Finish photometry notebooks

.jp_app_launcher_stellarphot.yaml

@@ -6,21 +6,21 @@
   type: notebook
   catalog: Stellarphot photometry
 
-- title: 2 - Seeing profile
-  description: Choose aperture settings
-  source: ../stellarphot/photometry/01-viewer-seeing-template.ipynb
+- title: 2 - Seeing profile and comparison stars
+  description: Choose aperture settings and stars to perform photometry on
+  source: ../stellarphot/02-seeing-and-comparison.ipynb
   icon: ../stellarphot/stellarphot-logo.svg
   cwd: not_used
   type: notebook
   catalog: Stellarphot photometry
 
-- title: 3 - Comparison stars
-  description: Choose comparison stars
-  source: ../stellarphot/photometry/02-comp-star-plotter-template.ipynb
-  icon: ../stellarphot/stellarphot-logo.svg
-  cwd: not_used
-  type: notebook
-  catalog: Stellarphot photometry
+# - title: 3 - Comparison stars
+#   description: Choose comparison stars
+#   source: ../stellarphot/photometry/02-comp-star-plotter-template.ipynb
+#   icon: ../stellarphot/stellarphot-logo.svg
+#   cwd: not_used
+#   type: notebook
+#   catalog: Stellarphot photometry
 
 - title: 4 - Review settings
   description: Choose comparison stars

pyproject.toml

@@ -25,6 +25,7 @@ dependencies = [
     "ipywidgets",
     "jupyter-app-launcher",
     "matplotlib",
+    "papermill",
     "pandas",
     "photutils >=1.9",
     "pydantic >=2",
@@ -178,4 +179,6 @@ filterwarnings = [
     'ignore:RADECSYS=:',
     # photutils changed the name of a function again
     'ignore:The make_gaussian_sources_image function is deprecated',
+    # papermill is using deprecated jupyter paths
+    'ignore:Jupyter is migrating its paths to use standard platformdirs:DeprecationWarning',
 ]

stellarphot/gui_tools/__init__.py

@@ -1,6 +1,6 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 
 from .comparison_functions import *
-from .fits_opener import *
 from .photometry_widget_functions import *
+from .profile_and_comps import *
 from .seeing_profile_functions import *

stellarphot/gui_tools/comparison_functions.py

@@ -13,7 +13,6 @@
     from astrowidgets.ginga import ImageWidget
 
 from stellarphot import SourceListData
-from stellarphot.gui_tools.fits_opener import FitsOpener
 from stellarphot.gui_tools.seeing_profile_functions import set_keybindings
 from stellarphot.settings import (
     PartialPhotometrySettings,
@@ -22,6 +21,7 @@
     ui_generator,
 )
 from stellarphot.settings.custom_widgets import SettingWithTitle
+from stellarphot.settings.fits_opener import FitsOpener
 from stellarphot.utils.comparison_utils import (
     crossmatch_APASS2VSX,
     in_field,
@@ -34,7 +34,7 @@
 DESC_STYLE = {"description_width": "initial"}
 
 
-def make_markers(iw, ccd, RD, vsx, ent, name_or_coord=None):
+def make_markers(iw, RD, vsx, ent, name_or_coord=None):
     """
     Add markers for APASS, TESS targets, VSX.  Also center on object/coordinate.
 
@@ -44,9 +44,6 @@ def make_markers(iw, ccd, RD, vsx, ent, name_or_coord=None):
     iw : `astrowidgets.ImageWidget`
         Ginga widget.
 
-    ccd : `astropy.nddata.CCDData`
-        Sample image.
-
     RD : `astropy.table.Table`
         Table with target information, including a
         `astropy.coordinates.SkyCoord` column.
@@ -66,7 +63,6 @@ def make_markers(iw, ccd, RD, vsx, ent, name_or_coord=None):
     None
         Markers are added to the image in Ginga widget.
     """
-    iw.load_nddata(ccd)
     iw.zoom_level = "fit"
 
     try:
@@ -278,17 +274,22 @@ def __init__(
             self._file_chooser.set_file(file, directory=directory)
             self._set_file(None)
 
+        # Save the source location settings
+        self.source_locations.savebuttonbar.bn_save.click()
+
         self._make_observers()
 
     def _init(self):
         """
         Handles aspects of initialization that need to be deferred until
         a file is chosen.
         """
-        self.ccd, self.vsx = set_up(
-            self._file_chooser.path.name,
-            directory_with_images=self._file_chooser.path.parent,
-        )
+        # Read in the ccd data here and load the image into viewer instead of doing
+        # it behind the scenes in set_up and make_markers
+        self.ccd = self.fits_file.ccd
+        self.fits_file.load_in_image_widget(self.iw)
+
+        self.vsx = set_up(self.ccd)
 
         apass, vsx_apass_angle, targets_apass_angle = crossmatch_APASS2VSX(
             self.ccd, self.targets_from_file, self.vsx
@@ -310,13 +311,16 @@ def _init(self):
 
         make_markers(
             self.iw,
-            self.ccd,
             self.targets_from_file,
             self.vsx,
             apass_comps,
             name_or_coord=self.target_coord,
         )
 
+    @property
+    def fits_file(self):
+        return self._file_chooser
+
     @property
     def photom_apertures_file(self):
         return self.source_locations.value["source_list_file"]
@@ -349,7 +353,6 @@ def _set_object(self):
             self.object_name.value = "<h2>Object unknown</h2>"
             self._object = ""
 
-        print(f"Object: {self._object}")
         # We have a name, try to get coordinates from it
         try:
             self.target_coord = SkyCoord.from_name(self._object)