 @@ def _start_chunk_inversion(self, model_config, alpha, rho, num_threads):
     def _initialize_with_overlappogram(self, overlappogram):
         self._overlappogram = overlappogram
 
+        if self._overlappogram.uncertainty is None:
+            warnings.warn("Running in weightless mode since no weights array was provided.", NoWeightsWarnings)
+
         if self._detector_row_range is None:
             self._detector_row_range = (0, overlappogram.data.shape[0])
         self.total_row_count = self._detector_row_range[1] - self._detector_row_range[0]
@@ -239,7 +243,7 @@ def _initialize_with_overlappogram(self, overlappogram):
 
         self._overlappogram.data[np.where(self._overlappogram.data < 0.0)] = 0.0
 
-        # initialize all result cubes
+        # initialize all results cubes
         self._overlappogram_height, self._overlappogram_width = self._overlappogram.data.shape
         self._em_data = np.zeros((self._overlappogram_height, self._num_slits, self._num_deps), dtype=np.float32)
         self._inversion_prediction = np.zeros((self._overlappogram_height, self._overlappogram_width), dtype=np.float32)

overlappogram/io.py

@@ -6,17 +6,23 @@
 __all__ = ["load_overlappogram", "load_response_cube", "save_em_cube", "save_spectral_cube", "save_prediction"]
 
 
-def load_overlappogram(image_path, weights_path) -> NDCube:
+def load_overlappogram(image_path: str, weights_path: str | None) -> NDCube:
     with fits.open(image_path) as image_hdul:
         image = image_hdul[0].data
         header = image_hdul[0].header
         wcs = WCS(image_hdul[0].header)
-    with fits.open(weights_path) as weights_hdul:
-        weights = weights_hdul[0].data
-    return NDCube(image, wcs=wcs, uncertainty=StdDevUncertainty(1 / weights), meta=dict(header))
 
+    if weights_path is None:
+        uncertainty = None
+    else:
+        with fits.open(weights_path) as weights_hdul:
+            weights = weights_hdul[0].data
+            uncertainty = StdDevUncertainty(1 / weights)
 
-def load_response_cube(path) -> NDCube:
+    return NDCube(image, wcs=wcs, uncertainty=uncertainty, meta=dict(header))
+
+
+def load_response_cube(path: str) -> NDCube:
     with fits.open(path) as hdul:
         response = hdul[0].data
         header = hdul[0].header
@@ -28,13 +34,13 @@ def load_response_cube(path) -> NDCube:
     return NDCube(response, wcs=wcs, meta=meta)
 
 
-def save_em_cube(cube, path, overwrite=True) -> None:
+def save_em_cube(cube, path: str, overwrite: bool = True) -> None:
     fits.writeto(path, cube, overwrite=overwrite)
 
 
-def save_prediction(prediction, path, overwrite=True) -> None:
+def save_prediction(prediction, path: str, overwrite: bool = True) -> None:
     fits.writeto(path, prediction, overwrite=overwrite)
 
 
-def save_spectral_cube(spectral_cube, path, overwrite=True) -> None:
+def save_spectral_cube(spectral_cube, path: str, overwrite: bool = True) -> None:
     fits.writeto(path, spectral_cube, overwrite=overwrite)

pyproject.toml

@@ -5,7 +5,7 @@ requires = ["setuptools",
 
 [project]
 name = "overlappogram"
-version = "0.0.3"
+version = "0.0.4"
 dependencies = ["numpy",
     "astropy",
     "scikit-learn",
@@ -19,7 +19,7 @@ dependencies = ["numpy",
     "click",
     "tqdm"
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 authors = [
     {name = "J. Marcus Hughes", email = "[email protected]"},
     {name = "Dyana Beabout", email = "[email protected]"},