Merge pull request #29 from lsst-uk/initial_data

Initial data class commit.

.gitignore

@@ -1,3 +1,5 @@
+**/.DS_Store
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

pyproject.toml

@@ -15,6 +15,8 @@ classifiers = [
 dynamic = ["version"]
 dependencies = [
     "ipykernel", # Support for Jupyter notebooks
+    "numpy",
+    "lsst-rsp"
 ]
 
 [project.urls]
@@ -38,6 +40,9 @@ dev = [
     "ipython", # Also used in building notebooks into Sphinx
 ]
 
+[project.scripts]
+adler = "adler.adler:main"
+
 [build-system]
 requires = [
     "setuptools>=62", # Used to build and package the Python project

src/adler/__init__.py

@@ -1,3 +1,2 @@
-from .example_module import greetings, meaning
-
-__all__ = ["greetings", "meaning"]
+from . import dataclasses
+from . import science

src/adler/adler.py

@@ -0,0 +1,26 @@
+import argparse
+
+from adler.dataclasses.AdlerPlanetoid import AdlerPlanetoid
+
+
+def runAdler(args):
+    planetoid = AdlerPlanetoid(args.ssoid)
+
+    planetoid.do_pretend_science()
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Runs Adler for a select planetoid and given user input.")
+
+    parser.add_argument("-s", "--ssoid", help="SSObject ID of planetoid.", type=str, required=True)
+
+    # can add arguments to specify a date range etc later
+    # alternatively we may start using a config file
+
+    args = parser.parse_args()
+
+    runAdler(args)
+
+
+if __name__ == "__main__":
+    main()

src/adler/dataclasses/AdlerPlanetoid.py

@@ -0,0 +1,71 @@
+from lsst.rsp import get_tap_service
+from adler.dataclasses.DataSchema import Observations, MPCORB, SSObject
+from adler.science.DummyScience import DummyScience
+
+
+class AdlerPlanetoid:
+    def __init__(self, ssObjectId, sql_filename=None):
+        self.ssObjectId = ssObjectId
+        self.sql_filename = sql_filename
+        # can also include date ranges at some point
+
+        # can draw from a local SQL database
+        if not sql_filename:
+            self.service = get_tap_service("ssotap")
+        else:
+            self.service = None
+
+        # this creates the AdlerPlanetoid.Observations, AdlerPlanetoid.MPCORB and
+        # AdlerPlanetoid.SSObject objects.
+        self.populate_observations()
+        self.populate_MPCORB()
+        self.populate_SSObject()
+
+    def populate_observations(self):
+        observations_sql_query = f"""
+            SELECT
+                ssObject.ssObjectId, mag, magErr, band, midpointMjdTai as mjd, ra, dec, phaseAngle,
+                topocentricDist, heliocentricDist
+            FROM
+                dp03_catalogs_10yr.ssObject
+                JOIN dp03_catalogs_10yr.diaSource ON dp03_catalogs_10yr.ssObject.ssObjectId   = dp03_catalogs_10yr.diaSource.ssObjectId
+                JOIN dp03_catalogs_10yr.ssSource  ON dp03_catalogs_10yr.diaSource.diaSourceId = dp03_catalogs_10yr.ssSource.diaSourceId
+            WHERE
+                ssObject.ssObjectId = {self.ssObjectId} and band='r'
+            """
+
+        self.Observations = Observations(
+            self.ssObjectId, observations_sql_query, self.service, self.sql_filename
+        )
+
+    def populate_MPCORB(self):
+        MPCORB_sql_query = f"""
+            SELECT
+                ssObjectId, mpcDesignation, mpcNumber, mpcH, mpcG, epoch, peri, node, incl, e, n, q, 
+                uncertaintyParameter, flags
+            FROM
+                dp03_catalogs_10yr.MPCORB
+            WHERE
+                ssObjectId = {self.ssObjectId}
+        """
+
+        self.MPCORB = MPCORB(self.ssObjectId, MPCORB_sql_query, self.service, self.sql_filename)
+
+    def populate_SSObject(self):
+        SSObject_sql_query = f"""
+            SELECT
+                discoverySubmissionDate, firstObservationDate, arc, numObs, 
+                r_H, r_G12, r_Herr, r_G12err, r_nData,
+                maxExtendedness, minExtendedness, medianExtendedness
+            FROM
+                dp03_catalogs_10yr.SSObject
+            WHERE
+                ssObjectId = {self.ssObjectId}
+        """
+
+        self.SSObject = SSObject(self.ssObjectId, SSObject_sql_query, self.service, self.sql_filename)
+
+    def do_pretend_science(self):
+        self.DummyScienceResult = DummyScience().science_result
+
+        print(self.DummyScienceResult)

