Merge branch 'main' into bdnyc-photometry

.github/workflows/python-app.yml

@@ -4,8 +4,6 @@
 name: Database Integration Tests
 
 on:
-  push:
-    branches: [ main ]
   pull_request:
     branches: [ main ]
   workflow_dispatch:  # manual execution

scripts/tutorials/generate_database.py

@@ -22,6 +22,7 @@
 db.load_database(DB_PATH, verbose=False)
 
 print('New db file generated.')
+print(os.listdir())
 
 # Close all connections
 db.session.close()

website/gen_info.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python
+"""
+Prints the info about the given object in this div
+
+Methods
+-------
+output
+    Converts inventory into JSON string
+main
+    Loads simple database, queries for a target and pulls out inventory
+"""
+# inbuilt libs
+import json
+
+# local libs
+from web_base import load_db, target_exists, target_argparse
+
+
+def output(inventory: dict):
+    """
+    Converts object inventory to json string
+
+    Parameters
+    ----------
+    inventory
+        The dictionary of data about given object
+
+    Returns
+    -------
+    inventory
+        The json string of data about given object
+
+    """
+    if 'Photometry' in inventory.keys():
+        del inventory['Photometry']  # will not print photometry data raw to page
+    inventory = json.dumps(inventory, indent=4)  # convert to json string and pretty print
+    return inventory
+
+
+def main(target: str):
+    """
+    Main module, loading simple database, querying and outputting object inventory as json string
+
+    Parameters
+    ----------
+    target
+        The name of the object to query database by
+
+    Returns
+    -------
+    inventory
+        The json string of the inventory for that object
+    """
+    db = load_db()  # load database
+    inventory = target_exists(db, target)  # query database for given object
+    inventory = output(inventory)  # converts inventory of object to string
+    return inventory
+
+
+if __name__ == '__main__' or 'bokeh' in __name__:
+    _tgt = target_argparse()  # if running from command line
+    main(_tgt)

website/gen_photo.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python
+"""
+Creates photometry table
+
+Attributes
+----------
+KNOWN_MAGS
+    Dictionary of photometric bands against central wavelength in microns
+
+Methods
+-------
+photometry_exists
+    Grabs photometry from object inventory on query
+main
+    Queries database for given object and finds photometry if it exists
+"""
+# local files
+from web_base import load_db, target_exists, target_argparse
+
+# global vars
+# TODO: expand known mags or use different method of initialising tables depending on if plotting photometry
+KNOWN_MAGS = {'WISE_W1': 3.368, 'WISE_W2': 4.618, 'WISE_W3': 12.082, 'WISE_W4': 22.194}  # central wave in microns
+
+
+def photometry_exists(inventory: dict):
+    """
+    Unpacks the photometry for an object
+
+    Parameters
+    ----------
+    inventory
+        Dictionary of the database output for that object
+    """
+    bands, mags, errs = [], [], []
+    try:
+        if 'Photometry' not in inventory.keys():
+            raise NotImplementedError('No "Photometry" key yet in db')
+        elif type(inventory['Photometry']) != list:
+            raise TypeError('Photometry entry needs to produce list')
+    except (NotImplementedError, TypeError):
+        bands = [*KNOWN_MAGS.keys(), ]
+        mags, errs = [None, ] * len(bands), [None, ] * len(bands)
+        return bands, mags, errs
+    else:
+        photo = inventory['Photometry']
+    for band in photo:
+        bands.append(band['band'])  # photometric band name
+        mags.append(band['magnitude'])  # magnitude for object
+        errs.append(band['magnitude_error'])  # magnitude error for object
+    return bands, mags, errs
+
+
+def main(target: str):
+    """
+    Main module
+
+    Parameters
+    ----------
+    target
+        Name of the target to be searched for, given as script argument
+    """
+    db = load_db()  # load simple database
+    inventory = target_exists(db, target)  # query database for given object
+    bands, mags, errs = photometry_exists(inventory)  # get lists for photometry
+    return bands, mags, errs
+
+
+if __name__ == '__main__' or 'bokeh' in __name__:
+    _tgt = target_argparse()  # pull target name from system arguments
+    main(_tgt)

