Merge branch 'HinodeXRT:main' into jslavin-patch-2

.pre-commit-config.yaml

@@ -5,11 +5,12 @@ ci:
 repos:
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.4.0
   hooks:
   - id: check-ast
   - id: trailing-whitespace
   - id: end-of-file-fixer
+    exclude: .*\.fits
   - id: check-merge-conflict
     exclude: .*\.rst
   - id: requirements-txt-fixer
@@ -19,8 +20,13 @@ repos:
   - id: check-toml
   - id: check-yaml
 
+- repo: https://github.com/tox-dev/pyproject-fmt
+  rev: 0.4.1
+  hooks:
+  - id: pyproject-fmt
+
 - repo: https://github.com/PyCQA/isort
-  rev: 5.10.1
+  rev: 5.11.4
   hooks:
   - id: isort
     name: isort
@@ -31,12 +37,12 @@ repos:
     - python
 
 - repo: https://github.com/psf/black
-  rev: 22.8.0
+  rev: 22.12.0
   hooks:
   - id: black
 
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.5.2
+  rev: 1.6.0
   hooks:
   - id: nbqa-black
     additional_dependencies:
@@ -50,12 +56,10 @@ repos:
     - --nbqa-mutate
 
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.4.0
+  rev: v2.5.0
   hooks:
   - id: pretty-format-ini
     args: [--autofix]
-  - id: pretty-format-toml
-    args: [--autofix]
   - id: pretty-format-yaml
     args: [--autofix]
 
@@ -74,10 +78,12 @@ repos:
   rev: v2.2.2
   hooks:
   - id: codespell
-    args: [--config pyproject.toml]
+    exclude: .*\.fits
+    additional_dependencies:
+    - tomli
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v2.38.2
+  rev: v3.3.1
   hooks:
   - id: pyupgrade
     args: [--keep-runtime-typing, --py38-plus]

docs/_substitutions.rst

@@ -7,6 +7,9 @@
 .. |Quantity| replace:: :class:`~astropy.units.Quantity`
 .. |TimeDelta| replace:: :class:`~astropy.time.TimeDelta`
 .. |Time| replace:: :class:`~astropy.time.Time`
+.. |Channel| replace:: :class:`~xrtpy.response.channel.Channel`
+.. |EffectiveAreaFundamental| replace:: :class:`~xrtpy.response.effective_area.EffectiveAreaFundamental`
+.. |TemperatureResponseFundamental| replace:: :class:`~xrtpy.response.temperature_response.TemperatureResponseFundamental`
 
 .. A workaround for nested inline literals so that the filename will get
    formatted like a file but will be a link. In the text, these get used

docs/examples.rst

@@ -21,6 +21,4 @@ Computing response functions
 .. nbgallery::
   :glob:
 
-  notebooks/*
-  notebooks/computing_functions/effective_area.ipynb
-  notebooks/computing_functions/temperature_response.ipynb
+  notebooks/computing_functions/*

docs/getting_started.rst

@@ -15,7 +15,7 @@ to explore properties of the XRT. Visit our Example page for detail example guid
 
 Channel
 -------
-Channel is an instrument configuration class that explores properties of the XRT. Channel offers a detailed review of instruments for a chosen
+|Channel| is an instrument configuration class that explores properties of the XRT. Channel offers a detailed review of instruments for a chosen
 filter channel including the Charge-Coupled Device (CCD), Entrance Filter, Focus-Filter(s), Geometry, and Mirror(s).
 
 

pyproject.toml

@@ -1,13 +1,19 @@
 [build-system]
-requires = ["setuptools >= 50.0",
-            "setuptools_scm >= 6.0",
-            "wheel >= 0.34.0"]  # ought to mirror 'requirements/build.txt'
 build-backend = "setuptools.build_meta"
+requires = [
+  "setuptools>=50",
+  "setuptools_scm>=6",
+  "wheel>=0.34",
+]  # ought to mirror 'requirements/build.txt'
 
 [tool.codespell]
 skip = "*.genx,*.geny,*.png,*egg*,.git,.hypothesis,.nox,.tox,.idea,__pycache__,_build"
 ignore-words-list = """
-circularly"""
+circularly,
+nd,
+sav,
+te
+"""
 