src/adler/dataclasses/DataSchema.py

@@ -0,0 +1,102 @@
+import numpy as np
+
+
+class DataSchema:
+    """Parent class for Observations (a join of DiaSource and SSSource), MPCORB
+    and SSObject data classes.
+    """
+
+    def __init__(self, ssObjectId, sql_query, service, sql_filename=None):
+        self.ssObjectId = ssObjectId
+        self.sql_query = sql_query
+        self.service = service
+
+        if not sql_filename:
+            self.data_table = self.get_RSP_table(self.sql_query)
+        else:
+            self.data_table = self.get_SQL_table(self.sql_query)
+
+    def get_RSP_table(self, sql_query):
+        rsp_table = self.service.search(sql_query).to_table()
+        return rsp_table
+
+    def get_SQL_table(self, sql_query, testing_filename):
+        pass
+
+    # should be one function to get whatever from the table and type accordingly
+    def get_array_from_table(self, column_name):
+        return np.array(self.data_table[column_name])
+
+    def get_string_from_table(self, column_name):
+        return str(self.data_table[column_name][0])
+
+    def get_float_from_table(self, column_name):
+        return float(self.data_table[column_name][0])
+
+    def get_int_from_table(self, column_name):
+        return int(self.data_table[column_name][0])
+
+
+class Observations(DataSchema):
+    """This is a SQL join of DiaSource and SSSource which contains all of the
+    observations of the object.
+    """
+
+    def __init__(self, ssObjectId, observations_query, service, sql_filename=None):
+        super().__init__(ssObjectId, observations_query, service, sql_filename)
+
+        # This populates each of the variables with a numpy array of the specific column.
+        # This should probably be moved to a constructor class method.
+        self.mag = self.get_array_from_table("mag")
+        self.magErr = self.get_array_from_table("magErr")
+        self.mjd = self.get_array_from_table("mjd")
+        self.ra = self.get_array_from_table("ra")
+        self.dec = self.get_array_from_table("dec")
+        self.phaseAngle = self.get_array_from_table("phaseAngle")
+        self.topocentricDist = self.get_array_from_table("topocentricDist")
+        self.heliocentricDist = self.get_array_from_table("heliocentricDist")
+
+        self.reduced_mag = self.mag - 5 * np.log10(self.topocentricDist * self.heliocentricDist)
+
+
+class MPCORB(DataSchema):
+    """Grabs information from MPCORB."""
+
+    def __init__(self, ssObjectId, observations_query, service, sql_filename=None):
+        super().__init__(ssObjectId, observations_query, service, sql_filename)
+
+        self.mpcDesignation = self.get_string_from_table("mpcDesignation")
+        self.mpcNumber = self.get_string_from_table("mpcNumber")
+        self.mpcH = self.get_float_from_table("mpcH")
+        self.mpcG = self.get_float_from_table("mpcH")
+        self.epoch = self.get_float_from_table("epoch")
+        self.peri = self.get_float_from_table("peri")
+        self.node = self.get_float_from_table("node")
+        self.incl = self.get_float_from_table("incl")
+        self.e = self.get_float_from_table("e")
+        self.n = self.get_float_from_table("n")
+        self.q = self.get_float_from_table("q")
+        self.uncertaintyParameter = self.get_string_from_table("uncertaintyParameter")
+        self.flags = self.get_string_from_table("flags")
+
+        # no mean anomaly, no a in MPCORB table
+
+
+class SSObject(DataSchema):
+    """Grabs information from MPCORB."""
+
+    def __init__(self, ssObjectId, observations_query, service, sql_filename=None):
+        super().__init__(ssObjectId, observations_query, service, sql_filename)
+
+        self.discoverySubmissionDate = self.get_float_from_table("discoverySubmissionDate")
+        self.firstObservationDate = self.get_float_from_table("firstObservationDate")
+        self.arc = self.get_float_from_table("arc")
+        self.numObs = self.get_int_from_table("numObs")
+        self.r_H = self.get_float_from_table("r_H")
+        self.r_G12 = self.get_float_from_table("r_G12")
+        self.r_Herr = self.get_float_from_table("r_Herr")
+        self.r_G12Err = self.get_float_from_table("r_G12err")
+        self.r_nData = self.get_int_from_table("r_nData")
+        self.maxExtendedness = self.get_float_from_table("maxExtendedness")
+        self.minExtendedness = self.get_float_from_table("minExtendedness")
+        self.medianExtendedness = self.get_float_from_table("medianExtendedness")

src/adler/science/DummyScience.py

@@ -0,0 +1,3 @@
+class DummyScience:
+    def __init__(self):
+        self.science_result = "look, science!"

tests/adler/dataclasses/dummy_test.py

@@ -0,0 +1,5 @@
+# placeholder test to ensure tests work
+
+
+def test_dummytest():
+    print("test complete")