pycfit 0.1.0__tar.gz

pycfit-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
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+# C extensions
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pycfit-0.1.0/LICENSE

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pycfit-0.1.0/MANIFEST.in

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+# Exclude specific files
+# All files which are tracked by git and not explicitly excluded here are included by setuptools_scm
+# Prune folders
+prune build
+prune docs/_build
+prune docs/api
+global-exclude *.pyc *.o
+
+# This subpackage is only used in development checkouts
+# and should not be included in built tarballs
+prune pycfit/_dev

pycfit-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pycfit
+Version: 0.1.0
+Summary: Component Fitting package
+Author-email: Ayris Narock <ayris.a.narock@nasa.gov>, Matthew Coon <matthew.t.coon@nasa.gov>
+License: Apache-2.0
+Project-URL: homepage, https://git.smce.nasa.gov/solo/spectral-fitting
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: astropy[all]>=7.0
+Requires-Dist: PyQt5
+Requires-Dist: qtpy
+Requires-Dist: pyqtgraph
+Dynamic: license-file
+
+# Python Component Fitting Tool  (pycfit)
+
+Python program to replicate many spectral fitting functions of the CFIT system from SolarSoft IDL.  
+
+
+
+# Installation
+
+ `pip install pycfit` 
+ 
+
+# Use
+```python
+#### Use interactive fitter to find an initial model based on an averaged spectra
+
+from pycfit import cfit_gui
+from pycfit.data import load_average_data
+
+# Load sample data
+avg_wavelength, avg_intensity, avg_uncertainty = load_average_data()
+
+# Call the GUI fitter
+model = cfit_gui(avg_wavelength, avg_intensity, uncertainty=avg_uncertainty)
+
+
+
+#### Use the interactive viewer to fit each point of the raster to the initial model
+#### and adjust or mask individual point fittings as needed
+
+from pycfit import cfit_grid_gui
+from pycfit.data import load_grid_data
+
+# Load a small-patch of sample data
+wavelength, intensity, uncertainty, mask = load_grid_data(patch=True)
+
+# Call the GUI inspector/fitter
+gridResults = cfit_grid_gui(model, wavelength, intensity, 
+                uncertainty=uncertainty, mask=mask, 
+                parallel=False)
+
+
+```
+
+
+# Contacts:
+### Software Maintenance:
+Ayris Narock:  ayris.a.narock@nasa.gov
+### NASA Official:
+Therese Kucera:  therese.a.kucera@nasa.gov
+
+
+
+# License
+
+This project is Copyright (c) National Aeronautics and Space Administration and licensed under
+the terms of the Apache Software License 2.0 license. This package is based upon
+the `Openastronomy packaging guide <https://github.com/OpenAstronomy/packaging-guide>`_
+which is licensed under the BSD 3-clause licence. See the licenses folder for
+more information.

pycfit-0.1.0/README.md

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+# Python Component Fitting Tool  (pycfit)
+
+Python program to replicate many spectral fitting functions of the CFIT system from SolarSoft IDL.  
+
+
+
+# Installation
+
+ `pip install pycfit` 
+ 
+
+# Use
+```python
+#### Use interactive fitter to find an initial model based on an averaged spectra
+
+from pycfit import cfit_gui
+from pycfit.data import load_average_data
+
+# Load sample data
+avg_wavelength, avg_intensity, avg_uncertainty = load_average_data()
+
+# Call the GUI fitter
+model = cfit_gui(avg_wavelength, avg_intensity, uncertainty=avg_uncertainty)
+
+
+
+#### Use the interactive viewer to fit each point of the raster to the initial model
+#### and adjust or mask individual point fittings as needed
+
+from pycfit import cfit_grid_gui
+from pycfit.data import load_grid_data
+
+# Load a small-patch of sample data
+wavelength, intensity, uncertainty, mask = load_grid_data(patch=True)
+
+# Call the GUI inspector/fitter
+gridResults = cfit_grid_gui(model, wavelength, intensity, 
+                uncertainty=uncertainty, mask=mask, 
+                parallel=False)
+
+
+```
+
+
+# Contacts:
+### Software Maintenance:
+Ayris Narock:  ayris.a.narock@nasa.gov
+### NASA Official:
+Therese Kucera:  therese.a.kucera@nasa.gov
+
+
+
+# License
+
+This project is Copyright (c) National Aeronautics and Space Administration and licensed under
+the terms of the Apache Software License 2.0 license. This package is based upon
+the `Openastronomy packaging guide <https://github.com/OpenAstronomy/packaging-guide>`_
+which is licensed under the BSD 3-clause licence. See the licenses folder for
+more information.