 [tool.gilesbot]
 

setup.cfg

@@ -86,6 +86,8 @@ developer =
 
 [options.package_data]
 xrtpy = data/*
+xrtpy.response = data/*.txt, data/*.geny
+xrtpy.response.tests = data/*/*/*.txt
 
 [tool:pytest]
 minversion = 5.4

xrtpy/response/effective_area.py

@@ -3,6 +3,8 @@
     "effective_area",
 ]
 
+
+import astropy.time
 import datetime
 import math
 import numpy as np
@@ -12,7 +14,7 @@
 import sunpy.time
 
 from astropy import units as u
-from datetime import timedelta
+from astropy.utils.data import get_pkg_data_filename
 from functools import cached_property
 from pathlib import Path
 from scipy import interpolate
@@ -50,11 +52,15 @@
 _filter_contam_file = scipy.io.readsav(_filter_contam_filename)
 
 # CCD contam geny files keys for time and date.
-_ccd_contamination_file_time = _ccd_contam_file["p1"]
+_ccd_contamination_file_time = astropy.time.Time(
+    _ccd_contam_file["p1"], format="utime", scale="utc"
+)
 _ccd_contamination = _ccd_contam_file["p2"]
 
 # Filter contam geny files keys for time and date.
-_filter_contamination_file_time = _filter_contam_file["p1"]
+_filter_contamination_file_time = astropy.time.Time(
+    _filter_contam_file["p1"], format="utime", scale="utc"
+)
 _filter_contamination = _filter_contam_file["p2"]
 
 
@@ -90,100 +96,44 @@ def observation_date(self) -> str:
     @observation_date.setter
     def observation_date(self, date):
         """Validating users requested observation date."""
-        astropy_time = sunpy.time.parse_time(date)  # Astropy time in utc
-        observation_date = astropy_time.datetime
+
+        observation_date = sunpy.time.parse_time(date)
 
         if observation_date <= epoch:
             raise ValueError(
-                f"Invalid date: {observation_date}.\n Date must be after September 22nd, 2006 21:36:00."
+                f"\nInvalid date: {observation_date.datetime}.\n"
+                f"Date must be after {epoch}."
             )
-        self._observation_date = observation_date
-
-    @property
-    def xrt_contam_on_ccd_geny_update(self):
-        """Return a string of the last time the file was modified."""
-        modified_time = os.path.getmtime(_ccd_contam_filename)
-        modified_time_dt = datetime.datetime.fromtimestamp(modified_time)
 
-        return modified_time_dt.strftime("%Y/%m/%d")
-
-    @property
-    def ccd_data_dates_to_seconds(self):
-        """Converting CCD data dates to datetimes."""
-
-        ccd_data_dates_dt = []
-        ccd_data_dates_to_seconds = []
-        for time in _ccd_contamination_file_time:
-            t0 = _ccd_contamination_file_time[0]
-            dt = time - t0
-            ccd_data_dates_dt.append(epoch + timedelta(0, dt))
-            ccd_data_dates_to_seconds.append(
-                float((epoch + timedelta(0, dt)).strftime("%S"))
-            )
+        modified_time_path = os.path.getmtime(_ccd_contam_filename)
+        modified_time = astropy.time.Time(modified_time_path, format="unix")
+        latest_available_ccd_data = _ccd_contamination_file_time[-1].datetime.strftime(
+            "%Y/%m/%d"
+        )
+        modified_time_datetime = datetime.datetime.fromtimestamp(
+            modified_time_path
+        ).strftime("%Y/%m/%d")
 