website/gen_plot.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+"""
+Generates the script and div for the bokeh plot of spectra
+
+Methods
+-------
+spectra_exists
+    Takes spectra from database for given object
+main
+    Queries database for given object and finds spectra
+"""
+# local files
+from web_base import load_db, target_exists, target_argparse
+
+
+def spectra_exists(inventory: dict):
+    """
+    Unpacks the spectra from the object inventory
+
+    Parameters
+    ----------
+    inventory
+        Dictionary of the database output for that object
+    Returns
+    -------
+    _
+        The spectra
+    """
+    try:
+        if 'Spectra' not in inventory.keys():
+            raise NotImplementedError('No "Spectra" key yet in db')
+    except NotImplementedError:
+        pass  # for now
+    # TODO: when implemented add the unpacking and handling of spectra here (astropy specutils?)
+    # TODO: including multiple spectra per object
+    return
+
+
+def main(target: str):
+    """
+    Main module
+
+    Parameters
+    ----------
+    target
+        Name of the target to be searched for, given as script argument
+    """
+    db = load_db()  # load simple database
+    inventory = target_exists(db, target)  # query database for given object
+    spectra = spectra_exists(inventory)  # pull spectra from database query
+    return spectra
+
+
+if __name__ == '__main__' or 'bokeh' in __name__:
+    _tgt = target_argparse()  # pull target name from system arguments
+    main(_tgt)