pycfit-0.1.0/pycfit/__init__.py

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+from .cfit_api import cfit, cfit_grid, cfit_gui, cfit_grid_gui
+from .version import version as __version__
+
+# Then you can be explicit to control what ends up in the namespace,
+__all__ = ['cfit', 'cfit_grid', 'cfit_gui', 'cfit_grid_gui']

pycfit-0.1.0/pycfit/_version.py

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+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.1.0'
+__version_tuple__ = version_tuple = (0, 1, 0)

pycfit-0.1.0/pycfit/cfit_api.py

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+"""
+Main API Functions
+"""
+import pickle
+from astropy.modeling import Model
+from qtpy.QtCore import Qt
+from qtpy.QtWidgets import QApplication
+from .function import FunctionFitter
+from .dialog import FitDialog
+from .grid import Grid
+from .dialog_grid import GridDialog
+
+
+
+## For Single Spectra ##
+def cfit(wavelength, intensity, uncertainty=None, function=None):
+    fitter = FunctionFitter(wavelength, intensity, uncertainty, function=function)
+    return fitter
+
+
+
+def cfit_gui(wavelength, intensity, uncertainty=None, function=None):
+    """
+    Single spectra fit GUI
+    Will return the astropy model that is stored at the time of GUI exit.
+    Meaning -- if you have done a "fit", and then adjusted your graphs, the
+    adjusted model is returned.
+
+    wavelength:  (1D array)
+    intensity:   (1D array)
+    uncertainty: (optional 1D array) Measurement uncertainty
+    function:  (opional.  astropy model or path to .pkl) 
+                Expects an astropy model object, plain or pickled 
+                If passed, loads this as the initial model state.
+                Otherwise, loads with no model at start
+    """
+    # create FunctionFitter object
+    if function:
+        try:
+            if isinstance(function, Model):
+                astroModel = function
+            else:
+                with open(function, 'rb') as pkl:
+                    astroModel = pickle.load(pkl)
+            fitter = FunctionFitter(wavelength, intensity, uncertainty, function=astroModel)
+            model_init = astroModel.copy()
+        except:
+            print(f'Bad function argument: {function}')
+            return
+    else:
+        fitter = FunctionFitter(wavelength, intensity, uncertainty)
+        model_init = None
+
+    # Create interactive fit dialog object
+    if hasattr(Qt, 'AA_EnableHighDpiScaling'):
+        QApplication.setAttribute(Qt.AA_EnableHighDpiScaling, True)
+    if hasattr(Qt, 'AA_UseHighDpiPixmaps'):
+        QApplication.setAttribute(Qt.AA_UseHighDpiPixmaps, True)
+
+    app = QApplication(['cfit_gui'])
+    fd = FitDialog(fitter=fitter)
+    if fd.exec_():
+        return fd.get_model()
+    else:
+        print('Canceled!')
+        return model_init
+
+
+def cfit_load(modelFile):
+    """Utility to load astropy Model from pickle"""
+    try:
+        with open(modelFile, 'rb') as pkl:
+            astroModel = pickle.load(pkl)
+        if isinstance(astroModel, Model):
+            return astroModel
+        else:
+            raise Exception()
+    except:
+        print(f'Bad pickle file path: {modelFile}')
+
+
+
+## For Grid of Spectras ##
+def cfit_grid(function, wavelength, intensity, uncertainty=None, mask=None, auto_fit=False, parallel=True):
+    GM = Grid(function, wavelength, intensity, uncertainty=uncertainty, mask=mask)
+    if auto_fit:
+        print("Fitting across the grid. This may take a few minutes . . . ")
+        GM.fit(parallel=parallel)
+
+    return GM
+
+
+def cfit_grid_gui(function, wavelength, intensity, uncertainty=None, mask=None, parallel=True):
+    GM = cfit_grid(function, wavelength, intensity, uncertainty=uncertainty, mask=mask, auto_fit=True, parallel=parallel)
+
+    # Create interactive fit dialog object
+    if hasattr(Qt, 'AA_EnableHighDpiScaling'):
+        QApplication.setAttribute(Qt.AA_EnableHighDpiScaling, True)
+    if hasattr(Qt, 'AA_UseHighDpiPixmaps'):
+        QApplication.setAttribute(Qt.AA_UseHighDpiPixmaps, True)
+
+    app = QApplication(['cfit_grid_gui'])
+    gd = GridDialog(GM)
+    if gd.exec_():
+        return gd.get_results()
+    else:
+        print('Canceled!')
+        return function
+        
+

pycfit-0.1.0/pycfit/data/__init__.py

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+import numpy as np
+from pathlib import Path
+
+def load_average_data():
+    """
+    Example data from SPICE mission
+    Average spectra from window 'O III 703 / Mg IX 706 (Merged)'
+
+    Returns a tuple: (wavelength, intensity, uncertainty)
+
+    Source file: solo_L2_spice-n-ras_20240425T121922_V22_251658647-000.fits
+    """
+
+    LOCAL_DIR = Path(__file__).parent
+    avg = np.load(LOCAL_DIR.joinpath('avg_data.npz'))
+
+    return avg['wavelength'], avg['intensity'], avg['uncertainty']
+
+
+def load_grid_data(patch=False):
+    """
+    Example data from SPICE mission
+    Raster spectra from window 'O III 703 / Mg IX 706 (Merged)'
+
+    Returns a tuple: (wavelength, intensity, uncertainty, mask)
+
+    Optional keyword "patch=True" will return only a 20x20 subset.
+    Otherwise, full raster is returned
+
+    Source file: solo_L2_spice-n-ras_20240425T121922_V22_251658647-000.fits
+    """
+
+    LOCAL_DIR = Path(__file__).parent
+
+    if patch:
+        data = np.load(LOCAL_DIR.joinpath('patch_data.npz'))
+    else:
+        data = np.load(LOCAL_DIR.joinpath('grid_data.npz'))
+
+    return data['wavelength'], data['intensity'], data['uncertainty'], data['mask']