-        if self.observation_date > ccd_data_dates_dt[-1]:
+        if observation_date > modified_time:
             raise ValueError(
-                "No contamination data is presently available for "
-                f"{self.observation_date}.\n The latest available data is on "
-                f"{ccd_data_dates_dt[-1]}.\n Contamination data is "
+                "\nNo contamination data is presently available for "
+                f"{observation_date.datetime}.\n The latest available data is on "
+                f"{latest_available_ccd_data}.\n Contamination data is "
                 "updated periodically. The last update was on "
-                f"{self.xrt_contam_on_ccd_geny_update}. If this is more "
+                f"{modified_time_datetime}. If this is more "
                 "than one month ago, please raise an issue at: "
                 "https://github.com/HinodeXRT/xrtpy/issues/new"
             )
-        return ccd_data_dates_to_seconds
-
-    @property
-    def ccd_observation_date_to_seconds(self):
-        """Converting users observation date into seconds with
-        respect to CCD contamination data. Used for interpolation."""
-
-        ccd_observation_date_to_seconds = []
-        for time in _ccd_contamination_file_time:
-            t0 = _ccd_contamination_file_time[0]
-            dt = time - t0
-            ccd_observation_date_to_seconds.append(
-                (self.observation_date + timedelta(0, dt)).strftime("%S")
-            )
-
-        return ccd_observation_date_to_seconds[0]
 
-    @property
-    def filter_observation_date_to_seconds(self):
-        """Converting users observation date into seconds with respect to filter contamination data. Used for interpolation."""
-
-        filter_observation_date_to_seconds = []
-        for time in _filter_contamination_file_time:
-            t0 = _filter_contamination_file_time[0]
-            dt = time - t0
-            filter_observation_date_to_seconds.append(
-                (self.observation_date + timedelta(0, dt)).strftime("%S")
-            )
-
-        return filter_observation_date_to_seconds[0]
-
-    @property
-    def filter_data_dates_to_seconds(self):
-        """Converting filter contamination data dates to datetimes."""
-
-        filter_data_dates_to_seconds = []
-        for time in _filter_contamination_file_time:
-            t0 = _filter_contamination_file_time[0]
-            dt = time - t0
-            filter_data_dates_to_seconds.append(
-                float((epoch + timedelta(0, dt)).strftime("%S"))
-            )
-
-        return filter_data_dates_to_seconds
+        self._observation_date = observation_date
 
     @property
     def contamination_on_CCD(self):
         """Calculation of contamination layer on the CCD, thickness given in Angstrom (Å)."""
-
         interpolater = scipy.interpolate.interp1d(
-            self.ccd_data_dates_to_seconds, _ccd_contamination, kind="linear"
+            _ccd_contamination_file_time.utime, _ccd_contamination, kind="linear"
         )
-        return interpolater(self.ccd_observation_date_to_seconds)
+        return interpolater(self.observation_date.utime)
 
     @property
     def filter_index_mapping_to_name(self):
@@ -200,25 +150,25 @@ def filter_wheel_number(self):
 
     @property
     def filter_data(self):
-        """Collecting filter data."""
+        """Collecting filter contamination data."""
         return _filter_contamination[self.filter_index_mapping_to_name][
             self.filter_wheel_number
         ]
 
     @property
     def contamination_on_filter(self) -> u.angstrom:
-        """
-        Thickness of the contamination layer on a filter."""
-
+        """Thickness of the contamination layer on a filter."""
         interpolater = scipy.interpolate.interp1d(
-            self.filter_data_dates_to_seconds, self.filter_data, kind="linear"
+            _filter_contamination_file_time.utime, self.filter_data, kind="linear"
         )
-        return interpolater(self.filter_observation_date_to_seconds)
+        return interpolater(self.observation_date.utime)
 
     @cached_property
     def n_DEHP_attributes(self):
         """Diethylhexylphthalate: Wavelength (nm), Delta, Beta."""
-        _n_DEHP_filename = Path(__file__).parent.absolute() / "data" / "n_DEHP.txt"
+        _n_DEHP_filename = get_pkg_data_filename(
+            "data/n_DEHP.txt", package="xrtpy.response"
+        )
 
         with open(_n_DEHP_filename) as n_DEHP:
             list_of_DEHP_attributes = []

xrtpy/util/time.py

@@ -2,10 +2,12 @@
     "epoch",
 ]
 
-from datetime import datetime, timedelta
+import astropy.time
+
+from datetime import timedelta
 
 # Hinode-XRT mission elapsed time "Epoch" is Sept 22, 2006 21:36:00.
-epoch = datetime(year=2006, month=9, day=22, hour=21, minute=36, second=0)
+epoch = astropy.time.Time("2006-09-22 21:36:00")
 
 
 def xrt_data_time_to_dt(data_time, epoch):