website/main.py

@@ -0,0 +1,162 @@
+"""
+Main bokeh serve host
+
+Methods
+-------
+info_box
+    The <pre> box to be filled with the object inventory
+photo_table
+    The empty photometric table to be populated with object photometry
+spectra_fig
+    The spectra for an object which will be populated with all object spectra
+main
+    Generating initial elements on current document and assigns callback to fill them on selection
+"""
+# 3rd party imports
+from bokeh.models import ColumnDataSource, PreText, DataTable, TableColumn
+from bokeh.plotting import curdoc, figure
+import numpy as np
+# local imports
+import splash_table as st
+import gen_info as geninfo
+import gen_plot as genspec
+import gen_photo as genphot
+
+
+def info_box():
+    """
+    Generates a <pre> box to be filled with the object inventory
+
+    Returns
+    -------
+    infopre
+        Bokeh PreText object with empty text
+    """
+    # TODO: fix the object info to be 2 column, fitting to surrounding div not relying on overflow-y
+    infopre = PreText(text='', sizing_mode='stretch_both', name='objectinfo')
+    return infopre
+
+
+def photo_table():
+    """
+    Creates an empty DataTable to be filled with photometric data
+
+    Returns
+    -------
+    photdt
+        Bokeh DataTable object containing columns linked to cds
+    cds
+        Bokeh ColumnDataSource containing null data
+    """
+    bands = [*genphot.KNOWN_MAGS.keys(), ]  # the photometric bands to start with
+    # TODO: change what bands are shown initially, do not need to be this restrictive list
+    data = dict(
+        bands=bands,  # photometric bands
+        vals=[None, ] * len(bands),  # null list for empty cells
+        valserr=[None, ] * len(bands)  # null list for empty cells
+    )
+    cds = ColumnDataSource(data)  # pass to bokeh columndatasource object
+    cols = [
+        TableColumn(field="bands", title="Band", width=100),  # the column for photometric bands
+        TableColumn(field="vals", title="Magnitude", width=100),  # the column for magnitudes
+        TableColumn(field="valserr", title="Error", width=100)  # the column for magnitude errors
+    ]
+    photdt = DataTable(source=cds, columns=cols, name='photodt',  # the cds to link to, columns and element id
+                       fit_columns=False, index_position=None,  # for making small width table and ignore index column
+                       width=300, height=150)  # set exact size (pixels)
+    return photdt, cds
+
+
+def spectra_fig():
+    """
+    Creates the empty figure and relevant ColumnDataSource
+
+    Returns
+    -------
+    specfig
+        Bokeh figure object for showing spectra
+    cds
+        Bokeh ColumnDataSource object relating to the spectral data
+    """
+    # TODO: think of a better way of doing multiple spectra on one plot, maybe call for each spectra in total number
+    # TODO: could add photometry to this plot, requires knowing mags, their central wavelengths and zero points
+    # TODO: decide what we want to see in splash view
+    # TODO: decide if we want it normalised or not
+    data = dict(
+        wave=np.linspace(0.1, 10, 100),  # initial view
+        flux=np.random.randn(100) * 0.5 + 1,  # some random flux data
+    )
+    cds = ColumnDataSource(data)  # pass to bokeh object
+    tooltips = [('Wavelength', '@wave'), ('Flux', '@flux')]  # tooltips for hovering
+    specfig = figure(tools='pan,box_zoom,wheel_zoom,reset,save,hover', tooltips=tooltips,  # bokeh tools
+                     sizing_mode='stretch_width', name='spectraplot', height=495,  # sizing and ids w height in pixels
+                     title='Empty Spectra', x_axis_label='Wavelength (um)', y_axis_label='Flux (erg/s/s/um)')  # format
+    specfig.line(source=cds, x='wave', y='flux')  # create line plot for spectra
+    # font sizing
+    specfig.title.text_font_size = '18pt'
+    specfig.xaxis.major_label_text_font_size = '14pt'
+    specfig.xaxis.axis_label_text_font_size = '16pt'
+    specfig.yaxis.major_label_text_font_size = '14pt'
+    specfig.yaxis.axis_label_text_font_size = '16pt'
+    return specfig, cds
+
+
+def main():
+    """
+    Generates initial elements in curdoc() and holds callback function
+
+    Methods
+    -------
+    update
+        The callback running on bokeh serve triggered on selection of row
+    """
+    def update(attrname, old, new):
+        """
+        Python callback function running in current document on selection of row.
+        The parameters shown are not used in shown script but are required in the bokeh callback manager
+
+        Parameters
+        ----------
+        attrname
+            The changing attribute (required under hood)
+        old
+            The old object (required under hood)
+        new
+            The new object (required under hood)
+        """
+        selected_index = dtcds.selected.indices[0]  # the index selected from datatable on page
+        data = dtcds.data  # the data in table
+        target = data['sname'][selected_index]  # pulling out object name
+
+        band, mags, magserr = genphot.main(target)  # grab photometric data fro given object
+        photcds.data['bands'] = band  # update photometric table with known bands
+        photcds.data['vals'] = mags  # update photometric table with corresponding magnitudes
+        photcds.data['valserr'] = magserr  # update photometric table with corresponding magnitude errors
+
+        inventory = geninfo.main(target)  # pull out full inventory (minus photometry) for given object
+        infopre.text = inventory  # update the object info text box
+
+        specfig.title.text = target  # change title on spectra to object name
+        # TODO: add spectra in here
+        return
+    # document title
+    curdoc().template_variables['title'] = 'Simple Browser'
+    curdoc().title = 'Simple Browser'
+
+    photdt, photcds = photo_table()  # create empty photometric table and relating cds object
+    curdoc().add_root(photdt)  # embed photometric table in page
+
+    infopre = info_box()  # create empty <pre> box for object info
+    curdoc().add_root(infopre)  # embed object info in page
+
+    specfig, specfigcds = spectra_fig()  # create empty bokeh figure and relating cds object
+    curdoc().add_root(specfig)  # embed spectra plot in page
+
+    dtcds, dt = st.main()  # the populated table of all sources, ra and dec
+    dtcds.selected.on_change('indices', update)  # assign python callback to be on row selection
+    curdoc().add_root(dt)  # embed full table in page
+    return
+
+
+if __name__ == '__main__' or 'bokeh' in __name__:  # nb. the latter condition is true when running in bokeh serve
+    main()